1
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Coleman OD, Macdonald J, Thomson B, Ward JA, Stubbs CJ, McAllister TE, Clark S, Amin S, Cao Y, Abboud MI, Zhang Y, Sanganee H, Huber KVM, Claridge TDW, Kawamura A. Cyclic peptides target the aromatic cage of a PHD-finger reader domain to modulate epigenetic protein function. Chem Sci 2023; 14:7136-7146. [PMID: 37416723 PMCID: PMC10321576 DOI: 10.1039/d2sc05944d] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/15/2023] [Indexed: 07/08/2023] Open
Abstract
Plant homeodomain fingers (PHD-fingers) are a family of reader domains that can recruit epigenetic proteins to specific histone modification sites. Many PHD-fingers recognise methylated lysines on histone tails and play crucial roles in transcriptional regulation, with their dysregulation linked to various human diseases. Despite their biological importance, chemical inhibitors for targeting PHD-fingers are very limited. Here we report a potent and selective de novo cyclic peptide inhibitor (OC9) targeting the Nε-trimethyllysine-binding PHD-fingers of the KDM7 histone demethylases, developed using mRNA display. OC9 disrupts PHD-finger interaction with histone H3K4me3 by engaging the Nε-methyllysine-binding aromatic cage through a valine, revealing a new non-lysine recognition motif for the PHD-fingers that does not require cation-π interaction. PHD-finger inhibition by OC9 impacted JmjC-domain mediated demethylase activity at H3K9me2, leading to inhibition of KDM7B (PHF8) but stimulation of KDM7A (KIAA1718), representing a new approach for selective allosteric modulation of demethylase activity. Chemoproteomic analysis showed selective engagement of OC9 with KDM7s in T cell lymphoblastic lymphoma SUP T1 cells. Our results highlight the utility of mRNA-display derived cyclic peptides for targeting challenging epigenetic reader proteins to probe their biology, and the broader potential of this approach for targeting protein-protein interactions.
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Affiliation(s)
- Oliver D Coleman
- School of Natural and Environmental Sciences - Chemistry, Newcastle University Newcastle NE1 7RU UK
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford Roosevelt Drive Old Road Campus Oxford OX3 7BN UK
| | - Jessica Macdonald
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Ben Thomson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Jennifer A Ward
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Old Road Campus Oxford OX3 7FZ UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford Oxford OX3 7FZ UK
| | - Christopher J Stubbs
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Cambridge CB4 0WG UK
| | - Tom E McAllister
- School of Natural and Environmental Sciences - Chemistry, Newcastle University Newcastle NE1 7RU UK
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford Roosevelt Drive Old Road Campus Oxford OX3 7BN UK
| | - Shane Clark
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Siddique Amin
- School of Natural and Environmental Sciences - Chemistry, Newcastle University Newcastle NE1 7RU UK
| | - Yimang Cao
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Martine I Abboud
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Yijia Zhang
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Hitesh Sanganee
- Emerging Innovations Unit, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - Kilian V M Huber
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Old Road Campus Oxford OX3 7FZ UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford Oxford OX3 7FZ UK
| | - Tim D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Akane Kawamura
- School of Natural and Environmental Sciences - Chemistry, Newcastle University Newcastle NE1 7RU UK
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford Roosevelt Drive Old Road Campus Oxford OX3 7BN UK
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2
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Yong JRJ, Kupče Ē, Claridge TDW. A general scheme for generating NMR supersequences combining high- and low-sensitivity experiments. Chem Commun (Camb) 2023. [PMID: 37272587 DOI: 10.1039/d3cc01472j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
NOAH supersequences are a way of collecting multiple 2D NMR experiments in a single measurement. So far, this approach has been limited to experiments with comparable sensitivity. Here, we propose a scheme which overcomes this limitation, combining experiments with very different sensitivities such as 1,1-ADEQUATE, 15N HMBC, and 13C HSQC.
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Affiliation(s)
- Jonathan R J Yong
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.
| | | | - Tim D W Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.
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3
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Abstract
There are few enantioconvergent reactions in which racemic substrates bearing multiple stereochemical features are converted into products with high levels of diastereo- and enantiocontrol. Here, we disclose a process for the highly enantio- and diastereoselective syntheses of medium ring lactams via an intramolecular counterion-directed C-alkylation reaction. The treatment of racemic biaryl anilides that exist as a complex mixture of enantiomers and diastereoisomeric conformers by virtue of multiple axes of restricted rotation with a quinidine-derived ammonium salt under basic conditions affords medium ring lactams bearing elements of both axial and point chirality via an enolate-driven configurational relaxation process. Thermal equilibration of the syn- and anti-product diasteroisomers has demonstrated that the barriers to bowl inversion are >124 kJ mol-1. We propose that the chiral ammonium salt differentiates between a complex and rapidly equilibrating mixture of enolate and rotational isomers, ultimately leading to highly enantioselective alkylative ring closure. This dynamic and enantioconvergent process offers an operationally simple approach to the synthesis of valuable chiral medium ring lactams for which there are few catalytic and enantioselective approaches.
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Affiliation(s)
- Ji-Yuan Du
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.,College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Tudor Balan
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Tim D W Claridge
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Martin D Smith
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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4
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Rabe P, Walla CC, Goodyear NK, Welsh J, Southwart R, Clifton I, Linyard JDS, Tumber A, Claridge TDW, Myers WK, Schofield CJ. Spectroscopic studies reveal details of substrate-induced conformational changes distant from the active site in isopenicillin N synthase. J Biol Chem 2022; 298:102249. [PMID: 35835215 PMCID: PMC9403350 DOI: 10.1016/j.jbc.2022.102249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/23/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/06/2022] Open
Abstract
Isopenicillin N synthase (IPNS) catalyzes formation of the β-lactam and thiazolidine rings of isopenicillin N from its linear tripeptide l-δ-(α-aminoadipoyl)-l-cysteinyl-d-valine (ACV) substrate in an iron- and dioxygen (O2)-dependent four-electron oxidation without precedent in current synthetic chemistry. Recent X-ray free-electron laser studies including time-resolved serial femtosecond crystallography show that binding of O2 to the IPNS–Fe(II)–ACV complex induces unexpected conformational changes in α-helices on the surface of IPNS, in particular in α3 and α10. However, how substrate binding leads to conformational changes away from the active site is unknown. Here, using detailed 19F NMR and electron paramagnetic resonance experiments with labeled IPNS variants, we investigated motions in α3 and α10 induced by binding of ferrous iron, ACV, and the O2 analog nitric oxide, using the less mobile α6 for comparison. 19F NMR studies were carried out on singly and doubly labeled α3, α6, and α10 variants at different temperatures. In addition, double electron–electron resonance electron paramagnetic resonance analysis was carried out on doubly spin-labeled variants. The combined spectroscopic and crystallographic results reveal that substantial conformational changes in regions of IPNS including α3 and α10 are induced by binding of ACV and nitric oxide. Since IPNS is a member of the structural superfamily of 2-oxoglutarate-dependent oxygenases and related enzymes, related conformational changes may be of general importance in nonheme oxygenase catalysis.
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Affiliation(s)
- Patrick Rabe
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.
| | - Carla C Walla
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Noelle K Goodyear
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jordan Welsh
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom; Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
| | - Rebecca Southwart
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Ian Clifton
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - James D S Linyard
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Tim D W Claridge
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - William K Myers
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK.
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.
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5
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Okokon JE, Etuk IC, Thomas PS, Drijfhout FP, Claridge TDW, Li WW. In vivo antihyperglycaemic and antihyperlipidemic activities and chemical constituents of Solanum anomalum. Biomed Pharmacother 2022; 151:113153. [PMID: 35598372 DOI: 10.1016/j.biopha.2022.113153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/11/2022] [Revised: 05/12/2022] [Accepted: 05/15/2022] [Indexed: 11/02/2022] Open
Abstract
Solanum anomalum is a plant used ethnomedically for the treatment of diabetes. The study was aimed to validate ethnomedical claims in rat model and identify the likely antidiabetic compounds. Leaf extract (70-210 mg/kg/day) and fractions (140 mg/kg/day) of S. anomalum were evaluated in hyperglycaemic rats induced using alloxan for effects on blood glucose, lipids and pancreas histology. Phytochemical characterisation of isolated compounds and their identification were performed using mass spectrometry and NMR spectroscopy. Bioinformatics tool was used to predict the possible protein targets of the identified bioactive compounds. The leaf extract/fractions on administration to diabetic rats caused significant lowering of fasting blood glucose of the diabetic rats during single dose study and on repeated administration of the extract. The hydroethanolic leaf extracts also enhanced glucose utilization capacity of the diabetic rats and caused significant lowering of glycosylated hemoglobin levels and elevation of insulin levels in the serum. Furthermore, triglycerides, LDL-cholesterol, and VLDL-cholesterol levels were lowered significantly, while HDL-cholesterol levels were also elevated in the treated diabetic rats. There was absence or few pathological signs in the treated hyperglycaemic rat pancreas compared to that present in the pancreas of control group. Diosgenin, 25(R)-diosgenin-3-O-α-L-rhamnopyranosyl-(1→4)-β-D-glucopyranoside, uracil, thymine, 1-octacosanol, and octacosane were isolated and identified. Protein phosphatases along with secreted proteins are predicted to be the major targets of diosgenin and the diosgenin glycoside. These results suggest that the leaf extract/fractions of S. anomalum possess antidiabetic and antihyperlipidemic properties, offer protection to the pancreas and stimulate insulin secretion, which can be attributable to the activities of its phytochemical constituents.
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Affiliation(s)
- Jude E Okokon
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, University of Uyo, Uyo, Nigeria.
| | - Idongesit C Etuk
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, University of Uyo, Uyo, Nigeria
| | - Paul S Thomas
- Department of Pharmacognosy and Natural Medicine, Faculty of Pharmacy, University of Uyo, Uyo, Nigeria
| | - Falko P Drijfhout
- Chemical Sciences Research Centre, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - Tim D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Wen-Wu Li
- School of Pharmacy and Bioengineering, Keele University, Stoke-on-Trent ST4 7QB, United Kingdom.
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6
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Patrick CW, Woods JF, Gawel P, Otteson CE, Thompson AL, Claridge TDW, Jasti R, Anderson HL. Polyyne [3]Rotaxanes: Synthesis via Dicobalt Carbonyl Complexes and Enhanced Stability. Angew Chem Int Ed Engl 2022; 61:e202116897. [PMID: 34995402 PMCID: PMC9302669 DOI: 10.1002/anie.202116897] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 12/10/2021] [Indexed: 01/08/2023]
Abstract
New strategies for synthesizing polyyne polyrotaxanes are being developed as an approach to stable carbyne “insulated molecular wires”. Here we report an active metal template route to polyyne [3]rotaxanes, using dicobalt carbonyl masked alkyne equivalents. We synthesized two [3]rotaxanes, both with the same C28 polyyne dumbbell component, one with a phenanthroline‐based macrocycle and one using a 2,6‐pyridyl cycloparaphenylene nanohoop. The thermal stabilities of the two rotaxanes were compared with that of the naked polyyne dumbbell in decalin at 80 °C, and the nanohoop rotaxane was found to be 4.5 times more stable.
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Affiliation(s)
- Connor W Patrick
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | - Joseph F Woods
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | - Przemyslaw Gawel
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | - Claire E Otteson
- Department of Chemistry and Biochemistry, Materials Science Institute, University of Oregon, Eugene, OR 97403, USA
| | - Amber L Thompson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | - Tim D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | - Ramesh Jasti
- Department of Chemistry and Biochemistry, Materials Science Institute, University of Oregon, Eugene, OR 97403, USA
| | - Harry L Anderson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
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7
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Abstract
![]()
NMR
supersequences allow multiple 2D NMR data sets to be acquired
in greatly reduced experiment durations through tailored detection
of NMR responses within concatenated modules. In NOAH (NMR by Ordered
Acquisition using 1H detection) experiments, up to five
modules can be combined (or even more when parallel modules are employed),
which in theory leads to thousands of plausible supersequences. However,
constructing a pulse program for a supersequence is highly time-consuming,
requires specialized knowledge, and is error-prone due to its complexity;
this has prevented the true potential of the NOAH concept from being
fully realized. We introduce here an online tool named GENESIS (GENEration
of Supersequences In Silico), available via https://nmr-genesis.co.uk,
which systematically generates pulse programs for arbitrary NOAH supersequences
compatible with Bruker spectrometers. The GENESIS website provides
a unified “one-stop” interface where users may obtain
customized supersequences for specific applications, together with
all associated acquisition and processing scripts, as well as detailed
instructions for running NOAH experiments. Furthermore, it enables
the rapid dissemination of new developments in NOAH sequences, such
as new modules or improvements to existing modules. Here, we present
several such enhancements, including options for solvent suppression,
new modules based on pure shift NMR, and improved artifact reduction
in HMBC and HMQC modules.
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Affiliation(s)
- Jonathan R J Yong
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - E Riks Kupče
- Bruker UK Ltd, R&D, Coventry CV4 9GH, United Kingdom
| | - Tim D W Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
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8
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Patrick CW, Woods JF, Gawel P, Otteson CE, Thompson AL, Claridge TDW, Jasti R, Anderson HL. Polyyne [3]rotaxanes: Synthesis via dicobalt carbonyl complexes and enhanced stability. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Harry Laurence Anderson
- University of Oxford Department of Chemistry 12 Mansfield RoadChemistry Research Laboratory OX1 3TA Oxford UNITED KINGDOM
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9
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Dulal P, Gharaei R, Berg A, Walters AA, Hawkins N, Claridge TDW, Kowal K, Neill S, Ritchie AJ, Ashfield R, Hill AVS, Tronci G, Russell SJ, Douglas AD. Publisher Correction: Characterisation of factors contributing to the performance of nonwoven fibrous matrices as substrates for adenovirus vectored vaccine stabilisation. Sci Rep 2021; 11:23361. [PMID: 34845277 PMCID: PMC8630089 DOI: 10.1038/s41598-021-02406-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Pawan Dulal
- Jenner Institute, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK.
| | - Robabeh Gharaei
- Clothworkers' Centre for Textile Materials Innovation for Healthcare, University of Leeds, Leeds, LS2 9JT, UK
| | - Adam Berg
- Jenner Institute, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Adam A Walters
- Jenner Institute, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Nicholas Hawkins
- Oxford Silk Group, ABRG, Department of Zoology, University of Oxford, Oxford, OX2 3RE, UK
| | - Tim D W Claridge
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Katarzyna Kowal
- Nonwovens Innovation and Research Institute Ltd, 169 Meanwood Road, Leeds, LS7 1SR, UK
| | - Steven Neill
- Nonwovens Innovation and Research Institute Ltd, 169 Meanwood Road, Leeds, LS7 1SR, UK
| | - Adam J Ritchie
- Jenner Institute, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Rebecca Ashfield
- Jenner Institute, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Adrian V S Hill
- Jenner Institute, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Giuseppe Tronci
- Clothworkers' Centre for Textile Materials Innovation for Healthcare, University of Leeds, Leeds, LS2 9JT, UK
| | - Stephen J Russell
- Clothworkers' Centre for Textile Materials Innovation for Healthcare, University of Leeds, Leeds, LS2 9JT, UK.,Nonwovens Innovation and Research Institute Ltd, 169 Meanwood Road, Leeds, LS7 1SR, UK
| | - Alexander D Douglas
- Jenner Institute, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK.
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10
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Abstract
The principles employed in parallel NMR and MRI are applied to NMR supersequences yielding as many as ten 2D NMR spectra in one measurement. We present a number of examples where two NOAH (NMR by Ordered Acquisition using 1H-detection) supersequences are recorded in parallel, thus dramatically increasing the information content obtained in a single NMR experiment. The two parallel supersequences entangled by time-sharing schemes (IPAP-seHSQC, HSQC-COSY, and HSQC-TOCSY) incorporate also modified (sequential and/or interleaved) conventional pulse schemes (modules), including HMBC, TOCSY, COSY, CLIP-COSY, NOESY, and ROESY. Such parallel supersequences can be tailored for specific applications, for instance, the analysis and characterization of molecular structure of complex organic molecules from a single measurement. In particular, the CASPER software was used to establish the structure of a tetrasaccharide, β-LNnTOMe, with a high degree of confidence from a single measurement involving a parallel NOAH-5 supersequence.
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Affiliation(s)
- Ēriks Kupče
- Bruker
UK Ltd, R&D, Banner
Lane, Coventry CV4 9GH, United Kingdom
| | - Jonathan R. J. Yong
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Tim D. W. Claridge
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
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11
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Dulal P, Gharaei R, Berg A, Walters AA, Hawkins N, Claridge TDW, Kowal K, Neill S, Ritchie AJ, Ashfield R, Hill AVS, Tronci G, Russell SJ, Douglas AD. Characterisation of factors contributing to the performance of nonwoven fibrous matrices as substrates for adenovirus vectored vaccine stabilisation. Sci Rep 2021; 11:20877. [PMID: 34686689 PMCID: PMC8536692 DOI: 10.1038/s41598-021-00065-4] [Citation(s) in RCA: 1] [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: 05/24/2021] [Accepted: 09/23/2021] [Indexed: 11/09/2022] Open
Abstract
Adenovirus vectors offer a platform technology for vaccine development. The value of the platform has been proven during the COVID-19 pandemic. Although good stability at 2-8 °C is an advantage of the platform, non-cold-chain distribution would have substantial advantages, in particular in low-income countries. We have previously reported a novel, potentially less expensive thermostabilisation approach using a combination of simple sugars and glass micro-fibrous matrix, achieving excellent recovery of adenovirus-vectored vaccines after storage at temperatures as high as 45 °C. This matrix is, however, prone to fragmentation and so not suitable for clinical translation. Here, we report an investigation of alternative fibrous matrices which might be suitable for clinical use. A number of commercially-available matrices permitted good protein recovery, quality of sugar glass and moisture content of the dried product but did not achieve the thermostabilisation performance of the original glass fibre matrix. We therefore further investigated physical and chemical characteristics of the glass fibre matrix and its components, finding that the polyvinyl alcohol present in the glass fibre matrix assists vaccine stability. This finding enabled us to identify a potentially biocompatible matrix with encouraging performance. We discuss remaining challenges for transfer of the technology into clinical use, including reliability of process performance.
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Affiliation(s)
- Pawan Dulal
- Jenner Institute, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK.
| | - Robabeh Gharaei
- grid.9909.90000 0004 1936 8403Clothworkers’ Centre for Textile Materials Innovation for Healthcare, University of Leeds, Leeds, LS2 9JT UK
| | - Adam Berg
- grid.270683.80000 0004 0641 4511Jenner Institute, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN UK
| | - Adam A. Walters
- grid.270683.80000 0004 0641 4511Jenner Institute, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN UK
| | - Nicholas Hawkins
- grid.4991.50000 0004 1936 8948Oxford Silk Group, ABRG, Department of Zoology, University of Oxford, Oxford, OX2 3RE UK
| | - Tim D. W. Claridge
- grid.4991.50000 0004 1936 8948Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA UK
| | - Katarzyna Kowal
- grid.436666.7Nonwovens Innovation and Research Institute Ltd, 169 Meanwood Road, Leeds, LS7 1SR UK
| | - Steven Neill
- grid.436666.7Nonwovens Innovation and Research Institute Ltd, 169 Meanwood Road, Leeds, LS7 1SR UK
| | - Adam J. Ritchie
- grid.270683.80000 0004 0641 4511Jenner Institute, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN UK
| | - Rebecca Ashfield
- grid.270683.80000 0004 0641 4511Jenner Institute, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN UK
| | - Adrian V. S. Hill
- grid.270683.80000 0004 0641 4511Jenner Institute, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN UK
| | - Giuseppe Tronci
- grid.9909.90000 0004 1936 8403Clothworkers’ Centre for Textile Materials Innovation for Healthcare, University of Leeds, Leeds, LS2 9JT UK
| | - Stephen J. Russell
- grid.9909.90000 0004 1936 8403Clothworkers’ Centre for Textile Materials Innovation for Healthcare, University of Leeds, Leeds, LS2 9JT UK ,grid.436666.7Nonwovens Innovation and Research Institute Ltd, 169 Meanwood Road, Leeds, LS7 1SR UK
| | - Alexander D. Douglas
- grid.270683.80000 0004 0641 4511Jenner Institute, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN UK
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12
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Schuller M, Butler RE, Ariza A, Tromans-Coia C, Jankevicius G, Claridge TDW, Kendall SL, Goh S, Stewart GR, Ahel I. Molecular basis for DarT ADP-ribosylation of a DNA base. Nature 2021; 596:597-602. [PMID: 34408320 DOI: 10.1038/s41586-021-03825-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [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: 10/29/2020] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
ADP-ribosyltransferases use NAD+ to catalyse substrate ADP-ribosylation1, and thereby regulate cellular pathways or contribute to toxin-mediated pathogenicity of bacteria2-4. Reversible ADP-ribosylation has traditionally been considered a protein-specific modification5, but recent in vitro studies have suggested nucleic acids as targets6-9. Here we present evidence that specific, reversible ADP-ribosylation of DNA on thymidine bases occurs in cellulo through the DarT-DarG toxin-antitoxin system, which is found in a variety of bacteria (including global pathogens such as Mycobacterium tuberculosis, enteropathogenic Escherichia coli and Pseudomonas aeruginosa)10. We report the structure of DarT, which identifies this protein as a diverged member of the PARP family. We provide a set of high-resolution structures of this enzyme in ligand-free and pre- and post-reaction states, which reveals a specialized mechanism of catalysis that includes a key active-site arginine that extends the canonical ADP-ribosyltransferase toolkit. Comparison with PARP-HPF1, a well-established DNA repair protein ADP-ribosylation complex, offers insights into how the DarT class of ADP-ribosyltransferases evolved into specific DNA-modifying enzymes. Together, our structural and mechanistic data provide details of this PARP family member and contribute to a fundamental understanding of the ADP-ribosylation of nucleic acids. We also show that thymine-linked ADP-ribose DNA adducts reversed by DarG antitoxin (functioning as a noncanonical DNA repair factor) are used not only for targeted DNA damage to induce toxicity, but also as a signalling strategy for cellular processes. Using M. tuberculosis as an exemplar, we show that DarT-DarG regulates growth by ADP-ribosylation of DNA at the origin of chromosome replication.
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Affiliation(s)
- Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rachel E Butler
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Antonio Ariza
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Gytis Jankevicius
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Biozentrum, University of Basel, Basel, Switzerland
| | - Tim D W Claridge
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Sharon L Kendall
- Centre for Emerging, Endemic and Exotic Disease, Pathology and Population Sciences, The Royal Veterinary College, Hatfield, UK
| | - Shan Goh
- Centre for Emerging, Endemic and Exotic Disease, Pathology and Population Sciences, The Royal Veterinary College, Hatfield, UK
| | - Graham R Stewart
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK.
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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13
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Yong JRJ, Hansen AL, Kupče Ē, Claridge TDW. Increasing sensitivity and versatility in NMR supersequences with new HSQC-based modules. J Magn Reson 2021; 329:107027. [PMID: 34246882 DOI: 10.1016/j.jmr.2021.107027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 05/22/2023]
Abstract
The sensitivity-enhanced HSQC, as well as HSQC-TOCSY, experiments have been modified for incorporation into NOAH (NMR by Ordered Acquisition using 1H detection) supersequences, adding diversity for 13C and 15N modules. Importantly, these heteronuclear modules have been specifically tailored to preserve the magnetisation required for subsequent acquisition of other heteronuclear or homonuclear modules in a supersequence. In addition, we present protocols for optimally combining HSQC and HSQC-TOCSY elements within the same supersequences, yielding high-quality 2D spectra suitable for structure characterisation but with greatly reduced experiment durations. We further demonstrate that these time savings can translate to increased detection sensitivity per unit time.
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Affiliation(s)
- Jonathan R J Yong
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Alexandar L Hansen
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH 43210, USA
| | - Ēriks Kupče
- Bruker UK Ltd., Banner Lane, Coventry CV4 9GH, UK
| | - Tim D W Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK.
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14
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Kupče Ē, Mote KR, Webb A, Madhu PK, Claridge TDW. Multiplexing experiments in NMR and multi-nuclear MRI. Prog Nucl Magn Reson Spectrosc 2021; 124-125:1-56. [PMID: 34479710 DOI: 10.1016/j.pnmrs.2021.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 05/22/2023]
Abstract
Multiplexing NMR experiments by direct detection of multiple free induction decays (FIDs) in a single experiment offers a dramatic increase in the spectral information content and often yields significant improvement in sensitivity per unit time. Experiments with multi-FID detection have been designed with both homonuclear and multinuclear acquisition, and the advent of multiple receivers on commercial spectrometers opens up new possibilities for recording spectra from different nuclear species in parallel. Here we provide an extensive overview of such techniques, designed for applications in liquid- and solid-state NMR as well as in hyperpolarized samples. A brief overview of multinuclear MRI is also provided, to stimulate cross fertilization of ideas between the two areas of research (NMR and MRI). It is shown how such techniques enable the design of experiments that allow structure elucidation of small molecules from a single measurement. Likewise, in biomolecular NMR experiments multi-FID detection allows complete resonance assignment in proteins. Probes with multiple RF microcoils routed to multiple NMR receivers provide an alternative way of increasing the throughput of modern NMR systems, effectively reducing the cost of NMR analysis and increasing the information content at the same time. Solid-state NMR experiments have also benefited immensely from both parallel and sequential multi-FID detection in a variety of multi-dimensional pulse schemes. We are confident that multi-FID detection will become an essential component of future NMR methodologies, effectively increasing the sensitivity and information content of NMR measurements.
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Affiliation(s)
- Ēriks Kupče
- Bruker UK Ltd., Banner Lane, Coventry CV4 9GH, United Kingdom.
| | - Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research-Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Andrew Webb
- Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Perunthiruthy K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research-Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Tim D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
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15
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16
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Abstract
Template-directed synthesis has been used to prepare a fully π-conjugated cyclic porphyrin octamer, composed of both β,meso,β-edge-fused porphyrin tape units and butadiyne-linked porphyrins. The UV-vis-NIR spectra of this partially fused nanoring show that π-conjugation extends around the whole macrocycle, and that it has a smaller HOMO-LUMO gap than its all-butadiyne-linked analogue, as predicted by TD-DFT calculations. The 1H NMR shifts of the bound templates confirm the disrupted aromaticity of the edge-fused porphyrins in the neutral nanoring. NMR oxidation titrations reveal the presence of a global paratropic ring current in its 4+ and 8+ oxidation states and of a global diatropic ring current in the 6+ state of the partially fused ring. The paratropic ring current in the 4+ oxidation state is about four times stronger than that in the all-butadiyne-linked cyclic octamer complex, whereas the diatropic current in the 6+ state is about 40% weaker. Two isomeric K-shaped tetrapyridyl templates with trifluoromethyl substituents at different positions were used to probe the distribution of the ring current in the 4+, 6+, and 8+ oxidation states by 19F NMR, demonstrating that the ring currents are global and homogeneous.
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Affiliation(s)
- Sebastian M Kopp
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, United Kingdom
| | - Henrik Gotfredsen
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, United Kingdom
| | - Jie-Ren Deng
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, United Kingdom
| | - Tim D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, United Kingdom
| | - Harry L Anderson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, United Kingdom
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17
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Aguilar JA, Cassani J, Probert F, Palace J, Claridge TDW, Botana A, Kenwright AM. Reliable, high-quality suppression of NMR signals arising from water and macromolecules: application to bio-fluid analysis. Analyst 2020; 144:7270-7277. [PMID: 31693024 DOI: 10.1039/c9an01005j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Analysis of metabolites in biofluids using nuclear magnetic resonance often requires the suppression of obscuring signals arising from water and macromolecules. This paper analyses the limitations of the pulse sequence most commonly used to achieve such suppression (presat-CPMG) and proposes new pulse sequences that do not share those limitations. The utility of these improved pulse sequences is demonstrated in a metabolomic study of multiple sclerosis (MS) patients.
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Affiliation(s)
- Juan A Aguilar
- Department of Chemistry. Durham University, South Road, Durham, DH1 3LE, UK.
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18
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Claridge TDW, Mayzel M, Kupče Ē. Triplet NOAH supersequences optimised for small molecule structure characterisation. Magn Reson Chem 2019; 57:946-952. [PMID: 31066946 DOI: 10.1002/mrc.4887] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 05/22/2023]
Abstract
A series of NMR supersequences are presented for the time-efficient structure characterisation of small molecules in the solution state. These triplet sequences provide HMBC, HSQC, and one homonuclear correlation experiment of choice according to the NMR by Ordered Acquisition using 1 H detection principle. The experiments are demonstrated to be compatible with non-uniform sampling schemes and may be acquired and processed under full automation.
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Affiliation(s)
- Tim D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, UK
| | - Maksim Mayzel
- Application Science CH, MRS Division, Bruker BioSpin AG, Fällanden, Switzerland
| | - Ēriks Kupče
- Advanced Applications Development, Bruker UK Ltd., Coventry, UK
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19
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Chatzopoulou M, Claridge TDW, Davies KE, Davies SG, Elsey DJ, Emer E, Fletcher AM, Harriman S, Robinson N, Rowley JA, Russell AJ, Tinsley JM, Weaver R, Wilkinson IVL, Willis NJ, Wilson FX, Wynne GM. Isolation, Structural Identification, Synthesis, and Pharmacological Profiling of 1,2-trans-Dihydro-1,2-diol Metabolites of the Utrophin Modulator Ezutromid. J Med Chem 2019; 63:2547-2556. [DOI: 10.1021/acs.jmedchem.9b01547] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Maria Chatzopoulou
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Tim D. W. Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Kay E. Davies
- Department of Physiology, Anatomy and Genetics, MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Stephen G. Davies
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - David J. Elsey
- Summit Therapeutics plc, 136a Eastern Avenue, Milton Park, Abingdon OX14 4SB, United Kingdom
| | - Enrico Emer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Ai M. Fletcher
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Shawn Harriman
- Summit Therapeutics plc, One Broadway, 14th Floor, Cambridge, Massachusetts 02142, United States
| | - Neil Robinson
- S.H.B. Enterprises Ltd., 55 Station Road, Beaconsfield HP19 1QL, United Kingdom
| | - Jessica A. Rowley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Angela J. Russell
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3PQ, United Kingdom
| | - Jonathon M. Tinsley
- Summit Therapeutics plc, 136a Eastern Avenue, Milton Park, Abingdon OX14 4SB, United Kingdom
| | - Richard Weaver
- XenoGesis Ltd., BioCity Nottingham, Pennyfoot Street, Nottingham NG1 1GF, United Kingdom
| | - Isabel V. L. Wilkinson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Nicky J. Willis
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Francis X. Wilson
- Summit Therapeutics plc, 136a Eastern Avenue, Milton Park, Abingdon OX14 4SB, United Kingdom
| | - Graham M. Wynne
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
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20
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Kupče Ē, Claridge TDW. New NOAH modules for structure elucidation at natural isotopic abundance. J Magn Reson 2019; 307:106568. [PMID: 31421539 DOI: 10.1016/j.jmr.2019.106568] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/26/2019] [Accepted: 08/05/2019] [Indexed: 05/22/2023]
Abstract
We introduce several new NOAH modules designed for NMR supersequences that allow structure elucidation of small organic molecules from a single measurement. We show that double isotope filters (ZZ-filters) increase the flexibility of module permutation within the NMR supersequences, optimising combinations exploiting 15N and 13C nuclides. The time-shared 2BOB module combined with the ZZ-HMBC module (yielding NOAH-2 BO) provides an example of extending the NMR supersequences with parallel experiments (here 2BOB) that are incompatible with sequential implementation. Finally, the PANSY-COSY module combined with the HSQC sequence (yielding NOAH-2 SC2) provides an example of incorporating multiple receiver experiments into NMR supersequences opening new avenues for designing information rich NMR experiments. The new NOAH supersequences were utilized in computer assisted structure elucidation (CASE) study accomplished using the CMCse software.
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Affiliation(s)
- Ēriks Kupče
- Bruker UK Limited, Banner Lane, Coventry CV4 9GH, UK.
| | - Tim D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
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21
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Robertson GP, Odell B, Kuprov I, Dixon DJ, Claridge TDW. Measuring Spin Relaxation Rates Using Satellite Exchange NMR Spectroscopy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Gerard P. Robertson
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA UK
| | - Barbara Odell
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA UK
| | - Ilya Kuprov
- School of Chemistry; University of Southampton; Highfield Campus Southampton SO17 1BJ UK
| | - Darren J. Dixon
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA UK
| | - Tim D. W. Claridge
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA UK
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22
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Robertson GP, Odell B, Kuprov I, Dixon DJ, Claridge TDW. Measuring Spin Relaxation Rates Using Satellite Exchange NMR Spectroscopy. Angew Chem Int Ed Engl 2018; 57:7498-7502. [PMID: 29575317 DOI: 10.1002/anie.201801322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 01/31/2018] [Indexed: 11/10/2022]
Abstract
An approach to the indirect measurement of nuclear spin relaxation rates of low-magnetogyric ratio (γ) nuclei using the process of satellite exchange is described. The method does not require the observation of, or even the ability to provide radio-frequency pulses to, the low-γ nucleus, but requires this to be scalar coupled to an NMR observable nucleus, such as 31 P or 1 H, making it especially attractive for the study of diamagnetic transition metals. In situations where spin relaxation is dominated by chemical shift anisotropy (CSA), the determination of the longitudinal spin relaxation time constant (T1 ) of the metal becomes possible, as illustrated for 195 Pt and 107/109 Ag.
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Affiliation(s)
- Gerard P Robertson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Barbara Odell
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Darren J Dixon
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Tim D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
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23
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McAllister TE, Yeh TL, Abboud MI, Leung IKH, Hookway ES, King ONF, Bhushan B, Williams ST, Hopkinson RJ, Münzel M, Loik ND, Chowdhury R, Oppermann U, Claridge TDW, Goto Y, Suga H, Schofield CJ, Kawamura A. Non-competitive cyclic peptides for targeting enzyme-substrate complexes. Chem Sci 2018; 9:4569-4578. [PMID: 29899950 PMCID: PMC5969509 DOI: 10.1039/c8sc00286j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/23/2018] [Indexed: 01/19/2023] Open
Abstract
Affinity reagents are of central importance for selectively identifying proteins and investigating their interactions. We report on the development and use of cyclic peptides, identified by mRNA display-based RaPID methodology, that are selective for, and tight binders of, the human hypoxia inducible factor prolyl hydroxylases (PHDs) - enzymes crucial in hypoxia sensing. Biophysical analyses reveal the cyclic peptides to bind in a distinct site, away from the enzyme active site pocket, enabling conservation of substrate binding and catalysis. A biotinylated cyclic peptide captures not only the PHDs, but also their primary substrate hypoxia inducible factor HIF1-α. Our work highlights the potential for tight, non-active site binding cyclic peptides to act as promising affinity reagents for studying protein-protein interactions.
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Affiliation(s)
- T E McAllister
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - T-L Yeh
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - M I Abboud
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - I K H Leung
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
- School of Chemical Sciences , The University of Auckland , Private Bag 92019 , Auckland 1142 , New Zealand
| | - E S Hookway
- Botnar Research Centre , NIHR Oxford Biomedical Research Unit , University of Oxford , Windmill Road , Oxford , OX3 7LD , UK
| | - O N F King
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - B Bhushan
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
- Division of Cardiovascular Medicine , Radcliffe Department of Medicine , University of Oxford , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
| | - S T Williams
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - R J Hopkinson
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - M Münzel
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - N D Loik
- Department of Chemistry , Graduate School of Science , The University of Tokyo , Tokyo 113-0033 , Japan
| | - R Chowdhury
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - U Oppermann
- Botnar Research Centre , NIHR Oxford Biomedical Research Unit , University of Oxford , Windmill Road , Oxford , OX3 7LD , UK
| | - T D W Claridge
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - Y Goto
- Department of Chemistry , Graduate School of Science , The University of Tokyo , Tokyo 113-0033 , Japan
| | - H Suga
- Department of Chemistry , Graduate School of Science , The University of Tokyo , Tokyo 113-0033 , Japan
- JST , CREST , The University of Tokyo , Tokyo 113-0033 , Japan
| | - C J Schofield
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - A Kawamura
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
- Division of Cardiovascular Medicine , Radcliffe Department of Medicine , University of Oxford , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
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24
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Cremers J, Haver R, Rickhaus M, Gong JQ, Favereau L, Peeks MD, Claridge TDW, Herz LM, Anderson HL. Template-Directed Synthesis of a Conjugated Zinc Porphyrin Nanoball. J Am Chem Soc 2018; 140:5352-5355. [PMID: 29638125 DOI: 10.1021/jacs.8b02552] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We report the template-directed synthesis of a π-conjugated 14-porphyrin nanoball. This structure consists of two intersecting nanorings containing six and 10 porphyrin units. Fluorescence upconversion spectroscopy experiments demonstrate that electronic excitation delocalizes over the whole three-dimensional π system in less than 0.3 ps if the nanoball is bound to its templates or over 2 ps if the nanoball is empty.
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Affiliation(s)
- Jonathan Cremers
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Oxford OX1 3TA , United Kingdom
| | - Renée Haver
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Oxford OX1 3TA , United Kingdom
| | - Michel Rickhaus
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Oxford OX1 3TA , United Kingdom
| | - Juliane Q Gong
- Clarendon Laboratory, Department of Physics , University of Oxford , Oxford OX1 3PU , United Kingdom
| | - Ludovic Favereau
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Oxford OX1 3TA , United Kingdom
| | - Martin D Peeks
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Oxford OX1 3TA , United Kingdom
| | - Tim D W Claridge
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Oxford OX1 3TA , United Kingdom
| | - Laura M Herz
- Clarendon Laboratory, Department of Physics , University of Oxford , Oxford OX1 3PU , United Kingdom
| | - Harry L Anderson
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Oxford OX1 3TA , United Kingdom
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25
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Abstract
New NOAH supersequences (NMR by Ordered Acquisition using 1H-detection) are introduced that allow fast structure elucidation of organic molecules from a single measurement.
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Affiliation(s)
| | - Tim D. W. Claridge
- Department of Chemistry
- University of Oxford
- Chemistry Research Laboratory
- Oxford
- UK
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26
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Jurynczyk M, Probert F, Yeo T, Tackley G, Claridge TDW, Cavey A, Woodhall MR, Arora S, Winkler T, Schiffer E, Vincent A, DeLuca G, Sibson NR, Isabel Leite M, Waters P, Anthony DC, Palace J. Metabolomics reveals distinct, antibody-independent, molecular signatures of MS, AQP4-antibody and MOG-antibody disease. Acta Neuropathol Commun 2017; 5:95. [PMID: 29208041 PMCID: PMC5718082 DOI: 10.1186/s40478-017-0495-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 11/13/2017] [Indexed: 11/11/2022] Open
Abstract
The overlapping clinical features of relapsing remitting multiple sclerosis (RRMS), aquaporin-4 (AQP4)-antibody (Ab) neuromyelitis optica spectrum disorder (NMOSD), and myelin oligodendrocyte glycoprotein (MOG)-Ab disease mean that detection of disease specific serum antibodies is the gold standard in diagnostics. However, antibody levels are not prognostic and may become undetectable after treatment or during remission. Therefore, there is still a need to discover antibody-independent biomarkers. We sought to discover whether plasma metabolic profiling could provide biomarkers of these three diseases and explore if the metabolic differences are independent of antibody titre. Plasma samples from 108 patients (34 RRMS, 54 AQP4-Ab NMOSD, and 20 MOG-Ab disease) were analysed by nuclear magnetic resonance spectroscopy followed by lipoprotein profiling. Orthogonal partial-least squares discriminatory analysis (OPLS-DA) was used to identify significant differences in the plasma metabolite concentrations and produce models (mathematical algorithms) capable of identifying these diseases. In all instances, the models were highly discriminatory, with a distinct metabolite pattern identified for each disease. In addition, OPLS-DA identified AQP4-Ab NMOSD patient samples with low/undetectable antibody levels with an accuracy of 92%. The AQP4-Ab NMOSD metabolic profile was characterised by decreased levels of scyllo-inositol and small high density lipoprotein particles along with an increase in large low density lipoprotein particles relative to both RRMS and MOG-Ab disease. RRMS plasma exhibited increased histidine and glucose, along with decreased lactate, alanine, and large high density lipoproteins while MOG-Ab disease plasma was defined by increases in formate and leucine coupled with decreased myo-inositol. Despite overlap in clinical measures in these three diseases, the distinct plasma metabolic patterns support their distinct serological profiles and confirm that these conditions are indeed different at a molecular level. The metabolites identified provide a molecular signature of each condition which is independent of antibody titre and EDSS, with potential use for disease monitoring and diagnosis.
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Affiliation(s)
- Maciej Jurynczyk
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Level 3, West Wing, Headley Way, Oxford, OX3 9DU, UK
- Department of Neurology, Medical University of Lodz, Lodz, Poland
| | - Fay Probert
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.
| | - Tianrong Yeo
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
- Department of Neurology, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore
| | - George Tackley
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Level 3, West Wing, Headley Way, Oxford, OX3 9DU, UK
| | - Tim D W Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Ana Cavey
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Level 3, West Wing, Headley Way, Oxford, OX3 9DU, UK
| | - Mark R Woodhall
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Level 3, West Wing, Headley Way, Oxford, OX3 9DU, UK
| | - Siddharth Arora
- Mathematical Institute, University of Oxford, Woodstock Rd, Oxford, OX2 6GC, UK
| | | | - Eric Schiffer
- Numares AG, Am Biopark 9, 93053, Regensburg, Germany
| | - Angela Vincent
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Level 3, West Wing, Headley Way, Oxford, OX3 9DU, UK
| | - Gabriele DeLuca
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Level 3, West Wing, Headley Way, Oxford, OX3 9DU, UK
| | - Nicola R Sibson
- Cancer Research UK & Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, OX37DQ, Oxford, UK
| | - M Isabel Leite
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Level 3, West Wing, Headley Way, Oxford, OX3 9DU, UK
| | - Patrick Waters
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Level 3, West Wing, Headley Way, Oxford, OX3 9DU, UK
| | - Daniel C Anthony
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.
| | - Jacqueline Palace
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Level 3, West Wing, Headley Way, Oxford, OX3 9DU, UK.
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Kupče Ē, Claridge TDW. NOAH: NMR Supersequences for Small Molecule Analysis and Structure Elucidation. Angew Chem Int Ed Engl 2017; 56:11779-11783. [DOI: 10.1002/anie.201705506] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/17/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Ēriks Kupče
- Bruker (UK) Ltd.; Banner Lane Coventry CV4 9GH UK
| | - Tim D. W. Claridge
- Department of Chemistry; University of Oxford; Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA UK
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Probert F, Ruiz-Rodado V, Vruchte DT, Nicoli ER, Claridge TDW, Wassif CA, Farhat N, Porter FD, Platt FM, Grootveld M. NMR analysis reveals significant differences in the plasma metabolic profiles of Niemann Pick C1 patients, heterozygous carriers, and healthy controls. Sci Rep 2017; 7:6320. [PMID: 28740230 PMCID: PMC5524790 DOI: 10.1038/s41598-017-06264-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 02/27/2017] [Accepted: 06/09/2017] [Indexed: 02/07/2023] Open
Abstract
Niemann-Pick type C1 (NPC1) disease is a rare autosomal recessive, neurodegenerative lysosomal storage disorder, which presents with a range of clinical phenotypes and hence diagnosis remains a challenge. In view of these difficulties, the search for a novel, NPC1-specific biomarker (or set of biomarkers) is a topic of much interest. Here we employed high-resolution 1H nuclear magnetic resonance spectroscopy coupled with advanced multivariate analysis techniques in order to explore and seek differences between blood plasma samples acquired from NPC1 (untreated and miglustat treated), heterozygote, and healthy control subjects. Using this approach, we were able to identify NPC1 disease with 91% accuracy confirming that there are significant differences in the NMR plasma metabolic profiles of NPC1 patients when compared to healthy controls. The discrimination between NPC1 (both miglustat treated and untreated) and healthy controls was dominated by lipoprotein triacylglycerol 1H NMR resonances and isoleucine. Heterozygote plasma samples displayed also increases in the intensities of selected lipoprotein triacylglycerol 1H NMR signals over those of healthy controls. The metabolites identified could represent useful biomarkers in the future and provide valuable insight in to the underlying pathology of NPC1 disease.
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Affiliation(s)
- Fay Probert
- Department of Pharmacology, De Montfort University, Leicester, UK.,Department of Pharmacology, University of Oxford, Oxford, UK
| | | | | | | | | | - Christopher A Wassif
- Department of Pharmacology, University of Oxford, Oxford, UK.,Section of Molecular Dysmorphology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institute of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Nicole Farhat
- Section of Molecular Dysmorphology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institute of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Forbes D Porter
- Section of Molecular Dysmorphology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institute of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Frances M Platt
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Martin Grootveld
- Department of Pharmacology, De Montfort University, Leicester, UK.
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Cremers J, Richert S, Kondratuk DV, Claridge TDW, Timmel CR, Anderson HL. Nanorings with copper(ii) and zinc(ii) centers: forcing copper porphyrins to bind axial ligands in heterometallated oligomers. Chem Sci 2016; 7:6961-6968. [PMID: 28451130 PMCID: PMC5355962 DOI: 10.1039/c6sc01809b] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 08/01/2016] [Indexed: 01/22/2023] Open
Abstract
The affinity of copper(ii) porphyrins for pyridine ligands is extremely weak, but oligo-pyridine templates can be used to direct the synthesis of Cu-containing cyclic porphyrin oligomers when they also have Zn centers. We report the synthesis of two heterometallated nanorings: a six-porphyrin ring prepared from a Zn/Cu/Zn linear trimer and a ten-porphyrin ring prepared from a Zn/Zn/Cu/Zn/Zn pentamer. Both these macrocycles have copper porphyrins at two specific positions across the diameter of the ring and zinc at other sites. The presence of a paramagnetic metal results in broadening of the 1H NMR spectra and reduces the relaxation time constants (T1 and T2). The changes in T1 provide quantitative information on the distance of each proton from the copper atom. The Zn/Zn/Cu/Zn/Zn linear porphyrin pentamer binds strongly to a penta-pyridyl template, despite the weakness of the Cu-N interaction, because of the chelate cooperativity of the neighboring Zn-N coordination. The stabilities of a family of four linear porphyrin pentamer complexes were determined by UV-vis-NIR titration and analyzed using a chemical double-mutant cycle. The results show that the free energy of interaction of a copper center to axial pyridine ligands is -6.2 kJ mol-1 when the entropy cost of bringing together the two molecules has already been paid by pyridine-zinc interactions. The development of template-directed approaches to the synthesis of nanorings with combinations of different metals at specific positions around the ring opens up many possibilities for controlling the photophysical behavior of these supramolecular systems and for probing their conformations by EPR.
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Affiliation(s)
- Jonathan Cremers
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , Oxford OX1 3TA , UK .
| | - Sabine Richert
- Department of Chemistry , University of Oxford , Centre for Advanced Electron Spin Resonance , Oxford OX1 3QR , UK
| | - Dmitry V Kondratuk
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , Oxford OX1 3TA , UK .
| | - Tim D W Claridge
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , Oxford OX1 3TA , UK .
| | - Christiane R Timmel
- Department of Chemistry , University of Oxford , Centre for Advanced Electron Spin Resonance , Oxford OX1 3QR , UK
| | - Harry L Anderson
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , Oxford OX1 3TA , UK .
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Pérez-Victoria I, Boutureira O, Claridge TDW, Davis BG. Glycosyldiselenides as lectin ligands detectable by NMR in biofluids. Chem Commun (Camb) 2016; 51:12208-11. [PMID: 26134709 DOI: 10.1039/c5cc03952e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The ability of glycosyldiselenides to act as lectin ligands and their selective detection in plasma by (77)Se NMR is reported.
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Affiliation(s)
- Ignacio Pérez-Victoria
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK.
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31
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Rousseaux SL, Gong JQ, Haver R, Odell B, Claridge TDW, Herz LM, Anderson HL. Self-Assembly of Russian Doll Concentric Porphyrin Nanorings. J Am Chem Soc 2015; 137:12713-8. [PMID: 26378660 PMCID: PMC4655919 DOI: 10.1021/jacs.5b07956] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Indexed: 12/17/2022]
Abstract
Electronic communication between concentric macrocycles with wave functions that extend around their circumferences can lead to remarkable behavior, as illustrated by multiwalled carbon nanotubes and photosynthetic chlorophyll arrays. However, it is difficult to hold one π-conjugated molecular ring inside another. Here, we show that ring-in-ring complexes, consisting of a 6-porphyrin ring locked inside a 12-porphyrin ring, can be assembled by placing different metals in the two rings (zinc and aluminum). A bridging ligand with carboxylate and imidazole binding sites forms spokes between the two rings, resulting in a highly cooperative supramolecular self-assembly process. Excitation is transferred from the inner 6-ring to the outer 12-ring of this Russian doll complex within 40 ps. These complexes lead to a form of template-directed synthesis in which one nanoring promotes formation of a larger concentric homologous ring; here, the effective template is an eight-component noncovalent assembly. Russian doll templating provides a new approach to amplifying the size of a covalent nanostructure.
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Affiliation(s)
- Sophie
A. L. Rousseaux
- Department
of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, United Kingdom
| | - Juliane Q. Gong
- Department
of Physics, University of Oxford, Clarendon Laboratory, Oxford OX1 3PU, United Kingdom
| | - Renée Haver
- Department
of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, United Kingdom
| | - Barbara Odell
- Department
of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, United Kingdom
| | - Tim D. W. Claridge
- Department
of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, United Kingdom
| | - Laura M. Herz
- Department
of Physics, University of Oxford, Clarendon Laboratory, Oxford OX1 3PU, United Kingdom
| | - Harry L. Anderson
- Department
of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, United Kingdom
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32
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Probert F, Ruiz-Rodado V, Zhang X, te Vruchte D, Claridge TDW, Edgar M, Tocchio AZ, Lachmann RH, Platt FM, Grootveld M. Urinary excretion and metabolism of miglustat and valproate in patients with Niemann-Pick type C1 disease: One- and two-dimensional solution-state (1)H NMR studies. J Pharm Biomed Anal 2015; 117:276-88. [PMID: 26397207 DOI: 10.1016/j.jpba.2015.08.011] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 08/04/2015] [Accepted: 08/09/2015] [Indexed: 10/23/2022]
Abstract
Niemann-Pick type C1 (NP-C1) disease is a neurodegenerative lysosomal storage disease for which the only approved therapy is miglustat (MGS). In this study we explored the applications and value of both one- and two-dimensional high-resolution NMR analysis strategies to the detection and quantification of MGS and its potential metabolites in urine samples collected from NP-C1 disease patients (n=47), and also applied these techniques to the analysis of the anticonvulsant drug valproate and one of its major metabolites in ca. 30% of these samples (i.e. from those who were also receiving this agent for the control of epileptic seizures). A combination of high-resolution 1D and 2D TOCSY/NOESY techniques confirmed the identity of MGS in the urinary (1)H NMR profiles of NP-C1 patients treated with this agent (n=25), and its quantification was readily achievable via electronic integration of selected 1D resonance intensities. However, this analysis provided little or no evidence for its metabolism in vivo, observations consistent with those acquired in corresponding experiments performed involving an in vitro microsomal system. Contrastingly, the major valproate metabolite 1-O-valproyl-β-glucuronide was readily detectable and quantifiable in 14/47 of the urine samples investigated, despite some resonance overlap problems (identification of this agent was confirmed by experiments involving equilibration of these samples with β-glucuronidase, a process liberating free valproate). In order to facilitate and validate the detection of MGS in urine specimens, full assignments of the (1)H NMR spectra of MGS in both buffered aqueous (pH 7.10) and deuterated methanol solvent systems were also made. The pharmacological and bioanalytical significance of data acquired are discussed, with special reference to the advantages offered by high-resolution NMR analysis.
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Affiliation(s)
- Fay Probert
- Leicester School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, UK
| | - Victor Ruiz-Rodado
- Leicester School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, UK
| | - Xiaoyu Zhang
- Leicester School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, UK; School of Pharmacy, China Pharmaceutical University, Jiangning Campus, 639 Longmian Avenue, Jiangning District, Nanjing, Jiangsu 211198 China
| | - Danielle te Vruchte
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Tim D W Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford Mansfield Road, Oxford OX1 3TA, UK
| | - Mark Edgar
- Department of Chemistry, Loughborough University, Loughborough, LE11 3TU, UK
| | - Anna Zonato Tocchio
- Leicester School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, UK
| | - Robin H Lachmann
- Charles Dent Metabolic Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | - Frances M Platt
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Martin Grootveld
- Leicester School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, UK.
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33
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Gray E, Larkin JR, Claridge TDW, Talbot K, Sibson NR, Turner MR. The longitudinal cerebrospinal fluid metabolomic profile of amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener 2015; 16:456-63. [PMID: 26121274 PMCID: PMC4720042 DOI: 10.3109/21678421.2015.1053490] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 04/19/2015] [Indexed: 11/25/2022]
Abstract
Neurochemical biomarkers are urgently sought in ALS. Metabolomic analysis of cerebrospinal fluid (CSF) using proton nuclear magnetic resonance ((1)H-NMR) spectroscopy is a highly sensitive method capable of revealing nervous system cellular pathology. The (1)H-NMR CSF metabolomic signature of ALS was sought in a longitudinal cohort. Six-monthly serial collection was performed in ALS patients across a range of clinical sub-types (n = 41) for up to two years, and in healthy controls at a single time-point (n = 14). A multivariate statistical approach, partial least squares discriminant analysis, was used to determine differences between the NMR spectra from patients and controls. Significantly predictive models were found using those patients with at least one year's interval between recruitment and the second sample. Glucose, lactate, citric acid and, unexpectedly, ethanol were the discriminating metabolites elevated in ALS. It is concluded that (1)H-NMR captured the CSF metabolomic signature associated with derangements in cellular energy utilization connected with ALS, and was most prominent in comparisons using patients with longer disease duration. The specific metabolites identified support the concept of a hypercatabolic state, possibly involving mitochondrial dysfunction specifically. Endogenous ethanol in the CSF may be an unrecognized novel marker of neuronal tissue injury in ALS.
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Affiliation(s)
- Elizabeth Gray
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
| | - James R. Larkin
- Cancer Research UK and Medical Research Council, Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK
| | | | - Kevin Talbot
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
| | - Nicola R. Sibson
- Cancer Research UK and Medical Research Council, Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK
| | - Martin R. Turner
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
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34
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Liu S, Kondratuk DV, Rousseaux SAL, Gil-Ramírez G, O'Sullivan MC, Cremers J, Claridge TDW, Anderson HL. Caterpillar track complexes in template-directed synthesis and correlated molecular motion. Angew Chem Int Ed Engl 2015; 54:5355-9. [PMID: 25683453 PMCID: PMC4471551 DOI: 10.1002/anie.201412293] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [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: 12/22/2014] [Revised: 01/29/2015] [Indexed: 01/05/2023]
Abstract
Small alterations to the structure of a star-shaped template totally change its mode of operation. The hexapyridyl template directs the conversion of a porphyrin dimer to the cyclic hexamer, but deleting one pyridine site changes the product to the cyclic decamer, while deleting two binding sites changes the product to the cyclic octamer. This surprising switch in selectivity is explained by the formation of 2:1 caterpillar track complexes, in which two template wheels bind inside the nanoring. Caterpillar track complexes can also be prepared by binding the hexapyridyl template inside the 8- and 10-porphyrin nanorings. NMR exchange spectroscopy (EXSY) experiments show that these complexes exhibit correlated motion, in which the conrotatory rotation of the two template wheels is coupled to rotation of the nanoring track. In the case of the 10-porphyrin system, the correlated motion can be locked by binding palladium(II) dichloride between the two templates.
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Affiliation(s)
- Shiqi Liu
- Department of Chemistry, University of Oxford, Chemistry Research LaboratoryOxford, OX1 3TA (UK)
| | - Dmitry V Kondratuk
- Department of Chemistry, University of Oxford, Chemistry Research LaboratoryOxford, OX1 3TA (UK)
| | - Sophie A L Rousseaux
- Department of Chemistry, University of Oxford, Chemistry Research LaboratoryOxford, OX1 3TA (UK)
| | - Guzmán Gil-Ramírez
- Department of Chemistry, University of Oxford, Chemistry Research LaboratoryOxford, OX1 3TA (UK)
| | - Melanie C O'Sullivan
- Department of Chemistry, University of Oxford, Chemistry Research LaboratoryOxford, OX1 3TA (UK)
| | - Jonathan Cremers
- Department of Chemistry, University of Oxford, Chemistry Research LaboratoryOxford, OX1 3TA (UK)
| | - Tim D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research LaboratoryOxford, OX1 3TA (UK)
| | - Harry L Anderson
- Department of Chemistry, University of Oxford, Chemistry Research LaboratoryOxford, OX1 3TA (UK)
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Liu S, Kondratuk DV, Rousseaux SAL, Gil-Ramírez G, O'Sullivan MC, Cremers J, Claridge TDW, Anderson HL. Caterpillar Track Complexes in Template-Directed Synthesis and Correlated Molecular Motion. ACTA ACUST UNITED AC 2015; 127:5445-5449. [PMID: 27546919 PMCID: PMC4974918 DOI: 10.1002/ange.201412293] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [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: 12/22/2014] [Revised: 01/29/2015] [Indexed: 01/03/2023]
Abstract
Small alterations to the structure of a star‐shaped template totally change its mode of operation. The hexapyridyl template directs the conversion of a porphyrin dimer to the cyclic hexamer, but deleting one pyridine site changes the product to the cyclic decamer, while deleting two binding sites changes the product to the cyclic octamer. This surprising switch in selectivity is explained by the formation of 2:1 caterpillar track complexes, in which two template wheels bind inside the nanoring. Caterpillar track complexes can also be prepared by binding the hexapyridyl template inside the 8‐ and 10‐porphyrin nanorings. NMR exchange spectroscopy (EXSY) experiments show that these complexes exhibit correlated motion, in which the conrotatory rotation of the two template wheels is coupled to rotation of the nanoring track. In the case of the 10‐porphyrin system, the correlated motion can be locked by binding palladium(II) dichloride between the two templates.
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Affiliation(s)
- Shiqi Liu
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA (UK)
| | - Dmitry V Kondratuk
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA (UK)
| | - Sophie A L Rousseaux
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA (UK)
| | - Guzmán Gil-Ramírez
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA (UK)
| | - Melanie C O'Sullivan
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA (UK)
| | - Jonathan Cremers
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA (UK)
| | - Tim D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA (UK)
| | - Harry L Anderson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA (UK)
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36
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Hutin M, Sprafke JK, Odell B, Anderson HL, Claridge TDW. A discrete three-layer stack aggregate of a linear porphyrin tetramer: solution-phase structure elucidation by NMR and X-ray scattering. J Am Chem Soc 2013; 135:12798-807. [PMID: 23909839 DOI: 10.1021/ja406015r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Formation of stacked aggregates can dramatically alter the properties of aromatic π-systems, yet the solution-phase structure elucidation of these aggregates is often impossible because broad distributions of species are formed, giving uninformative spectroscopic data. Here, we show that a butadiyne-linked zinc porphyrin tetramer forms a remarkably well-defined aggregate, consisting of exactly three molecules, in a parallel stacked arrangement (in chloroform at room temperature; concentration 1 mM-0.1 μM). The aggregate has a mass of 14.7 kDa. Unlike most previously reported aggregates, it gives sharp NMR resonances and aggregation is in slow exchange on the NMR time scale. The structure was elucidated using a range of NMR techniques, including diffusion-editing, (1)H-(29)Si HMBC, (1)H-(1)H COSY, TOCSY and NOESY, and (1)H-(13)C edited HSQC spectroscopy. Surprisingly, the (1)H-(1)H COSY spectrum revealed many long-range residual dipolar couplings (RDCs), and detailed analysis of magnetic field-induced (1)H-(13)C RDCs provided further evidence for the structural model. The size and shape of the aggregate is supported by small-angle X-ray scattering (SAXS) data. It adopts a geometry that maximizes van der Waals contact between the porphyrins, while avoiding clashes between side chains. The need for interdigitation of the side chains prevents formation of stacks consisting of more than three layers. Although a detailed analysis has only been carried out for one compound (the tetramer), comparison with the NMR spectra of other oligomers indicates that they form similar three-layer stacks. In all cases, aggregation can be prevented by addition of pyridine, although at low pyridine concentrations, disaggregation takes many hours to reach equilibrium.
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Affiliation(s)
- Marie Hutin
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
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Koduri ND, Hileman B, Cox JD, Scott H, Hoang P, Robbins A, Bowers K, Tsebaot L, Miao K, Castaneda M, Coffin M, Wei G, Claridge TDW, Roberts KP, Hussaini SR. Acceleration of the Eschenmoser coupling reaction by sonication: efficient synthesis of enaminones. RSC Adv 2013. [DOI: 10.1039/c2ra22033d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Combettes LE, Clausen-Thue P, King MA, Odell B, Thompson AL, Gouverneur V, Claridge TDW. Back Cover: Conformational Analysis of Fluorinated Pyrrolidines Using 19F- 1H Scalar Couplings and Heteronuclear NOEs (Chem. Eur. J. 41/2012). Chemistry 2012. [DOI: 10.1002/chem.201290181] [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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Combettes LE, Clausen-Thue P, King MA, Odell B, Thompson AL, Gouverneur V, Claridge TDW. Conformational analysis of fluorinated pyrrolidines using 19F-1H scalar couplings and heteronuclear NOEs. Chemistry 2012; 18:13133-41. [PMID: 22991298 DOI: 10.1002/chem.201201577] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Indexed: 11/07/2022]
Abstract
A series of 3-fluoropyrrolidines have been studied to investigate the influence of the stereoelectronic fluorine gauche effect on ring conformations in the solid state by single-crystal X-ray analysis and in solution phase by NMR spectroscopy. As part of these studies 1D (19)F-(1)H heteronuclear NOE (HOESY) experiments have been optimised for applications to small molecules and are described in detail. These have been employed to estimate (19)F-(1)H internuclear distances and were combined with vicinal (3)J(F,H) and (3)J(H,H) scalar coupling constants to analyse the ring conformations. Where possible the derived solution-phase structural data have been compared with those of the crystalline state. The results demonstrate the influence of the gauche effect in stabilising C(γ)-exo conformations of the fluorinated pyrrolidines. It was further shown that when steric interactions were also present, this conformational bias was diminished and the contribution of the alternative C(γ)-endo conformation was seen to increase in solution at lower sample temperatures.
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Affiliation(s)
- Lorraine E Combettes
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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Combettes LE, Schuler M, Patel R, Bonillo B, Odell B, Thompson AL, Claridge TDW, Gouverneur V. Synthesis of 3-Fluoropyrrolidines and 4-Fluoropyrrolidin-2-ones from Allylic Fluorides. Chemistry 2012; 18:13126-32. [DOI: 10.1002/chem.201201576] [Citation(s) in RCA: 12] [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] [Received: 05/06/2012] [Indexed: 11/06/2022]
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41
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Zapata F, Caballero A, White NG, Claridge TDW, Costa PJ, Félix V, Beer PD. Fluorescent charge-assisted halogen-bonding macrocyclic halo-imidazolium receptors for anion recognition and sensing in aqueous media. J Am Chem Soc 2012; 134:11533-41. [PMID: 22703526 DOI: 10.1021/ja302213r] [Citation(s) in RCA: 166] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The synthesis and anion binding properties of a new family of fluorescent halogen bonding (XB) macrocyclic halo-imidazolium receptors are described. The receptors contain chloro-, bromo-, and iodo-imidazolium motifs incorporated into a cyclic structure using naphthalene spacer groups. The large size of the iodine atom substituents resulted in the isolation of anti and syn conformers of the iodo-imidazoliophane, whereas the chloro- and bromo-imidazoliophane analogues exhibit solution dynamic conformational behavior. The syn iodo-imidazoliophane isomer forms novel dimeric isostructural XB complexes of 2:2 stoichiometry with bromide and iodide anions in the solid state. Solution phase DOSY NMR experiments indicate iodide recognition takes place via cooperative convergent XB-iodide 1:1 stoichiometric binding in aqueous solvent mixtures. (1)H NMR and fluorescence spectroscopic titration experiments with a variety of anions in the competitive CD(3)OD/D(2)O (9:1) aqueous solvent mixture demonstrated the bromo- and syn iodo-imidazoliophane XB receptors to bind selectively iodide and bromide respectively, and sense these halide anions exclusively via a fluorescence response. The protic-, chloro-, and anti iodo-imidazoliophane receptors proved to be ineffectual anion complexants in this aqueous methanolic solvent mixture. Computational DFT and molecular dynamics simulations corroborate the experimental observations that bromo- and syn iodo-imidazoliophane XB receptors form stable cooperative convergent XB associations with bromide and iodide.
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Affiliation(s)
- Fabiola Zapata
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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Abstract
Sulfate templation has been used in the synthesis of a novel tris-urea-based triply interlocked capsule, whose structure has been verified by DOSY NMR, mass spectrometry and molecular modelling investigations.
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Affiliation(s)
- Yitong Li
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, UK OX1 3TA
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43
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Manzano BR, Jalón FA, Ortiz IM, Soriano ML, Torre FGDL, Elguero J, Maestro MA, Mereiter K, Claridge TDW. Self-assembly of Ligands Designed for the Building of a New Type of [2 × 2] Metallic Grid. Anion Encapsulation and Diffusion NMR Spectroscopy. Inorg Chem 2007; 47:413-28. [PMID: 17910436 DOI: 10.1021/ic701117a] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [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: 11/30/2022]
Abstract
The ligands 4,6-bis(pyrazol-1-yl)pyrimidine (bpzpm), 4,6-bis(3,5-dimethylpyrazol-1-yl)pyrimidine (bpz(*)pm), 4,6-bis(4-methylpyrazol-1-yl)pyrimidine (Mebpzpm), and 3,6-bis(3,5-dimethylpyrazol-1-yl)pyridazine (ppdMe) were synthesized and were made to react with Cu(I) centers in the presence of different counteranions. Different [2 x 2] metallic grids were obtained. With ligands bpzpm, bpz*pm, and Mebpzpm, a new type of grid was obtained where the facing ligands were divergent and two counteranions (BF(4-) or PF(6-)) were hosted in the resulting cavities and exhibit C-H...F and anion...pi interactions in the solid state. The presence of methyl groups on the pyrazolyl rings induced several distortions in the structure. In complexes with the ligand ppdMe, there were found two groups of parallel ligands in the grid, and the cavities generated were smaller. The counteranions were situated outside the grid, and the facing ligands exhibited aromatic pi-pi stacking interactions. Anion-pi interactions involving the pyridazine ring were found. The behavior in solution of the new derivatives with a special emphasis on the cation-anion interactions was studied by UV-vis and NMR spectroscopy. Diffusion NMR experiments performed for some complexes allowed us to conclude that weak cation-anion interactions exist in solution, with the counteranions undergoing fast exchange on the diffusion time scale between the free and ion-paired states.
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Affiliation(s)
- Blanca R Manzano
- Departamento de Química InorgAnica, OrgAnica y Bioquímica, Facultad de Químicas, IRICA, Universidad de Castilla-La Mancha, Avda Camilo José Cela, 10, E-13071 Ciudad Real, Spain.
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Affiliation(s)
- Seong-Ho Shin
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
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Affiliation(s)
- Heather W Daniell
- Department of Chemistry, Oxford University, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
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Abstract
Here we present the first synthesis of a [3]rotaxane with two dumbbell components threaded through a single gamma-cyclodextrin macrocycle. This synthesis is carried out in two steps: first one dumbbell is synthesized threaded through the macrocycle to give a [2]rotaxane, then a second dumbbell is synthesized through the remaining cavity of the [2]rotaxane. We have synthesized a hetero- [3]rotaxane with one stilbene and one cyanine dye threaded through gamma-cyclodextrin, which exhibits quantitative energy transfer between the two encapsulated dyes. The stilbene [2]rotaxane intermediate in this synthesis has a remarkably high affinity for suitably shaped hydrophobic guests in aqueous solution, facilitating the synthesis of [3]rotaxanes and suggesting possible applications in sensors.
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Affiliation(s)
- Eric J F Klotz
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK
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Cheetham AG, Hutchings MG, Claridge TDW, Anderson HL. Enzymatic Synthesis and Photoswitchable Enzymatic Cleavage of a Peptide-Linked Rotaxane. Angew Chem Int Ed Engl 2006; 45:1596-9. [PMID: 16456900 DOI: 10.1002/anie.200504064] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Andrew G Cheetham
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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Cheetham AG, Hutchings MG, Claridge TDW, Anderson HL. Enzymatic Synthesis and Photoswitchable Enzymatic Cleavage of a Peptide-Linked Rotaxane. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200504064] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Buston JEH, Claridge TDW, Heyes SJ, Leech MA, Moloney MG, Prout K, Stevenson M. Structural investigations of a lead(iv) tetraacetate–pyridine complex. Dalton Trans 2005:3195-203. [PMID: 16172645 DOI: 10.1039/b506366c] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A 1 : 1 crystalline complex of lead(IV) tetraacetate and pyridine (LTA-py) has been prepared. The single-crystal X-ray structure, at 296 and 150 K, establishes the presence of a relatively short Pb-N bond (2.307 A) within an intriguing seven-coordinate lead inner sphere consisting of the pyridine ligand and two bidentate and two monodentate acetate ligands. The pyridine occupies a surprising amount of the available coordination space and has induced a dramatic change in coordination compared to the four chelating acetate ligands found in lead tetraacetate (LTA). Thermal measurements (TGA/DSC) indicate the de-coordination of pyridine and its loss from the solid between 360 and 380 K. (207)Pb CP/MAS NMR spectroscopy also demonstrates the existence of the Pb-N bond through observation of (1)J((207)Pb,(14)N)= 63 Hz and a (207)Pb-(14)N dipolar coupling constant, of 149 Hz. The solid-state (207)Pb NMR parameters are used to give insight into the coordination environment of Pb(iv) in LTA-py. In solution, ligand exchange is rapid on chemical shift and J-coupling time scales. A (207)Pb NMR study of the titration of an LTA solution by pyridine yields a stability constant for LTA-py of K = 1.5 M(-1) and predicts it to have a (207)Pb NMR chemical shift essentially identical to that observed by CP/MAS NMR in the solid state. This correlation between the solid state and solution indicates that the seven-coordinate LTA-py structure found in the crystalline state does persist in solution, and this could further explain why the addition of pyridine has such profound effects on lead(IV) carboxylate-mediated organic reactions. Simulations of exchange-broadened line shapes of (13)C CP/MAS NMR spectra in the temperature regime above 280 K indicate local motion of the pyridine rings in the form of 180 degrees jumps (activation energy 72.5 kJ mol(-1)); these are first such ring flips reported for a coordinated pyridine ligand.
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Affiliation(s)
- Jonathan E H Buston
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
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Claridge TDW, Pérez-Victoria I. Enhanced 13C resolution in semi-selective HMbC: a band-selective, constant-time HMBC for complex organic structure elucidation by NMR. Org Biomol Chem 2004; 1:3632-4. [PMID: 14649890 DOI: 10.1039/b307122g] [Citation(s) in RCA: 74] [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: 11/21/2022]
Abstract
A semi-selective 2D HMBC experiment is described which yields high-resolution in the indirect carbon-13 dimension by suppressing homonuclear proton coupling modulations and so provides an NMR technique suitable for the structure elucidation of organic compounds which exhibit particularly crowded carbon-13 spectra.
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Affiliation(s)
- Tim D W Claridge
- Dyson Perrins Laboratory Department of Chemistry, University of Oxford, South Parks Road, Oxford, UK OX1 3QY.
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