1
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Lykins J, Moschitto MJ, Zhou Y, Filippova EV, Le HV, Tomita T, Fox BA, Bzik DJ, Su C, Rajagopala SV, Flores K, Spano F, Woods S, Roberts CW, Hua C, El Bissati K, Wheeler KM, Dovgin S, Muench SP, McPhillie M, Fishwick CW, Anderson WF, Lee PJ, Hickman M, Weiss LM, Dubey JP, Lorenzi HA, Silverman RB, McLeod RL. From TgO/GABA-AT, GABA, and T-263 Mutant to Conception of Toxoplasma. iScience 2024; 27:108477. [PMID: 38205261 PMCID: PMC10776954 DOI: 10.1016/j.isci.2023.108477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 04/28/2023] [Accepted: 11/13/2023] [Indexed: 01/12/2024] Open
Abstract
Toxoplasma gondii causes morbidity, mortality, and disseminates widely via cat sexual stages. Here, we find T. gondii ornithine aminotransferase (OAT) is conserved across phyla. We solve TgO/GABA-AT structures with bound inactivators at 1.55 Å and identify an inactivator selective for TgO/GABA-AT over human OAT and GABA-AT. However, abrogating TgO/GABA-AT genetically does not diminish replication, virulence, cyst-formation, or eliminate cat's oocyst shedding. Increased sporozoite/merozoite TgO/GABA-AT expression led to our study of a mutagenized clone with oocyst formation blocked, arresting after forming male and female gametes, with "Rosetta stone"-like mutations in genes expressed in merozoites. Mutations are similar to those in organisms from plants to mammals, causing defects in conception and zygote formation, affecting merozoite capacitation, pH/ionicity/sodium-GABA concentrations, drawing attention to cyclic AMP/PKA, and genes enhancing energy or substrate formation in TgO/GABA-AT-related-pathways. These candidates potentially influence merozoite's capacity to make gametes that fuse to become zygotes, thereby contaminating environments and causing disease.
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Affiliation(s)
- Joseph Lykins
- Pritzker School of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Matthew J. Moschitto
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208-3113, USA
| | - Ying Zhou
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Ekaterina V. Filippova
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hoang V. Le
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208-3113, USA
| | - Tadakimi Tomita
- Division of Parasitology, Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Barbara A. Fox
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - David J. Bzik
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Chunlei Su
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Seesandra V. Rajagopala
- Department of Infectious Diseases, The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Kristin Flores
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Furio Spano
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Stuart Woods
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow Scotland, UK
| | - Craig W. Roberts
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow Scotland, UK
| | - Cong Hua
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Kamal El Bissati
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Kelsey M. Wheeler
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Sarah Dovgin
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Stephen P. Muench
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, The University of Leeds, Leeds, West York LS2 9JT, UK
| | - Martin McPhillie
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Colin W.G. Fishwick
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Pharmacology, Northwestern University, Chicago, IL 60611, USA
| | - Patricia J. Lee
- Division of Experimental Therapeutics, Military Malaria Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Mark Hickman
- Division of Experimental Therapeutics, Military Malaria Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Louis M. Weiss
- Division of Parasitology, Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jitender P. Dubey
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Hernan A. Lorenzi
- Department of Infectious Diseases, The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Richard B. Silverman
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208-3113, USA
- Department of Pharmacology, Northwestern University, Chicago, IL 60611, USA
| | - Rima L. McLeod
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
- Department of Pediatrics (Infectious Diseases), Institute of Genomics, Genetics, and Systems Biology, Global Health Center, Toxoplasmosis Center, CHeSS, The College, University of Chicago, Chicago, IL 60637, USA
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2
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Maity AN, Chen JR, Ke SC. Exploring the mechanism of action of lysine 5,6-aminomutase using EPR and ENDOR spectroscopies. Methods Enzymol 2022; 669:197-228. [PMID: 35644172 DOI: 10.1016/bs.mie.2021.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Radical enzymes orchestrate challenging chemical transformations by devising strategies to tame the highly reactive radical intermediates. Electron paramagnetic resonance (EPR) spectroscopy is the most suitable technique to study various aspects of the radical enzymes. Lysine 5,6-aminomutase (5,6-LAM) is one such radical enzyme and employs coenzyme B12 and pyridoxal 5'-phosphate (PLP) to catalyze the 1,2-amino shift reaction through a radical mechanism. 5,6-LAM accepts either d-lysine or l-β-lysine as the substrate. EPR and electron nuclear double resonance (ENDOR) spectroscopies have played major roles in deciphering the mechanism of action of 5,6-LAM, while density functional theoretical (DFT) computation and synthetic isotopologues have played supporting roles. This comprehensive toolkit has revealed that 5,6-LAM undergoes large-scale conformational movement to bring PLP and coenzyme B12 close together, which allows the reaction to progress. The conformational change also closes the active site, which protects the radical intermediates and enables their transformation to product without unwanted side reactions. The substrate-related radical (S•), which is spin-coupled with Co2+ generated from homolysis of the CoC bond in coenzyme B12, was unequivocally characterized when a substrate analog, 4-thia-l-lysine, and isotopologues of it were reacted with 5,6-LAM. Studies with substrate analogs revealed a unique "odd-even" correlation with opening of the closed state. Moreover, mutagenesis studies identified the contributions that conserved residues in 5,6-LAM make toward binding of the substrate. Further studies with a cofactor analog, PLP-N-oxide, have shed light on various aspects of the mechanism of action of 5,6-LAM.
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Affiliation(s)
| | - Jun-Ru Chen
- Department of Physics, National Dong Hwa University, Hualien, Taiwan
| | - Shyue-Chu Ke
- Department of Physics, National Dong Hwa University, Hualien, Taiwan.
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3
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Silverman RB. Design and Mechanism of GABA Aminotransferase Inactivators. Treatments for Epilepsies and Addictions. Chem Rev 2018; 118:4037-4070. [PMID: 29569907 PMCID: PMC8459698 DOI: 10.1021/acs.chemrev.8b00009] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
When the brain concentration of the inhibitory neurotransmitter γ-aminobutyric acid (GABA) diminishes below a threshold level, the excess neuronal excitation can lead to convulsions. This imbalance in neurotransmission can be corrected by inhibition of the enzyme γ-aminobutyric acid aminotransferase (GABA-AT), which catalyzes the conversion of GABA to the excitatory neurotransmitter l-glutamic acid. It also has been found that raising GABA levels can antagonize the rapid elevation and release of dopamine in the nucleus accumbens, which is responsible for the reward response in addiction. Therefore, the design of new inhibitors of GABA-AT, which increases brain GABA levels, is an important approach to new treatments for epilepsy and addiction. This review summarizes findings over the last 40 or so years of mechanism-based inactivators (unreactive compounds that require the target enzyme to catalyze their conversion to the inactivating species, which inactivate the enzyme prior to their release) of GABA-AT with emphasis on their catalytic mechanisms of inactivation, presented according to organic chemical mechanism, with minimal pharmacology, except where important for activity in epilepsy and addiction. Patents, abstracts, and conference proceedings are not covered in this review. The inactivation mechanisms described here can be applied to the inactivations of a wide variety of unrelated enzymes.
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Affiliation(s)
- Richard B. Silverman
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois, 60208-3113, United States
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4
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Zigmond E, Ya’acov AB, Lee H, Lichtenstein Y, Shalev Z, Smith Y, Zolotarov L, Ziv E, Kalman R, Le HV, Lu H, Silverman RB, Ilan Y. Suppression of Hepatocellular Carcinoma by Inhibition of Overexpressed Ornithine Aminotransferase. ACS Med Chem Lett 2015; 6:840-4. [PMID: 26288681 DOI: 10.1021/acsmedchemlett.5b00153] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 05/29/2015] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma is the second leading cause of cancer death worldwide. DNA microarray analysis identified the ornithine aminotransferase (OAT) gene as a prominent gene overexpressed in hepatocellular carcinoma (HCC) from Psammomys obesus. In vitro studies demonstrated inactivation of OAT by gabaculine (1), a neurotoxic natural product, which suppressed in vitro proliferation of two HCC cell lines. Alpha-fetoprotein (AFP) secretion, a biomarker for HCC, was suppressed by gabaculine in both cell lines, but not significantly. Because of the active site similarity between GABA aminotransferase (GABA-AT) and OAT, a library of 24 GABA-AT inhibitors was screened to identify a more selective inhibitor of OAT. (1S,3S)-3-Amino-4-(hexafluoropropan-2-ylidene)cyclopentane-1-carboxylic acid (2) was found to be an inactivator of OAT that only weakly inhibits GABA-AT, l-aspartate aminotransferase, and l-alanine aminotransferase. In vitro administration of 2 significantly suppressed AFP secretion in both Hep3B and HepG2 HCC cells; in vivo, 2 significantly suppressed AFP serum levels and tumor growth in HCC-harboring mice, even at 0.1 mg/kg. Overexpression of the OAT gene in HCC and the ability to block the growth of HCC by OAT inhibitors support the role of OAT as a potential therapeutic target to inhibit HCC growth. This is the first demonstration of suppression of HCC by an OAT inactivator.
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Affiliation(s)
| | | | - Hyunbeom Lee
- Department of Chemistry,
Department of Molecular Biosciences, Chemistry of Life Processes Institute,
and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208, United States
| | | | | | | | | | | | | | - Hoang V. Le
- Department of Chemistry,
Department of Molecular Biosciences, Chemistry of Life Processes Institute,
and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208, United States
| | - Hejun Lu
- Department of Chemistry,
Department of Molecular Biosciences, Chemistry of Life Processes Institute,
and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard B. Silverman
- Department of Chemistry,
Department of Molecular Biosciences, Chemistry of Life Processes Institute,
and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208, United States
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5
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Gökcan H, Konuklar FAS. Stereoelectronic explanations for the mechanistic details of transimination and HF elimination reactions. J Mol Graph Model 2014; 51:173-83. [PMID: 24929816 DOI: 10.1016/j.jmgm.2014.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 11/26/2022]
Abstract
The β-fluoroamines are commonly used as substrate analogs to determine the mechanistic details of enzymatic reactions. Presence of fluorine atom gives rise to the alterations in the electronic profile and the pKa of molecules which results in mechanistic deviations. The fluorine-substituted mechanism-based substrate analogs are widely used in the inactivation of pyridoxal 5'-phosphate (PLP)-dependent enzymes. The presence of fluorine atom also alters the sequence of reactions taking place in PLP-dependent enzymes where the HF elimination reaction appears in between the transimination and inactivation reactions. Despite the amount of the works on β-fluoroamines, the effect of stereoelectronic differences on the transimination and HF elimination reactions taking place in PLP-dependent enzymes has not been investigated yet. A density functional theory study is conducted to elucidate mechanistic details of the reactions occurring in PLP-dependent enzymes. In order to understand the mechanistic insights of different isomers and the effect of the fluorine atom, 4-amino-3-fluorobutanoic acid (3-F-GABA) enantiomers are chosen to be investigated besides 4-aminobutanoic acid (GABA), which is the natural substrate for γ-aminobutyric acid aminotransferase (GABA-AT). The investigated β-fluoroamines are the experimentally proposed potential inhibitors of PLP-dependent enzyme GABA-AT.
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Affiliation(s)
- Hatice Gökcan
- Istanbul Technical University, Informatics Institute, Computational Science and Engineering Division, Ayazağa Campus, 34496 Maslak, Istanbul, Turkey
| | - F Aylin Sungur Konuklar
- Istanbul Technical University, Informatics Institute, Computational Science and Engineering Division, Ayazağa Campus, 34496 Maslak, Istanbul, Turkey.
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6
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Okubo M, Kawaguchi M. Rat submandibular gland perfusion method for clarifying inhibitory regulation of GABAA receptor. J Pharmacol Sci 2013; 122:42-50. [PMID: 23685805 DOI: 10.1254/jphs.12241fp] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
GABA is an inhibitory transmitter found in rat salivary gland. However, the inhibitory potential of GABA on salivary secretion is unclear. Using an in vivo cannulation method, intraperitoneal administration of GABA was ineffective in the absence of gabaculine, a GABA transaminase inhibitor, on pilocarpine-induced salivary secretion, suggesting that GABA was rendered metabolically inactive before reaching the salivary gland. We hypothesized that the action of a drug on the salivary glands could be measured directly using a submandibular gland perfusion system. The submandibular gland artery, veins, and duct were cannulated in situ so that physiological functions such as innervation would not be compromised. Hank's balanced salt solution (pH 7.4) was perfused at a rate of 0.5 ml/min together with 1 μM carbachol (CCh) over a 5-min period every 30 min. Amount of secreted saliva showed no change to the recurrent addition of CCh to the perfusate. GABA or muscimol dose-dependently inhibited CCh-induced salivary secretion. This effect was blocked by bicuculline, a GABA(A)-receptor (GABA(A)-R) antagonist, and enhanced by clonazepam, a central-type benzodiazepine-receptor agonist. These results suggest that salivary secretion is suppressed by GABA(A)-R in rat salivary gland and that the perfusion method used was effective in clarifying inhibitory regulation of GABA(A)-R.
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Affiliation(s)
- Migiwa Okubo
- Oral Health Science Center hrc8, Tokyo Dental College, Japan.
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7
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Sayer C, Isupov MN, Westlake A, Littlechild JA. Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:564-76. [PMID: 23519665 PMCID: PMC3606037 DOI: 10.1107/s0907444912051670] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/21/2012] [Indexed: 11/10/2022]
Abstract
The crystal structures and inhibitor complexes of two industrially important ω-aminotransferase enzymes from Pseudomonas aeruginosa and Chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. The two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the Pseudomonas enzyme shows activity towards the amino donor β-alanine, whilst the Chromobacterium enzyme does not. Both enzymes show activity towards S-α-methylbenzylamine (MBA), with the Chromobacterium enzyme having a broader substrate range. The crystal structure of the P. aeruginosa enzyme has been solved in the holo form and with the inhibitor gabaculine bound. The C. violaceum enzyme has been solved in the apo and holo forms and with gabaculine bound. The structures of the holo forms of both enzymes are quite similar. There is little conformational difference observed between the inhibitor complex and the holoenzyme for the P. aeruginosa aminotransferase. In comparison, the crystal structure of the C. violaceum gabaculine complex shows significant structural rearrangements from the structures of both the apo and holo forms of the enzyme. It appears that the different rigidity of the protein scaffold contributes to the substrate specificity observed for the two ω-aminotransferases.
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Affiliation(s)
- Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Michail N. Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Aaron Westlake
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Jennifer A. Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
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8
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Chen YH, Maity AN, Frey PA, Ke SC. Mechanism-based Inhibition Reveals Transitions between Two Conformational States in the Action of Lysine 5,6-Aminomutase: A Combination of Electron Paramagnetic Resonance Spectroscopy, Electron Nuclear Double Resonance Spectroscopy, and Density Functional Theory Study. J Am Chem Soc 2012; 135:788-94. [DOI: 10.1021/ja309603a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yung-Han Chen
- Physics Department, National Dong Hwa University, Hualien, Taiwan 97401
| | | | - Perry A. Frey
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
53726, United States
| | - Shyue-Chu Ke
- Physics Department, National Dong Hwa University, Hualien, Taiwan 97401
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9
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Shi C, Aldrich CC. Design and synthesis of potential mechanism-based inhibitors of the aminotransferase BioA involved in biotin biosynthesis. J Org Chem 2012; 77:6051-8. [PMID: 22724679 DOI: 10.1021/jo3008435] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BioA, a pyridoxal 5'-phosphate (PLP) dependent aminotransferase, catalyzes the second step of biotin biosynthesis, converting 7-keto-8-aminopelargonic acid (KAPA) into 7,8-diaminopelargonic acid (DAPA). Amiclenomycin (ACM) isolated from cultures of different Streptomyces strains is a potent mechanism-based inhibitor of BioA that operates via an aromatization mechanism, irreversibly labeling the PLP cofactor. However, ACM is plagued by inherent chemical stability. Herein we describe the synthesis of four inhibitors, inspired by ACM but containing an allylic amine as the chemical warhead, designed to both improve stability and operate via a complementary Michael addition-pathway upon enzymatic oxidation of the allylic amine substrate to an enimine. Acyclic analogue M-1 contains a terminal olefin as the pro-Michael acceptor. The synthesis of M-1 features an alkyne-zipper reaction and the Overman rearrangement as key synthetic operations. The cyclic analogues M-2/3/4 contain either an endocyclic or exocyclic olefin as the pro-Michael acceptor. These were all prepared using a common strategy employing DIBAL reduction of a precursor bicyclic lactam, followed by in situ Horner-Wadsworth-Emmons (HWE) olefination as the key synthetic steps.
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Affiliation(s)
- Ce Shi
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
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10
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Sayer C, Bommer M, Isupov M, Ward J, Littlechild J. Crystal structure and substrate specificity of the thermophilic serine:pyruvate aminotransferase fromSulfolobus solfataricus. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:763-72. [DOI: 10.1107/s0907444912011274] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 03/14/2012] [Indexed: 11/10/2022]
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11
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Gökcan H, Konuklar FAS. Theoretical study on HF elimination and aromatization mechanisms: a case of pyridoxal 5' phosphate-dependent enzyme. J Org Chem 2012; 77:5533-43. [PMID: 22646918 DOI: 10.1021/jo3005815] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyridoxal 5-phosphate (PLP), the phosphorylated and the oxidized form of vitamin B6 is an organic cofactor. PLP forms a Schiff base with the ϵ-amino group of a lysine residue of PLP-dependent enzymes. γ-Aminobutyric acid (GABA) aminotransferase is a PLP-dependent enzyme that degrades GABA to succinic semialdehyde, while reduction of GABA concentration in the brain causes convolution besides several neurological diseases. The fluorine-containing substrate analogues for the inactivation of the GABA-AT are synthesized extensively in cases where the inactivation mechanisms involve HF elimination. Although two proposed mechanisms are present for the HF elimination, the details of the base-induced HF elimination are not well identified. In this density functional theory (DFT) study, fluorine-containing substrate analogue, 5-amino-2-fluorocyclohex-3-enecarboxylic acid, is particularly chosen in order to explain the details of the HF elimination reactions. On the other hand, the experimental studies revealed that aromatization competes with Michael addition mechanism in the presence of 5-amino-2-fluorocyclohex-3-enecarboxylic acid. The results allowed us to draw a conclusion for the nature of HF elimination, besides the elucidation of the mechanism preference for the inactivation mechanism. Furthermore, the solvent phase calculations carried out in this study ensure that the proton transfer steps should be assisted either by a water molecule or a base for lower activation energy barriers.
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Affiliation(s)
- Hatice Gökcan
- Informatics Institute, Computational Science and Engineering Programme, Istanbul Technical University, Ayazağa Campus 34469, Maslak, Istanbul, Turkey
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12
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Shi C, Geders TW, Park SW, Wilson DJ, Boshoff HI, Orisadipe A, Barry CE, Schnappinger D, Finzel BC, Aldrich CC. Mechanism-based inactivation by aromatization of the transaminase BioA involved in biotin biosynthesis in Mycobaterium tuberculosis. J Am Chem Soc 2011; 133:18194-201. [PMID: 21988601 PMCID: PMC3222238 DOI: 10.1021/ja204036t] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BioA catalyzes the second step of biotin biosynthesis, and this enzyme represents a potential target to develop new antitubercular agents. Herein we report the design, synthesis, and biochemical characterization of a mechanism-based inhibitor (1) featuring a 3,6-dihydropyrid-2-one heterocycle that covalently modifies the pyridoxal 5'-phosphate (PLP) cofactor of BioA through aromatization. The structure of the PLP adduct was confirmed by MS/MS and X-ray crystallography at 1.94 Å resolution. Inactivation of BioA by 1 was time- and concentration-dependent and protected by substrate. We used a conditional knock-down mutant of M. tuberculosis to demonstrate the antitubercular activity of 1 correlated with BioA expression, and these results provide support for the designed mechanism of action.
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Affiliation(s)
- Ce Shi
- Center for Drug Design, Academic Health Center, University of Minnesota, MN, 55455, United States
| | - Todd W. Geders
- Department of Medicinal Chemistry, University of Minnesota, MN, 55455, United States
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, United States
| | - Daniel J. Wilson
- Center for Drug Design, Academic Health Center, University of Minnesota, MN, 55455, United States
| | - Helena I. Boshoff
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, United States
| | - Abayomi Orisadipe
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, United States
| | - Clifton E. Barry
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, United States
| | - Barry C. Finzel
- Department of Medicinal Chemistry, University of Minnesota, MN, 55455, United States
| | - Courtney C. Aldrich
- Center for Drug Design, Academic Health Center, University of Minnesota, MN, 55455, United States
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13
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Liu D, Pozharski E, Fu M, Silverman RB, Ringe D. Mechanism of inactivation of Escherichia coli aspartate aminotransferase by (S)-4-amino-4,5-dihydro-2-furancarboxylic acid . Biochemistry 2010; 49:10507-15. [PMID: 21033689 PMCID: PMC3013228 DOI: 10.1021/bi101325z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As a potential drug to treat neurological diseases, the mechanism-based inhibitor (S)-4-amino-4,5-dihydro-2-furancarboxylic acid (S-ADFA) has been found to inhibit the γ-aminobutyric acid aminotransferase (GABA-AT) reaction. To circumvent the difficulties in structural studies of a S-ADFA-enzyme complex using GABA-AT, l-aspartate aminotransferase (l-AspAT) from Escherichia coli was used as a model PLP-dependent enzyme. Crystal structures of the E. coli aspartate aminotransferase with S-ADFA bound to the active site were obtained via cocrystallization at pH 7.5 and 8. The complex structures suggest that S-ADFA inhibits the transamination reaction by forming adducts with the catalytic lysine 246 via a covalent bond while producing 1 equiv of pyridoxamine 5'-phosphate (PMP). Based on the structures, formation of the K246-S-ADFA adducts requires a specific initial binding configuration of S-ADFA in the l-AspAT active site, as well as deprotonation of the ε-amino group of lysine 246 after the formation of the quinonoid and/or ketimine intermediate in the overall inactivation reaction.
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Affiliation(s)
- Dali Liu
- Departments of Biochemistry and Chemistry, and Rosenstiel Basic Sciences Research Center MS029, Brandeis University, Waltham, Massachusetts 02454-9110
| | - Edwin Pozharski
- Departments of Biochemistry and Chemistry, and Rosenstiel Basic Sciences Research Center MS029, Brandeis University, Waltham, Massachusetts 02454-9110
| | - Mengmeng Fu
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, the Center for Molecular Innovation and Drug Discovery and Chemistry of Life Processes Institute, Northwestern University, and Evanston, Illinois 60208-3113
| | - Richard B. Silverman
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, the Center for Molecular Innovation and Drug Discovery and Chemistry of Life Processes Institute, Northwestern University, and Evanston, Illinois 60208-3113
| | - Dagmar Ringe
- Departments of Biochemistry and Chemistry, and Rosenstiel Basic Sciences Research Center MS029, Brandeis University, Waltham, Massachusetts 02454-9110
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14
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Glucose promotion of GABA metabolism contributes to the stimulation of insulin secretion in β-cells. Biochem J 2010; 431:381-9. [PMID: 20695849 DOI: 10.1042/bj20100714] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We have demonstrated recently that branched-chain α-keto acid stimulation of insulin secretion is dependent on islet GABA (γ-aminobutyric acid) metabolism: GABA transamination to succinic semialdehyde is increased by 2-oxoglutarate, generated in α-keto acid transamination to its corresponding α-amino acid. The present work was aimed at investigating whether glucose also promotes islet GABA metabolism and whether the latter contributes to the stimulation of insulin secretion. Glucose (20 mM) decreased both the content and release of islet GABA. Gabaculine (1 mM), a GABA transaminase inhibitor, partially suppressed the secretory response of rat perifused islets to 20 mM glucose at different L-glutamine concentrations (0, 1 and 10 mM), as well as the glucose-induced decrease in islet GABA. The drug also reduced islet ATP content and the ATP/ADP ratio at 20 mM glucose. Exogenous succinic semialdehyde induced a dose-dependent increase in islet GABA content by reversal of GABA transamination and a biphasic insulin secretion in the absence of glucose. It depolarized isolated β-cells and triggered action potential firing, accompanied by a reduction of membrane currents through ATP-sensitive K(+) channels. The gene expression and enzyme activity of GABA transaminase were severalfold higher than that of 2-oxoglutarate dehydrogenase in islet homogenates. We conclude that, at high glucose concentrations, there is an increased diversion of glucose metabolism from the citric acid cycle into the 'GABA shunt'. Semialdehyde succinic acid is a cell-permeant 'GABA-shunt' metabolite that increases ATP and the ATP/ADP ratio, depolarizes β-cells and stimulates insulin secretion. In summary, an increased islet GABA metabolism may trigger insulin secretion.
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15
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Lepore BW, Liu D, Peng Y, Fu M, Yasuda C, Manning JM, Silverman RB, Ringe D. Chiral discrimination among aminotransferases: inactivation by 4-amino-4,5-dihydrothiophenecarboxylic acid. Biochemistry 2010; 49:3138-47. [PMID: 20192272 DOI: 10.1021/bi902052x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mechanism-based inhibitors such as cycloserine and gabaculine can inactivate aminotransferases via reactions of the compounds with the pyridoxal phosphate cofactor forming an irreversible adduct. The reaction is chirally specific in that any one enzyme usually only recognizes one enantiomer of the inactivator. For instance, l-aspartate aminotransferase (l-AspAT) is inactivated by 4-amino-4,5-dihydro-2-thiophenecarboxylic acid (ADTA), however, only by the S-isomer. We have now shown that d-amino acid aminotransferase (d-a-AT) is irreversibly inactivated by the R-isomer of the same compound. The X-ray crystal structure (PDB code: 3LQS ) of the inactivated enzyme shows that in the product the enzyme no longer makes a Schiff base linkage to the pyridoxal 5'-phosphate (PLP) cofactor, and instead the compound has formed a derivative of the cofactor. The adduct is similar to that formed between d-cycloserine and d-a-AT or alanine racemase (Ala-Rac) in that the thiophene ring of R-ADTA is intact and seems to be aromatic. The plane of the ring is rotated by nearly 90 degrees with respect to the plane of the pyridine ring of the cofactor, in comparison with the enzyme inactivated by cycloserine. Based on the structure of the product, the mechanism of inactivation most probably involves a transamination followed by aromatization to form an aromatic thiophene ring.
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Affiliation(s)
- Bryan W Lepore
- Graduate Program in Bioorganic Chemistry, Graduate Program in Biophysics and Biochemistry, Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA
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16
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Maity AN, Hsieh CP, Huang MH, Chen YH, Tang KH, Behshad E, Frey PA, Ke SC. Evidence for Conformational Movement and Radical Mechanism in the Reaction of 4-Thia-l-lysine with Lysine 5,6-Aminomutase. J Phys Chem B 2009; 113:12161-3. [DOI: 10.1021/jp905357a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amarendra N. Maity
- Physics Department, National Dong Hwa University, Hualien, Taiwan 974-01, Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53726
| | - Chih-Pin Hsieh
- Physics Department, National Dong Hwa University, Hualien, Taiwan 974-01, Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53726
| | - Ming-Hui Huang
- Physics Department, National Dong Hwa University, Hualien, Taiwan 974-01, Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53726
| | - Yung-Han Chen
- Physics Department, National Dong Hwa University, Hualien, Taiwan 974-01, Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53726
| | - Kuo-Hsiang Tang
- Physics Department, National Dong Hwa University, Hualien, Taiwan 974-01, Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53726
| | - Elham Behshad
- Physics Department, National Dong Hwa University, Hualien, Taiwan 974-01, Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53726
| | - Perry A. Frey
- Physics Department, National Dong Hwa University, Hualien, Taiwan 974-01, Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53726
| | - Shyue-Chu Ke
- Physics Department, National Dong Hwa University, Hualien, Taiwan 974-01, Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53726
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17
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Wang Z, Yuan H, Nikolic D, Van Breemen RB, Silverman RB. (+/-)-(1S,2R,5S)-5-Amino-2-fluorocyclohex-3-enecarboxylic acid. A potent GABA aminotransferase inactivator that irreversibly inhibits via an elimination-aromatization pathway. Biochemistry 2006; 45:14513-22. [PMID: 17128990 PMCID: PMC2570588 DOI: 10.1021/bi061592m] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inhibition of gamma-aminobutyric acid aminotransferase (GABA-AT) increases the concentration of GABA, an inhibitory neurotransmitter in human brain, which could have therapeutic applications for a variety of neurological diseases, including epilepsy. On the basis of studies of several previously synthesized conformationally restricted GABA-AT inhibitors, (+/-)-(1S,2R,5S)-5-amino-2-fluorocyclohex-3-enecarboxylic acid (12) was designed as a mechanism-based inactivator. This compound was shown to irreversibly inhibit GABA-AT; substrate protects the enzyme from inactivation. Mechanistic experiments demonstrated the loss of one fluoride ion per active site during inactivation and the formation of N-m-carboxyphenylpyridoxamine 5'-phosphate (26), the same product generated by inactivation of GABA-AT by gabaculine (8). An elimination-aromatization mechanism is proposed to account for these results.
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Affiliation(s)
- Zhiyong Wang
- Department of Chemistry, Center for Drug Discovery and Chemical Biology, Northwestern University, Evanston, Illinois 60208-3113, USA
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18
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Wang Z, Silverman RB. Syntheses and evaluation of fluorinated conformationally restricted analogues of GABA as potential inhibitors of GABA aminotransferase. Bioorg Med Chem 2006; 14:2242-52. [PMID: 16314106 DOI: 10.1016/j.bmc.2005.11.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2005] [Revised: 11/01/2005] [Accepted: 11/02/2005] [Indexed: 11/21/2022]
Abstract
Inhibition of gamma-aminobutyric acid aminotransferase (GABA-AT) could raise the concentration of GABA, an inhibitory neurotransmitter in the human brain, and could have therapeutic applications for a variety of neurological diseases including epilepsy. Four fluorine-containing analogues of GABA with conformations restricted by a cyclohexane ring system were designed and synthesized, but unlike some of their five-membered ring counterparts, minimal inhibition of GABA-AT was observed. It is likely that the rigid chair conformation of these compounds cannot be accommodated well in the enzyme's active site.
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Affiliation(s)
- Zhiyong Wang
- Department of Chemistry, Center for Drug Discovery and Chemical Biology, Northwestern University, Evanston, IL 60208-3113, USA
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19
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Beleboni RO, Carolino ROG, Pizzo AB, Castellan-Baldan L, Coutinho-Netto J, dos Santos WF, Coimbra NC. Pharmacological and biochemical aspects of GABAergic neurotransmission: pathological and neuropsychobiological relationships. Cell Mol Neurobiol 2005; 24:707-28. [PMID: 15672674 DOI: 10.1007/s10571-004-6913-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
1. The GABAergic neurotransmission has been implicated in the modulation of many neural networks in forebrain, midbrain and hindbrain, as well as, in several neurological disorders. 2. The complete comprehension of GABA system neurochemical properties and the search for approaches in identifying new targets for the treatment of neural diseases related to GABAergic pathway are of the extreme relevance. 3. The present review will be focused on the pharmacology and biochemistry of the GABA metabolism, GABA receptors and transporters. In addition, the pathological and psychobiological implications related to GABAergic neurotransmission will be considered.
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Affiliation(s)
- Renê Oliveira Beleboni
- Departament of Biochemistry and Immunology, School of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
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20
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Fu M, Silverman RB. Inactivation of gamma-aminobutyric acid aminotransferase by (S)-4-amino-4,5-dihydro-2-furancarboxylic acid does not proceed by the expected aromatization mechanism. Bioorg Med Chem Lett 2004; 14:203-6. [PMID: 14684328 DOI: 10.1016/j.bmcl.2003.09.065] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inactivation of pyridoxal 5'-phosphate (PLP)-dependent gamma-aminobutryic acid aminotransferase by (S)-4-amino-4,5-dihydro-2-furancarboxylic acid (SADFA) gives pyridoxamine 5'-phosphate, not the expected SADFA-PLP aromatization product. Inactivation appears to proceed by a Michael addition/hydrolysis mechanism instead.
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Affiliation(s)
- Mengmeng Fu
- Department of Chemistry, Northwestern University, Evanston, IL 60208-3113, USA
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21
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Mann S, Lesage D, Tabet JC, Marquet A. Identification of the products of reaction between pyridoxal phosphate and amiclenomycin and other related 1-amino-cyclohexa-2,5-dienes. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00782-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Sandmark J, Mann S, Marquet A, Schneider G. Structural basis for the inhibition of the biosynthesis of biotin by the antibiotic amiclenomycin. J Biol Chem 2002; 277:43352-8. [PMID: 12218056 DOI: 10.1074/jbc.m207239200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The antibiotic amiclenomycin blocks the biosynthesis of biotin by inhibiting the pyridoxal-phosphate-dependent enzyme diaminopelargonic acid synthase. Inactivation of the enzyme is stereoselective, i.e. the cis isomer of amiclenomycin is a potent inhibitor, whereas the trans isomer is much less reactive. The crystal structure of the complex of the holoenzyme and amiclenomycin at 1.8 A resolution reveals that the internal aldimine linkage between the cofactor and the side chain of the catalytic residue Lys-274 is broken. Instead, a covalent bond is formed between the 4-amino nitrogen of amiclenomycin and the C4' carbon atom of pyridoxal-phosphate. The electron density for the bound inhibitor suggests that aromatization of the cyclohexadiene ring has occurred upon formation of the covalent adduct. This process could be initiated by proton abstraction at the C4 carbon atom of the cyclohexadiene ring, possibly by the proximal side chain of Lys-274, leading to the tautomer Schiff base followed by the removal of the second allylic hydrogen. The carboxyl tail of the amiclenomycin moiety forms a salt link to the conserved residue Arg-391 in the substrate-binding site. Modeling suggests steric hindrance at the active site as the determinant of the weak inhibiting potency of the trans isomer.
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Affiliation(s)
- Jenny Sandmark
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
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23
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Abstract
We describe the first synthesis of amiclenomycin, a natural product that has been found to inhibit biotin biosynthesis and, as a consequence, to exhibit antibiotic properties. Structure 1, with a trans relationship between the ring substituents. had previously been proposed for amiclenomycin on the basis of its 1H NMR spectrum. We have prepared the trans and cis isomers 1 and 2 by unequivocal routes and we conclude that the natural product is in fact the cis isomer 2. The properly substituted cyclohexadienyl rings were constructed first. A cycloaddition reaction between 1,2-di(phenylsulfonyl)ethylene and the N-allyloxycarbonyl diene 13, followed by reductive elimination of the phenylsulfinyl groups, gave the cis isomer 15. To obtain the trans isomer, the O-trimethylsilyl diene was used to give the cis hydroxylated Diels-Alder adduct 33, which was transformed into the corresponding trans amino derivative by means of a Mitsunobu reaction. The L-alpha-amino acid functionality was introduced by means of a Strecker reaction on the aldehydes 16 and 42, followed by enzymatic hydrolysis with immobilised pronase.
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Affiliation(s)
- Stéphane Mann
- Laboratoire de Chimie Organique Biologique, Université Paris VI, UMR CNRS 7613, France
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