Co-reporter:Dr. Ēriks Kupče; Tim D. W. Claridge
Angewandte Chemie 2017 Volume 129(Issue 39) pp:11941-11945
Publication Date(Web):2017/09/18
DOI:10.1002/ange.201705506
AbstractNested NMR experiments combining up to five conventional NMR pulse sequences into one supersequence are introduced. The core 2D NMR techniques routinely employed in small molecule NMR spectroscopy, such as HSQC, HMQC, HMBC, COSY, NOESY, TOCSY, and similar, can be recorded in a single measurement. In this way the data collection time may be dramatically reduced and sample throughput increased for basic NMR applications, such as structure elucidation and verification in synthetic, medicinal, and natural product chemistry.
Co-reporter:Dr. Ēriks Kupče; Tim D. W. Claridge
Angewandte Chemie International Edition 2017 Volume 56(Issue 39) pp:11779-11783
Publication Date(Web):2017/09/18
DOI:10.1002/anie.201705506
AbstractNested NMR experiments combining up to five conventional NMR pulse sequences into one supersequence are introduced. The core 2D NMR techniques routinely employed in small molecule NMR spectroscopy, such as HSQC, HMQC, HMBC, COSY, NOESY, TOCSY, and similar, can be recorded in a single measurement. In this way the data collection time may be dramatically reduced and sample throughput increased for basic NMR applications, such as structure elucidation and verification in synthetic, medicinal, and natural product chemistry.
Co-reporter:A. Khan, R. K. Leśniak, J. Brem, A. M. Rydzik, H. Choi, I. K. H. Leung, M. A. McDonough, C. J. Schofield and T. D. W. Claridge
MedChemComm 2016 vol. 7(Issue 5) pp:873-880
Publication Date(Web):17 Feb 2016
DOI:10.1039/C6MD00004E
γ-Butyrobetaine hydroxylase (BBOX) is a 2-oxoglutarate (2OG) dependent oxygenase that catalyses the stereoselective C-3 hydroxylation of γ-butyrobetaine (GBB) to give L-carnitine. L-Carnitine is involved in fatty acid metabolism in all animals and in some prokaryotes, and BBOX is a current drug target for the treatment of myocardial infarction. We describe the development and application of 1H NMR GBB/2OG reporter based assays employing paramagnetic relaxation enhancement to monitor inhibitor binding to the BBOX active site. In a single experiment, the method assesses inhibitors for competitive binding with 2OG or GBB, or both. The method was exemplified with a set of isoquinoline-based inhibitors; the results reveal structure–activity relationships that were not predicted from crystallographic studies, with some inhibitors competing 2OG only and some competing both 2OG and GBB. The method will also be applicable to work on the inhibition of other 2OG oxygenases.
Co-reporter:Tharindi D. Panduwawala, Laia Josa-Culleré, Ilya Kuprov, Barbara Odell, Mark G. Moloney, and Timothy D. W. Claridge
The Journal of Organic Chemistry 2016 Volume 81(Issue 10) pp:4142-4148
Publication Date(Web):May 5, 2016
DOI:10.1021/acs.joc.6b00458
Anomalous cross-peaks observed in the NOESY spectra of 2,4-disubstituted thiazolidines and oxazolidines that cannot be attributed to classical dipolar NOE or chemical exchange peaks have been investigated experimentally and computationally and have been shown to arise from scalar cross-relaxation of the first kind. This process is stimulated by the relatively slow modulation of scalar couplings and, for the systems studied, arises from slow on–off proton exchange of the amino nitrogen, a process influenced by solution temperature, acidity, and concentration. The mechanism is likely to be significant for many systems in which proton exchange occurs on the millisecond time scale, and misinterpretation of these cross-peaks may lead to erroneous conclusions should their true origins not be recognized.
Co-reporter:Ignacio Pérez-Victoria, Omar Boutureira, Tim D. W. Claridge and Benjamin G. Davis
Chemical Communications 2015 vol. 51(Issue 61) pp:12208-12211
Publication Date(Web):24 Jun 2015
DOI:10.1039/C5CC03952E
The ability of glycosyldiselenides to act as lectin ligands and their selective detection in plasma by 77Se NMR is reported.
Co-reporter:Dr. Ilya Kuprov; David M. Hodgson;Johannes Kloesges;Christopher I. Pearson;Dr. Barbara Odell; Timothy D. W. Claridge
Angewandte Chemie 2015 Volume 127( Issue 12) pp:3768-3772
Publication Date(Web):
DOI:10.1002/ange.201410271
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.
Co-reporter:Kelvin E. Jackson, Claire L. Mortimer, Barbara Odell, Jeffrey M. McKenna, Timothy D. W. Claridge, Robert S. Paton, and David M. Hodgson
The Journal of Organic Chemistry 2015 Volume 80(Issue 20) pp:9838-9846
Publication Date(Web):September 24, 2015
DOI:10.1021/acs.joc.5b01804
1H 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).
Co-reporter:Dr. Ilya Kuprov; David M. Hodgson;Johannes Kloesges;Christopher I. Pearson;Dr. Barbara Odell; Timothy D. W. Claridge
Angewandte Chemie International Edition 2015 Volume 54( Issue 12) pp:3697-3701
Publication Date(Web):
DOI:10.1002/anie.201410271
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.
Co-reporter:Anna M. Rydzik;Jürgen Brem;Ser S. vanBerkel;Inga Pfeffer;Anne Makena;Dr. Timothy D. W. Claridge; Christopher J. Schofield
Angewandte Chemie 2014 Volume 126( Issue 12) pp:
Publication Date(Web):
DOI:10.1002/ange.201401104
Co-reporter:Anna M. Rydzik;Jürgen Brem;Ser S. vanBerkel;Inga Pfeffer;Anne Makena;Dr. Timothy D. W. Claridge; Christopher J. Schofield
Angewandte Chemie International Edition 2014 Volume 53( Issue 12) pp:
Publication Date(Web):
DOI:10.1002/anie.201401104
Co-reporter:Anna M. Rydzik;Jürgen Brem;Ser S. vanBerkel;Inga Pfeffer;Anne Makena;Dr. Timothy D. W. Claridge; Christopher J. Schofield
Angewandte Chemie International Edition 2014 Volume 53( Issue 12) pp:3129-3133
Publication Date(Web):
DOI:10.1002/anie.201310866
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 19F 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.
Co-reporter:Anna M. Rydzik;Jürgen Brem;Ser S. vanBerkel;Inga Pfeffer;Anne Makena;Dr. Timothy D. W. Claridge; Christopher J. Schofield
Angewandte Chemie 2014 Volume 126( Issue 12) pp:3193-3197
Publication Date(Web):
DOI:10.1002/ange.201310866
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 19F 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.
Co-reporter:Marie Hutin ; Johannes K. Sprafke ; Barbara Odell ; Harry L. Anderson ;Tim D. W. Claridge
Journal of the American Chemical Society 2013 Volume 135(Issue 34) pp:12798-12807
Publication Date(Web):August 2, 2013
DOI:10.1021/ja406015r
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, 1H–29Si HMBC, 1H–1H COSY, TOCSY and NOESY, and 1H–13C edited HSQC spectroscopy. Surprisingly, the 1H–1H COSY spectrum revealed many long-range residual dipolar couplings (RDCs), and detailed analysis of magnetic field-induced 1H–13C 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.
Co-reporter:Ivanhoe K. H. Leung ; Marina Demetriades ; Adam P. Hardy ; Clarisse Lejeune ; Tristan J. Smart ; Andrea Szöllössi ; Akane Kawamura ; Christopher J. Schofield
Journal of Medicinal Chemistry 2013 Volume 56(Issue 2) pp:547-555
Publication Date(Web):December 12, 2012
DOI:10.1021/jm301583m
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 KD 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.
Co-reporter:Luc Henry, Ivanhoe K.H. Leung, Timothy D.W. Claridge, Christopher J. Schofield
Bioorganic & Medicinal Chemistry Letters 2012 Volume 22(Issue 15) pp:4975-4978
Publication Date(Web):1 August 2012
DOI:10.1016/j.bmcl.2012.06.024
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.
Co-reporter:Lorraine E. Combettes;Philip Clausen-Thue;Dr. Michael A. King;Dr. Barbara Odell;Dr. Amber L. Thompson; Véronique Gouverneur;Dr. Tim D. W. Claridge
Chemistry - A European Journal 2012 Volume 18( Issue 41) pp:13133-13141
Publication Date(Web):
DOI:10.1002/chem.201201577
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 19F–1H heteronuclear NOE (HOESY) experiments have been optimised for applications to small molecules and are described in detail. These have been employed to estimate 19F–1H internuclear distances and were combined with vicinal 3J(F,H) and 3J(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 Cγ-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 Cγ-endo conformation was seen to increase in solution at lower sample temperatures.
Co-reporter:Lorraine E. Combettes;Dr. Marie Schuler;Rakesh Patel;Baltasar Bonillo;Dr. Barbara Odell;Dr. Amber L. Thompson;Dr. Tim D. W. Claridge; Véronique Gouverneur
Chemistry - A European Journal 2012 Volume 18( Issue 41) pp:13126-13132
Publication Date(Web):
DOI:10.1002/chem.201201576
Abstract
Various 3-fluoropyrrolidines and 4-fluoropyrrolidin-2-ones were prepared by 5-exo-trig iodocyclisation from allylic fluorides bearing a pending nitrogen nucleophile. These bench-stable precursors were made accessible upon electrophilic fluorination of the corresponding allylsilanes. The presence of the allylic fluorine substituent induces syn-stereocontrol upon iodocyclisation with diastereomeric ratios ranging from 10:1 to > 20:1 for all N-tosyl-3-fluoropent-4-en-1-amines and amides. The sense and level of stereocontrol is strikingly similar to the corresponding iodocyclisation of structurally related allylic fluorides bearing pending oxygen nucleophiles. These results suggest that the syn selectivity observed upon ring closure involves I2–π complexes with the fluorine positioned inside.
Co-reporter:Lorraine E. Combettes;Philip Clausen-Thue;Dr. Michael A. King;Dr. Barbara Odell;Dr. Amber L. Thompson; Véronique Gouverneur;Dr. Tim D. W. Claridge
Chemistry - A European Journal 2012 Volume 18( Issue 41) pp:
Publication Date(Web):
DOI:10.1002/chem.201290181
Co-reporter:Ivanhoe K. H. Leung, Tom Brown Jr, Christopher J. Schofield and Timothy D. W. Claridge
MedChemComm 2011 vol. 2(Issue 5) pp:390-395
Publication Date(Web):07 Mar 2011
DOI:10.1039/C1MD00011J
Dynamic combinatorial chemistry (DCC) is a potentially useful method for the identification of biomacromolecule ligands; however, the number of reactions applicable to DCC in aqueous solution is limited. We report studies that investigate the reversible reaction of boronic acids with alcohols as an approach to enzyme inhibition, employing α-chymotrypsin as a model system. NMR techniques (11B NMR and 1H waterLOGSY) were used to observe ternary complexes of boronic acids, sugars and α-chymotrypsin, and were useful for distinguishing preferentially binding combinations of boronic acids and sugars. The results reveal that both the propensity of boronate ester formation in solution and affinity of the boronate ester for the target enzyme determine whether ternary complex formation is observed. The results also provide proof of principle for the boronate ester approach to DCC versusprotein targets.
Co-reporter:Ivanhoe K. H. Leung ; Emily Flashman ; Kar Kheng Yeoh ; Christopher J. Schofield
Journal of Medicinal Chemistry 2010 Volume 53(Issue 2) pp:867-875
Publication Date(Web):December 21, 2009
DOI:10.1021/jm901537q
This report demonstrates that solvent water relaxation measurements can be used for quantitative screening of ligand binding and for mechanistic investigations of enzymes containing paramagnetic metal centers by using conventional NMR instrumentation at high field. The method was exemplified using prolyl hydroxylase domain containing enzyme 2 (PHD2), a human enzyme involved in hypoxic sensing, with Mn(II) substituting for Fe(II) at the active site. KD values were determined for inhibitors that hinder access of water to the paramagnetic center. This technique is also useful for investigating the mechanism of suitable metalloenzymes, including order of ligand binding and modes of inhibition.
Co-reporter:Richard J. Hopkinson, Philippa S. Barlow, Christopher J. Schofield and Timothy D. W. Claridge
Organic & Biomolecular Chemistry 2010 vol. 8(Issue 21) pp:4915-4920
Publication Date(Web):24 Aug 2010
DOI:10.1039/C0OB00208A
Within cells it is proposed that a major mechanism for the metabolism of formaldehyde is via its reaction with glutathione (GSH) to form S-hydroxymethylglutathione (HMG), which undergoes subsequent oxidation. In addition to HMG and the previously reported (5R,10S)-5-(carboxymethylcarbamoyl)-7-oxo-3-thia-1,6-diazabicyclo[4.4.1]undecane-10-carboxylic acid (BiGF2), NMR studies on the reaction of GSH with formaldehyde reveal two previously unassigned monocyclic structures. The results imply that the biologically relevant reactions between aldehydes and peptides/proteins may be more complex than presently perceived.
Co-reporter:Sebastian Kemper, Mitul K. Patel, James C. Errey, Benjamin G. Davis, Jonathan A. Jones, Timothy D.W. Claridge
Journal of Magnetic Resonance 2010 Volume 203(Issue 1) pp:1-10
Publication Date(Web):March 2010
DOI:10.1016/j.jmr.2009.11.015
In the application of saturation transfer difference (STD) experiments to the study of protein–ligand interactions, the relaxation of the ligand is one of the major influences on the experimentally observed STD factors, making interpretation of these difficult when attempting to define a group epitope map (GEM). In this paper, we describe a simplification of the relaxation matrix that may be applied under specified experimental conditions, which results in a simplified equation reflecting the directly transferred magnetisation rate from the protein onto the ligand, defined as the summation over the whole protein of the protein–ligand cross-relaxation multiplied by with the fractional saturation of the protein protons. In this, the relaxation of the ligand is accounted for implicitly by inclusion of the experimentally determined longitudinal relaxation rates. The conditions under which this “group epitope mapping considering relaxation of the ligand” (GEM-CRL) can be applied were tested on a theoretical model system, which demonstrated only minor deviations from that predicted by the full relaxation matrix calculations (CORCEMA-ST) [7]. Furthermore, CORCEMA-ST calculations of two protein–saccharide complexes (Jacalin and TreR) with known crystal structures were performed and compared with experimental GEM-CRL data. It could be shown that the GEM-CRL methodology is superior to the classical group epitope mapping approach currently used for defining ligand–protein proximities. GEM-CRL is also useful for the interpretation of CORCEMA-ST results, because the transferred magnetisation rate provides an additional parameter for the comparison between measured and calculated values. The independence of this parameter from the above mentioned factors can thereby enhance the value of CORCEMA-ST calculations.
Co-reporter:Ignacio Pérez-Victoria, Sebastian Kemper, Mitul K. Patel, John M. Edwards, James C. Errey, Lucia F. Primavesi, Matthew J. Paul, Timothy D. W. Claridge and Benjamin G. Davis
Chemical Communications 2009 (Issue 39) pp:5862-5864
Publication Date(Web):19 Aug 2009
DOI:10.1039/B913489A
The binding kinetics of disaccharides trehalose and trehalose-6-phosphate to repressor protein TreR have been determined using STD NMR and shed light on the contrasting biological roles of these two sugars.
Co-reporter:Ludovic Drouin Dr.;E.Cristina Stanca-Kaposta Dr.;Priptal Saundh;AntonyJ. Fairbanks Dr.;Sebastian Kemper;TimothyD.W. Claridge Dr.;JohnP. Simons
Chemistry - A European Journal 2009 Volume 15( Issue 16) pp:4057-4069
Publication Date(Web):
DOI:10.1002/chem.200802179
Co-reporter:Timothy D.W. Claridge, Beatrice Lopez-Ortega, Sarah F. Jenkinson, George W.J. Fleet
Tetrahedron: Asymmetry 2008 Volume 19(Issue 8) pp:984-988
Publication Date(Web):1 May 2008
DOI:10.1016/j.tetasy.2008.03.029
Co-reporter:Tim D. W. Claridge and Ignacio Pérez-Victoria
Organic & Biomolecular Chemistry 2003 vol. 1(Issue 21) pp:3632-3634
Publication Date(Web):24 Jul 2003
DOI:10.1039/B307122G
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.
Co-reporter:Richard J. Hopkinson, Philippa S. Barlow, Christopher J. Schofield and Timothy D. W. Claridge
Organic & Biomolecular Chemistry 2010 - vol. 8(Issue 21) pp:NaN4920-4920
Publication Date(Web):2010/08/24
DOI:10.1039/C0OB00208A
Within cells it is proposed that a major mechanism for the metabolism of formaldehyde is via its reaction with glutathione (GSH) to form S-hydroxymethylglutathione (HMG), which undergoes subsequent oxidation. In addition to HMG and the previously reported (5R,10S)-5-(carboxymethylcarbamoyl)-7-oxo-3-thia-1,6-diazabicyclo[4.4.1]undecane-10-carboxylic acid (BiGF2), NMR studies on the reaction of GSH with formaldehyde reveal two previously unassigned monocyclic structures. The results imply that the biologically relevant reactions between aldehydes and peptides/proteins may be more complex than presently perceived.
Co-reporter:Ignacio Pérez-Victoria, Omar Boutureira, Tim D. W. Claridge and Benjamin G. Davis
Chemical Communications 2015 - vol. 51(Issue 61) pp:NaN12211-12211
Publication Date(Web):2015/06/24
DOI:10.1039/C5CC03952E
The ability of glycosyldiselenides to act as lectin ligands and their selective detection in plasma by 77Se NMR is reported.
Co-reporter:Ignacio Pérez-Victoria, Sebastian Kemper, Mitul K. Patel, John M. Edwards, James C. Errey, Lucia F. Primavesi, Matthew J. Paul, Timothy D. W. Claridge and Benjamin G. Davis
Chemical Communications 2009(Issue 39) pp:NaN5864-5864
Publication Date(Web):2009/08/19
DOI:10.1039/B913489A
The binding kinetics of disaccharides trehalose and trehalose-6-phosphate to repressor protein TreR have been determined using STD NMR and shed light on the contrasting biological roles of these two sugars.