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Karunanithy G, Cnossen A, Müller H, Peeks MD, Rees NH, Claridge TDW, Anderson HL, Baldwin AJ. Harnessing NMR relaxation interference effects to characterise supramolecular assemblies. Chem Commun (Camb) 2016; 52:7450-3. [DOI: 10.1039/c6cc02544g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Supramolecular assemblies can show unusual splitting patterns in their NMR spectra, with the magnitude of the effect increasing with molecular size. A simple NMR relaxation experiment reveals the origin of the effect and provides information on tumbling rates and local electronic structure.
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Hopkinson RJ, Leung IKH, Smart TJ, Rose NR, Henry L, Claridge TDW, Schofield CJ. Studies on the Glutathione-Dependent Formaldehyde-Activating Enzyme from Paracoccus denitrificans. PLoS One 2015; 10:e0145085. [PMID: 26675168 PMCID: PMC4682968 DOI: 10.1371/journal.pone.0145085] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/26/2015] [Indexed: 12/15/2022] Open
Abstract
Formaldehyde is a toxin and carcinogen that is both an environmental pollutant and an endogenous metabolite. Formaldehyde metabolism, which is probably essential for all aerobic cells, likely proceeds via multiple mechanisms, including via a glutathione-dependent pathway that is widely conserved in bacteria, plants and animals. However, it is unclear whether the first step in the glutathione-dependent pathway (i.e. formation of S-hydroxymethylglutathione (HMG)) is enzyme-catalysed. We report studies on glutathione-dependent formaldehyde-activating enzyme (GFA) from Paracoccus denitrificans, which has been proposed to catalyse HMG formation from glutathione and formaldehyde on the basis of studies using NMR exchange spectroscopy (EXSY). Although we were able to replicate the EXSY results, time course experiments unexpectedly imply that GFA does not catalyse HMG formation under standard conditions. However, GFA was observed to bind glutathione using NMR and mass spectrometry. Overall, the results reveal that GFA binds glutathione but does not directly catalyse HMG formation under standard conditions. Thus, it is possible that GFA acts as a glutathione carrier that acts to co-localise glutathione and formaldehyde in a cellular context.
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Kamps JJAG, Khan A, Choi H, Lesniak RK, Brem J, Rydzik AM, McDonough MA, Schofield CJ, Claridge TDW, Mecinović J. Cation-π Interactions Contribute to Substrate Recognition in γ-Butyrobetaine Hydroxylase Catalysis. Chemistry 2015; 22:1270-6. [PMID: 26660433 PMCID: PMC4736438 DOI: 10.1002/chem.201503761] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Indexed: 11/08/2022]
Abstract
γ-Butyrobetaine hydroxylase (BBOX) is a non-heme Fe(II) - and 2-oxoglutarate-dependent oxygenase that catalyzes the stereoselective hydroxylation of an unactivated C-H bond of γ-butyrobetaine (γBB) in the final step of carnitine biosynthesis. BBOX contains an aromatic cage for the recognition of the positively charged trimethylammonium group of the γBB substrate. Enzyme binding and kinetic analyses on substrate analogues with P and As substituting for N in the trimethylammonium group show that the analogues are good BBOX substrates, which follow the efficiency trend N(+) >P(+) >As(+). The results reveal that an uncharged carbon analogue of γBB is not a BBOX substrate, thus highlighting the importance of the energetically favorable cation-π interactions in productive substrate recognition.
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Pereira R, Wolstenhulme J, Sandford G, Claridge TDW, Gouverneur V, Cvengroš J. Synthesis and characterization of a novel N-F reagent derived from the ethano-Tröger's base: (1)J(FN) coupling constants as a signature for the N-F bond. Chem Commun (Camb) 2015; 52:1606-9. [PMID: 26658721 DOI: 10.1039/c5cc08375c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Methylation of 2,8-dimethyl-6H,12H-5,11-ethanodibenzo[b,f][1,5]-diazocine (ethano-Tröger's base) with methyl iodide followed by ion metathesis and fluorination with N-fluoro-2,3,4,5,6-pentachloropyridinium triflate affords a new electrophilic N-F reagent, that is more reactive than Selectfluor. 2D (19)F-(15)N HMQC experiments provide (1)JNF coupling constants which are diagnostic for the N-F functional group.
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Jackson KE, Mortimer CL, Odell B, McKenna JM, Claridge TDW, Paton RS, Hodgson DM. α- and α'-Lithiation-Electrophile Trapping of N-Thiopivaloyl and N-tert-Butoxythiocarbonyl α-Substituted Azetidines: Rationalization of the Regiodivergence Using NMR and Computation. J Org Chem 2015; 80:9838-46. [PMID: 26401908 DOI: 10.1021/acs.joc.5b01804] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
(1)H NMR and computational analyses provide insight into the regiodivergent (α- and α'-) lithiation-electrophile trapping of N-thiopivaloyl- and N-(tert-butoxythiocarbonyl)-α-alkylazetidines. The magnitudes of the rotation barriers in these azetidines indicate that rotamer interconversions do not occur at the temperature and on the time scale of the lithiations. The NMR and computational studies support the origin of regioselectivity as being thiocarbonyl-directed lithiation from the lowest energy amide-like rotameric forms (cis for N-thiopivaloyl and trans for N-tert-butoxythiocarbonyl).
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Bassolino G, Sovdat T, Soares Duarte A, Lim JM, Schnedermann C, Liebel M, Odell B, Claridge TDW, Fletcher SP, Kukura P. Barrierless Photoisomerization of 11-cis Retinal Protonated Schiff Base in Solution. J Am Chem Soc 2015; 137:12434-7. [DOI: 10.1021/jacs.5b06492] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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57
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Dickens AM, Larkin JR, Davis BG, Griffin JL, Claridge TDW, Sibson NR, Anthony DC. NMR-Based Metabolomics Separates the Distinct Stages of Disease in a Chronic Relapsing Model of Multiple Sclerosis. J Neuroimmune Pharmacol 2015; 10:435-44. [PMID: 26155956 DOI: 10.1007/s11481-015-9622-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/24/2015] [Indexed: 10/23/2022]
Abstract
Relapsing experimental allergic encephalomyelitis (Cr-EAE) is commonly used to explore the pathogenesis and efficacy of new therapies for MS, but it is unclear whether the metabolome of Cr-EAE is comparable to human multiple sclerosis (MS). For MS, the diagnosis and staging can be achieved by metabolomics on blood using a combination of magnetic resonance spectroscopy and partial least squares discriminant analysis (PLS-DA). Here, we sought to discover whether this approach could be used to differentiate between sequential disease states in Cr-EAE and whether the same metabolites would be discriminatory. Urine and plasma samples were obtained at different time-points from a clinically relevant model of MS. Using PLS-DA modelling for the urine samples furnished some predictive models, but could not discriminate between all disease states. However, PLS-DA modelling of the plasma samples was able to distinguish between animals with clinically silent disease (day 10, 28) and animals with active disease (day 14, 38). We were also able to distinguish Cr-EAE mice from naive mice at all-time points and control mice, treated with complete Freund's adjuvant alone, at day 14 and 38. Key metabolites that underpin these models included fatty acids, glucose and taurine. Two of these metabolites, fatty acids and glucose, were also key metabolites in separating relapsing-remitting MS from secondary-progressive MS in the human study. These results demonstrate the sensitivity of this metabolomics approach for distinguishing between different disease states. Furthermore, some, but not all, of the changes in metabolites were conserved in humans and the mouse model, which could be useful for future drug development.
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MESH Headings
- Animals
- Disease Models, Animal
- Disease Progression
- Encephalomyelitis, Autoimmune, Experimental/blood
- Encephalomyelitis, Autoimmune, Experimental/metabolism
- Encephalomyelitis, Autoimmune, Experimental/urine
- Magnetic Resonance Spectroscopy/methods
- Metabolomics/methods
- Mice
- Mice, Biozzi
- Models, Theoretical
- Multiple Sclerosis, Relapsing-Remitting/blood
- Multiple Sclerosis, Relapsing-Remitting/metabolism
- Multiple Sclerosis, Relapsing-Remitting/urine
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Al-Qahtani K, Jabeen B, Sekirnik R, Riaz N, Claridge TDW, Schofield CJ, McCullagh JSO. The broad spectrum 2-oxoglutarate oxygenase inhibitor N-oxalylglycine is present in rhubarb and spinach leaves. PHYTOCHEMISTRY 2015; 117:456-461. [PMID: 26196940 DOI: 10.1016/j.phytochem.2015.06.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 06/24/2015] [Accepted: 06/29/2015] [Indexed: 02/11/2024]
Abstract
2-Oxoglutarate (2OG) and ferrous iron dependent oxygenases are involved in many biological processes in organisms ranging from humans (where some are therapeutic targets) to plants. These enzymes are of significant biomedicinal interest because of their roles in hypoxic signaling and epigenetic regulation. Synthetic N-oxalylglycine (NOG) has been identified as a broad-spectrum 2OG oxygenase inhibitor and is currently widely used in studies on the hypoxic response and chromatin modifications in animals. We report the identification of NOG as a natural product present in Rheum rhabarbarum (rhubarb) and Spinach oleracea (spinach) leaves; NOG was not observed in Escherchia coli or human embryonic kidney cells (HEK 293T). The finding presents the possibility that NOG plays a natural role in regulating gene expression by inhibiting 2OG dependent oxygenases. This has significance because tricarboxylic acid cycle (TCA) intermediate inhibition of 2OG dependent oxygenases has attracted major interest in cancer research.
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Chan MC, Atasoylu O, Hodson E, Tumber A, Leung IKH, Chowdhury R, Gómez-Pérez V, Demetriades M, Rydzik AM, Holt-Martyn J, Tian YM, Bishop T, Claridge TDW, Kawamura A, Pugh CW, Ratcliffe PJ, Schofield CJ. Potent and Selective Triazole-Based Inhibitors of the Hypoxia-Inducible Factor Prolyl-Hydroxylases with Activity in the Murine Brain. PLoS One 2015; 10:e0132004. [PMID: 26147748 PMCID: PMC4492579 DOI: 10.1371/journal.pone.0132004] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/09/2015] [Indexed: 01/01/2023] Open
Abstract
As part of the cellular adaptation to limiting oxygen availability in animals, the expression of a large set of genes is activated by the upregulation of the hypoxia-inducible transcription factors (HIFs). Therapeutic activation of the natural human hypoxic response can be achieved by the inhibition of the hypoxia sensors for the HIF system, i.e. the HIF prolyl-hydroxylases (PHDs). Here, we report studies on tricyclic triazole-containing compounds as potent and selective PHD inhibitors which compete with the 2-oxoglutarate co-substrate. One compound (IOX4) induces HIFα in cells and in wildtype mice with marked induction in the brain tissue, revealing that it is useful for studies aimed at validating the upregulation of HIF for treatment of cerebral diseases including stroke.
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60
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Rydzik AM, Leung IKH, Kochan GT, Loik ND, Henry L, McDonough MA, Claridge TDW, Schofield CJ. Comparison of the substrate selectivity and biochemical properties of human and bacterial γ-butyrobetaine hydroxylase. Org Biomol Chem 2015; 12:6354-8. [PMID: 25030770 DOI: 10.1039/c4ob01167h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
2-Oxoglutarate and iron dependent oxygenases have potential for the stereoselective hydroxylation of amino acids and related compounds. The biochemical and kinetic properties of recombinant γ-butyrobetaine hydroxylase from human and Pseudomonas sp. AK1 were compared. The results reveal differences between the two BBOXs, including in their stimulation by ascorbate. Despite their closely related sequences, the two enzymes also display different substrate selectivities, including for the production of (di)hydroxylated betaines, implying use of engineered BBOXs for biocatalytic purposes may be productive.
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61
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Baranowski MR, Nowicka A, Rydzik AM, Warminski M, Kasprzyk R, Wojtczak BA, Wojcik J, Claridge TDW, Kowalska J, Jemielity J. Synthesis of fluorophosphate nucleotide analogues and their characterization as tools for ¹⁹F NMR studies. J Org Chem 2015; 80:3982-97. [PMID: 25816092 DOI: 10.1021/acs.joc.5b00337] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
To broaden the scope of existing methods based on (19)F nucleotide labeling, we developed a new method for the synthesis of fluorophosphate (oligo)nucleotide analogues containing an O to F substitution at the terminal position of the (oligo)phosphate moiety and evaluated them as tools for (19)F NMR studies. Using three efficient and comprehensive synthetic approaches based on phosphorimidazolide chemistry and tetra-n-butylammonium fluoride, fluoromonophosphate, or fluorophosphate imidazolide as fluorine sources, we prepared over 30 fluorophosphate-containing nucleotides, varying in nucleobase type (A, G, C, U, m(7)G), phosphate chain length (from mono to tetra), and presence of additional phosphate modifications (thio, borano, imido, methylene). Using fluorophosphate imidazolide as fluorophosphorylating reagent for 5'-phosphorylated oligos we also synthesized oligonucleotide 5'-(2-fluorodiphosphates), which are potentially useful as (19)F NMR hybridization probes. The compounds were characterized by (19)F NMR and evaluated as (19)F NMR molecular probes. We found that fluorophosphate nucleotide analogues can be used to monitor activity of enzymes with various specificities and metal ion requirements, including human DcpS enzyme, a therapeutic target for spinal muscular atrophy. The compounds can also serve as reporter ligands for protein binding studies, as exemplified by studying interaction of fluorophosphate mRNA cap analogues with eukaryotic translation initiation factor (eIF4E).
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Brem J, Struwe WB, Rydzik AM, Tarhonskaya H, Pfeffer I, Flashman E, van Berkel SS, Spencer J, Claridge TDW, McDonough MA, Benesch JLP, Schofield CJ. Studying the active-site loop movement of the São Paolo metallo-β-lactamase-1†Electronic supplementary information (ESI) available: Procedures for protein expression and purification, 19F-labelling, crystallisation, data collection, and structure determination, table of crystallographic data, table of crystallographic parameters and refinement statistics, figures showing binding mode and distances, procedures for mass spectrometry measurements, differential scanning fluorimetry measurements, stopped-flow measurements and other kinetics measurements. See DOI: 10.1039/c4sc01752hClick here for additional data file. Chem Sci 2015; 6:956-963. [PMID: 25717359 PMCID: PMC4333608 DOI: 10.1039/c4sc01752h] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 10/24/2014] [Indexed: 11/21/2022] Open
Abstract
Metallo-β-lactamases (MBLs) catalyse the hydrolysis of almost all β-lactam antibiotics. We report biophysical and kinetic studies on the São Paulo MBL (SPM-1), which reveal its Zn(ii) ion usage and mechanism as characteristic of the clinically important di-Zn(ii) dependent B1 MBL subfamily. Biophysical analyses employing crystallography, dynamic 19F NMR and ion mobility mass spectrometry, however, reveal that SPM-1 possesses loop and mobile element regions characteristic of the B2 MBLs. These include a mobile α3 region which is important in catalysis and determining inhibitor selectivity. SPM-1 thus appears to be a hybrid B1/B2 MBL. The results have implications for MBL evolution and inhibitor design.
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Kuprov I, Hodgson DM, Kloesges J, Pearson CI, Odell B, Claridge TDW. Anomalous Nuclear Overhauser Effects in Carbon-Substituted Aziridines: Scalar Cross-Relaxation of the First Kind. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kuprov I, Hodgson DM, Kloesges J, Pearson CI, Odell B, Claridge TDW. Anomalous nuclear Overhauser effects in carbon-substituted aziridines: scalar cross-relaxation of the first kind. Angew Chem Int Ed Engl 2015; 54:3697-701. [PMID: 25631552 PMCID: PMC4506550 DOI: 10.1002/anie.201410271] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 11/24/2014] [Indexed: 11/15/2022]
Abstract
Anomalous NOESY cross-peaks that cannot be explained by dipolar cross-relaxation or chemical exchange are described for carbon-substituted aziridines. The origin of these is identified as scalar cross-relaxation of the first kind, as demonstrated by a complete theoretical description of this relaxation process and by computational simulation of the NOESY spectra. It is shown that this process relies on the stochastic modulation of J-coupling by conformational transitions, which in the case of aziridines arise from inversion at the nitrogen center. The observation of scalar cross-relaxation between protons does not appear to have been previously reported for NOESY spectra. Conventional analysis would have assigned the cross-peaks as being indicative of a chemical exchange process occurring between correlated spins, were it not for the fact that the pairs of nuclei displaying them cannot undergo such exchange.
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65
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Tarhonskaya H, Chowdhury R, Leung IKH, Loik ND, McCullagh JSO, Claridge TDW, Schofield CJ, Flashman E. Investigating the contribution of the active site environment to the slow reaction of hypoxia-inducible factor prolyl hydroxylase domain 2 with oxygen. Biochem J 2014; 463:363-72. [PMID: 25120187 DOI: 10.1042/bj20140779] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024]
Abstract
The prolyl hydroxylase domain proteins (PHDs) catalyse the post-translational hydroxylation of the hypoxia-inducible factor (HIF), a modification that regulates the hypoxic response in humans. The PHDs are Fe(II)/2-oxoglutarate (2OG) oxygenases; their catalysis is proposed to provide a link between cellular HIF levels and changes in O2 availability. Transient kinetic studies have shown that purified PHD2 reacts slowly with O2 compared with some other studied 2OG oxygenases, a property which may be related to its hypoxia-sensing role. PHD2 forms a stable complex with Fe(II) and 2OG; crystallographic and kinetic analyses indicate that an Fe(II)-co-ordinated water molecule, which must be displaced before O2 binding, is relatively stable in the active site of PHD2. We used active site substitutions to investigate whether these properties are related to the slow reaction of PHD2 with O2. While disruption of 2OG binding in a R383K variant did not accelerate O2 activation, we found that substitution of the Fe(II)-binding aspartate for a glutamate residue (D315E) manifested significantly reduced Fe(II) binding, yet maintained catalytic activity with a 5-fold faster reaction with O2. The results inform on how the precise active site environment of oxygenases can affect rates of O2 activation and provide insights into limiting steps in PHD catalysis.
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66
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Dickens AM, Larkin JR, Griffin JL, Cavey A, Matthews L, Turner MR, Wilcock GK, Davis BG, Claridge TDW, Palace J, Anthony DC, Sibson NR. A type 2 biomarker separates relapsing-remitting from secondary progressive multiple sclerosis. Neurology 2014; 83:1492-9. [PMID: 25253748 PMCID: PMC4222850 DOI: 10.1212/wnl.0000000000000905] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 06/04/2014] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVE We tested whether it is possible to differentiate relapsing-remitting (RR) from secondary progressive (SP) disease stages in patients with multiple sclerosis (MS) using a combination of nuclear magnetic resonance (NMR) metabolomics and partial least squares discriminant analysis (PLS-DA) of biofluids, which makes no assumptions on the underlying mechanisms of disease. METHODS Serum samples were obtained from patients with primary progressive MS (PPMS), SPMS, and RRMS; patients with other neurodegenerative conditions; and age-matched controls. Samples were analyzed by NMR and PLS-DA models were derived to separate disease groups. RESULTS The PLS-DA models for serum samples from patients with MS enabled reliable differentiation between RRMS and SPMS. This approach also identified significant differences between the metabolite profiles of each of the MS groups (PP, SP, and RR) and the healthy controls, as well as predicting disease group membership with high specificity and sensitivity. CONCLUSIONS NMR metabolomics analysis of serum is a sensitive and robust method for differentiating between different stages of MS, yielding diagnostic markers without a priori knowledge of disease pathogenesis. Critically, this study identified and validated a type II biomarker for the RR to SP transition in patients with MS. This approach may be of considerable benefit in categorizing patients for treatment and as an outcome measure in future clinical trials. CLASSIFICATION OF EVIDENCE This study provides Class II evidence that serum metabolite profiles accurately distinguish patients with different subtypes and stages of MS.
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67
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Rydzik AM, Leung IKH, Kochan GT, McDonough MA, Claridge TDW, Schofield CJ. Oxygenase-catalyzed desymmetrization of N,N-dialkyl-piperidine-4-carboxylic acids. Angew Chem Int Ed Engl 2014; 53:10925-7. [PMID: 25164544 PMCID: PMC4497603 DOI: 10.1002/anie.201406125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Indexed: 12/14/2022]
Abstract
γ-Butyrobetaine hydroxylase (BBOX) is a 2-oxoglutarate dependent oxygenase that catalyzes the final hydroxylation step in the biosynthesis of carnitine. BBOX was shown to catalyze the oxidative desymmetrization of achiral N,N-dialkyl piperidine-4-carboxylates to give products with two or three stereogenic centers.
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Rydzik AM, Leung IKH, Kochan GT, McDonough MA, Claridge TDW, Schofield CJ. Oxygenase-Catalyzed Desymmetrization ofN,N-Dialkyl-piperidine-4-carboxylic Acids. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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69
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Tarhonskaya H, Szöllössi A, Leung IKH, Bush JT, Henry L, Chowdhury R, Iqbal A, Claridge TDW, Schofield CJ, Flashman E. Studies on Deacetoxycephalosporin C Synthase Support a Consensus Mechanism for 2-Oxoglutarate Dependent Oxygenases. Biochemistry 2014; 53:2483-93. [DOI: 10.1021/bi500086p] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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70
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Rydzik AM, Brem J, van Berkel SS, Pfeffer I, Makena A, Claridge TDW, Schofield CJ. Cover Picture: Monitoring Conformational Changes in the NDM-1 Metallo-β-lactamase by 19F NMR Spectroscopy (Angew. Chem. Int. Ed. 12/2014). Angew Chem Int Ed Engl 2014. [DOI: 10.1002/anie.201401104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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71
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Rydzik AM, Brem J, van Berkel SS, Pfeffer I, Makena A, Claridge TDW, Schofield CJ. Monitoring conformational changes in the NDM-1 metallo-β-lactamase by 19F NMR spectroscopy. Angew Chem Int Ed Engl 2014; 53:3129-33. [PMID: 24615874 PMCID: PMC4499255 DOI: 10.1002/anie.201310866] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Indexed: 12/26/2022]
Abstract
The New Delhi metallo-β-lactamase (NDM-1) is involved in the emerging antibiotic resistance problem. Development of metallo-β-lactamases (MBLs) inhibitors has proven challenging, due to their conformational flexibility. Here we report site-selective labeling of NDM-1 with 1,1,1-trifluoro-3-bromo acetone (BFA), and its use to study binding events and conformational changes upon ligand-metal binding using (19) F NMR spectroscopy. The results demonstrate different modes of binding of known NDM-1 inhibitors, including L- and D-captopril by monitoring the changing chemical environment of the active-site loop of NDM-1. The method described will be applicable to other MBLs and more generally to monitoring ligand-induced conformational changes.
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Tarhonskaya H, Rydzik AM, Leung IKH, Loik ND, Chan MC, Kawamura A, McCullagh JSO, Claridge TDW, Flashman E, Schofield CJ. Non-enzymatic chemistry enables 2-hydroxyglutarate-mediated activation of 2-oxoglutarate oxygenases. Nat Commun 2014; 5:3423. [PMID: 24594748 PMCID: PMC3959194 DOI: 10.1038/ncomms4423] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 02/10/2014] [Indexed: 01/08/2023] Open
Abstract
Accumulation of (R)-2-hydroxyglutarate in cells results from mutations to isocitrate dehydrogenase that correlate with cancer. A recent study reports that (R)-, but not (S)-2-hydroxyglutarate, acts as a co-substrate for the hypoxia-inducible factor prolyl hydroxylases via enzyme-catalysed oxidation to 2-oxoglutarate. Here we investigate the mechanism of 2-hydroxyglutarate-enabled activation of 2-oxoglutarate oxygenases, including prolyl hydroxylase domain 2, the most important human prolyl hydroxylase isoform. We observe that 2-hydroxyglutarate-enabled catalysis by prolyl hydroxylase domain 2 is not enantiomer-specific and is stimulated by ferrous/ferric ion and reducing agents including L-ascorbate. The results reveal that 2-hydroxyglutarate is oxidized to 2-oxoglutarate non-enzymatically, likely via iron-mediated Fenton-chemistry, at levels supporting in vitro catalysis by 2-oxoglutarate oxygenases. Succinic semialdehyde and succinate are also identified as products of 2-hydroxyglutarate oxidation. Overall, the results rationalize the reported effects of 2-hydroxyglutarate on catalysis by prolyl hydroxylases in vitro and suggest that non-enzymatic 2-hydroxyglutarate oxidation may be of biological interest.
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Rydzik AM, Brem J, van Berkel SS, Pfeffer I, Makena A, Claridge TDW, Schofield CJ. Titelbild: Monitoring Conformational Changes in the NDM-1 Metallo-β-lactamase by19F NMR Spectroscopy (Angew. Chem. 12/2014). Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201401104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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74
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Rydzik AM, Brem J, van Berkel SS, Pfeffer I, Makena A, Claridge TDW, Schofield CJ. Monitoring Conformational Changes in the NDM-1 Metallo-β-lactamase by19F NMR Spectroscopy. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310866] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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75
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Rydzik AM, Leung IKH, Thalhammer A, Kochan GT, Claridge TDW, Schofield CJ. Fluoromethylated derivatives of carnitine biosynthesis intermediates – synthesis and applications. Chem Commun (Camb) 2014; 50:1175-7. [DOI: 10.1039/c3cc47581f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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76
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van Berkel SS, Nettleship JE, Leung IKH, Brem J, Choi H, Stuart DI, Claridge TDW, McDonough MA, Owens RJ, Ren J, Schofield CJ. Binding of (5S)-penicilloic acid to penicillin binding protein 3. ACS Chem Biol 2013; 8:2112-6. [PMID: 23899657 DOI: 10.1021/cb400200h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
β-Lactam antibiotics react with penicillin binding proteins (PBPs) to form relatively stable acyl-enzyme complexes. We describe structures derived from the reaction of piperacillin with PBP3 (Pseudomonas aeruginosa) including not only the anticipated acyl-enzyme complex but also an unprecedented complex with (5S)-penicilloic acid, which was formed by C-5 epimerization of the nascent (5R)-penicilloic acid product. Formation of the complex was confirmed by solution studies, including NMR. Together, these results will be useful in the design of new PBP inhibitors and raise the possibility that noncovalent PBP inhibition by penicilloic acids may be of clinical relevance.
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77
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Hopkinson RJ, Walport LJ, Münzel M, Rose NR, Smart TJ, Kawamura A, Claridge TDW, Schofield CJ. Is JmjC Oxygenase Catalysis Limited to Demethylation? Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303282] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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78
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Hopkinson RJ, Walport LJ, Münzel M, Rose NR, Smart TJ, Kawamura A, Claridge TDW, Schofield CJ. Is JmjC oxygenase catalysis limited to demethylation? Angew Chem Int Ed Engl 2013; 52:7709-13. [PMID: 23788451 PMCID: PMC3798130 DOI: 10.1002/anie.201303282] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Indexed: 01/01/2023]
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79
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Yang M, Hardy AP, Chowdhury R, Loik ND, Scotti JS, McCullagh JSO, Claridge TDW, McDonough MA, Ge W, Schofield CJ. Substrate Selectivity Analyses of Factor Inhibiting Hypoxia-Inducible Factor. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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80
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Yang M, Hardy AP, Chowdhury R, Loik ND, Scotti JS, McCullagh JSO, Claridge TDW, McDonough MA, Ge W, Schofield CJ. Substrate selectivity analyses of factor inhibiting hypoxia-inducible factor. Angew Chem Int Ed Engl 2013; 52:1700-4. [PMID: 23296631 DOI: 10.1002/anie.201208046] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Indexed: 11/06/2022]
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81
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Leung IKH, Demetriades M, Hardy AP, Lejeune C, Smart TJ, Szöllössi A, Kawamura A, Schofield CJ, Claridge TDW. Reporter ligand NMR screening method for 2-oxoglutarate oxygenase inhibitors. J Med Chem 2013; 56:547-55. [PMID: 23234607 DOI: 10.1021/jm301583m] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The human 2-oxoglutarate (2OG) dependent oxygenases belong to a family of structurally related enzymes that play important roles in many biological processes. We report that competition-based NMR methods, using 2OG as a reporter ligand, can be used for quantitative and site-specific screening of ligand binding to 2OG oxygenases. The method was demonstrated using hypoxia inducible factor hydroxylases and histone demethylases, and K(D) values were determined for inhibitors that compete with 2OG at the metal center. This technique is also useful as a screening or validation tool for inhibitor discovery, as exemplified by work with protein-directed dynamic combinatorial chemistry.
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82
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Hamed RB, Henry L, Gomez-Castellanos JR, Asghar A, Brem J, Claridge TDW, Schofield CJ. Stereoselective preparation of lipidated carboxymethyl-proline/pipecolic acid derivatives via coupling of engineered crotonases with an alkylmalonyl-CoA synthetase. Org Biomol Chem 2013; 11:8191-6. [DOI: 10.1039/c3ob41525b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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83
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Raskatov JA, Thompson AL, Cowley AR, Claridge TDW, Brown JM. Chiral recognition in contact ion-pairs; observation, characterization and analysis. Chem Sci 2013. [DOI: 10.1039/c3sc51096d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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84
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Brennan MB, Claridge TDW, Compton RG, Davies SG, Fletcher AM, Henstridge MC, Hewings DS, Kurosawa W, Lee JA, Roberts PM, Schoonen AK, Thomson JE. Ammonium-directed olefinic epoxidation: kinetic and mechanistic insights. J Org Chem 2012; 77:7241-61. [PMID: 22827448 DOI: 10.1021/jo3010556] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ammonium-directed olefinic epoxidations of a range of differentially N-substituted cyclic allylic and homoallylic amines (derived from cyclopentene, cyclohexene, and cycloheptene) have been investigated, and the reaction kinetics have been analyzed. The results of these studies suggest that both the ring size and the identity of the substituents on nitrogen are important in determining both the overall rate and the stereochemical outcome of the epoxidation reaction. In general, secondary amines or tertiary amines with nonsterically demanding substituents on nitrogen are superior to tertiary amines with sterically demanding substituents on nitrogen in their ability to promote the oxidation reaction. Furthermore, in all cases examined, the ability of the (in situ formed) ammonium substituent to direct the stereochemical course of the epoxidation reaction is either comparable or superior to that of the analogous hydroxyl substituent. Much slower rates of ring-opening of the intermediate epoxides are observed in cyclopentene-derived and cycloheptene-derived allylic amines as compared with their cyclohexene-derived allylic and homoallylic amine counterparts, allowing for isolation of these intermediates in both of the former cases.
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85
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Rydzik AM, Leung IKH, Kochan GT, Thalhammer A, Oppermann U, Claridge TDW, Schofield CJ. Development and Application of a Fluoride-Detection-Based Fluorescence Assay for γ-Butyrobetaine Hydroxylase. Chembiochem 2012; 13:1559-63. [DOI: 10.1002/cbic.201200256] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Indexed: 01/30/2023]
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86
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Henry L, Leung IKH, Claridge TDW, Schofield CJ. γ-Butyrobetaine hydroxylase catalyses a Stevens type rearrangement. Bioorg Med Chem Lett 2012; 22:4975-8. [PMID: 22765904 DOI: 10.1016/j.bmcl.2012.06.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 06/10/2012] [Accepted: 06/11/2012] [Indexed: 11/24/2022]
Abstract
γ-Butyrobetaine hydroxylase (BBOX) is a 2-oxoglutarate and Fe(II)-dependent oxygenase that catalyses the final step of L-carnitine biosynthesis in animals. BBOX catalyses the oxidation of 3-(2,2,2-trimethylhydrazinium)propionate (THP), a clinically used BBOX inhibitor, to form multiple products including 3-amino-4-(methyamino)butanoic acid (AMBA), which is proposed to be formed via a Stevens type rearrangement mechanism. We report the synthesis of AMBA and confirm that it is a product of the BBOX catalysed oxidation of THP. AMBA reacts with formaldehyde, which is produced enzymatically by BBOX, to give a cyclic adduct.
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87
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Demetriades M, Leung IKH, Chowdhury R, Chan MC, McDonough MA, Yeoh KK, Tian YM, Claridge TDW, Ratcliffe PJ, Woon ECY, Schofield CJ. Dynamic Combinatorial Chemistry Employing Boronic Acids/Boronate Esters Leads to Potent Oxygenase Inhibitors. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202000] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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88
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Demetriades M, Leung IKH, Chowdhury R, Chan MC, McDonough MA, Yeoh KK, Tian YM, Claridge TDW, Ratcliffe PJ, Woon ECY, Schofield CJ. Dynamic Combinatorial Chemistry Employing Boronic Acids/Boronate Esters Leads to Potent Oxygenase Inhibitors. Angew Chem Int Ed Engl 2012; 51:6672-5. [DOI: 10.1002/anie.201202000] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Indexed: 11/05/2022]
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89
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Sagar R, Rudić S, Gamblin DP, Scanlan EM, Vaden TD, Odell B, Claridge TDW, Simons JP, Davis BG. Conformational effects in sugar ions: spectroscopic investigations in the gas phase and in solution. Chem Sci 2012. [DOI: 10.1039/c2sc20341c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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90
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Hamed RB, Henry L, Gomez-Castellanos JR, Mecinović J, Ducho C, Sorensen JL, Claridge TDW, Schofield CJ. Crotonase Catalysis Enables Flexible Production of Functionalized Prolines and Carbapenams. J Am Chem Soc 2011; 134:471-9. [DOI: 10.1021/ja208318d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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91
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Sprafke JK, Odell B, Claridge TDW, Anderson HL. “Alles-oder-Nichts”-Kooperativität bei der Selbstorganisation eines Annulen-Sandwichs. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008087] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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92
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Sprafke JK, Odell B, Claridge TDW, Anderson HL. All-or-Nothing Cooperative Self-Assembly of an Annulene Sandwich. Angew Chem Int Ed Engl 2011; 50:5572-5. [DOI: 10.1002/anie.201008087] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Indexed: 11/05/2022]
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93
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Chowdhury R, Yeoh KK, Tian YM, Hillringhaus L, Bagg EA, Rose NR, Leung IKH, Li XS, Woon ECY, Yang M, McDonough MA, King ON, Clifton IJ, Klose RJ, Claridge TDW, Ratcliffe PJ, Schofield CJ, Kawamura A. The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. EMBO Rep 2011; 12:463-9. [PMID: 21460794 PMCID: PMC3090014 DOI: 10.1038/embor.2011.43] [Citation(s) in RCA: 755] [Impact Index Per Article: 58.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 02/21/2011] [Accepted: 02/22/2011] [Indexed: 02/07/2023] Open
Abstract
Mutations in isocitrate dehydrogenases (IDHs) have a gain-of-function effect leading to R(-)-2-hydroxyglutarate (R-2HG) accumulation. By using biochemical, structural and cellular assays, we show that either or both R- and S-2HG inhibit 2-oxoglutarate (2OG)-dependent oxygenases with varying potencies. Half-maximal inhibitory concentration (IC(50)) values for the R-form of 2HG varied from approximately 25 μM for the histone N(ɛ)-lysine demethylase JMJD2A to more than 5 mM for the hypoxia-inducible factor (HIF) prolyl hydroxylase. The results indicate that candidate oncogenic pathways in IDH-associated malignancy should include those that are regulated by other 2OG oxygenases than HIF hydroxylases, in particular those involving the regulation of histone methylation.
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94
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Yang M, Chowdhury R, Ge W, Hamed RB, McDonough MA, Claridge TDW, Kessler BM, Cockman ME, Ratcliffe PJ, Schofield CJ. Factor-inhibiting hypoxia-inducible factor (FIH) catalyses the post-translational hydroxylation of histidinyl residues within ankyrin repeat domains. FEBS J 2011; 278:1086-97. [PMID: 21251231 PMCID: PMC3569879 DOI: 10.1111/j.1742-4658.2011.08022.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Factor-inhibiting hypoxia-inducible factor (FIH) is an Fe(II)/2-oxoglutarate-dependent dioxygenase that acts as a negative regulator of the hypoxia-inducible factor (HIF) by catalysing β-hydroxylation of an asparaginyl residue in its C-terminal transcriptional activation domain (CAD). In addition to the hypoxia-inducible factor C-terminal transcriptional activation domain (HIF-CAD), FIH also catalyses asparaginyl hydroxylation of many ankyrin repeat domain-containing proteins, revealing a broad sequence selectivity. However, there are few reports on the selectivity of FIH for the hydroxylation of specific residues. Here, we report that histidinyl residues within the ankyrin repeat domain of tankyrase-2 can be hydroxylated by FIH. NMR and crystallographic analyses show that the histidinyl hydroxylation occurs at the β-position. The results further expand the scope of FIH-catalysed hydroxylations.
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95
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Li WW, Claridge TDW, Li Q, Wormald MR, Davis BG, Bayley H. Tuning the cavity of cyclodextrins: altered sugar adaptors in protein pores. J Am Chem Soc 2011; 133:1987-2001. [PMID: 21244029 DOI: 10.1021/ja1100867] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyclodextrins (CDs) have been widely used in host-guest molecular recognition because of their chiral and hydrophobic cavities. For example, β-cyclodextrin (βCD) lodged as a molecular adaptor in protein pores such as α-hemolysin (αHL) is used for stochastic sensing. Here, we have tuned the cavity and overall size of βCD by replacing a single oxygen atom in its ring skeleton by a disulfide unit in two different configurations to both expand our ability to detect analytes and understand the interactions of βCD with protein pores. The three-dimensional structures of the two stereoisomeric CDs have been determined by the combined application of NMR spectroscopy and molecular simulation and show distorted conformations as compared to natural βCD. The interactions of these synthetic βCD analogues with mutant αHL protein pores and guest molecules were studied by single-channel electrical recording. The dissociation rate constants for both disulfide CDs from the mutant pores show ∼1000-fold increase as compared to those of unaltered βCD, but are ∼10-fold lower than the dissociation rate constants for βCD from wild-type αHL. Both of the skeleton-modified CDs show altered selectivity toward guest molecules. Our approach expands the breadth in sensitivity and diversity of sensing with protein pores and suggests structural parameters useful for CD design, particularly in the creation of asymmetric cavities.
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96
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Mantri M, Loik ND, Hamed RB, Claridge TDW, McCullagh JSO, Schofield CJ. The 2-oxoglutarate-dependent oxygenase JMJD6 catalyses oxidation of lysine residues to give 5S-hydroxylysine residues. Chembiochem 2011; 12:531-4. [PMID: 22238144 DOI: 10.1002/cbic.201000641] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2010] [Indexed: 02/05/2023]
Abstract
Amino acid analyses reveal that JMJD6-catalysed hydroxylation of RNA-splicing regulatory protein fragments occurs to give hydroxylysine products with 5S stereochemistry. This contrasts with collagen lysyl hydroxylases, which give 5R-hydroxylated products. The work suggests that more than one subfamily of lysyl hydroxylases has evolved and illustrates the importance of stereochemical assignments in proteomic analyses.
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97
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Serpell CJ, Thomas O, Odell B, Claridge TDW, Chall R, Thompson AL, Beer PD. Dimeric self-association of an isophthalamide macrocycle in solution and the solid state. CrystEngComm 2011. [DOI: 10.1039/c1ce05271c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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98
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Leung IKH, Brown Jr T, Schofield CJ, Claridge TDW. An approach to enzyme inhibition employing reversible boronate ester formation. MEDCHEMCOMM 2011. [DOI: 10.1039/c1md00011j] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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99
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Yang M, Ge W, Chowdhury R, Claridge TDW, Kramer HB, Schmierer B, McDonough MA, Gong L, Kessler BM, Ratcliffe PJ, Coleman ML, Schofield CJ. Asparagine and aspartate hydroxylation of the cytoskeletal ankyrin family is catalyzed by factor-inhibiting hypoxia-inducible factor. J Biol Chem 2010; 286:7648-60. [PMID: 21177872 PMCID: PMC3045019 DOI: 10.1074/jbc.m110.193540] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Factor-inhibiting hypoxia-inducible factor (FIH) catalyzes the β-hydroxylation of an asparagine residue in the C-terminal transcriptional activation domain of the hypoxia inducible factor (HIF), a modification that negatively regulates HIF transcriptional activity. FIH also catalyzes the hydroxylation of highly conserved Asn residues within the ubiquitous ankyrin repeat domain (ARD)-containing proteins. Hydroxylation has been shown to stabilize localized regions of the ARD fold in the case of a three-repeat consensus ankyrin protein, but this phenomenon has not been demonstrated for the extensive naturally occurring ARDs. Here we report that the cytoskeletal ankyrin family are substrates for FIH-catalyzed hydroxylations. We show that the ARD of ankyrinR is multiply hydroxylated by FIH both in vitro and in endogenous proteins purified from human and mouse erythrocytes. Hydroxylation of the D34 region of ankyrinR ARD (ankyrin repeats 13–24) increases its conformational stability and leads to a reduction in its interaction with the cytoplasmic domain of band 3 (CDB3), demonstrating the potential for FIH-catalyzed hydroxylation to modulate protein-protein interactions. Unexpectedly we found that aspartate residues in ankyrinR and ankyrinB are hydroxylated and that FIH-catalyzed aspartate hydroxylation also occurs in other naturally occurring AR sequences. The crystal structure of an FIH variant in complex with an Asp-substrate peptide together with NMR analyses of the hydroxylation product identifies the 3S regio- and stereoselectivity of the FIH-catalyzed Asp hydroxylation, revealing a previously unprecedented posttranslational modification.
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100
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Claridge TDW, Davies SG, Lee JA, Nicholson RL, Roberts PM, Russell AJ, Smith AD, Toms SM. Highly (E)-selective Wadsworth-Emmons reactions promoted by methylmagnesium bromide. Org Lett 2010; 10:5437-40. [PMID: 18975957 DOI: 10.1021/ol802212e] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An experimentally simple protocol for the very highly (E)-selective Wadsworth-Emmons reaction [(E):(Z) selectivities in excess of 180:1 in some cases] of a range of straight-chain and branched aliphatic, substituted aromatic, and base-sensitive aldehydes via reaction with an alkyl diethylphosphonoacetate and MeMgBr is reported.
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