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Marchesani F, Rebecchi F, Pieroni M, Faggiano S, Annunziato G, Spaggiari C, Bruno S, Rinaldi S, Giaccari R, Costantino G, Campanini B. Chemical Probes to Investigate Central Nervous System Disorders: Design, Synthesis and Mechanism of Action of a Potent Human Serine Racemase Inhibitor. ACS Med Chem Lett 2024; 15:1298-1305. [PMID: 39140049 PMCID: PMC11318019 DOI: 10.1021/acsmedchemlett.4c00174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 08/15/2024] Open
Abstract
The intricate signaling network within the central nervous system (CNS) involving N-methyl-d-aspartate receptors (NMDARs) has been recognized as a key player in severe neurodegenerative diseases. The indirect modulation of NMDAR-mediated neurotransmission through inhibition of serine racemase (SR)-the enzyme responsible for the synthesis of the NMDAR coagonist d-serine-has been suggested as a therapeutic strategy to treat these conditions. Despite the inherent challenges posed by SR conformational flexibility, a ligand-based drug design strategy has successfully produced a series of potent covalent inhibitors structurally related to amino acid analogues. Among these inhibitors, O-(2-([1,1'-biphenyl]-4-yl)-1-carboxyethyl)hydroxylammonium chloride (28) has emerged as a valuable candidate with a K d of about 5 μM, which makes it one of the most potent hSR inhibitors reported to date. This molecule is expected to inspire the identification of selective hSR inhibitors that might find applications as tools in the study and treatment of several CNS pathologies.
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Affiliation(s)
| | | | - Marco Pieroni
- Department
of Food and Drug, University of Parma, 43124 Parma, Italy
- P4T
Group, University of Parma, 43124 Parma, Italy
- Interdepartmental
Research Center for the Innovation of Health Products “Biopharmanet-tec”, University of Parma, 43124 Parma, Italy
- Centro
Interdipartimentale Misure (CIM) “G. Casnati”, University of Parma, 43124 Parma, Italy
| | - Serena Faggiano
- Department
of Food and Drug, University of Parma, 43124 Parma, Italy
- Institute
of Biophysics, National Research Council, 56124 Pisa, Italy
| | - Giannamaria Annunziato
- Department
of Food and Drug, University of Parma, 43124 Parma, Italy
- Centro
Interdipartimentale Misure (CIM) “G. Casnati”, University of Parma, 43124 Parma, Italy
| | - Chiara Spaggiari
- Department
of Food and Drug, University of Parma, 43124 Parma, Italy
| | - Stefano Bruno
- Department
of Food and Drug, University of Parma, 43124 Parma, Italy
- Interdepartmental
Research Center for the Innovation of Health Products “Biopharmanet-tec”, University of Parma, 43124 Parma, Italy
| | - Sofia Rinaldi
- Department
of Food and Drug, University of Parma, 43124 Parma, Italy
| | - Roberta Giaccari
- Department
of Food and Drug, University of Parma, 43124 Parma, Italy
| | - Gabriele Costantino
- Department
of Food and Drug, University of Parma, 43124 Parma, Italy
- Interdepartmental
Research Center for the Innovation of Health Products “Biopharmanet-tec”, University of Parma, 43124 Parma, Italy
- Centro
Interdipartimentale Misure (CIM) “G. Casnati”, University of Parma, 43124 Parma, Italy
| | - Barbara Campanini
- Department
of Food and Drug, University of Parma, 43124 Parma, Italy
- Interdepartmental
Research Center for the Innovation of Health Products “Biopharmanet-tec”, University of Parma, 43124 Parma, Italy
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Katane M, Homma H. Biosynthesis and Degradation of Free D-Amino Acids and Their Physiological Roles in the Periphery and Endocrine Glands. Biol Pharm Bull 2024; 47:562-579. [PMID: 38432912 DOI: 10.1248/bpb.b23-00485] [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: 03/05/2024]
Abstract
It was long believed that D-amino acids were either unnatural isomers or laboratory artifacts, and that the important functions of amino acids were exerted only by L-amino acids. However, recent investigations have revealed a variety of D-amino acids in mammals that play important roles in physiological functions, including free D-serine and D-aspartate that are crucial in the central nervous system. The functions of several D-amino acids in the periphery and endocrine glands are also receiving increasing attention. Here, we present an overview of recent advances in elucidating the physiological roles of D-amino acids, especially in the periphery and endocrine glands.
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Affiliation(s)
- Masumi Katane
- Medicinal Research Laboratories, Graduate School of Pharmaceutical Sciences, Kitasato University
| | - Hiroshi Homma
- Laboratory of Analytical Chemistry, Graduate School of Pharmaceutical Sciences, Kitasato University
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3
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Wu S, Zhou J, Zhang H, Barger SW. Serine Racemase Expression Differentiates Aging from Alzheimer's Brain. Curr Alzheimer Res 2022; 19:494-502. [PMID: 35929621 DOI: 10.2174/1567205019666220805105106] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 01/27/2023]
Abstract
Aging is an inevitable process characterized by progressive loss of physiological integrity and increased susceptibility to cancer, diabetes, cardiovascular, and neurodegenerative diseases; aging is the primary risk factor for Alzheimer's disease (AD), the most common cause of dementia. AD is characterized by brain pathology, including extracellular deposition of amyloid aggregation and intracellular accumulation of neurofibrillary tangles composed of hyperphosphorylated tau protein. In addition, losses of synapses and a wide range of neurons are pivotal pathologies in the AD brain. Accumulating evidence demonstrates hypoactivation of hippocampal neural networks in the aging brain, whereas AD-related mild cognitive impairment (AD-MCI) begins with hyperactivation, followed by a diminution of hippocampal activity as AD develops. The biphasic trends of the activity of the hippocampal neural network are consistent with the alteration of N-methyl-D-aspartate receptor (NMDA-R) activity from aging to prodromal (AD-MCI) to mid-/late stage AD. D-serine, a product of racemization catalyzed by serine racemase (SR), is an important co-agonist of the NMDA-R which is involved in synaptic events including neurotransmission, synaptogenesis, long-term potentiation (LTP), development, and excitotoxicity. SR and D-serine are decreased in the hippocampus of the aging brain, correlating with impairment of cognitive function. By contrast, SR is increased in AD brain, which is associated with a greater degree of cognitive dysfunction. Emerging studies suggest that D-serine levels in the brain or in cerebral spinal fluid from AD patients are higher than in age-matched controls, but the results are inconsistent. Very recently, serum D-serine levels in AD were reported to correlate with sex and clinical dementia rating (CDR) stage. This review will discuss alterations of NMDA-R and SR in aging and AD brain, and the mechanisms underlying the differential regulation of SR will be probed. Collectively, we propose that SR may be a molecular switch that distinguishes the effects of aging from those of AD on the brain.
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Affiliation(s)
- Shengzhou Wu
- School of Optometry and Ophthalmology and the Eye Hospital, Wenzhou Medical University, State Key Laboratory of Optometry, Wenzhou, Zhejiang 325003, P.R. China
| | - Jing Zhou
- School of Optometry and Ophthalmology and the Eye Hospital, Wenzhou Medical University, State Key Laboratory of Optometry, Wenzhou, Zhejiang 325003, P.R. China
| | - He Zhang
- School of Optometry and Ophthalmology and the Eye Hospital, Wenzhou Medical University, State Key Laboratory of Optometry, Wenzhou, Zhejiang 325003, P.R. China.,College of Life and Environmental Sciences, Wenzhou University, Wenzhou, Zhejiang, P.R. China
| | - Steven W Barger
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock AR, USA.,Geriatric Research, Education & Clinical Center, Central Arkansas Veterans Healthcare System, Little Rock AR, USA
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4
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Koulouris CR, Gardiner SE, Harris TK, Elvers KT, Mark Roe S, Gillespie JA, Ward SE, Grubisha O, Nicholls RA, Atack JR, Bax BD. Tyrosine 121 moves revealing a ligandable pocket that couples catalysis to ATP-binding in serine racemase. Commun Biol 2022; 5:346. [PMID: 35410329 PMCID: PMC9001717 DOI: 10.1038/s42003-022-03264-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/14/2022] [Indexed: 11/23/2022] Open
Abstract
Human serine racemase (hSR) catalyses racemisation of L-serine to D-serine, the latter of which is a co-agonist of the NMDA subtype of glutamate receptors that are important in synaptic plasticity, learning and memory. In a 'closed' hSR structure containing the allosteric activator ATP, the inhibitor malonate is enclosed between the large and small domains while ATP is distal to the active site, residing at the dimer interface with the Tyr121 hydroxyl group contacting the α-phosphate of ATP. In contrast, in 'open' hSR structures, Tyr121 sits in the core of the small domain with its hydroxyl contacting the key catalytic residue Ser84. The ability to regulate SR activity by flipping Tyr121 from the core of the small domain to the dimer interface appears to have evolved in animals with a CNS. Multiple X-ray crystallographic enzyme-fragment structures show Tyr121 flipped out of its pocket in the core of the small domain. Data suggest that this ligandable pocket could be targeted by molecules that inhibit enzyme activity.
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Affiliation(s)
- Chloe R Koulouris
- Sussex Drug Discovery Centre, University of Sussex, Brighton, BN1 9QG, UK
| | - Sian E Gardiner
- Medicines Discovery Institute, Cardiff University, Cardiff, CF10 3AT, UK
| | - Tessa K Harris
- Medicines Discovery Institute, Cardiff University, Cardiff, CF10 3AT, UK
| | - Karen T Elvers
- Medicines Discovery Institute, Cardiff University, Cardiff, CF10 3AT, UK
| | - S Mark Roe
- Department of Biochemistry and Biomedicine, University of Sussex, Brighton, BN1 9QJ, UK
| | - Jason A Gillespie
- Medicines Discovery Institute, Cardiff University, Cardiff, CF10 3AT, UK
| | - Simon E Ward
- Medicines Discovery Institute, Cardiff University, Cardiff, CF10 3AT, UK
| | - Olivera Grubisha
- Medicines Discovery Institute, Cardiff University, Cardiff, CF10 3AT, UK
| | - Robert A Nicholls
- MRC Laboratory of Molecular Biology, Francis Crick Ave, CB2 0QH, Cambridge, UK
| | - John R Atack
- Medicines Discovery Institute, Cardiff University, Cardiff, CF10 3AT, UK.
| | - Benjamin D Bax
- Medicines Discovery Institute, Cardiff University, Cardiff, CF10 3AT, UK.
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Dyakin VV, Wisniewski TM, Lajtha A. Racemization in Post-Translational Modifications Relevance to Protein Aging, Aggregation and Neurodegeneration: Tip of the Iceberg. Symmetry (Basel) 2021; 13:455. [PMID: 34350031 PMCID: PMC8330555 DOI: 10.3390/sym13030455] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Homochirality of DNA and prevalent chirality of free and protein-bound amino acids in a living organism represents the challenge for modern biochemistry and neuroscience. The idea of an association between age-related disease, neurodegeneration, and racemization originated from the studies of fossils and cataract disease. Under the pressure of new results, this concept has a broader significance linking protein folding, aggregation, and disfunction to an organism's cognitive and behavioral functions. The integrity of cognitive function is provided by a delicate balance between the evolutionarily imposed molecular homo-chirality and the epigenetic/developmental impact of spontaneous and enzymatic racemization. The chirality of amino acids is the crucial player in the modulation the structure and function of proteins, lipids, and DNA. The collapse of homochirality by racemization is the result of the conformational phase transition. The racemization of protein-bound amino acids (spontaneous and enzymatic) occurs through thermal activation over the energy barrier or by the tunnel transfer effect under the energy barrier. The phase transition is achieved through the intermediate state, where the chirality of alpha carbon vanished. From a thermodynamic consideration, the system in the homo-chiral (single enantiomeric) state is characterized by a decreased level of entropy. The oscillating protein chirality is suggesting its distinct significance in the neurotransmission and flow of perceptual information, adaptive associative learning, and cognitive laterality. The common pathological hallmarks of neurodegenerative disorders include protein misfolding, aging, and the deposition of protease-resistant protein aggregates. Each of the landmarks is influenced by racemization. The brain region, cell type, and age-dependent racemization critically influence the functions of many intracellular, membrane-bound, and extracellular proteins including amyloid precursor protein (APP), TAU, PrP, Huntingtin, α-synuclein, myelin basic protein (MBP), and collagen. The amyloid cascade hypothesis in Alzheimer's disease (AD) coexists with the failure of amyloid beta (Aβ) targeting drug therapy. According to our view, racemization should be considered as a critical factor of protein conformation with the potential for inducing order, disorder, misfolding, aggregation, toxicity, and malfunctions.
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Affiliation(s)
- Victor V. Dyakin
- Virtual Reality Perception Lab (VRPL), The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
| | - Thomas M. Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, New York University School of Medicine, New York, NY 10016, USA
| | - Abel Lajtha
- Center for Neurochemistry, The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
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6
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Lei H, Yang T, Mahmood S, Abo-Ismail M, Roy BC, Li C, Plastow GS, Bruce HL. A genome-wide case-control association study of dark cutting in beef cattle. CANADIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1139/cjas-2019-0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genetic architecture of dark cutting was investigated with a case-control genome-wide association study on two groups of beef cattle analyzed separately and together (combined group). Groups I (n = 64) and II (n = 150) were genotyped using the 70K GeneSeek Genomic Profiler for Beef Cattle-HD and the 50K Illumina BovineSNP50v2 BeadChip, respectively. Dark cutting was analyzed as a binary trait (case versus control) using logistic regression in an additive model implemented in PLINK version 1.9. Significant loci were not identified when correcting for multiple testing (false discovery rate), suggesting that the trait is not controlled by genes with big effects, or the sample size was not large enough to detect these major genes. Regions harbouring single-nucleotide polymorphisms (SNPs) with a raw p < 0.01 using 1 MB window were analyzed for gene function using the ingenuity pathway analysis. For groups I, II, and the combined group, 449, 301, and 191 SNPs were identified, respectively. Genes identified were involved in pyruvic acid modification and release, 2-deoxyglucose clearance and disposal, sucrose recognition, energy production, and metabolism of carbohydrate. Although detected SNP associations require validation in a large population, results suggested the possibility for marker-assisted or genomic selection of beef cattle to reduce dark cutting.
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Affiliation(s)
- Huaigang Lei
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Tianfu Yang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Shahid Mahmood
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Mohammed Abo-Ismail
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Department of Animal Science, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Bimol C. Roy
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Changxi Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, 6000 C&E Trail, Lacombe, AB T4L 1W1, Canada
| | - Graham S. Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Heather L. Bruce
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
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7
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Marchesani F, Gianquinto E, Autiero I, Michielon A, Campanini B, Faggiano S, Bettati S, Mozzarelli A, Spyrakis F, Bruno S. The allosteric interplay between S-nitrosylation and glycine binding controls the activity of human serine racemase. FEBS J 2020; 288:3034-3054. [PMID: 33249721 DOI: 10.1111/febs.15645] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022]
Abstract
Human serine racemase (hSR) catalyzes the biosynthesis of D-serine, an obligatory co-agonist of the NMDA receptors. It was previously found that the reversible S-nitrosylation of Cys113 reduces hSR activity. Here, we show by site-directed mutagenesis, fluorescence spectroscopy, mass spectrometry, and molecular dynamics that S-nitrosylation stabilizes an open, less-active conformation of the enzyme. The reaction of hSR with either NO or nitroso donors is conformation-dependent and occurs only in the conformation stabilized by the allosteric effector ATP, in which the ε-amino group of Lys114 acts as a base toward the thiol group of Cys113. In the closed conformation stabilized by glycine-an active-site ligand of hSR-the side chain of Lys114 moves away from that of Cys113, while the carboxyl side-chain group of Asp318 moves significantly closer, increasing the thiol pKa and preventing the reaction. We conclude that ATP binding, glycine binding, and S-nitrosylation constitute a three-way regulation mechanism for the tight control of hSR activity. We also show that Cys113 undergoes H2 O2 -mediated oxidation, with loss of enzyme activity, a reaction also dependent on hSR conformation.
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Affiliation(s)
- Francesco Marchesani
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Italy
| | - Eleonora Gianquinto
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Italy
| | - Ida Autiero
- Molecular Horizon Srl, Bettona, PG, Italy.,Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini, Napoli, Italy
| | - Annalisa Michielon
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Italy
| | - Barbara Campanini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Italy
| | - Serena Faggiano
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Italy.,Consiglio Nazionale delle Ricerche, Istituto di Biofisica, Pisa, Italy
| | - Stefano Bettati
- Consiglio Nazionale delle Ricerche, Istituto di Biofisica, Pisa, Italy.,Dipartimento di Medicina e Chirurgia, Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Italy.,Consiglio Nazionale delle Ricerche, Istituto di Biofisica, Pisa, Italy
| | - Francesca Spyrakis
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Italy
| | - Stefano Bruno
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Italy
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8
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Identification of an l-serine/l-threonine dehydratase with glutamate racemase activity in mammals. Biochem J 2020; 477:4221-4241. [DOI: 10.1042/bcj20200721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/12/2020] [Accepted: 10/20/2020] [Indexed: 02/02/2023]
Abstract
Recent investigations have shown that multiple d-amino acids are present in mammals and these compounds have distinctive physiological functions. Free d-glutamate is present in various mammalian tissues and cells and in particular, it is presumably correlated with cardiac function, and much interest is growing in its unique metabolic pathways. Recently, we first identified d-glutamate cyclase as its degradative enzyme in mammals, whereas its biosynthetic pathway in mammals is unclear. Glutamate racemase is a most probable candidate, which catalyzes interconversion between d-glutamate and l-glutamate. Here, we identified the cDNA encoding l-serine dehydratase-like (SDHL) as the first mammalian clone with glutamate racemase activity. This rat SDHL had been deposited in mammalian databases as a protein of unknown function and its amino acid sequence shares ∼60% identity with that of l-serine dehydratase. Rat SDHL was expressed in Escherichia coli, and the enzymatic properties of the recombinant were characterized. The results indicated that rat SDHL is a multifunctional enzyme with glutamate racemase activity in addition to l-serine/l-threonine dehydratase activity. This clone is hence abbreviated as STDHgr. Further experiments using cultured mammalian cells confirmed that d-glutamate was synthesized and l-serine and l-threonine were decomposed. It was also found that SDHL (STDHgr) contributes to the homeostasis of several other amino acids.
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Michielon A, Marchesani F, Faggiano S, Giaccari R, Campanini B, Bettati S, Mozzarelli A, Bruno S. Human serine racemase is inhibited by glyceraldehyde 3-phosphate, but not by glyceraldehyde 3-phosphate dehydrogenase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140544. [PMID: 32971286 DOI: 10.1016/j.bbapap.2020.140544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/14/2020] [Accepted: 09/19/2020] [Indexed: 11/28/2022]
Abstract
Murine serine racemase (SR), the enzyme responsible for the biosynthesis of the neuromodulator d-serine, was reported to form a complex with glyceraldehyde 3-phosphate dehydrogenase (GAPDH), resulting in SR inhibition. In this work, we investigated the interaction between the two human orthologues. We were not able to observe neither the inhibition nor the formation of the SR-GAPDH complex. Rather, hSR is inhibited by the hGAPDH substrate glyceraldehyde 3-phosphate (G3P) in a time- and concentration-dependent fashion, likely through a covalent reaction of the aldehyde functional group. The inhibition was similar for the two G3P enantiomers but it was not observed for structurally similar aldehydes. We ruled out a mechanism of inhibition based on the competition with either pyridoxal phosphate (PLP) - described for other PLP-dependent enzymes when incubated with small aldehydes - or ATP. Nevertheless, the inhibition time course was affected by the presence of hSR allosteric and orthosteric ligands, suggesting a conformation-dependence of the reaction.
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Affiliation(s)
- Annalisa Michielon
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Francesco Marchesani
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Serena Faggiano
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy; Istituto di Biofisica, CNR, Via G. Moruzzi 1, 56124 Pisa, Italy
| | - Roberta Giaccari
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Barbara Campanini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Stefano Bettati
- Dipartimento di Medicina e Chirurgia, Via Volturno 39, 43125 Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy; Istituto di Biofisica, CNR, Via G. Moruzzi 1, 56124 Pisa, Italy
| | - Stefano Bruno
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy.
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TGFβ1-Smad3 signaling mediates the formation of a stable serine racemase dimer in microglia. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140447. [DOI: 10.1016/j.bbapap.2020.140447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/14/2020] [Accepted: 05/17/2020] [Indexed: 12/13/2022]
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11
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Gu SX, Wang HF, Zhu YY, Chen FE. Natural Occurrence, Biological Functions, and Analysis of D-Amino Acids. PHARMACEUTICAL FRONTS 2020. [DOI: 10.1055/s-0040-1713820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AbstractThis review covers the recent development on the natural occurrence, functional elucidations, and analysis of amino acids of the D (dextro) configuration. In the pharmaceutical field, amino acids are not only used directly as clinical drugs and nutriments, but also widely applied as starting materials, catalysts, or chiral ligands for the synthesis of active pharmaceutical ingredients. Earler belief hold that only L-amino acids exist in nature and D-amino acids were artificial products. However, increasing evidence indicates that D-amino acids are naturally occurring in living organisms including human beings, plants, and microorganisms, playing important roles in biological processes. While D-amino acids have similar physical and chemical characteristics with their respective L-enantiomers in an achiral measurement, the biological functions of D-amino acids are remarkably different from those of L-ones. With the rapid development of chiral analytical techniques for D-amino acids, studies on the existence, formation mechanisms, biological functions as well as relevant physiology and pathology of D-amino acids have achieved great progress; however, they are far from being sufficiently explored.
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Affiliation(s)
- Shuang-Xi Gu
- Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan, People's Republic of China
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan, People's Republic of China
| | - Hai-Feng Wang
- Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan, People's Republic of China
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan, People's Republic of China
| | - Yuan-Yuan Zhu
- School of Chemistry & Environmental Engineering, Wuhan Institute of Technology, Wuhan, People's Republic of China
| | - Fen-Er Chen
- Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan, People's Republic of China
- Department of Chemistry, Fudan University, Shanghai, People's Republic of China
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Zhang H, Lu J, Wu S. Sp4 controls constitutive expression of neuronal serine racemase and NF-E2-related factor-2 mediates its induction by valproic acid. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194597. [PMID: 32603878 DOI: 10.1016/j.bbagrm.2020.194597] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/12/2020] [Accepted: 06/21/2020] [Indexed: 01/10/2023]
Abstract
Serine racemase (SR) synthesizes l-type serine to its enantimor, d-serine which participates in physiological processes and in pathological conditions. In the central nervous system, SR is highly expressed in neurons and astrocytes but expressed at relatively lower amount in microglia. However, the mechanism by which SR is highly expessed in neurons is hitherto unknown. We report that the SR mRNA and protein levels in Neuro-2a were increased by valproic acid (VPA), a neuron differentiation stimulator as well as a histone deacetylase inhibitor. SR proximal promoter contained nine putative Sp-binding elements and in the exon 1, three putative anti-oxidant elements (AREs) were conservative among human, rat, and mouse genome. The promoter constructs including 5'-, 3'-fragment, and full length fragment from mouse were individually cloned into a luciferase reporter. Using dual-luciferase assay, the promoter harboring 3'-fragment contained much lower activity than the construct containing 5'-fragment which was though resistant to VPA induction, relative to 3'-fragment. Overexpression of Sp4 or Nrf2 increased whereas knockdown of either decreased Srr mRNA and SR protein. Using site-directed mutagenesis, mutation of Sp-binding elements or AREs in the constructs significantly decreased luciferase activity of the corresponding promoter construct. With chromatin immunoprecipitation, Sp4 was demonstrated to interact directly with the Sp-binding elements whereas Nrf2 bound AREs in Srr mRNA promoter. Altogether, our study highlights that Sp4 controls constitutive expression of SR in neuron and VPA mediates SR expression in N2A cells which is associated with its effect on neuron differentiation, that is, the effect is mediated via Nrf2.
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Affiliation(s)
- He Zhang
- School of Optometry and Ophthalmology and the Eye Hospital, Wenzhou Medical University, China; State Key Laboratory of Optometry, Ophthalmology, and Visual Science, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China
| | - Jinfang Lu
- School of Optometry and Ophthalmology and the Eye Hospital, Wenzhou Medical University, China; School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Shengzhou Wu
- School of Optometry and Ophthalmology and the Eye Hospital, Wenzhou Medical University, China; State Key Laboratory of Optometry, Ophthalmology, and Visual Science, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China.
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13
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Chen M, Liu CT, Tang Y. Discovery and Biocatalytic Application of a PLP-Dependent Amino Acid γ-Substitution Enzyme That Catalyzes C-C Bond Formation. J Am Chem Soc 2020; 142:10506-10515. [PMID: 32434326 DOI: 10.1021/jacs.0c03535] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pyridoxal phosphate (PLP)-dependent enzymes can catalyze transformations of l-amino acids at α, β, and γ positions. These enzymes are frequently involved in the biosynthesis of nonproteinogenic amino acids as building blocks of natural products and are attractive biocatalysts. Here, we report the discovery of a two-step enzymatic synthesis of (2S,6S)-6-methyl pipecolate 1, from the biosynthetic pathway of citrinadin. The key enzyme CndF is PLP-dependent and catalyzes the synthesis of (S)-2-amino-6-oxoheptanoate 3 that is in equilibrium with the cyclic Schiff base. The second enzyme CndE is a stereoselective imine reductase that gives 1. Biochemical characterization of CndF showed this enzyme performs γ-elimination of O-acetyl-l-homoserine to generate the vinylglycine ketimine, which is subjected to nucleophilic attack by acetoacetate to form the new Cγ-Cδ bond in 3 and complete the γ-substitution reaction. CndF displays promiscuity toward different β-keto carboxylate and esters. With use of an Aspergillus strain expressing CndF and CndE, feeding various alkyl-β-keto esters led to the biosynthesis of 6-substituted l-pipecolates. The discovery of CndF expands the repertoire of reactions that can be catalyzed by PLP-dependent enzymes.
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Affiliation(s)
- Mengbin Chen
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Chun-Ting Liu
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
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14
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Bacterial production of maize and human serine racemases as partially active inclusion bodies for d-serine synthesis. Enzyme Microb Technol 2020; 137:109547. [DOI: 10.1016/j.enzmictec.2020.109547] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 01/31/2023]
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15
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Bodkin JA, Coleman MJ, Godfrey LJ, Carvalho CM, Morgan CJ, Suckow RF, Anderson T, Ongur D, Kaufman MJ, Lewandowski KE, Siegel AJ, Waldstreicher E, Grochowski CM, Javitt DC, Rujescu D, Hebbring S, Weinshilboum R, Rodriguez SB, Kirchhoff C, Visscher T, Vuckovic A, Fialkowski A, McCarthy S, Malhotra D, Sebat J, Goff DC, Hudson JI, Lupski JR, Coyle JT, Rudolph U, Levy DL. Targeted Treatment of Individuals With Psychosis Carrying a Copy Number Variant Containing a Genomic Triplication of the Glycine Decarboxylase Gene. Biol Psychiatry 2019; 86:523-535. [PMID: 31279534 PMCID: PMC6745274 DOI: 10.1016/j.biopsych.2019.04.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 04/17/2019] [Accepted: 04/17/2019] [Indexed: 02/08/2023]
Abstract
BACKGROUND The increased mutational burden for rare structural genomic variants in schizophrenia and other neurodevelopmental disorders has so far not yielded therapies targeting the biological effects of specific mutations. We identified two carriers (mother and son) of a triplication of the gene encoding glycine decarboxylase, GLDC, presumably resulting in reduced availability of the N-methyl-D-aspartate receptor coagonists glycine and D-serine and N-methyl-D-aspartate receptor hypofunction. Both carriers had a diagnosis of a psychotic disorder. METHODS We carried out two double-blind, placebo-controlled clinical trials of N-methyl-D-aspartate receptor augmentation of psychotropic drug treatment in these two individuals. Glycine was used in the first clinical trial, and D-cycloserine was used in the second one. RESULTS Glycine or D-cycloserine augmentation of psychotropic drug treatment each improved psychotic and mood symptoms in placebo-controlled trials. CONCLUSIONS These results provide two independent proof-of-principle demonstrations of symptom relief by targeting a specific genotype and explicitly link an individual mutation to the pathophysiology of psychosis and treatment response.
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Affiliation(s)
| | | | | | | | | | | | | | - Dost Ongur
- McLean Hospital, Belmont, MA.,Harvard Medical School, Boston, MA
| | - Marc J. Kaufman
- McLean Hospital, Belmont, MA.,Harvard Medical School, Boston, MA
| | | | - Arthur J. Siegel
- McLean Hospital, Belmont, MA.,Harvard Medical School, Boston, MA
| | | | | | - Daniel C. Javitt
- Columbia University Medical Center, New York, NY.,Nathan Kline Institute, Orangeburg, NY
| | - Dan Rujescu
- Department of Psychiatry, Psychotherapy, and Psychosomatics, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Scott Hebbring
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, WI
| | | | | | | | | | | | | | | | | | | | - Donald C. Goff
- Nathan Kline Institute, Orangeburg, NY.,Department of Psychiatry, New York University Langone Medical Center, New York, NY
| | - James I. Hudson
- McLean Hospital, Belmont, MA.,Harvard Medical School, Boston, MA
| | | | - Joseph T. Coyle
- McLean Hospital, Belmont, MA.,Harvard Medical School, Boston, MA
| | - Uwe Rudolph
- McLean Hospital, Belmont, MA.,Harvard Medical School, Boston, MA
| | - Deborah L. Levy
- McLean Hospital, Belmont, MA.,Harvard Medical School, Boston, MA
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16
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Graham DL, Beio ML, Nelson DL, Berkowitz DB. Human Serine Racemase: Key Residues/Active Site Motifs and Their Relation to Enzyme Function. Front Mol Biosci 2019; 6:8. [PMID: 30918891 PMCID: PMC6424897 DOI: 10.3389/fmolb.2019.00008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/12/2019] [Indexed: 01/06/2023] Open
Abstract
Serine racemase (SR) is the first racemase enzyme to be identified in human biology and converts L-serine to D-serine, an important neuronal signaling molecule that serves as a co-agonist of the NMDA (N-methyl-D-aspartate) receptor. This overview describes key molecular features of the enzyme, focusing on the side chains and binding motifs that control PLP (pyridoxal phosphate) cofactor binding as well as activity modulation through the binding of both divalent cations and ATP, the latter showing allosteric modulation. Discussed are catalytically important residues in the active site including K56 and S84—the si- and re-face bases, respectively,—and R135, a residue that appears to play a critical role in the binding of both negatively charged alternative substrates and inhibitors. The interesting bifurcated mechanism followed by this enzyme whereby substrate L-serine can be channeled either into D-serine (racemization pathway) or into pyruvate (β-elimination pathway) is discussed extensively, as are studies that focus on a key loop region (the so-called “triple serine loop”), the modification of which can be used to invert the normal in vitro preference of this enzyme for the latter pathway over the former. The possible cross-talk between the PLP enzymes hSR and hCBS (human cystathionine β-synthase) is discussed, as the former produces D-serine and the latter produces H2S, both of which stimulate the NMDAR and both of which have been implicated in neuronal infarction pursuant to ischemic stroke. Efforts to gain a more complete mechanistic understanding of these PLP enzymes are expected to provide valuable insights for the development of specific small molecule modulators of these enzymes as tools to study their roles in neuronal signaling and in modulation of NMDAR function.
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Affiliation(s)
- Danielle L Graham
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Matthew L Beio
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - David L Nelson
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
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17
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Raboni S, Marchetti M, Faggiano S, Campanini B, Bruno S, Marchesani F, Margiotta M, Mozzarelli A. The Energy Landscape of Human Serine Racemase. Front Mol Biosci 2019; 5:112. [PMID: 30687716 PMCID: PMC6333871 DOI: 10.3389/fmolb.2018.00112] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/26/2018] [Indexed: 12/17/2022] Open
Abstract
Human serine racemase is a pyridoxal 5′-phosphate (PLP)-dependent dimeric enzyme that catalyzes the reversible racemization of L-serine and D-serine and their dehydration to pyruvate and ammonia. As D-serine is the co-agonist of the N-methyl-D-aspartate receptors for glutamate, the most abundant excitatory neurotransmitter in the brain, the structure, dynamics, function, regulation and cellular localization of serine racemase have been investigated in detail. Serine racemase belongs to the fold-type II of the PLP-dependent enzyme family and structural models from several orthologs are available. The comparison of structures of serine racemase co-crystallized with or without ligands indicates the presence of at least one open and one closed conformation, suggesting that conformational flexibility plays a relevant role in enzyme regulation. ATP, Mg2+, Ca2+, anions, NADH and protein interactors, as well as the post-translational modifications nitrosylation and phosphorylation, finely tune the racemase and dehydratase activities and their relative reaction rates. Further information on serine racemase structure and dynamics resulted from the search for inhibitors with potential therapeutic applications. The cumulative knowledge on human serine racemase allowed obtaining insights into its conformational landscape and into the mechanisms of cross-talk between the effector binding sites and the active site.
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Affiliation(s)
- Samanta Raboni
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | - Serena Faggiano
- Department of Food and Drug, University of Parma, Parma, Italy.,Institute of Biophysics, National Research Council, Pisa, Italy
| | | | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | | | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma, Parma, Italy.,Institute of Biophysics, National Research Council, Pisa, Italy.,National Institute of Biostructures and Biosystems, Rome, Italy
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18
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Billard JM. Changes in Serine Racemase-Dependent Modulation of NMDA Receptor: Impact on Physiological and Pathological Brain Aging. Front Mol Biosci 2018; 5:106. [PMID: 30555832 PMCID: PMC6282039 DOI: 10.3389/fmolb.2018.00106] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/09/2018] [Indexed: 02/02/2023] Open
Abstract
The N-methyl-D-Aspartate glutamate receptors (NMDARs) are pivotal for the functional and morphological plasticity that are required in neuronal networks for efficient brain activities and notably for cognitive-related abilities. Because NMDARs are heterogeneous in subunit composition and associated with multiple functional regulatory sites, their efficacy is under the tonic influence of numerous allosteric modulations, whose dysfunction generally represents the first step generating pathological states. Among the enzymatic candidates, serine racemase (SR) has recently gathered an increasing interest considering that it tightly regulates the production of d-serine, an amino acid now viewed as the main endogenous co-agonist necessary for NMDAR activation. Nowadays, SR deregulation is associated with a wide range of neurological and psychiatric diseases including schizophrenia, amyotrophic lateral sclerosis, and depression. This review aims at compelling the most recent experimental evidences indicating that changes in SR-related modulation of NMDARs also govern opposite functional dysfunctions in physiological and pathological (Alzheimer's disease) aging that finally results in memory disabilities in both cases. It also highlights SR as a relevant alternative target for new pharmacological strategies aimed at preventing functional alterations and cognitive impairments linked to the aging process.
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19
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Kato Y, Hin N, Maita N, Thomas AG, Kurosawa S, Rojas C, Yorita K, Slusher BS, Fukui K, Tsukamoto T. Structural basis for potent inhibition of d-amino acid oxidase by thiophene carboxylic acids. Eur J Med Chem 2018; 159:23-34. [PMID: 30265959 PMCID: PMC6193832 DOI: 10.1016/j.ejmech.2018.09.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/10/2018] [Accepted: 09/14/2018] [Indexed: 12/15/2022]
Abstract
A series of thiophene-2-carboxylic acids and thiophene-3-carboxylic acids were identified as a new class of DAO inhibitors. Structure-activity relationship (SAR) studies revealed that small substituents are well-tolerated on the thiophene ring of both the 2-carboxylic acid and 3-carboxylic acid scaffolds. Crystal structures of human DAO in complex with potent thiophene carboxylic acids revealed that Tyr224 was tightly stacked with the thiophene ring of the inhibitors, resulting in the disappearance of the secondary pocket observed with other DAO inhibitors. Molecular dynamics simulations of the complex revealed that Tyr224 preferred the stacked conformation irrespective of whether Tyr224 was stacked or not in the initial state of the simulations. MM/GBSA indicated a substantial hydrophobic interaction between Tyr244 and the thiophene-based inhibitor. In addition, the active site was tightly closed with an extensive network of hydrogen bonds including those from Tyr224 in the stacked conformation. The introduction of a large branched side chain to the thiophene ring markedly decreased potency. These results are in marked contrast to other DAO inhibitors that can gain potency with a branched side chain extending to the secondary pocket due to Tyr224 repositioning. These insights should be of particular importance in future efforts to optimize DAO inhibitors with novel scaffolds.
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Affiliation(s)
- Yusuke Kato
- Institute for Enzyme Research, Tokushima University, Tokushima, 770-8503, Japan
| | - Niyada Hin
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Nobuo Maita
- Institute for Enzyme Research, Tokushima University, Tokushima, 770-8503, Japan
| | - Ajit G Thomas
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Sumire Kurosawa
- Institute for Enzyme Research, Tokushima University, Tokushima, 770-8503, Japan
| | - Camilo Rojas
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Kazuko Yorita
- Institute for Enzyme Research, Tokushima University, Tokushima, 770-8503, Japan
| | - Barbara S Slusher
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD, 21205, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Kiyoshi Fukui
- Institute for Enzyme Research, Tokushima University, Tokushima, 770-8503, Japan.
| | - Takashi Tsukamoto
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD, 21205, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD, 21205, USA
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20
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Glutamine 89 is a key residue in the allosteric modulation of human serine racemase activity by ATP. Sci Rep 2018; 8:9016. [PMID: 29899358 PMCID: PMC5998037 DOI: 10.1038/s41598-018-27227-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/25/2018] [Indexed: 11/17/2022] Open
Abstract
Serine racemase (SR) catalyses two reactions: the reversible racemisation of L-serine and the irreversible dehydration of L- and D-serine to pyruvate and ammonia. SRs are evolutionarily related to serine dehydratases (SDH) and degradative threonine deaminases (TdcB). Most SRs and TdcBs – but not SDHs – are regulated by nucleotides. SR binds ATP cooperatively and the nucleotide allosterically stimulates the serine dehydratase activity of the enzyme. A H-bond network comprising five residues (T52, N86, Q89, E283 and N316) and water molecules connects the active site with the ATP-binding site. Conservation analysis points to Q89 as a key residue for the allosteric communication, since its mutation to either Met or Ala is linked to the loss of control of activity by nucleotides. We verified this hypothesis by introducing the Q89M and Q89A point mutations in the human SR sequence. The allosteric communication between the active site and the allosteric site in both mutants is almost completely abolished. Indeed, the stimulation of the dehydratase activity by ATP is severely diminished and the binding of the nucleotide is no more cooperative. Ancestral state reconstruction suggests that the allosteric control by nucleotides established early in SR evolution and has been maintained in most eukaryotic lineages.
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21
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Szilágyi B, Kovács P, Ferenczy GG, Rácz A, Németh K, Visy J, Szabó P, Ilas J, Balogh GT, Monostory K, Vincze I, Tábi T, Szökő É, Keserű GM. Discovery of isatin and 1H-indazol-3-ol derivatives as d-amino acid oxidase (DAAO) inhibitors. Bioorg Med Chem 2018; 26:1579-1587. [DOI: 10.1016/j.bmc.2018.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/27/2018] [Accepted: 02/03/2018] [Indexed: 01/23/2023]
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22
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Choi H, Roh D, Yoon S, Choi S, Kwon S, Kang S, Moon J, Han H, Beitz AJ, Lee J. Differential involvement of ipsilateral and contralateral spinal cord astrocyte D-serine in carrageenan-induced mirror-image pain: role of σ1 receptors and astrocyte gap junctions. Br J Pharmacol 2018; 175:558-572. [PMID: 29172248 PMCID: PMC5773966 DOI: 10.1111/bph.14109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 11/04/2017] [Accepted: 11/17/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND AND PURPOSE Although we have recently demonstrated that spinal astrocyte gap junctions mediate the development of mirror-image pain (MIP), it is still unclear which astrocyte-derived factor is responsible for the development of MIP and how its production is controlled. In the present study, we focused on the role of ipsilateral versus contralateral D-serine in the development of MIP and investigated the possible involvement of σ1 receptors and gap junctions in astrocyte D-serine production. EXPERIMENTAL APPROACH Following carrageenan injection, mechanical allodynia was tested at various time points to examine the effect of individual drugs. Immunohistochemistry and Western blot analyses were performed to clarify the expression levels of spinal D-serine, serine racemase, σ1 receptors and connexin 43. KEY RESULTS The expression of ipsilateral D-serine was up-regulated during the early phase of inflammation, while contralateral D-serine increased during the later phase of inflammation. The pharmacological inhibition of D-serine during the early phase blocked the development of both ipsilateral and contralateral mechanical allodynia. However, the inhibition of D-serine during the later phase of inflammation blocked contralateral, but not ipsilateral mechanical allodynia. Furthermore, the inhibition of σ1 receptors during the earlier phase of inflammation inhibited the increase in ipsilateral D-serine. Conversely, the blockade of astrocyte gap junctions suppressed the up-regulation of contralateral D-serine during the later phase of inflammation. CONCLUSION AND IMPLICATIONS Spinal astrocyte D-serine plays an important role in the development of mirror-image pain. Furthermore, σ1 receptors and astrocyte gap junction signalling mediate ipsilateral and contralateral D-serine production respectively.
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Affiliation(s)
- Hoon‐Seong Choi
- Department of Veterinary Physiology, BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary MedicineSeoul National UniversitySeoulKorea
| | - Dae‐Hyun Roh
- Department of Oral Physiology, School of DentistryKyung Hee UniversitySeoulKorea
| | - Seo‐Yeon Yoon
- Pain Cognitive Function Research Center, Department of Brain and Cognitive Sciences, College of Natural SciencesSeoul National UniversitySeoulKorea
| | - Sheu‐Ran Choi
- Department of Veterinary Physiology, BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary MedicineSeoul National UniversitySeoulKorea
| | | | - Suk‐Yun Kang
- KM Fundamental Research DivisionKorea Institute of Oriental MedicineDaejeonKorea
| | - Ji‐Young Moon
- Animal Protection & Welfare DivisionAnimal and Plant Quarantine AgencyGimcheonKorea
| | - Ho‐Jae Han
- Department of Veterinary Physiology, BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary MedicineSeoul National UniversitySeoulKorea
| | - Alvin J Beitz
- Department of Veterinary and Biomedical Sciences, College of Veterinary MedicineUniversity of MinnesotaSaint PaulMNUSA
| | - Jang‐Hern Lee
- Department of Veterinary Physiology, BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary MedicineSeoul National UniversitySeoulKorea
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23
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Mizobuchi T, Nonaka R, Yoshimura M, Abe K, Takahashi S, Kera Y, Goto M. Crystal structure of a pyridoxal 5'-phosphate-dependent aspartate racemase derived from the bivalve mollusc Scapharca broughtonii. Acta Crystallogr F Struct Biol Commun 2017; 73:651-656. [PMID: 29199985 PMCID: PMC5713669 DOI: 10.1107/s2053230x17015813] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/30/2017] [Indexed: 11/10/2022] Open
Abstract
Aspartate racemase (AspR) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that is responsible for D-aspartate biosynthesis in vivo. To the best of our knowledge, this is the first study to report an X-ray crystal structure of a PLP-dependent AspR, which was resolved at 1.90 Å resolution. The AspR derived from the bivalve mollusc Scapharca broughtonii (SbAspR) is a type II PLP-dependent enzyme that is similar to serine racemase (SR) in that SbAspR catalyzes both racemization and dehydration. Structural comparison of SbAspR and SR shows a similar arrangement of the active-site residues and nucleotide-binding site, but a different orientation of the metal-binding site. Superposition of the structures of SbAspR and of rat SR bound to the inhibitor malonate reveals that Arg140 recognizes the β-carboxyl group of the substrate aspartate in SbAspR. It is hypothesized that the aromatic proline interaction between the domains, which favours the closed form of SbAspR, influences the arrangement of Arg140 at the active site.
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Affiliation(s)
- Taichi Mizobuchi
- Department of Biomolecular Science, Graduate School of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Risako Nonaka
- Department of Biomolecular Science, Graduate School of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Motoki Yoshimura
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Katsumasa Abe
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Shouji Takahashi
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Yoshio Kera
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Masaru Goto
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
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24
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Tremiño L, Forcada-Nadal A, Contreras A, Rubio V. Studies on cyanobacterial protein PipY shed light on structure, potential functions, and vitamin B 6 -dependent epilepsy. FEBS Lett 2017; 591:3431-3442. [PMID: 28914444 DOI: 10.1002/1873-3468.12841] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 08/21/2017] [Accepted: 09/01/2017] [Indexed: 11/11/2022]
Abstract
The Synechococcus elongatus COG0325 gene pipY functionally interacts with the nitrogen regulatory gene pipX. As a first step toward a molecular understanding of such interactions, we characterized PipY. This 221-residue protein is monomeric and hosts pyridoxal phosphate (PLP), binding it with limited affinity and losing it upon incubation with D-cycloserine. PipY crystal structures with and without PLP reveal a single-domain monomer folded as the TIM barrel of type-III fold PLP enzymes, with PLP highly exposed, fitting a role for PipY in PLP homeostasis. The mobile PLP phosphate-anchoring C-terminal helix might act as a trigger for PLP exchange. Exploiting the universality of COG0325 functions, we used PipY in site-directed mutagenesis studies to shed light on disease causation by epilepsy-associated mutations in the human COG0325 gene PROSC.
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Affiliation(s)
- Lorena Tremiño
- Instituto de Biomedicina de Valencia (IBV-CSIC), CIBER de Enfermedades Raras (CIBERER-ISCIII), Valencia, Spain
| | - Alicia Forcada-Nadal
- Instituto de Biomedicina de Valencia (IBV-CSIC), CIBER de Enfermedades Raras (CIBERER-ISCIII), Valencia, Spain.,Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Spain
| | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Spain
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia (IBV-CSIC), CIBER de Enfermedades Raras (CIBERER-ISCIII), Valencia, Spain
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25
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Wang W, Sun J, Xiao W, Jiang L, Wang R, Fan J. Change of the N-terminal codon bias combined with tRNA supplementation outperforms the selected fusion tags for production of human d-amino acid oxidase as active inclusion bodies. Biotechnol Lett 2017; 39:1733-1740. [DOI: 10.1007/s10529-017-2413-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/18/2017] [Indexed: 11/29/2022]
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26
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Abstract
More than half a century ago researchers thought that D-amino acids had a minor function compared to L-enantiomers in biological processes. Many evidences have shown that D-amino acids are present in high concentration in microorganisms, plants, mammals and humans and fulfil specific biological functions. In the brain of mammals, D-serine (D-Ser) acts as a co-agonist of the N-methyl-D-aspartate (NMDA)-type glutamate receptors, responsible for learning, memory and behaviour. D-Ser metabolism is relevant for disorders associated with an altered function of the NMDA receptor, such as schizophrenia, ischemia, epilepsy and neurodegenerative disorders. On the other hand, D-aspartate (D-Asp) is one of the major regulators of adult neurogenesis and plays an important role in the development of endocrine function. D-Asp is present in the neuroendocrine and endocrine tissues and testes, and regulates the synthesis and secretion of hormones and spermatogenesis. Also food proteins contain D-amino acids that are naturally originated or processing-induced under conditions such as high temperatures, acid and alkali treatments and fermentation processes. The presence of D-amino acids in dairy products denotes thermal and alkaline treatments and microbial contamination. Two enzymes are involved in the metabolism of D-amino acids: amino acid racemase in the synthesis and D-amino acid oxidase in the degradation.
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27
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Bruno S, Margiotta M, Marchesani F, Paredi G, Orlandi V, Faggiano S, Ronda L, Campanini B, Mozzarelli A. Magnesium and calcium ions differentially affect human serine racemase activity and modulate its quaternary equilibrium toward a tetrameric form. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:381-387. [PMID: 28089597 DOI: 10.1016/j.bbapap.2017.01.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/21/2016] [Accepted: 01/05/2017] [Indexed: 11/18/2022]
Abstract
Serine racemase is the pyridoxal 5'-phosphate dependent enzyme that catalyzes both production and catabolism of d-serine, a co-agonist of the NMDA glutamate receptors. Mg2+, or, alternatively, Ca2+, activate human serine racemase by binding both at a specific site and - as ATP-metal complexes - at a distinct ATP binding site. We show that Mg2+ and Ca2+ bind at the metal binding site with a 4.5-fold difference in affinity, producing a similar thermal stabilization and partially shifting the dimer-tetramer equilibrium in favour of the latter. The ATP-Ca2+ complex produces a 2-fold lower maximal activation in comparison to the ATP-Mg2+ complex and exhibits a 3-fold higher EC50. The co-presence of ATP and metals further stabilizes the tetramer. In consideration of the cellular concentrations of Mg2+ and Ca2+, even taking into account the fluctuations of the latter, these results point to Mg2+ as the sole physiologically relevant ligand both at the metal binding site and at the ATP binding site. The stabilization of the tetramer by both metals and ATP-metal complexes suggests a quaternary activation mechanism mediated by 5'-phosphonucleotides similar to that observed in the distantly related prokaryotic threonine deaminases. This allosteric mechanism has never been observed before in mammalian fold type II pyridoxal 5'-phosphate dependent enzymes.
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Affiliation(s)
| | | | | | - Gianluca Paredi
- Interdepartment Center SITEIA.PARMA, University of Parma, Italy
| | | | | | - Luca Ronda
- Department of Neurosciences, University of Parma, Italy
| | | | - Andrea Mozzarelli
- Department of Pharmacy, University of Parma, Italy; Institute of Biophysics, CNR, Pisa, Italy; National Institute of Biostructures and Biomolecules, Rome, Italy
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28
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Kato E, Matsuzawa R, Kobayashi S, Fukushima T, Maekawa M, Hori Y. Effects of pregabalin on spinal d-serine content and NMDA receptor-mediated synaptic transmission in mice with neuropathic pain. Neurosci Lett 2017; 636:270-275. [DOI: 10.1016/j.neulet.2016.10.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/23/2016] [Accepted: 10/24/2016] [Indexed: 10/20/2022]
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29
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Merino-Gracia J, Zamora-Carreras H, Bruix M, Rodríguez-Crespo I. Molecular Basis for the Protein Recognition Specificity of the Dynein Light Chain DYNLT1/Tctex1: CHARACTERIZATION OF THE INTERACTION WITH ACTIVIN RECEPTOR IIB. J Biol Chem 2016; 291:20962-20975. [PMID: 27502274 DOI: 10.1074/jbc.m116.736884] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Indexed: 01/19/2023] Open
Abstract
It has been suggested that DYNLT1, a dynein light chain known to bind to various cellular and viral proteins, can function both as a molecular clamp and as a microtubule-cargo adapter. Recent data have shown that the DYNLT1 homodimer binds to two dynein intermediate chains to subsequently link cargo proteins such as the guanine nucleotide exchange factor Lfc or the small GTPases RagA and Rab3D. Although over 20 DYNLT1-interacting proteins have been reported, the exact sequence requirements that enable their association to the canonical binding groove or to the secondary site within the DYNLT1 surface are unknown. We describe herein the sequence recognition properties of the hydrophobic groove of DYNLT1 known to accommodate dynein intermediate chain. Using a pepscan approach, we have substituted each amino acid within the interacting peptide for all 20 natural amino acids and identified novel binding sequences. Our data led us to propose activin receptor IIB as a novel DYNLT1 ligand and suggest that DYNLT1 functions as a molecular dimerization engine bringing together two receptor monomers in the cytoplasmic side of the membrane. In addition, we provide evidence regarding a dual binding mode adopted by certain interacting partners such as Lfc or the parathyroid hormone receptor. Finally, we have used NMR spectroscopy to obtain the solution structure of human DYNLT1 forming a complex with dynein intermediate chain of ∼74 kDa; it is the first mammalian structure available.
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Affiliation(s)
- Javier Merino-Gracia
- From the Departamento Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain and
| | - Héctor Zamora-Carreras
- Departamento Química Física Biológica, Instituto Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Marta Bruix
- Departamento Química Física Biológica, Instituto Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Ignacio Rodríguez-Crespo
- From the Departamento Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain and
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30
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Katane M, Saitoh Y, Uchiyama K, Nakayama K, Saitoh Y, Miyamoto T, Sekine M, Uda K, Homma H. Characterization of a homologue of mammalian serine racemase fromCaenorhabditis elegans: the enzyme is not critical for the metabolism of serinein vivo. Genes Cells 2016; 21:966-77. [DOI: 10.1111/gtc.12398] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/24/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Masumi Katane
- Laboratory of Biomolecular Science; Graduate School of Pharmaceutical Sciences; Kitasato University; 5-9-1 Shirokane Minato-ku Tokyo 108-8641 Japan
| | - Yuki Saitoh
- Laboratory of Biomolecular Science; Graduate School of Pharmaceutical Sciences; Kitasato University; 5-9-1 Shirokane Minato-ku Tokyo 108-8641 Japan
| | - Keita Uchiyama
- Laboratory of Biomolecular Science; Graduate School of Pharmaceutical Sciences; Kitasato University; 5-9-1 Shirokane Minato-ku Tokyo 108-8641 Japan
| | - Kazuki Nakayama
- Laboratory of Biomolecular Science; Graduate School of Pharmaceutical Sciences; Kitasato University; 5-9-1 Shirokane Minato-ku Tokyo 108-8641 Japan
| | - Yasuaki Saitoh
- Laboratory of Biomolecular Science; Graduate School of Pharmaceutical Sciences; Kitasato University; 5-9-1 Shirokane Minato-ku Tokyo 108-8641 Japan
| | - Tetsuya Miyamoto
- Laboratory of Biomolecular Science; Graduate School of Pharmaceutical Sciences; Kitasato University; 5-9-1 Shirokane Minato-ku Tokyo 108-8641 Japan
| | - Masae Sekine
- Laboratory of Biomolecular Science; Graduate School of Pharmaceutical Sciences; Kitasato University; 5-9-1 Shirokane Minato-ku Tokyo 108-8641 Japan
| | - Kouji Uda
- Laboratory of Biochemistry; Faculty of Science; Kochi University; 2-5-1 Akebono-cho Kochi-shi Kochi 780-8520 Japan
| | - Hiroshi Homma
- Laboratory of Biomolecular Science; Graduate School of Pharmaceutical Sciences; Kitasato University; 5-9-1 Shirokane Minato-ku Tokyo 108-8641 Japan
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31
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Abstract
Homochirality is fundamental for life. L-Amino acids are exclusively used as substrates for the polymerization and formation of peptides and proteins in living systems. However, D- amino acids were recently detected in various living organisms, including mammals. Of these D-amino acids, D-serine has been most extensively studied. D-Serine was found to play an important role as a neurotransmitter in the human central nervous system (CNS) by binding to the N-methyl- D-aspartate receptor (NMDAr). D-Serine binds with high affinity to a co-agonist site at the NMDAr and, along with glutamate, mediates several vital physiological and pathological processes, including NMDAr transmission, synaptic plasticity and neurotoxicity. Therefore, a key role for D-serine as a determinant of NMDAr mediated neurotransmission in mammalian CNS has been suggested. In this context, we review the known functions of D-serine in human physiology, such as CNS development, and pathology, such as neuro-psychiatric and neurodegenerative diseases related to NMDAr dysfunction.
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32
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Rojas C, Alt J, Ator NA, Thomas AG, Wu Y, Hin N, Wozniak K, Ferraris D, Rais R, Tsukamoto T, Slusher BS. D-Amino-Acid Oxidase Inhibition Increases D-Serine Plasma Levels in Mouse But not in Monkey or Dog. Neuropsychopharmacology 2016; 41:1610-9. [PMID: 26471255 PMCID: PMC4832022 DOI: 10.1038/npp.2015.319] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 10/09/2015] [Accepted: 10/10/2015] [Indexed: 12/23/2022]
Abstract
D-serine has been shown to improve positive, negative, and cognitive symptoms when used as add-on therapy for the treatment of schizophrenia. However, D-serine has to be administered at high doses to observe clinical effects. This is thought to be due to D-serine undergoing oxidation by D-amino-acid oxidase (DAAO) before it reaches the brain. Consequently, co-administration of D-serine with a DAAO inhibitor could be a way to lower the D-serine dose required to treat schizophrenia. Early studies in rodents to evaluate this hypothesis showed that concomitant administration of structurally distinct DAAO inhibitors with D-serine enhanced plasma and brain D-serine levels in rodents compared with administration of D-serine alone. In the present work we used three potent DAAO inhibitors and confirmed previous results in mice. In a follow-up effort, we evaluated plasma D-serine levels in monkeys after oral administration of D-serine in the presence or absence of these DAAO inhibitors. Even though the compounds reached steady state plasma concentrations exceeding their Ki values by >60-fold, plasma D-serine levels remained the same as those in the absence of DAAO inhibitors. Similar results were obtained with dogs. In summary, in contrast to rodents, DAAO inhibition in monkeys and dogs did not influence the exposure to exogenously administered D-serine. Results could be due to differences in D-serine metabolism and/or clearance mechanisms and suggest that the role of DAAO in the metabolism of D-serine is different across species. These data provide caution regarding the utility of DAAO inhibition for patients with schizophrenia.
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Affiliation(s)
- Camilo Rojas
- Johns Hopkins Drug Discovery, Baltimore, MD, USA,Department of Molecular and Comparative Pathobiology, Baltimore, MD, USA
| | - Jesse Alt
- Johns Hopkins Drug Discovery, Baltimore, MD, USA
| | - Nancy A Ator
- Department of Psychiatry and Behavioral Sciences, Baltimore, MD, USA
| | | | - Ying Wu
- Johns Hopkins Drug Discovery, Baltimore, MD, USA
| | - Niyada Hin
- Johns Hopkins Drug Discovery, Baltimore, MD, USA
| | | | | | - Rana Rais
- Johns Hopkins Drug Discovery, Baltimore, MD, USA,Department of Neurology, Baltimore, MD, USA
| | - Takashi Tsukamoto
- Johns Hopkins Drug Discovery, Baltimore, MD, USA,Department of Neurology, Baltimore, MD, USA
| | - Barbara S Slusher
- Johns Hopkins Drug Discovery, Baltimore, MD, USA,Department of Psychiatry and Behavioral Sciences, Baltimore, MD, USA,Department of Neurology, Baltimore, MD, USA,Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA,Department of Neurology, Johns Hopkins University, 855 North Wolfe, Suite 277, Baltimore, MD 21205, USA, Tel: +1 410 614 0662, Fax: +1 410 614 0659, E-mail:
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33
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Singh NS, Rutkowska E, Plazinska A, Khadeer M, Moaddel R, Jozwiak K, Bernier M, Wainer IW. Ketamine Metabolites Enantioselectively Decrease Intracellular D-Serine Concentrations in PC-12 Cells. PLoS One 2016; 11:e0149499. [PMID: 27096720 PMCID: PMC4838237 DOI: 10.1371/journal.pone.0149499] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/16/2016] [Indexed: 01/18/2023] Open
Abstract
D-Serine is an endogenous NMDA receptor co-agonist that activates synaptic NMDA receptors modulating neuronal networks in the cerebral cortex and plays a key role in long-term potentiation of synaptic transmission. D-serine is associated with NMDA receptor neurotoxicity and neurodegeneration and elevated D-serine concentrations have been associated with Alzheimer's and Parkinsons' diseases and amyotrophic lateral sclerosis. Previous studies have demonstrated that the ketamine metabolites (rac)-dehydronorketamine and (2S,6S)-hydroxynorketamine decrease intracellular D-serine concentrations in a concentration dependent manner in PC-12 cells. In the current study, PC-12 cells were incubated with a series of ketamine metabolites and the IC50 values associated with attenuated intracellular D-serine concentrations were determined. The results demonstrate that structural and stereochemical features of the studied compounds contribute to the magnitude of the inhibitory effect with (2S,6S)-hydroxynorketamine and (2R,6R)-hydroxynorketamine displaying the most potent inhibition with IC50 values of 0.18 ± 0.04 nM and 0.68 ± 0.09 nM. The data was utilized to construct a preliminary 3D-QSAR/pharmacophore model for use in the design of new and more efficient modulators of D-serine.
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Affiliation(s)
- Nagendra S. Singh
- Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, United States of America
| | - Ewelina Rutkowska
- Department of Biopharmacy, Medical University of Lublin, Lublin, Poland
| | - Anita Plazinska
- Department of Biopharmacy, Medical University of Lublin, Lublin, Poland
| | - Mohammed Khadeer
- Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, United States of America
| | - Ruin Moaddel
- Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, United States of America
| | - Krzysztof Jozwiak
- Department of Biopharmacy, Medical University of Lublin, Lublin, Poland
| | - Michel Bernier
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, United States of America
| | - Irving W. Wainer
- Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, United States of America
- * E-mail:
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34
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Zhang H, Kuang XL, Chang Y, Lu J, Jiang H, Wu S. Reduced serine racemase expression in aging rat cerebellum is associated with oxidative DNA stress and hypermethylation in the promoter. Brain Res 2015; 1629:221-30. [PMID: 26505919 DOI: 10.1016/j.brainres.2015.10.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 10/16/2015] [Accepted: 10/17/2015] [Indexed: 12/16/2022]
Abstract
Regulation of serine racemase (SR) occurs at transcriptional and translational levels; post-translational modification, cytosolic distribution as well as allosteric effect regulate SR activity. In this study, we report a new route of SR regulation, i.e. oxidative stress and hypermethylation of the srr (gene of SR) promoter correlate with its reduced transcription in aging rat cerebella. We first showed that the mRNA and protein level of srr were decreased in the homogenates of rat cerebellum at age 12 months compared with the counterparts from age 20 days. The reduction of SR protein level in aging cerebella was evidenced by decreased immunostaining observed in the cell body of granule cells or Purkinje cells. Staining for 8-hydroxy-2'-deoxyguanosine (8-OHdG), a marker for oxidative stress to DNA, was much stronger in granule cell or Purkinje cell nuclei from rat cerebella at 12 months compared with staining at 20 days. We further detected srr promoter hypermethylation at 12 months compared with that at 20 days by use of bisulfite sequencing PCR, coinciding with elevated protein levels of DNA methyltransferase 1 (DNMT1) in homogenates of aging cerebella. In vitro, we demonstrated that chronic treatment with the oxidant, menadione (VK3), reduced srr mRNA levels, which was reversed by the DNA demethylating agent 5-Aza-dC-2'-deoxycytidine (5-Aza-dC) in primary cerebellar granule cell cultures. Together, the in vivo and ex vivo results suggest that oxidative DNA stress and srr promoter hypermethylation are associated with reduced srr gene transcription and corresponding reduced protein expression in aging cerebella.
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Affiliation(s)
- He Zhang
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China; State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China
| | - Xiu-Li Kuang
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China; State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China
| | - Yuhua Chang
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China; State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China
| | - Jinfang Lu
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang, China
| | - Haiyan Jiang
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China; State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China
| | - Shengzhou Wu
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China; State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China.
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35
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Moon JY, Choi SR, Roh DH, Yoon SY, Kwon SG, Choi HS, Kang SY, Han HJ, Kim HW, Beitz AJ, Oh SB, Lee JH. Spinal sigma-1 receptor activation increases the production of D-serine in astrocytes which contributes to the development of mechanical allodynia in a mouse model of neuropathic pain. Pharmacol Res 2015; 100:353-64. [PMID: 26316425 DOI: 10.1016/j.phrs.2015.08.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 08/05/2015] [Accepted: 08/20/2015] [Indexed: 12/21/2022]
Abstract
We have previously demonstrated that activation of the spinal sigma-1 receptor (Sig-1R) plays an important role in the development of mechanical allodynia (MA) via secondary activation of the N-methyl-d-aspartate (NMDA) receptor. Sig-1Rs have been shown to localize to astrocytes, and blockade of Sig-1Rs inhibits the pathologic activation of astrocytes in neuropathic mice. However, the mechanism by which Sig-1R activation in astrocytes modulates NMDA receptors in neurons is currently unknown. d-serine, synthesized from l-serine by serine racemase (Srr) in astrocytes, is an endogenous co-agonist for the NMDA receptor glycine site and can control NMDA receptor activity. Here, we investigated the role of d-serine in the development of MA induced by spinal Sig-1R activation in chronic constriction injury (CCI) mice. The production of d-serine and Srr expression were both significantly increased in the spinal cord dorsal horn post-CCI surgery. Srr and d-serine were only localized to astrocytes in the superficial dorsal horn, while d-serine was also localized to neurons in the deep dorsal horn. Moreover, we found that Srr exists in astrocytes that express Sig-1Rs. The CCI-induced increase in the levels of d-serine and Srr was attenuated by sustained intrathecal treatment with the Sig-1R antagonist, BD-1047 during the induction phase of neuropathic pain. In behavioral experiments, degradation of endogenous d-serine with DAAO, or selective blockade of Srr by LSOS, effectively reduced the development of MA, but not thermal hyperalgesia in CCI mice. Finally, BD-1047 administration inhibited the development of MA and this inhibition was reversed by intrathecal treatment with exogenous d-serine. These findings demonstrate for the first time that the activation of Sig-1Rs increases the expression of Srr and d-serine in astrocytes. The increased production of d-serine induced by CCI ultimately affects dorsal horn neurons that are involved in the development of MA in neuropathic mice.
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Affiliation(s)
- Ji-Young Moon
- KM Fundamental Research Division, Korea Institute of Oriental Medicine, Daejeon 305-811, Republic of Korea
| | - Sheu-Ran Choi
- Department of Veterinary Physiology, BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul 151-742, Republic of Korea
| | - Dae-Hyun Roh
- Department of Maxillofacial Tissue Regeneration, Kyung Hee University School of Dentistry, Seoul 130-701, Republic of Korea
| | - Seo-Yeon Yoon
- Pain Cognitive Function Research Center, Department of Brain and Cognitive Sciences College of Natural Sciences, Dental Research Institute and Department of Neurobiology and Physiology, School of Dentistry, Seoul National University, Seoul 110-749, Republic of Korea
| | - Soon-Gu Kwon
- Department of Veterinary Physiology, BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hoon-Seong Choi
- Department of Veterinary Physiology, BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul 151-742, Republic of Korea
| | - Suk-Yun Kang
- KM Fundamental Research Division, Korea Institute of Oriental Medicine, Daejeon 305-811, Republic of Korea
| | - Ho-Jae Han
- Department of Veterinary Physiology, BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hyun-Woo Kim
- Department of Physiology, Institute of Brain Research, Chungnam National University Medical School, Daejeon 301-747, Republic of Korea
| | - Alvin J Beitz
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Seog-Bae Oh
- Pain Cognitive Function Research Center, Department of Brain and Cognitive Sciences College of Natural Sciences, Dental Research Institute and Department of Neurobiology and Physiology, School of Dentistry, Seoul National University, Seoul 110-749, Republic of Korea
| | - Jang-Hern Lee
- Department of Veterinary Physiology, BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul 151-742, Republic of Korea.
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36
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Hin N, Duvall B, Ferraris D, Alt J, Thomas AG, Rais R, Rojas C, Wu Y, Wozniak K, Slusher BS, Tsukamoto T. 6-Hydroxy-1,2,4-triazine-3,5(2H,4H)-dione Derivatives as Novel D-Amino Acid Oxidase Inhibitors. J Med Chem 2015; 58:7258-72. [PMID: 26309148 PMCID: PMC5003509 DOI: 10.1021/acs.jmedchem.5b00482] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Indexed: 02/04/2023]
Abstract
A series of 2-substituted 6-hydroxy-1,2,4-triazine-3,5(2H,4H)-dione derivatives were synthesized as inhibitors of D-amino acid oxidase (DAAO). Many compounds in this series were found to be potent DAAO inhibitors, with IC50 values in the double-digit nanomolar range. The 6-hydroxy-1,2,4-triazine-3,5(2H,4H)-dione pharmacophore appears metabolically resistant to O-glucuronidation unlike other structurally related DAAO inhibitors. Among them, 6-hydroxy-2-(naphthalen-1-ylmethyl)-1,2,4-triazine-3,5(2H,4H)-dione 11h was found to be selective over a number of targets and orally available in mice. Furthermore, oral coadministration of D-serine with 11h enhanced the plasma levels of D-serine in mice compared to the oral administration of D-serine alone, demonstrating its ability to serve as a pharmacoenhancer of D-serine.
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Affiliation(s)
- Niyada Hin
- Brain Science Institute, Department of Neurology, and Department of
Molecular and Comparative
Pathobiology, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Bridget Duvall
- Brain Science Institute, Department of Neurology, and Department of
Molecular and Comparative
Pathobiology, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Dana Ferraris
- Brain Science Institute, Department of Neurology, and Department of
Molecular and Comparative
Pathobiology, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Jesse Alt
- Brain Science Institute, Department of Neurology, and Department of
Molecular and Comparative
Pathobiology, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Ajit G. Thomas
- Brain Science Institute, Department of Neurology, and Department of
Molecular and Comparative
Pathobiology, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Rana Rais
- Brain Science Institute, Department of Neurology, and Department of
Molecular and Comparative
Pathobiology, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Camilo Rojas
- Brain Science Institute, Department of Neurology, and Department of
Molecular and Comparative
Pathobiology, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Ying Wu
- Brain Science Institute, Department of Neurology, and Department of
Molecular and Comparative
Pathobiology, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Krystyna
M. Wozniak
- Brain Science Institute, Department of Neurology, and Department of
Molecular and Comparative
Pathobiology, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Barbara S. Slusher
- Brain Science Institute, Department of Neurology, and Department of
Molecular and Comparative
Pathobiology, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Takashi Tsukamoto
- Brain Science Institute, Department of Neurology, and Department of
Molecular and Comparative
Pathobiology, Johns Hopkins University, Baltimore, Maryland 21205, United States
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37
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Furuse M. Screening of central functions of amino acids and their metabolites for sedative and hypnotic effects using chick models. Eur J Pharmacol 2015; 762:382-93. [DOI: 10.1016/j.ejphar.2015.06.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 11/29/2022]
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Beato C, Pecchini C, Cocconcelli C, Campanini B, Marchetti M, Pieroni M, Mozzarelli A, Costantino G. Cyclopropane derivatives as potential human serine racemase inhibitors: unveiling novel insights into a difficult target. J Enzyme Inhib Med Chem 2015; 31:645-52. [PMID: 26133542 DOI: 10.3109/14756366.2015.1057720] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
d-Serine is the co-agonist of NMDA receptors and binds to the so-called glycine site. d-Serine is synthesized by human serine racemase (SR). Over activation of NMDA receptors is involved in many neurodegenerative diseases and, therefore, the inhibition of SR might represent a novel strategy for the treatment of these pathologies. SR is a very difficult target, with only few compounds so far identified exhibiting weak inhibitory activity. This study was aimed at the identification of novel SR inhibitor by mimicking malonic acid, the best-known SR inhibitor, with a cyclopropane scaffold. We developed, synthesized, and tested a series of cyclopropane dicarboxylic acid derivatives, complementing the synthetic effort with molecular docking. We identified few compounds that bind SR in high micromolar range with a lack of significant correlation between experimental and predicted binding affinities. The thorough analysis of the results can be exploited for the development of more potent SR inhibitors.
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Affiliation(s)
- Claudia Beato
- a Dipartimento di Farmacia , Università degli studi di Parma , Parma , Italy
| | - Chiara Pecchini
- a Dipartimento di Farmacia , Università degli studi di Parma , Parma , Italy
| | - Chiara Cocconcelli
- a Dipartimento di Farmacia , Università degli studi di Parma , Parma , Italy
| | - Barbara Campanini
- a Dipartimento di Farmacia , Università degli studi di Parma , Parma , Italy
| | | | - Marco Pieroni
- a Dipartimento di Farmacia , Università degli studi di Parma , Parma , Italy
| | - Andrea Mozzarelli
- a Dipartimento di Farmacia , Università degli studi di Parma , Parma , Italy .,b Istituto Nazionale Biostrutture e Biosistemi -- Consorzio Interuniversitario , Roma , Italy , and.,c Istituto di Biofisica, CNR , Pisa , Italy
| | - Gabriele Costantino
- a Dipartimento di Farmacia , Università degli studi di Parma , Parma , Italy
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39
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Singh NS, Zarate CA, Moaddel R, Bernier M, Wainer IW. What is hydroxynorketamine and what can it bring to neurotherapeutics? Expert Rev Neurother 2015; 14:1239-42. [PMID: 25331415 DOI: 10.1586/14737175.2014.971760] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
(R,S)-Ketamine was initially developed as an anesthetic agent and its pharmacological properties were determined on the basis of this clinical use. However, pharmacological studies in rat led to the development of the 'Ketamine Paradigm', whereby (R,S)-ketamine and its N-demethylated metabolite (R,S)-norketamine were deemed the active compounds whereas the other ketamine metabolites were considered inactive. Recent in vivo and in vitro studies with (2S,6S)-hydroxynorketamine, a previously identified 'inactive' metabolite, have demonstrated that this compound is an active and selective inhibitor of the α7 subtype of the nicotinic acetylcholine receptor and that this activity contributes to the pharmacological responses associated with the antidepressant activity of (R,S)-ketamine. Thus, it appears that it is necessary to reassess the 'Ketamine Paradigm' in regards to the use of sub-anesthetic doses of (R,S)-ketamine in the treatment of treatment-resistant depression.
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Affiliation(s)
- Nagendra S Singh
- Laboratory of Clinical Investigation, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD , USA
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40
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Nitoker N, Major DT. Understanding the Reaction Mechanism and Intermediate Stabilization in Mammalian Serine Racemase Using Multiscale Quantum-Classical Simulations. Biochemistry 2014; 54:516-27. [DOI: 10.1021/bi500984m] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Neta Nitoker
- Department
of Chemistry and
the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department
of Chemistry and
the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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41
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Vorlová B, Nachtigallová D, Jirásková-Vaníčková J, Ajani H, Jansa P, Rezáč J, Fanfrlík J, Otyepka M, Hobza P, Konvalinka J, Lepšík M. Malonate-based inhibitors of mammalian serine racemase: kinetic characterization and structure-based computational study. Eur J Med Chem 2014; 89:189-97. [PMID: 25462239 DOI: 10.1016/j.ejmech.2014.10.043] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 10/14/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
Overactivation of NMDA receptors has been implicated in various neuropathological conditions, including brain ischaemia, neurodegenerative disorders and epilepsy. Production of d-serine, an NMDA receptor co-agonist, from l-serine is catalyzed in vivo by the pyridoxal-5'-phosphate (PLP)-dependent enzyme serine racemase. Specific inhibition of this enzyme has been proposed as a promising strategy for treatment of neurological conditions caused by NMDA receptor dysfunction. Here we present the synthesis and activity analysis of a series of malonate-based inhibitors of mouse serine racemase (mSR). The compounds possessed IC50 values ranging from 40 ± 11 mM for 2,2-bis(hydroxymethyl)malonate down to 57 ± 1 μM for 2,2-dichloromalonate, the most effective competitive mSR inhibitor known to date. The structure-activity relationship of the whole series in the human orthologue (hSR) was interpreted using Glide docking, WaterMap analysis of hydration and quantum mechanical calculations based on the X-ray structure of the hSR/malonate complex. Docking into the hSR active site with three thermodynamically favourable water molecules was able to discern qualitatively between good and weak inhibitors. Further improvement in ranking was obtained using advanced PM6-D3H4X/COSMO semiempirical quantum mechanics-based scoring which distinguished between the compounds with IC50 better/worse than 2 mM. We have thus not only found a new potent hSR inhibitor but also worked out a computer-assisted protocol to rationalize the binding affinity which will thus aid in search for more effective SR inhibitors. Novel, potent hSR inhibitors may represent interesting research tools as well as drug candidates for treatment of diseases associated with NMDA receptor overactivation.
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Affiliation(s)
- Barbora Vorlová
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Department of Biochemistry, Faculty of Natural Science, Charles University, Albertov 6, 128 43 Prague 2, Czech Republic
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Jana Jirásková-Vaníčková
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Department of Biochemistry, Faculty of Natural Science, Charles University, Albertov 6, 128 43 Prague 2, Czech Republic
| | - Haresh Ajani
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46 Olomouc, Czech Republic
| | - Petr Jansa
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Jan Rezáč
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46 Olomouc, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46 Olomouc, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Department of Biochemistry, Faculty of Natural Science, Charles University, Albertov 6, 128 43 Prague 2, Czech Republic.
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.
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42
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Canu N, Ciotti MT, Pollegioni L. Serine racemase: a key player in apoptosis and necrosis. Front Synaptic Neurosci 2014; 6:9. [PMID: 24795622 PMCID: PMC4000995 DOI: 10.3389/fnsyn.2014.00009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 03/28/2014] [Indexed: 12/14/2022] Open
Abstract
A fine balance between cell survival and cell death is required to sculpt the nervous system during development. However, an excess of cell death can occur following trauma, exposure to neurotoxins or alcohol, and some developmental and neurodegenerative diseases, such as Alzheimer's disease (AD). N-Methyl-D-aspartate receptors (NMDARs) support synaptic plasticity and survival of many neuronal populations whereas inappropriate activation may promote various forms of cell death, apoptosis, and necrosis representing the two extremes of a continuum of cell death processes both “in vitro” and “in vivo.” Hence, by identifying the switches controlling pro-survival vs. apoptosis and apoptosis vs. pro-excitotoxic outcome of NMDAR stimulation, NMDAR modulators could be developed that selectively block the cell death enhancing pro-survival signaling or synaptic plasticity mediated by NMDAR. Among these modulators, a role is emerging for the enzyme serine racemase (SR) that synthesizes D-serine, a key co-agonist with glutamate at NMDAR. This review summarizes the experimental evidence from “in vitro” neuronal cultures—with special emphasis on cerebellar granule neurons (CGNs)—and “in vivo” models of neurodegeneration, where the dual role of the SR/D-serine pathway as a master regulator of apoptosis and the apoptosis-necrosis shift will be discussed.
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Affiliation(s)
- Nadia Canu
- Dipartimento di Medicina dei Sistemi, Università degli Studi di Roma Roma, Italy ; Istituto di Biologia Cellulare e Neurobiologia, Consiglio Nazionale delle Ricerche Roma, Italy
| | - Maria Teresa Ciotti
- Istituto di Biologia Cellulare e Neurobiologia, Consiglio Nazionale delle Ricerche Roma, Italy
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria Varese, Italy ; Centro Interuniversitario di Ricerca in Biotecnologie Proteiche "The Protein Factory," Politecnico di Milano, ICRM-CNR Milano and Università degli studi dell'Insubria Milano, Italy
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43
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Abstract
SIGNIFICANCE Hydrogen sulfide (H2S) has been recognized as a physiological mediator with a variety of functions. It regulates synaptic transmission, vascular tone, inflammation, transcription, and angiogenesis; protects cells from oxidative stress and ischemia-reperfusion injury; and promotes healing of ulcers. RECENT ADVANCES In addition to cystathionine β-synthase and cystathionine γ-lyase, 3-mercaptopyruvate sulfurtransferase along with cysteine aminotransferase was recently demonstrated to produce H2S. Even in bacteria, H2S produced by these enzymes functions as a defense against antibiotics, suggesting that the cytoprotective effect of H2S is a universal defense mechanism in organisms from bacteria to mammals. CRITICAL ISSUES The functional form of H2S-undissociated H2S gas, dissociated HS ion, or some other form of sulfur-has not been identified. FUTURE DIRECTIONS The regulation of H2S production by three enzymes may lead to the identification of the physiological signals that are required to release H2S. The identification of the physiological functions of other forms of sulfur may also help understand the biological significance of H2S.
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Affiliation(s)
- Hideo Kimura
- NCNP, National Institute of Neuroscience , Kodaira, Japan
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44
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Conserved pyridoxal protein that regulates Ile and Val metabolism. J Bacteriol 2013; 195:5439-49. [PMID: 24097949 DOI: 10.1128/jb.00593-13] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli YggS is a member of the highly conserved uncharacterized protein family that binds pyridoxal 5'-phosphate (PLP). To assist with the functional assignment of the YggS family, in vivo and in vitro analyses were performed using a yggS-deficient E. coli strain (ΔyggS) and a purified form of YggS, respectively. In the stationary phase, the ΔyggS strain exhibited a completely different intracellular pool of amino acids and produced a significant amount of l-Val in the culture medium. The log-phase ΔyggS strain accumulated 2-ketobutyrate, its aminated compound 2-aminobutyrate, and, to a lesser extent, l-Val. It also exhibited a 1.3- to 2.6-fold increase in the levels of Ile and Val metabolic enzymes. The fact that similar phenotypes were induced in wild-type E. coli by the exogenous addition of 2-ketobutyrate and 2-aminobutyrate indicates that the 2 compounds contribute to the ΔyggS phenotypes. We showed that the initial cause of the keto acid imbalance was the reduced availability of coenzyme A (CoA); supplementation with pantothenate, which is a CoA precursor, fully reversed phenotypes conferred by the yggS mutation. The plasmid-borne expression of YggS and orthologs from Bacillus subtilis, Saccharomyces cerevisiae, and humans fully rescued the ΔyggS phenotypes. Expression of a mutant YggS lacking PLP-binding ability, however, did not reverse the ΔyggS phenotypes. These results demonstrate for the first time that YggS controls Ile and Val metabolism by modulating 2-ketobutyrate and CoA availability. Its function depends on PLP, and it is highly conserved in a wide range species, from bacteria to humans.
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45
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Singh NS, Paul RK, Torjman MC, Wainer IW. Gabapentin and (S)-pregabalin decrease intracellular D-serine concentrations in PC-12 cells. Neurosci Lett 2013; 535:90-4. [PMID: 23274708 PMCID: PMC3566374 DOI: 10.1016/j.neulet.2012.12.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 12/11/2012] [Accepted: 12/13/2012] [Indexed: 10/27/2022]
Abstract
The effects of gabapentin (GBP) and (S)-pregabalin (PGB) on the intracellular concentrations of d-serine and the expression of serine racemase (SR) in PC-12 cells were determined. Intracellular d-serine concentrations were determined using an enantioselective capillary electrophoresis assay with laser-induced fluorescence detection. Increasing concentrations of GBP, 0.1-20μM, produced a significant decrease in d-serine concentration relative to control, 22.9±6.7% at 20μM (*p<0.05), with an IC(50) value of 3.40±0.29μM. Increasing concentrations of PGB, 0.1-10μM, produced a significant decrease in d-serine concentration relative to control, 25.3±7.6% at 10μM (*p<0.05), with an IC(50) value of 3.38±0.21μM. The compounds had no effect on the expression of monomeric-SR or dimeric-SR as determined by Western blotting. The results suggest that incubation of PC-12 cells with GBP and PGB reduced the basal activity of SR, which is most likely a result of the decreased Ca(2+) flux produced via interaction of the drugs with the α(2)-δ subunit of voltage-gated calcium channels. d-Serine is a co-agonist of the N-methyl d-aspartate receptor (NMDAR) and reduced d-serine concentrations have been associated with reduced NMDAR activity. Thus, GBP and PGB may act as indirect antagonists of NMDAR, a mechanism that may contribute to the clinical effects of the drugs in neuropathic pain.
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Affiliation(s)
- Nagendra S Singh
- Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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46
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Wolosker H, Mori H. Serine racemase: an unconventional enzyme for an unconventional transmitter. Amino Acids 2012; 43:1895-904. [PMID: 22847782 DOI: 10.1007/s00726-012-1370-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Accepted: 07/14/2012] [Indexed: 12/19/2022]
Abstract
The discovery of large amounts of D-serine in the brain challenged the dogma that only L-amino acids are relevant for eukaryotes. The levels of D-serine in the brain are higher than many L-amino acids and account for as much as one-third of L-serine levels. Several studies in the last decades have demonstrated a role of D-serine as an endogenous agonist of N-methyl-D-aspartate receptors (NMDARs). D-Serine is required for NMDAR activity during normal neurotransmission as well as NMDAR overactivation that takes place in neurodegenerative conditions. Still, there are many unanswered questions about D-serine neurobiology, including regulation of its synthesis, release and metabolism. Here, we review the mechanisms of D-serine synthesis by serine racemase and discuss the lessons we can learn from serine racemase knockout mice, focusing on the roles attributed to D-serine and its cellular origin.
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Affiliation(s)
- Herman Wolosker
- Department of Biochemistry, B. Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, 31096, Haifa, Israel.
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47
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Wang W, Barger SW. Cross-linking of serine racemase dimer by reactive oxygen species and reactive nitrogen species. J Neurosci Res 2012; 90:1218-29. [PMID: 22354542 PMCID: PMC3323679 DOI: 10.1002/jnr.22832] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 10/06/2011] [Accepted: 10/23/2011] [Indexed: 11/11/2022]
Abstract
Serine racemase (SR) is the only identified enzyme in mammals responsible for isomerization of L-serine to D-serine, a coagonist at N-methyl-D-aspartate (NMDA) receptors in the forebrain. Our previous data showed that an apparent SR dimer resistant to sodium dodecyl sulfate and β-mercaptoethanol was elevated in microglial cells after proinflammatory activation. Because the activation of microglia is typically associated with an oxidative burst, oxidative cross-linking between SR subunits was speculated. In this study, an siRNA technique was employed to confirm the identity of this SR dimer band. The oxidative species potentially responsible for the cross-linking was investigated with recombinant SR protein. The data indicate that nitric oxide, peroxynitrite, and hydroxyl radical were the likely candidates, whereas superoxide and hydrogen peroxide per se failed to contribute. Furthermore, the mechanism of formation of SR dimer by peroxynitrite oxidation was studied by mass spectrometry. A disulfide bond between Cys₆ and Cys₁₁₃ was identified in 3-morpholinosydnonimine hydrochloride (SIN-1)-treated SR monomer and dimer. Activity assays indicated that SIN-1 treatment decreased SR activity, confirming our previous conclusion that noncovalent dimer is the most active form of SR. These findings suggest a compensatory feedback in which the consequences of neuroinflammation might dampen D-serine production to limit excitotoxic stimulation of NMDA receptors.
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Affiliation(s)
- Wei Wang
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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48
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Henneberger C, Bard L, Rusakov DA. D-Serine: a key to synaptic plasticity? Int J Biochem Cell Biol 2012; 44:587-90. [PMID: 22266400 PMCID: PMC3375648 DOI: 10.1016/j.biocel.2012.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 01/04/2012] [Accepted: 01/05/2012] [Indexed: 11/29/2022]
Abstract
Two discoveries have put D-serine in the spotlight of neuroscience. First, D-serine was detected in brain tissue at high levels. Second, it was found to act on the N-methyl-D-aspartate receptor (NMDAR). This receptor is central to use-dependent synaptic plasticity, the cellular process which is widely believed to underlie learning. The ensuing quest for the mechanisms of D-serine synthesis, release and clearance, as well as for its physiological significance has provided a wealth of experimental evidence implicating D-serine in synaptic plasticity. However some key questions remain unanswered. Which cells release D-serine and upon what stimuli? Is D-serine supply dynamically regulated? What is the fate of released D-serine? Answering these questions appears to be an essential step in our understanding of how NMDARs trigger synaptic plasticity and learning. This review will highlight some recent advances and avenues of enquiry in dynamic D-serine signaling in the mammalian brain with emphasis on neurophysiology.
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49
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Baumgart F, Aicart-Ramos C, Rodriguez-Crespo I. Preparation and assay of recombinant serine racemase. Methods Mol Biol 2012; 794:357-366. [PMID: 21956576 DOI: 10.1007/978-1-61779-331-8_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Serine racemase is a glial and neuronal enzyme that reversibly converts L-serine to D-serine, an endogenous co-agonist of N-methyl-D-aspartate receptor type glutamate receptors (NMDARs). Here we present methods to recombinantly express and purify serine racemase in bacteria and two complementary ways to determine D-serine levels in unknown samples. Furthermore, a detailed protocol of serine racemase activity assays is described that can be used to screen for activators and inhibitors in vitro.
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Affiliation(s)
- Florian Baumgart
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
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50
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Abstract
D-Amino acids play important physiological roles in the mammalian body. Recent investigations revealed that, in mammals, D-amino acids are synthesized from their corresponding L-enantiomers via amino acid racemase. This article describes a method used to measure amino acid racemase activity by high-performance liquid chromatography (HPLC). The assay involves fluorogenic chiral derivatization of amino acids with a newly developed reagent, and enantioseparation of D- and L-amino acid derivatives by HPLC. The method is accurate and reliable, and can be automated using a programmable autosampling injector.
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Affiliation(s)
- Masumi Katane
- Department of Pharmaceutical Life Sciences, Kitasato University, Minatoku, Tokyo, Japan
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