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Woodman TJ, Lloyd MD. Analysis of enzyme reactions using NMR techniques: A case study with α-methylacyl-CoA racemase (AMACR). Methods Enzymol 2023; 690:159-209. [PMID: 37858529 DOI: 10.1016/bs.mie.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
α-Methylacyl-CoA racemase (AMACR; P504S) catalyzes the conversion of R-2-methylacyl-CoA esters into their corresponding S-2-methylacyl-CoA epimers enabling their degradation by β-oxidation. The enzyme also catalyzes the key epimerization reaction in the pharmacological activation pathway of ibuprofen and related drugs. AMACR protein levels and enzymatic activity are increased in prostate cancer, and the enzyme is a recognized drug target. Key to the development of novel treatments based on AMACR inhibition is the development of functional assays. Synthesis of substrates and purification of recombinant human AMACR are described. Incubation of R- or S-2-methylacyl-CoA esters with AMACR in vitro resulted in formation of epimers (at a near 1-1 ratio at equilibrium) via removal of their α-protons to form an enolate intermediate followed by reprotonation. Conversion can be conveniently followed by incubation in buffer containing 2H2O followed by 1H NMR analysis to monitor conversion of the α-methyl doublet to a single peak upon deuterium incorporation. Incubation of 2-methylacyl-CoA esters containing leaving groups results in an elimination reaction, which was also characterized by 1H NMR. The synthesis of substrates, including a double labeled substrate for mechanistic studies, and subsequent analysis is also described.
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Affiliation(s)
- Timothy J Woodman
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom.
| | - Matthew D Lloyd
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom.
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Mojanaga OO, Acharya KR, Lloyd MD. Recombinant protein production for structural and kinetic studies: A case study using M. tuberculosis α-methylacyl-CoA racemase (MCR). Methods Enzymol 2023; 690:1-37. [PMID: 37858526 DOI: 10.1016/bs.mie.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Modern drug discovery is a target-driven approach in which a particular protein such as an enzyme is implicated in the disease process. Commonly, small-molecule drugs are identified using screening, rational design, and structural biology approaches. Drug screening, testing and optimization is typically conducted in vitro, and copious amounts of protein are required. The advent of recombinant DNA technologies has resulted in a rise in proteins purified by affinity techniques, typically by incorporating an "affinity tag" at the N- or C-terminus. Use of these tagged proteins and affinity techniques comes with a host of issues. This chapter describes the production of an untagged enzyme, α-methylacyl-CoA racemase (MCR) from Mycobacterium tuberculosis, using a recombinant E. coli system. Purification of the enzyme on a 100 mg scale using tandem anion-exchange chromatographies (DEAE-sepharose and RESOURCE-Q columns), and size-exclusion chromatographies is described. A modified protocol allowing the purification of cationic proteins is also described, based on tandem cation-exchange chromatographies (using CM-sepharose and RESOURCE-S columns) and size-exclusion chromatographies. The resulting MCR protein is suitable for biochemical and structural biology applications. The described protocols have wide applicability to the purification of other recombinant proteins and enzymes without using affinity chromatography.
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Affiliation(s)
- Otsile O Mojanaga
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom
| | - K Ravi Acharya
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom.
| | - Matthew D Lloyd
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom.
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3
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Bearne SL. Design and evaluation of substrate-product analog inhibitors for racemases and epimerases utilizing a 1,1-proton transfer mechanism. Methods Enzymol 2023; 690:397-444. [PMID: 37858537 DOI: 10.1016/bs.mie.2023.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Racemases and epimerases catalyze the inversion of stereochemistry at asymmetric carbon atoms to generate stereoisomers that often play important roles in normal and pathological physiology. Consequently, there is interest in developing inhibitors of these enzymes for drug discovery. A strategy for the rational design of substrate-product analog (SPA) inhibitors of racemases and epimerases utilizing a direct 1,1-proton transfer mechanism is elaborated. This strategy assumes that two groups on the asymmetric carbon atom remain fixed at active-site binding determinants, while the hydrogen and third, motile group move during catalysis, with the latter potentially traveling between an R- and S-pocket at the active site. SPAs incorporate structural features of the substrate and product, often with geminal disubstitution on the asymmetric carbon atom to simultaneously present the motile group to both the R- and S-pockets. For racemases operating on substrates bearing three polar groups (glutamate, aspartate, and serine racemases) or with compact, hydrophobic binding pockets (proline racemase), substituent motion is limited and the design strategy furnishes inhibitors with poor or modest binding affinities. The approach is most successful when substrates have a large, motile hydrophobic group that binds at a plastic and/or capacious hydrophobic site. Potent inhibitors were developed for mandelate racemase, isoleucine epimerase, and α-methylacyl-CoA racemase using the SPA inhibitor design strategy, exhibiting binding affinities ranging from substrate-like to exceeding that of the substrate by 100-fold. This rational approach for designing inhibitors of racemases and epimerases having the appropriate active-site architectures is a useful strategy for furnishing compounds for drug development.
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Affiliation(s)
- Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada; Department of Chemistry, Dalhousie University, Halifax, NS, Canada.
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Lloyd MD, Yevglevskis M, Nathubhai A, James TD, Threadgill MD, Woodman TJ. Racemases and epimerases operating through a 1,1-proton transfer mechanism: reactivity, mechanism and inhibition. Chem Soc Rev 2021; 50:5952-5984. [PMID: 34027955 PMCID: PMC8142540 DOI: 10.1039/d0cs00540a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Racemases and epimerases catalyse changes in the stereochemical configurations of chiral centres and are of interest as model enzymes and as biotechnological tools. They also occupy pivotal positions within metabolic pathways and, hence, many of them are important drug targets. This review summarises the catalytic mechanisms of PLP-dependent, enolase family and cofactor-independent racemases and epimerases operating by a deprotonation/reprotonation (1,1-proton transfer) mechanism and methods for measuring their catalytic activity. Strategies for inhibiting these enzymes are reviewed, as are specific examples of inhibitors. Rational design of inhibitors based on substrates has been extensively explored but there is considerable scope for development of transition-state mimics and covalent inhibitors and for the identification of inhibitors by high-throughput, fragment and virtual screening approaches. The increasing availability of enzyme structures obtained using X-ray crystallography will facilitate development of inhibitors by rational design and fragment screening, whilst protein models will facilitate development of transition-state mimics.
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Affiliation(s)
- Matthew D Lloyd
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
| | - Maksims Yevglevskis
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and CatSci Ltd., CBTC2, Capital Business Park, Wentloog, Cardiff CF3 2PX, UK
| | - Amit Nathubhai
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and University of Sunderland, School of Pharmacy & Pharmaceutical Sciences, Sciences Complex, Sunderland SR1 3SD, UK
| | - Tony D James
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK and School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, People's Republic of China
| | - Michael D Threadgill
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Aberystwyth SY23 3BY, UK
| | - Timothy J Woodman
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
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6
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Kong G, Lee H, Tran Q, Kim C, Park J, Kwon SH, Kim SH, Park J. Current Knowledge on the Function of α-Methyl Acyl-CoA Racemase in Human Diseases. Front Mol Biosci 2020; 7:153. [PMID: 32760737 PMCID: PMC7372137 DOI: 10.3389/fmolb.2020.00153] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/18/2020] [Indexed: 01/22/2023] Open
Abstract
Branched chain fatty acids perform very important functions in human diet and drug metabolism. they cannot be metabolized in mitochondria and are instead processed and degraded in peroxisomes due to the presence of methyl groups on the carbon chains. Oxidative degradation pathways for lipids include α- and β-oxidation and several pathways. In all metabolic pathways, α-methyl acyl-CoA racemase (AMACR) plays an essential role by regulating the metabolism of lipids and drugs. AMACR regulates β-oxidation of branched chain lipids in peroxisomes and mitochondria and promotes chiral reversal of 2-methyl acids. AMACR defects cause sensory-motor neuronal and liver abnormalities in humans. These phenotypes are inherited and are caused by mutations in AMACR. In addition, AMACR has been found to be overexpressed in prostate cancer. In addition, the protein levels of AMACR have increased significantly in many types of cancer. Therefore, AMACR may be an important marker in tumors. In this review, a comprehensive overview of AMACR studies in human disease will be described.
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Affiliation(s)
- Gyeyeong Kong
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, South Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Hyunji Lee
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, South Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Quangdon Tran
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, South Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Chaeyeong Kim
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, South Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Jisoo Park
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, South Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, South Korea
- Department of Life Science, Hyehwa Liberal Arts College, LINC Plus Project Group, Daejeon University, Daejeon, South Korea
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, South Korea
| | - Seon-Hwan Kim
- Department of Neurosurgery, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Jongsun Park
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, South Korea
- Department of Medical Science, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon, South Korea
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Petrova YD, Wadda K, Nathubhai A, Yevglevskis M, Mitchell PJ, James TD, Threadgill MD, Woodman TJ, Lloyd MD. Identification of novel small-molecule inhibitors of α-methylacyl-CoA racemase (AMACR; P504S) and structure-activity relationships. Bioorg Chem 2019; 92:103264. [PMID: 31536955 DOI: 10.1016/j.bioorg.2019.103264] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 12/24/2022]
Abstract
α-Methylacyl-CoA racemase (AMACR; P504S; EC 5.1.99.4) catalyses epimerization of 2-methylacyl-CoAs and is important for the degradation of branched-chain fatty acids and the pharmacological activation of ibuprofen and related drugs. It is also a novel drug target for prostate and other cancers. However, development of AMACR as a drug target has been hampered by the difficulties in assaying enzyme activity. Consequently, reported inhibitors have been rationally designed acyl-CoA esters, which are delivered as their carboxylate prodrugs. The novel colorimetric assay for AMACR based on the elimination of 2,4-dinitrophenolate was developed for high-throughput screening and 20,387 'drug-like compounds' were screened, with a throughput of 768 compounds assayed per day. Pyrazoloquinolines and pyrazolopyrimidines were identified as novel scaffolds and investigated as AMACR inhibitors. The most potent inhibitors have IC50 values of ~2 µM. The pyrazoloquinoline inhibitor 10a displayed uncompetitive inhibition, whilst 10j displayed mixed competitive inhibition. The pyrazolopyrimidine inhibitor 11k displayed uncompetitive inhibition. This is the first report of the identification of specific drug-like small-molecule AMACR inhibitors by high-throughput screening. Pyrazoloquinolines and pyrazolopyrimidines may also be useful as inhibitors of other CoA-utilizing enzymes.
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Affiliation(s)
- Yoana D Petrova
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Katty Wadda
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK; Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Amit Nathubhai
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK; School of Pharmacy and Pharmaceutical Sciences, Sciences Complex, City Campus, Dale Building, Room 121, Sunderland SR1 3SD, UK(1)
| | - Maksims Yevglevskis
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Paul J Mitchell
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Tony D James
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Michael D Threadgill
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Timothy J Woodman
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Matthew D Lloyd
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
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Yevglevskis M, Nathubhai A, Wadda K, Lee GL, Al-Rawi S, Jiao T, Mitchell PJ, James TD, Threadgill MD, Woodman TJ, Lloyd MD. Novel 2-arylthiopropanoyl-CoA inhibitors of α-methylacyl-CoA racemase 1A (AMACR; P504S) as potential anti-prostate cancer agents. Bioorg Chem 2019; 92:103263. [PMID: 31536953 DOI: 10.1016/j.bioorg.2019.103263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 10/26/2022]
Abstract
α-Methylacyl-CoA racemase (AMACR; P504S) catalyses an essential step in the degradation of branched-chain fatty acids and the activation of ibuprofen and related drugs. AMACR has gained much attention as a drug target and biomarker, since it is found at elevated levels in prostate cancer and several other cancers. Herein, we report the synthesis of 2-(phenylthio)propanoyl-CoA derivatives which provided potent AMACR inhibitory activity (IC50 = 22-100 nM), as measured by the AMACR colorimetric activity assay. Inhibitor potency positively correlates with calculated logP, although 2-(3-benzyloxyphenylthio)propanoyl-CoA and 2-(4-(2-methylpropoxy)phenylthio)propanoyl-CoA were more potent than predicted by this parameter. Subsequently, carboxylic acid precursors were evaluated against androgen-dependent LnCaP prostate cancer cells and androgen-independent Du145 and PC3 prostate cancer cells using the MTS assay. All tested precursor acids showed inhibitory activity against LnCaP, Du145 and PC3 cells at 500 µM, but lacked activity at 100 µM. This is the first extensive structure-activity relationship study on the influence of side-chain interactions on the potency of novel rationally designed AMACR inhibitors.
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Affiliation(s)
- Maksims Yevglevskis
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Amit Nathubhai
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK; University of Sunderland, School of Pharmacy and Pharmaceutical Sciences, Sciences Complex, Sunderland SR1 3SD, UK(1)
| | - Katty Wadda
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK; Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Guat L Lee
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Suzanne Al-Rawi
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Tingying Jiao
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK; School of Pharmaceutical Sciences, Shandong University, Jinan, People's Republic of China
| | - Paul J Mitchell
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Tony D James
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Michael D Threadgill
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Timothy J Woodman
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Matthew D Lloyd
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
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9
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Yevglevskis M, Lee GL, Nathubhai A, Petrova YD, James TD, Threadgill MD, Woodman TJ, Lloyd MD. Structure-activity relationships of rationally designed AMACR 1A inhibitors. Bioorg Chem 2018; 79:145-154. [PMID: 29751320 DOI: 10.1016/j.bioorg.2018.04.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 12/12/2022]
Abstract
α-Methylacyl-CoA racemase (AMACR; P504S) is a promising novel drug target for prostate and other cancers. Assaying enzyme activity is difficult due to the reversibility of the 'racemisation' reaction and the difficulties in the separation of epimeric products; consequently few inhibitors have been described and no structure-activity relationship study has been performed. This paper describes the first structure-activity relationship study, in which a series of 23 known and potential rational AMACR inhibitors were evaluated. AMACR was potently inhibited (IC50 = 400-750 nM) by ibuprofenoyl-CoA and derivatives. Potency was positively correlated with inhibitor lipophilicity. AMACR was also inhibited by straight-chain and branched-chain acyl-CoA esters, with potency positively correlating with inhibitor lipophilicity. 2-Methyldecanoyl-CoAs were ca. 3-fold more potent inhibitors than decanoyl-CoA, demonstrating the importance of the 2-methyl group for effective inhibition. Elimination substrates and compounds with modified acyl-CoA cores were also investigated, and shown to be potent inhibitors. These results are the first to demonstrate structure-activity relationships of rational AMACR inhibitors and that potency can be predicted by acyl-CoA lipophilicity. The study also demonstrates the utility of the colorimetric assay for thorough inhibitor characterisation.
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Affiliation(s)
- Maksims Yevglevskis
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Guat L Lee
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Amit Nathubhai
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Yoana D Petrova
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Tony D James
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Michael D Threadgill
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Timothy J Woodman
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Matthew D Lloyd
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
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Pal M, Easton NM, Yaphe H, Bearne SL. Potent dialkyl substrate-product analogue inhibitors and inactivators of α-methylacyl-coenzyme A racemase from Mycobacterium tuberculosis by rational design. Bioorg Chem 2018; 77:640-650. [PMID: 29502025 DOI: 10.1016/j.bioorg.2018.01.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/28/2018] [Accepted: 01/30/2018] [Indexed: 12/15/2022]
Abstract
Rational approaches for the design of enzyme inhibitors furnish powerful strategies for developing pharmaceutical agents and tools for probing biological mechanisms. A new strategy for the development of gem-disubstituted substrate-product analogues as inhibitors of racemases and epimerases is elaborated using α-methylacyl-coenzyme A racemase from Mycobacterium tuberculosis (MtMCR) as a model enzyme. MtMCR catalyzes the epimerization at C2 of acyl-CoA substrates, a key step in the metabolism of branched-chain fatty acids. Moreover, the human enzyme is a potential target for the development of therapeutic agents directed against prostate cancer. We show that rationally designed, N,N-dialkylcarbamoyl-CoA substrate-product analogues inactivate MtMCR. Binding greatly exceeds that of the substrate, (S)-ibuprofenoyl-CoA, up to ∼250-fold and is proportional to the alkyl chain length (4-12 carbons) with the N,N-didecyl and N,N-didodecyl species having competitive inhibition constants with values of 1.9 ± 0.2 μM and 0.42 ± 0.04 μM, respectively. The presence of two decyl chains enhanced binding over a single decyl chain by ∼204-fold. Overall, the results reveal that gem-disubstituted substrate-product analogues can yield extremely potent inhibitors of an epimerase with a capacious active site.
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Affiliation(s)
- Mohan Pal
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Nicole M Easton
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Hannah Yaphe
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Department of Chemistry, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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11
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Yevglevskis M, Lee GL, Nathubhai A, Petrova YD, James TD, Threadgill MD, Woodman TJ, Lloyd MD. A novel colorimetric assay for α-methylacyl-CoA racemase 1A (AMACR; P504S) utilizing the elimination of 2,4-dinitrophenolate. Chem Commun (Camb) 2017; 53:5087-5090. [DOI: 10.1039/c7cc00476a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A versatile continuous colorimetric assay for AMACR is reported.
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Affiliation(s)
- Maksims Yevglevskis
- Drug & Target Development
- Department of Pharmacy & Pharmacology
- University of Bath
- Bath BA2 7AY
- UK
| | - Guat L. Lee
- Drug & Target Development
- Department of Pharmacy & Pharmacology
- University of Bath
- Bath BA2 7AY
- UK
| | - Amit Nathubhai
- Drug & Target Development
- Department of Pharmacy & Pharmacology
- University of Bath
- Bath BA2 7AY
- UK
| | - Yoana D. Petrova
- Drug & Target Development
- Department of Pharmacy & Pharmacology
- University of Bath
- Bath BA2 7AY
- UK
| | - Tony D. James
- Department of Chemistry
- University of Bath
- Bath BA2 7AY
- UK
| | - Michael D. Threadgill
- Drug & Target Development
- Department of Pharmacy & Pharmacology
- University of Bath
- Bath BA2 7AY
- UK
| | - Timothy J. Woodman
- Drug & Target Development
- Department of Pharmacy & Pharmacology
- University of Bath
- Bath BA2 7AY
- UK
| | - Matthew D. Lloyd
- Drug & Target Development
- Department of Pharmacy & Pharmacology
- University of Bath
- Bath BA2 7AY
- UK
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12
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Jolly P, Miodek A, Yang DK, Chen LC, Lloyd MD, Estrela P. Electro-Engineered Polymeric Films for the Development of Sensitive Aptasensors for Prostate Cancer Marker Detection. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00443] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | | | - Deng-Kai Yang
- Department
of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Lin-Chi Chen
- Department
of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
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13
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Pal M, Khanal M, Marko R, Thirumalairajan S, Bearne SL. Rational design and synthesis of substrate-product analogue inhibitors of α-methylacyl-coenzyme A racemase from Mycobacterium tuberculosis. Chem Commun (Camb) 2016; 52:2740-3. [PMID: 26759836 DOI: 10.1039/c5cc08096g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
2,2-Bis(4-isobutylphenyl)propanoyl-CoA and 2,2-bis(4-t-butylphenyl)propanoyl-CoA are rationally designed, gem-disubstituted substrate-product analogues that competitively inhibit α-methylacyl-coenzyme A racemase from Mycobacterium tuberculosis with Ki values of 16.9 ± 0.6 and 21 ± 4 μM, respectively, exceeding the enzyme's affinity for the substrate by approximately 5-fold.
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Affiliation(s)
- Mohan Pal
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Mandar Khanal
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Ryan Marko
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Srinath Thirumalairajan
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Stephen L Bearne
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada. and Department of Chemistry, Dalhousie University, Halifax, NS B3H 4R2, Canada
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14
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Kavianinia I, Kunalingam L, Harris PWR, Cook GM, Brimble MA. Total Synthesis and Stereochemical Revision of the Anti-Tuberculosis Peptaibol Trichoderin A. Org Lett 2016; 18:3878-81. [DOI: 10.1021/acs.orglett.6b01886] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Iman Kavianinia
- School
of Biological Sciences, The University of Auckland, 3A Symonds
Street, Auckland 1010, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - Lavanya Kunalingam
- School
of Biological Sciences, The University of Auckland, 3A Symonds
Street, Auckland 1010, New Zealand
| | - Paul W. R. Harris
- School
of Biological Sciences, The University of Auckland, 3A Symonds
Street, Auckland 1010, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - Gregory M. Cook
- Maurice
Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
- Department
of Microbiology and Immunology, School of Medical Sciences, University of Otago, 720 Cumberland Street, Dunedin 9054, New Zealand
| | - Margaret A. Brimble
- School
of Biological Sciences, The University of Auckland, 3A Symonds
Street, Auckland 1010, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
- School
of Chemical Sciences, The University of Auckland, 23 Symonds
Street, Auckland 1010, New Zealand
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15
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Wilkes H, Buckel W, Golding BT, Rabus R. Metabolism of Hydrocarbons in n-Alkane-Utilizing Anaerobic Bacteria. J Mol Microbiol Biotechnol 2016; 26:138-51. [PMID: 26959725 DOI: 10.1159/000442160] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The glycyl radical enzyme-catalyzed addition of n-alkanes to fumarate creates a C-C-bond between two concomitantly formed stereogenic carbon centers. The configurations of the two diastereoisomers of the product resulting from n-hexane activation by the n-alkane-utilizing denitrifying bacterium strain HxN1, i.e. (1-methylpentyl)succinate, were assigned as (2S,1'R) and (2R,1'R). Experiments with stereospecifically deuterated n-(2,5-2H2)hexanes revealed that exclusively the pro-S hydrogen atom is abstracted from C2 of the n-alkane by the enzyme and later transferred back to C3 of the alkylsuccinate formed. These results indicate that the alkylsuccinate-forming reaction proceeds with an inversion of configuration at the carbon atom (C2) of the n-alkane forming the new C-C-bond, and thus stereochemically resembles a SN2-type reaction. Therefore, the reaction may occur in a concerted manner, which may avoid the highly energetic hex-2-yl radical as an intermediate. The reaction is associated with a significant primary kinetic isotope effect (kH/kD ≥3) for hydrogen, indicating that the homolytic C-H-bond cleavage is involved in the first irreversible step of the reaction mechanism. The (1-methylalkyl)succinate synthases of n-alkane-utilizing anaerobic bacteria apparently have very broad substrate ranges enabling them to activate not only aliphatic but also alkyl-aromatic hydrocarbons. Thus, two denitrifiers and one sulfate reducer were shown to convert the nongrowth substrate toluene to benzylsuccinate and further to the dead-end product benzoyl-CoA. For this purpose, however, the modified β-oxidation pathway known from alkylbenzene-utilizing bacteria was not employed, but rather the pathway used for n-alkane degradation involving CoA ligation, carbon skeleton rearrangement and decarboxylation. Furthermore, various n-alkane- and alkylbenzene-utilizing denitrifiers and sulfate reducers were found to be capable of forming benzyl alcohols from diverse alkylbenzenes, putatively via dehydrogenases. The thermophilic sulfate reducer strain TD3 forms n-alkylsuccinates during growth with n-alkanes or crude oil, which, based on the observed patterns of homologs, do not derive from a terminal activation of n-alkanes.
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Affiliation(s)
- Heinz Wilkes
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
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16
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Yevglevskis M, Lee GL, Sun J, Zhou S, Sun X, Kociok-Köhn G, James TD, Woodman TJ, Lloyd MD. A study on the AMACR catalysed elimination reaction and its application to inhibitor testing. Org Biomol Chem 2016; 14:612-622. [PMID: 26537174 PMCID: PMC4718014 DOI: 10.1039/c5ob01541c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 10/27/2015] [Indexed: 12/15/2022]
Abstract
α-Methylacyl-CoA racemase (AMACR; P504S) catalyses a key step in the degradation of branched-chain fatty acids and is important for the pharmacological activation of Ibuprofen and related drugs. Levels of AMACR are increased in prostate and other cancers, and it is a drug target. Development of AMACR as a drug target is hampered by lack of a convenient assay. AMACR irreversibly catalyses the elimination of HF from 3-fluoro-2-methylacyl-CoA substrates, and this reaction was investigated for use as an assay. Several known inhibitors and alternative substrates reduced conversion of 3-fluoro-2-methyldecanoyl-CoA by AMACR, as determined by (1)H NMR. The greatest reduction of activity was observed with known potent inhibitors. A series of novel acyl-CoA esters with aromatic side chains were synthesised for testing as chromophoric substrates. These acyl-CoA esters were converted to unsaturated products by AMACR, but their use was limited by non-enzymatic elimination. Fluoride sensors were also investigated as a method of quantifying released fluoride and thus AMACR activity. These sensors generally suffered from high background signal and lacked reproducibility under the assay conditions. In summary, the elimination reaction can be used to characterise inhibitors, but it was not possible to develop a convenient colorimetric or fluorescent assay using 3-fluoro-2-methylacyl-CoA substrates.
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Affiliation(s)
- Maksims Yevglevskis
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
| | - Guat L. Lee
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
| | - Jenny Sun
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
- Department of Pharmacy , Shandong University , People's Republic of China
| | - Shiyi Zhou
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
- Department of Pharmacy , Shandong University , People's Republic of China
| | - Xiaolong Sun
- Department of Chemistry , University of Bath , Claverton Down , Bath BA2 7AY , UK
| | - Gabriele Kociok-Köhn
- Department of Chemistry , University of Bath , Claverton Down , Bath BA2 7AY , UK
| | - Tony D. James
- Department of Chemistry , University of Bath , Claverton Down , Bath BA2 7AY , UK
| | - Timothy J. Woodman
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
| | - Matthew D. Lloyd
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
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17
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Yevglevskis M, Lee GL, Threadgill MD, Woodman TJ, Lloyd MD. The perils of rational design--unexpected irreversible elimination of fluoride from 3-fluoro-2-methylacyl-CoA esters catalysed by α-methylacyl-CoA racemase (AMACR; P504S). Chem Commun (Camb) 2015; 50:14164-6. [PMID: 25277991 DOI: 10.1039/c4cc06127f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
α-Methylacyl-CoA racemase (AMACR; P504S) catalyses 'racemization' of 2-methylacyl-CoAs, the activation of R-ibuprofen and is a promising cancer drug target. Human recombinant AMACR 1A catalyses elimination of 3-fluoro-2-methyldecanoyl-CoAs to give E-2-methyldec-2-enoyl-CoA and fluoride anion, a previously unknown reaction. 'Racemization' of 2-methyldec-3-enoyl-CoAs was also catalysed, without double bond migration.
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Affiliation(s)
- Maksims Yevglevskis
- Medicinal Chemistry, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
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18
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Yevglevskis M, Bowskill CR, Chan CCY, Heng JHJ, Threadgill MD, Woodman TJ, Lloyd MD. A study on the chiral inversion of mandelic acid in humans. Org Biomol Chem 2015; 12:6737-44. [PMID: 25050409 DOI: 10.1039/c3ob42515k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mandelic acid is a chiral metabolite of the industrial pollutant styrene and is used in chemical skin peels, as a urinary antiseptic and as a component of other medicines. In humans, S-mandelic acid undergoes rapid chiral inversion to R-mandelic acid by an undefined pathway but it has been proposed to proceed via the acyl-CoA esters, S- and R-2-hydroxy-2-phenylacetyl-CoA, in an analogous pathway to that for Ibuprofen. This study investigates chiral inversion of mandelic acid using purified human recombinant enzymes known to be involved in the Ibuprofen chiral inversion pathway. Both S- and R-2-hydroxy-2-phenylacetyl-CoA were hydrolysed to mandelic acid by human acyl-CoA thioesterase-1 and -2 (ACOT1 and ACOT2), consistent with a possible role in the chiral inversion pathway. However, human α-methylacyl-CoA racemase (AMACR; P504S) was not able to catalyse exchange of the α-proton of S- and R-2-hydroxy-2-phenylacetyl-CoA, a requirement for chiral inversion. Both S- and R-2-phenylpropanoyl-CoA were epimerised by AMACR, showing that it is the presence of the hydroxy group that prevents epimerisation of R- and S-2-hydroxy-2-phenylacetyl-CoAs. The results show that it is unlikely that 2-hydroxy-2-phenylacetyl-CoA is an intermediate in the chiral inversion of mandelic acid, and that the chiral inversion of mandelic acid is via a different pathway to that of Ibuprofen and related drugs.
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Affiliation(s)
- Maksims Yevglevskis
- Medicinal Chemistry, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom.
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19
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Qu X, Allan A, Chui G, Hutchings TJ, Jiao P, Johnson L, Leung WY, Li PK, Steel GR, Thompson AS, Threadgill MD, Woodman TJ, Lloyd MD. Hydrolysis of ibuprofenoyl-CoA and other 2-APA-CoA esters by human acyl-CoA thioesterases-1 and -2 and their possible role in the chiral inversion of profens. Biochem Pharmacol 2013; 86:1621-5. [PMID: 24041740 DOI: 10.1016/j.bcp.2013.08.067] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 08/29/2013] [Accepted: 08/30/2013] [Indexed: 11/16/2022]
Abstract
Ibuprofen and related 2-arylpropanoic acid (2-APA) drugs are often given as a racemic mixture and the R-enantiomers undergo activation in vivo by metabolic chiral inversion. The chiral inversion pathway consists of conversion of the drug to the coenzyme A ester (by an acyl-CoA synthetase) followed by chiral inversion by α-methylacyl-CoA racemase (AMACR; P504S). The enzymes responsible for hydrolysis of the product S-2-APA-CoA ester to the active S-2-APA drug have not been identified. In this study, conversion of a variety of 2-APA-CoA esters by human acyl-CoA thioesterase-1 and -2 (ACOT-1 and -2) was investigated. Human recombinant ACOT-1 and -2 (ACOT-1 and -2) were both able to efficiently hydrolyse a variety of 2-APA-CoA substrates. Studies with the model substrates R- and S-2-methylmyristoyl-CoA showed that both enzymes were able to efficiently hydrolyse both of the epimeric substrates with (2R)- and (2S)- methyl groups. ACOT-1 is located in the cytosol and is able to hydrolyse 2-APA-CoA esters exported from the mitochondria and peroxisomes for inhibition of cyclo-oxygenase-1 and -2 in the endoplasmic reticulum. It is a prime candidate to be the enzyme responsible for the pharmacological action of chiral inverted drugs. ACOT-2 activity may be important in 2-APA toxicity effects and for the regulation of mitochondrial free coenzyme A levels. These results support the idea that 2-APA drugs undergo chiral inversion via a common pathway.
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Affiliation(s)
- Xiao Qu
- Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
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20
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Lloyd MD, Yevglevskis M, Lee GL, Wood PJ, Threadgill MD, Woodman TJ. α-Methylacyl-CoA racemase (AMACR): Metabolic enzyme, drug metabolizer and cancer marker P504S. Prog Lipid Res 2013; 52:220-30. [DOI: 10.1016/j.plipres.2013.01.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 10/27/2022]
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21
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Cao B, Chen X, Yamaryo-Botte Y, Richardson MB, Martin KL, Khairallah GN, Rupasinghe TW, O’Flaherty RM, O’Hair RA, Ralton JE, Crellin PK, Coppel RL, McConville MJ, Williams SJ. Synthesis, Structural Elucidation, And Biochemical Analysis of Immunoactive Glucuronosyl Diacylglycerides of Mycobacteria and Corynebacteria. J Org Chem 2013; 78:2175-90. [DOI: 10.1021/jo302508e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Paul K. Crellin
- Department of Microbiology, Monash University, Victoria 3800, Australia
| | - Ross L. Coppel
- Department of Microbiology, Monash University, Victoria 3800, Australia
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22
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Sharma S, Bhaumik P, Schmitz W, Venkatesan R, Hiltunen JK, Conzelmann E, Juffer AH, Wierenga RK. The Enolization Chemistry of a Thioester-Dependent Racemase: The 1.4 Å Crystal Structure of a Reaction Intermediate Complex Characterized by Detailed QM/MM Calculations. J Phys Chem B 2012; 116:3619-29. [DOI: 10.1021/jp210185m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Satyan Sharma
- Biocenter Oulu and Department
of Biochemistry, University of Oulu, P.O.
Box 3000, Oulu, FI-90014, Finland
| | - Prasenjit Bhaumik
- Protein Structure Section, Macromolecular
Crystallography Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Werner Schmitz
- Theodor-Boveri-Institut für
Biowissenschaften (Biozentrum) der Universität Würzburg, Am Hubland, D-97074 Würzburg,
Germany
| | - Rajaram Venkatesan
- Biocenter Oulu and Department
of Biochemistry, University of Oulu, P.O.
Box 3000, Oulu, FI-90014, Finland
| | - J. Kalervo Hiltunen
- Biocenter Oulu and Department
of Biochemistry, University of Oulu, P.O.
Box 3000, Oulu, FI-90014, Finland
| | - Ernst Conzelmann
- Theodor-Boveri-Institut für
Biowissenschaften (Biozentrum) der Universität Würzburg, Am Hubland, D-97074 Würzburg,
Germany
| | - André H. Juffer
- Biocenter Oulu and Department
of Biochemistry, University of Oulu, P.O.
Box 3000, Oulu, FI-90014, Finland
| | - Rik K. Wierenga
- Biocenter Oulu and Department
of Biochemistry, University of Oulu, P.O.
Box 3000, Oulu, FI-90014, Finland
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23
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Jarling R, Sadeghi M, Drozdowska M, Lahme S, Buckel W, Rabus R, Widdel F, Golding BT, Wilkes H. Stereochemical investigations reveal the mechanism of the bacterial activation of n-alkanes without oxygen. Angew Chem Int Ed Engl 2011; 51:1334-8. [PMID: 22127985 DOI: 10.1002/anie.201106055] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Indexed: 11/11/2022]
Affiliation(s)
- René Jarling
- Organische Geochemie, Helmholtz-Zentrum Potsdam, Deutsches GeoForschungsZentrum GFZ, Haus B228, Telegrafenberg, 14473 Potsdam, Germany
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24
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Jarling R, Sadeghi M, Drozdowska M, Lahme S, Buckel W, Rabus R, Widdel F, Golding BT, Wilkes H. Stereochemische Untersuchungen enthüllen den Mechanismus der sauerstofffreien Aktivierung von n-Alkanen durch Bakterien. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106055] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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Morgenroth A, Urusova EA, Dinger C, Al-Momani E, Kull T, Glatting G, Frauendorf H, Jahn O, Mottaghy FM, Reske SN, Zlatopolskiy BD. New Molecular Markers for Prostate Tumor Imaging: A Study on 2-Methylene Substituted Fatty Acids as New AMACR Inhibitors. Chemistry 2011; 17:10144-50. [DOI: 10.1002/chem.201003176] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 05/09/2011] [Indexed: 11/10/2022]
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26
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Wilson BA, Wang H, Nacev BA, Mease RC, Liu JO, Pomper MG, Isaacs WB. High-throughput screen identifies novel inhibitors of cancer biomarker α-methylacyl coenzyme A racemase (AMACR/P504S). Mol Cancer Ther 2011; 10:825-38. [PMID: 21441411 PMCID: PMC3423201 DOI: 10.1158/1535-7163.mct-10-0902] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
α-methylacyl coenzyme A racemase (AMACR) is a metabolic enzyme whose overexpression has been shown to be a diagnostic indicator of prostatic adenocarcinoma and other solid tumors. Here, we confirm that attenuation of AMACR expression diminishes the growth of prostate cancer cell lines by using stably expressed short-hairpin RNA constructs. This observation strongly suggests that the AMACR enzyme may be a target for therapeutic inhibition in prostate cancer. To this end, we report here a novel assay capable of screening libraries of diverse small molecules for inhibitors of AMACR activity. This assay facilitated the screening of approximately 5,000 unique compounds and the discovery of 7 distinct chemical entities capable of inhibiting AMACR at low micromolar concentrations. The most potent inhibitor discovered is the seleno-organic compound ebselen oxide [inhibitory concentration (IC(50)): 0.80 μmol/L]. The parent compound, ebselen (IC(50): 2.79 μmol/L), is a covalent inactivator of AMACR (K(I)((inact)): 24 μmol/L). Two of the AMACR inhibitors are selectively toxic to prostate cancer cell lines (LAPC4/LNCaP/PC3) that express AMACR compared to a normal prostate fibroblast cell line (WPMY1) that does not express the protein. This report shows the first high-throughput screen for the discovery of novel AMACR inhibitors, characterizes the first nonsubstrate-based inhibitors, and validates that AMACR is a viable chemotherapeutic target in vitro.
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Affiliation(s)
- Brice A.P. Wilson
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD
- James Buchanan Brady Urological Institute, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Haofan Wang
- Department of Radiology and Radiological Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Benjamin A. Nacev
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ronnie C. Mease
- Department of Radiology and Radiological Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jun O. Liu
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Martin G. Pomper
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Radiology and Radiological Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - William B. Isaacs
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD
- James Buchanan Brady Urological Institute, The Johns Hopkins University School of Medicine, Baltimore, MD
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27
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Woodman TJ, Wood PJ, Thompson AS, Hutchings TJ, Steel GR, Jiao P, Threadgill MD, Lloyd MD. Chiral inversion of 2-arylpropionyl-CoA esters by human α-methylacyl-CoA racemase 1A (P504S)—a potential mechanism for the anti-cancer effects of ibuprofen. Chem Commun (Camb) 2011; 47:7332. [DOI: 10.1039/c1cc10763a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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28
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Berretta R, Moscato P. Cancer biomarker discovery: the entropic hallmark. PLoS One 2010; 5:e12262. [PMID: 20805891 PMCID: PMC2923618 DOI: 10.1371/journal.pone.0012262] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Accepted: 06/26/2010] [Indexed: 12/29/2022] Open
Abstract
Background It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods. Methodology/Principal Findings Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer. Conclusions/Significance We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-througput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases.
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Affiliation(s)
- Regina Berretta
- Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, The University of Newcastle, Callaghan, New South Wales, Australia
- Information Based Medicine Program, Hunter Medical Research Institute, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Pablo Moscato
- Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, The University of Newcastle, Callaghan, New South Wales, Australia
- Information Based Medicine Program, Hunter Medical Research Institute, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
- Australian Research Council Centre of Excellence in Bioinformatics, Callaghan, New South Wales, Australia
- * E-mail:
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29
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Sattar FA, Darley DJ, Politano F, Woodman TJ, Threadgill MD, Lloyd MD. Unexpected stereoselective exchange of straight-chain fatty acyl-CoA alpha-protons by human alpha-methylacyl-CoA racemase 1A (P504S). Chem Commun (Camb) 2010; 46:3348-50. [PMID: 20442897 DOI: 10.1039/c002509g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Alpha-methylacyl-CoA racemase (AMACR; P504S) catalysed exchange of straight-chain fatty acyl-CoA alpha-protons. One alpha-proton was removed in each catalytic cycle, with the pro-S proton preferred. This reaction was most efficient for straight-chain substrates with longer side-chains. 2-Methyldecanoyl-CoA underwent alpha-proton exchange 3x more efficiently (as judged by K(cat)/K(m)) than decanoyl-CoA.
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Affiliation(s)
- Fouzia A Sattar
- Medicinal Chemistry, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
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30
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Ouazia D, Bearne SL. A continuous assay for alpha-methylacyl-coenzyme A racemase using circular dichroism. Anal Biochem 2009; 398:45-51. [PMID: 19854148 DOI: 10.1016/j.ab.2009.10.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Revised: 10/20/2009] [Accepted: 10/21/2009] [Indexed: 12/22/2022]
Abstract
alpha-Methylacyl-coenzyme A racemase (AMACR) catalyzes the epimerization of (2R)- and (2S)-methyl branched fatty acyl-coenzyme A (CoA) thioesters. AMACR is a biomarker for prostate cancer and a putative target for the development of therapeutic agents directed against the disease. To facilitate development of AMACR inhibitors, a continuous circular dichroism (CD)-based assay has been developed. The open reading frame encoding AMACR from Mycobacterium tuberculosis (MCR) was subcloned into a pET15b vector, and the enzyme was overexpressed and purified using metal ion affinity chromatography. The rates of MCR-catalyzed epimerization of either (2R)- or (2S)-ibuprofenoyl-CoA were determined by following the change in ellipticity at 279nm in the presence of octyl-beta-d-glucopyranoside (0.2%). MCR exhibited slightly higher affinity for (2R)-ibuprofenoyl-CoA (K(m)=48+/-5microM, k(cat)=291+/-30s(-1)), but turned over (2S)-ibuprofenoyl-CoA (K(m)=86+/-6microM, k(cat)=450+/-14s(-1)) slightly faster. MCR expressed as a fusion protein bearing an N-terminal His(6)-tag had a catalytic efficiency (k(cat)/K(m)) that was reduced 22% and 47% in the 2S-->2R and 2R-->2S directions, respectively, relative to untagged enzyme. The continuous CD-based assay offers an economical and efficient alternative method to the labor-intensive, fixed-time assays currently used to measure AMACR activity.
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Affiliation(s)
- Dahmane Ouazia
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5
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