51
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Lingard H, Han JT, Thompson AL, Leung IKH, Scott RTW, Thompson S, Hamilton AD. Diphenylacetylene-linked peptide strands induce bidirectional β-sheet formation. Angew Chem Int Ed Engl 2014; 53:3650-3. [PMID: 24554626 DOI: 10.1002/anie.201309353] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 12/17/2013] [Indexed: 12/31/2022]
Abstract
In the search for synthetic mimics of protein secondary structures relevant to the mediation of protein-protein interactions, we have synthesized a series of tetrasubstituted diphenylacetylenes that display β-sheet structures in two directions. Extensive X-ray crystallographic and NMR solution phase studies are consistent with these proteomimetics adopting sheet structures, displaying both hydrophobic and hydrophilic amino acid side chains.
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Lingard H, Han JT, Thompson AL, Leung IKH, Scott RTW, Thompson S, Hamilton AD. Diphenylacetylene-Linked Peptide Strands Induce Bidirectional β-Sheet Formation. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309353] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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53
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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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54
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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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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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Bush JT, Walport LJ, McGouran JF, Leung IKH, Berridge G, van Berkel SS, Basak A, Kessler BM, Schofield CJ. The Ugi four-component reaction enables expedient synthesis and comparison of photoaffinity probes. Chem Sci 2013. [DOI: 10.1039/c3sc51708j] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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57
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Rose NR, Woon ECY, Tumber A, Walport LJ, Chowdhury R, Li XS, King ONF, Lejeune C, Ng SS, Krojer T, Chan MC, Rydzik AM, Hopkinson RJ, Che KH, Daniel M, Strain-Damerell C, Gileadi C, Kochan G, Leung IKH, Dunford J, Yeoh KK, Ratcliffe PJ, Burgess-Brown N, von Delft F, Muller S, Marsden B, Brennan PE, McDonough MA, Oppermann U, Klose RJ, Schofield CJ, Kawamura A. Plant growth regulator daminozide is a selective inhibitor of human KDM2/7 histone demethylases. J Med Chem 2012; 55:6639-43. [PMID: 22724510 DOI: 10.1021/jm300677j] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The JmjC oxygenases catalyze the N-demethylation of N(ε)-methyl lysine residues in histones and are current therapeutic targets. A set of human 2-oxoglutarate analogues were screened using a unified assay platform for JmjC demethylases and related oxygenases. Results led to the finding that daminozide (N-(dimethylamino)succinamic acid, 160 Da), a plant growth regulator, selectively inhibits the KDM2/7 JmjC subfamily. Kinetic and crystallographic studies reveal that daminozide chelates the active site metal via its hydrazide carbonyl and dimethylamino groups.
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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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59
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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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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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61
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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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62
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Rotili D, Altun M, Kawamura A, Wolf A, Fischer R, Leung IKH, Mackeen MM, Tian YM, Ratcliffe PJ, Mai A, Kessler BM, Schofield CJ. A photoreactive small-molecule probe for 2-oxoglutarate oxygenases. ACTA ACUST UNITED AC 2011; 18:642-654. [PMID: 21609845 DOI: 10.1016/j.chembiol.2011.03.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 03/01/2011] [Accepted: 03/02/2011] [Indexed: 11/29/2022]
Abstract
2-oxoglutarate (2-OG)-dependent oxygenases have diverse roles in human biology. The inhibition of several 2-OG oxygenases is being targeted for therapeutic intervention, including for cancer, anemia, and ischemic diseases. We report a small-molecule probe for 2-OG oxygenases that employs a hydroxyquinoline template coupled to a photoactivable crosslinking group and an affinity-purification tag. Following studies with recombinant proteins, the probe was shown to crosslink to 2-OG oxygenases in human crude cell extracts, including to proteins at endogenous levels. This approach is useful for inhibitor profiling, as demonstrated by crosslinking to the histone demethylase FBXL11 (KDM2A) in HEK293T nuclear extracts. The results also suggest that small-molecule probes may be suitable for substrate identification studies.
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63
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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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64
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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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65
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Leung IKH, Flashman E, Yeoh KK, Schofield CJ, Claridge TDW. Using NMR solvent water relaxation to investigate metalloenzyme-ligand binding interactions. J Med Chem 2010; 53:867-75. [PMID: 20025281 DOI: 10.1021/jm901537q] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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. K(D) 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.
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