1
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Watt JM, Graeff R, Potter BVL. Small Molecule CD38 Inhibitors: Synthesis of 8-Amino- N1-inosine 5'-monophosphate, Analogues and Early Structure-Activity Relationship. Molecules 2021; 26:molecules26237165. [PMID: 34885748 PMCID: PMC8658804 DOI: 10.3390/molecules26237165] [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: 11/08/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/23/2022] Open
Abstract
Although a monoclonal antibody targeting the multifunctional ectoenzyme CD38 is an FDA-approved drug, few small molecule inhibitors exist for this enzyme that catalyzes inter alia the formation and metabolism of the N1-ribosylated, Ca2+-mobilizing, second messenger cyclic adenosine 5′-diphosphoribose (cADPR). N1-Inosine 5′-monophosphate (N1-IMP) is a fragment directly related to cADPR. 8-Substituted-N1-IMP derivatives, prepared by degradation of cyclic parent compounds, inhibit CD38-mediated cADPR hydrolysis more efficiently than related cyclic analogues, making them attractive for inhibitor development. We report a total synthesis of the N1-IMP scaffold from adenine and a small initial compound series that facilitated early delineation of structure-activity parameters, with analogues evaluated for inhibition of CD38-mediated hydrolysis of cADPR. The 5′-phosphate group proved essential for useful activity, but substitution of this group by a sulfonamide bioisostere was not fruitful. 8-NH2-N1-IMP is the most potent inhibitor (IC50 = 7.6 μM) and importantly HPLC studies showed this ligand to be cleaved at high CD38 concentrations, confirming its access to the CD38 catalytic machinery and demonstrating the potential of our fragment approach.
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Affiliation(s)
- Joanna M. Watt
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK;
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Richard Graeff
- Department of Physiology, University of Hong Kong, Hong Kong, China;
| | - Barry V. L. Potter
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK;
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
- Correspondence: ; Tel.: +44-1865-271945
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2
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Maemoto Y, Shimizu Y, Katoh R, Ito A. Naturally occurring small molecule compounds that target histone deacetylases and their potential applications in cancer therapy. J Antibiot (Tokyo) 2021; 74:667-676. [PMID: 34426659 DOI: 10.1038/s41429-021-00459-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 02/06/2023]
Abstract
Epigenetics is defined as the heritable alteration of gene expression without change to the DNA sequence. Epigenetic abnormalities play a role in various diseases, including cancer. Epigenetic regulation of gene expression occurs through histone chemical modifications and DNA methylation. Lysine acetylation is one of the major histone chemical modifications essential for epigenetic gene expression. Histone acetylation is reversibly regulated by histone acetyltransferases and histone deacetylases, which are molecular targets for cancer therapy. There has been an explosion of research in epigenetic-related drug discovery, and accordingly many small molecule compounds have been developed. Notably, several small molecule inhibitors of histone deacetylases have been approved for the treatment of cancer. This review will introduce natural products, their derivative inhibitors of histone deacetylases, and their clinical development.
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Affiliation(s)
- Yuki Maemoto
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Yuki Shimizu
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Ryu Katoh
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Akihiro Ito
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan.
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3
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Zachos I, Döring M, Tafertshofer G, Simon RC, Sieber V. carba‐Nicotinamid‐Adenin‐Dinukleotid‐Phosphat: Robuster Cofaktor für die Redox‐Biokatalyse. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202017027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ioannis Zachos
- Lehrstuhl für Chemie der biogenen Rohstoffe Campus Straubing für Biotechnologie und Nachhaltigkeit Technische Universität München Schulgasse 16 94315 Straubing Deutschland
| | - Manuel Döring
- Lehrstuhl für Chemie der biogenen Rohstoffe Campus Straubing für Biotechnologie und Nachhaltigkeit Technische Universität München Schulgasse 16 94315 Straubing Deutschland
- Synbiofoundry@TUM Technische Universität München Schulgasse 22 94315 Straubing Deutschland
| | - Georg Tafertshofer
- Roche Diagnostics GmbH DOZCBE.-6164 Nonnenwald 2 82377 Penzberg Deutschland
| | - Robert C. Simon
- Roche Diagnostics GmbH DOZCBE.-6164 Nonnenwald 2 82377 Penzberg Deutschland
| | - Volker Sieber
- Lehrstuhl für Chemie der biogenen Rohstoffe Campus Straubing für Biotechnologie und Nachhaltigkeit Technische Universität München Schulgasse 16 94315 Straubing Deutschland
- Synbiofoundry@TUM Technische Universität München Schulgasse 22 94315 Straubing Deutschland
- Katalytisches Forschungszentrum Technische Universität München Ernst-Otto-Fischer-Straße 1 85748 Garching Deutschland
- School of Chemistry and Molecular Biosciences The University of Queensland 68 Copper Road St. Lucia 4072 Australien
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4
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Zachos I, Döring M, Tafertshofer G, Simon RC, Sieber V. carba Nicotinamide Adenine Dinucleotide Phosphate: Robust Cofactor for Redox Biocatalysis. Angew Chem Int Ed Engl 2021; 60:14701-14706. [PMID: 33719153 PMCID: PMC8252718 DOI: 10.1002/anie.202017027] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/22/2021] [Indexed: 12/21/2022]
Abstract
Here we report a new robust nicotinamide dinucleotide phosphate cofactor analog (carba-NADP+ ) and its acceptance by many enzymes in the class of oxidoreductases. Replacing one ribose oxygen with a methylene group of the natural NADP+ was found to enhance stability dramatically. Decomposition experiments at moderate and high temperatures with the cofactors showed a drastic increase in half-life time at elevated temperatures since it significantly disfavors hydrolysis of the pyridinium-N-glycoside bond. Overall, more than 27 different oxidoreductases were successfully tested, and a thorough analytical characterization and comparison is given. The cofactor carba-NADP+ opens up the field of redox-biocatalysis under harsh conditions.
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Affiliation(s)
- Ioannis Zachos
- Chair of Chemistry of Biogenic ResourcesCampus Straubing for Biotechnology and SustainabilityTechnical University of MunichSchulgasse 1694315StraubingGermany
| | - Manuel Döring
- Chair of Chemistry of Biogenic ResourcesCampus Straubing for Biotechnology and SustainabilityTechnical University of MunichSchulgasse 1694315StraubingGermany
- Synbiofoundry@TUMTechnical University of MunichSchulgasse 2294315StraubingGermany
| | | | - Robert C. Simon
- Roche Diagnostics GmbHDOZCBE.-6164Nonnenwald 282377PenzbergGermany
| | - Volker Sieber
- Chair of Chemistry of Biogenic ResourcesCampus Straubing for Biotechnology and SustainabilityTechnical University of MunichSchulgasse 1694315StraubingGermany
- Synbiofoundry@TUMTechnical University of MunichSchulgasse 2294315StraubingGermany
- Catalytic Research CenterTechnical University of MunichErnst-Otto-Fischer-Strasse 185748GarchingGermany
- School of Chemistry and Molecular BiosciencesThe University of Queensland68 Copper RoadSt. Lucia4072Australia
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5
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Badawy AAB. Tryptophan Metabolism: A Versatile Area Providing Multiple Targets for Pharmacological Intervention. EGYPTIAN JOURNAL OF BASIC AND CLINICAL PHARMACOLOGY 2019; 9:10.32527/2019/101415. [PMID: 31105983 PMCID: PMC6520243 DOI: 10.32527/2019/101415] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The essential amino acid L-tryptophan (Trp) undergoes extensive metabolism along several pathways, resulting in production of many biologically active metabolites which exert profound effects on physiological processes. The disturbance in Trp metabolism and disposition in many disease states provides a basis for exploring multiple targets for pharmaco-therapeutic interventions. In particular, the kynurenine pathway of Trp degradation is currently at the forefront of immunological research and immunotherapy. In this review, I shall consider mammalian Trp metabolism in health and disease and outline the intervention targets. It is hoped that this account will provide a stimulus for pharmacologists and others to conduct further studies in this rich area of biomedical research and therapeutics.
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6
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Dai Z, Zhang XN, Nasertorabi F, Cheng Q, Pei H, Louie SG, Stevens RC, Zhang Y. Facile chemoenzymatic synthesis of a novel stable mimic of NAD . Chem Sci 2018; 9:8337-8342. [PMID: 30568770 PMCID: PMC6256357 DOI: 10.1039/c8sc03899f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/14/2018] [Indexed: 01/01/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) is an essential cofactor participating in a variety of important enzyme-catalyzed physiological and pathophysiological processes. Analogues of NAD+ provide key and valuable agents for investigating NAD+-dependent enzymes. In this study, we report the preparation of a novel stable NAD+ mimic, 4'-thioribose NAD+ (S-NAD+), using a facile and efficient chemoenzymatic approach. Substrate activity assays indicated the resulting S-NAD+ is chemically inert to human CD38 and sirtuin 2 enzymes, but capable of participating in redox reactions in a manner similar to NAD+. X-ray crystallographic analysis revealed binding of S-NAD+ to the active site of human CD38 and critical residues involved in leaving group activation and catalysis. By more closely mimicking NAD+ in geometry and electrostatics, the generated S-NAD+ offers a unique and important tool that can be extended to study enzymes utilizing NAD+.
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Affiliation(s)
- Zhefu Dai
- Department of Pharmacology and Pharmaceutical Sciences , School of Pharmacy , University of Southern California , 1985 Zonal Ave , Los Angeles , CA 90089 , USA .
| | - Xiao-Nan Zhang
- Department of Pharmacology and Pharmaceutical Sciences , School of Pharmacy , University of Southern California , 1985 Zonal Ave , Los Angeles , CA 90089 , USA .
| | - Fariborz Nasertorabi
- Departments of Biological Sciences and Chemistry , Bridge Institute , Michelson Center for Convergent Bioscience , University of Southern California , Los Angeles , CA 90089 , USA .
| | - Qinqin Cheng
- Department of Pharmacology and Pharmaceutical Sciences , School of Pharmacy , University of Southern California , 1985 Zonal Ave , Los Angeles , CA 90089 , USA .
| | - Hua Pei
- Titus Family Department of Clinical Pharmacy , School of Pharmacy , University of Southern California , 1985 Zonal Ave , Los Angeles , CA 90089 , USA
| | - Stan G Louie
- Titus Family Department of Clinical Pharmacy , School of Pharmacy , University of Southern California , 1985 Zonal Ave , Los Angeles , CA 90089 , USA
| | - Raymond C Stevens
- Departments of Biological Sciences and Chemistry , Bridge Institute , Michelson Center for Convergent Bioscience , University of Southern California , Los Angeles , CA 90089 , USA .
| | - Yong Zhang
- Department of Pharmacology and Pharmaceutical Sciences , School of Pharmacy , University of Southern California , 1985 Zonal Ave , Los Angeles , CA 90089 , USA .
- Department of Chemistry , Dornsife College of Letters, Arts and Sciences , University of Southern California , Los Angeles , CA 90089 , USA
- Norris Comprehensive Cancer Center , University of Southern California , Los Angeles , CA 90089 , USA
- Research Center for Liver Diseases , University of Southern California , Los Angeles , CA 90089 , USA
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7
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Chini EN, Chini CCS, Espindola Netto JM, de Oliveira GC, van Schooten W. The Pharmacology of CD38/NADase: An Emerging Target in Cancer and Diseases of Aging. Trends Pharmacol Sci 2018; 39:424-436. [PMID: 29482842 DOI: 10.1016/j.tips.2018.02.001] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/23/2018] [Accepted: 02/03/2018] [Indexed: 10/18/2022]
Abstract
Recent reports indicate that intracellular NAD levels decline in tissues during chronological aging, and that therapies aimed at increasing cellular NAD levels could have beneficial effects in many age-related diseases. The protein CD38 (cluster of differentiation 38) is a multifunctional enzyme that degrades NAD and modulates cellular NAD homeostasis. At the physiological level, CD38 has been implicated in the regulation of metabolism and in the pathogenesis of multiple conditions including aging, obesity, diabetes, heart disease, asthma, and inflammation. Interestingly, many of these functions are mediated by CD38 enzymatic activity. In addition, CD38 has also been identified as a cell-surface marker in hematologic cancers such as multiple myeloma, and a cytotoxic anti-CD38 antibody has been approved by the FDA for use in this disease. Although this is a remarkable development, killing CD38-positive tumor cells with cytotoxic anti-CD38 antibodies is only one of the potential pharmacological uses of targeting CD38. The present review discusses the biology of the CD38 enzyme and the current state of development of pharmacological tools aimed at CD38, and explores how these agents may represent a novel approach for treating human conditions including cancer, metabolic disease, and diseases of aging.
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Affiliation(s)
- Eduardo N Chini
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
| | - Claudia C S Chini
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Jair Machado Espindola Netto
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Guilherme C de Oliveira
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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8
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Second messenger analogues highlight unexpected substrate sensitivity of CD38: total synthesis of the hybrid "L-cyclic inosine 5'-diphosphate ribose". Sci Rep 2017; 7:16100. [PMID: 29170518 PMCID: PMC5700923 DOI: 10.1038/s41598-017-16388-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 11/13/2017] [Indexed: 02/07/2023] Open
Abstract
The multifunctional, transmembrane glycoprotein human CD38 catalyses the synthesis of three key Ca2+-mobilising messengers, including cyclic adenosine 5′-diphosphate ribose (cADPR), and CD38 knockout studies have revealed the relevance of the related signalling pathways to disease. To generate inhibitors of CD38 by total synthesis, analogues based on the cyclic inosine 5′-diphosphate ribose (cIDPR) template were synthesised. In the first example of a sugar hybrid cIDPR analogue, “L-cIDPR”, the natural “northern” N1-linked D-ribose of cADPR was replaced by L-ribose. L-cIDPR is surprisingly still hydrolysed by CD38, whereas 8-Br-L-cIDPR is not cleaved, even at high enzyme concentrations. Thus, the inhibitory activity of L-cIDPR analogues appears to depend upon substitution of the base at C-8; 8-Br-L-cIDPR and 8-NH2-L-cIDPR inhibit CD38-mediated cADPR hydrolysis (IC50 7 μM and 21 µM respectively) with 8-Br-L-cIDPR over 20-fold more potent than 8-Br-cIDPR. In contrast, L-cIDPR displays a comparative 75-fold reduction in activity, but is only ca 2-fold less potent than cIDPR itself. Molecular modelling was used to explore the interaction of the CD38 catalytic residue Glu-226 with the “northern” ribose. We propose that Glu226 still acts as the catalytic residue even for an L-sugar substrate. 8-Br-L-cIDPR potentially binds non-productively in an upside-down fashion. Results highlight the key role of the “northern” ribose in the interaction of cADPR with CD38.
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9
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Badawy AAB. Kynurenine Pathway of Tryptophan Metabolism: Regulatory and Functional Aspects. Int J Tryptophan Res 2017; 10:1178646917691938. [PMID: 28469468 PMCID: PMC5398323 DOI: 10.1177/1178646917691938] [Citation(s) in RCA: 654] [Impact Index Per Article: 93.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/11/2017] [Indexed: 12/21/2022] Open
Abstract
Regulatory and functional aspects of the kynurenine (K) pathway (KP) of tryptophan (Trp) degradation are reviewed. The KP accounts for ~95% of dietary Trp degradation, of which 90% is attributed to the hepatic KP. During immune activation, the minor extrahepatic KP plays a more active role. The KP is rate-limited by its first enzyme, Trp 2,3-dioxygenase (TDO), in liver and indoleamine 2,3-dioxygenase (IDO) elsewhere. TDO is regulated by glucocorticoid induction, substrate activation and stabilization by Trp, cofactor activation by heme, and end-product inhibition by reduced nicotinamide adenine dinucleotide (phosphate). IDO is regulated by IFN-γ and other cytokines and by nitric oxide. The KP disposes of excess Trp, controls hepatic heme synthesis and Trp availability for cerebral serotonin synthesis, and produces immunoregulatory and neuroactive metabolites, the B3 “vitamin” nicotinic acid, and oxidized nicotinamide adenine dinucleotide. Various KP enzymes are undermined in disease and are targeted for therapy of conditions ranging from immunological, neurological, and neurodegenerative conditions to cancer.
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Affiliation(s)
- Abdulla A-B Badawy
- Cardiff School of Health Sciences, Cardiff Metropolitan University, Cardiff, UK
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10
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Deshpande DA, Guedes AGP, Lund FE, Subramanian S, Walseth TF, Kannan MS. CD38 in the pathogenesis of allergic airway disease: Potential therapeutic targets. Pharmacol Ther 2016; 172:116-126. [PMID: 27939939 DOI: 10.1016/j.pharmthera.2016.12.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
CD38 is an ectoenzyme that catalyzes the conversion of β-nicotinamide adenine dinucleotide (β-NAD) to cyclic adenosine diphosphoribose (cADPR) and adenosine diphosphoribose (ADPR) and NADP to nicotinic acid adenine dinucleotide phosphate (NAADP) and adenosine diphosphoribose-2'-phosphate (ADPR-P). The metabolites of NAD and NADP have roles in calcium signaling in different cell types including airway smooth muscle (ASM) cells. In ASM cells, inflammatory cytokines augment CD38 expression and to a greater magnitude in cells from asthmatics, indicating a greater capacity for the generation of cADPR and ADPR in ASM from asthmatics. CD38 deficient mice develop attenuated airway responsiveness to inhaled methacholine following allergen sensitization and challenge compared to wild-type mice indicating its potential role in asthma. Regulation of CD38 expression in ASM cells is achieved by mitogen activated protein kinases, specific isoforms of PI3 kinases, the transcription factors NF-κB and AP-1, and post-transcriptionally by microRNAs. This review will focus on the role of CD38 in intracellular calcium regulation in ASM, contribution to airway inflammation and airway hyperresponsiveness in mouse models of allergic airway inflammation, the transcriptional and post-transcriptional mechanisms of regulation of expression, and outline approaches to inhibit its expression and activity.
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Affiliation(s)
| | - Alonso G P Guedes
- Department of Veterinary Clinical Sciences, University of Minnesota at Twin Cities, USA
| | - Frances E Lund
- Department of Microbiology, University of Alabama at Birmingham, USA
| | | | - Timothy F Walseth
- Department of Pharmacology, University of Minnesota at Twin Cities, USA
| | - Mathur S Kannan
- Department of Veterinary and Biomedical Sciences, University of Minnesota at Twin Cities, USA.
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11
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Abstract
The sirtuins form a superfamily of evolutionarily conserved NAD+-dependent protein N-ϵ-acyl-lysine (AcK) deacylases with roles in a variety of key cellular processes. Sirtuins have a broadly conserved overall structure with a catalytic site formed by a hydrophobic channel between the NAD+-binding Rossmann fold domain and a smaller Zn2+-binding domain. Schistosomes express five members of the sirtuin family and generic sirtuin inhibitors induce apoptosis and death in schistosome larvae, the disruption of adult worm pairs, inhibition of egg laying and damage to the male and female worm reproductive systems. Sirtuins in schistosomes and other parasitic flatworms present structural differences from their human orthologues that should allow the development of selective inhibitors that can be developed as drug leads.
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12
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Swarbrick J, Graeff R, Zhang H, Thomas MP, Hao Q, Potter BVL. Cyclic adenosine 5'-diphosphate ribose analogs without a "southern" ribose inhibit ADP-ribosyl cyclase-hydrolase CD38. J Med Chem 2014; 57:8517-29. [PMID: 25226087 PMCID: PMC4207131 DOI: 10.1021/jm501037u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cyclic adenosine 5'-diphosphate ribose (cADPR) analogs based on the cyclic inosine 5'-diphosphate ribose (cIDPR) template were synthesized by recently developed stereo- and regioselective N1-ribosylation. Replacing the base N9-ribose with a butyl chain generates inhibitors of cADPR hydrolysis by the human ADP-ribosyl cyclase CD38 catalytic domain (shCD38), illustrating the nonessential nature of the "southern" ribose for binding. Butyl substitution generally improves potency relative to the parent cIDPRs, and 8-amino-N9-butyl-cIDPR is comparable to the best noncovalent CD38 inhibitors to date (IC50 = 3.3 μM). Crystallographic analysis of the shCD38:8-amino-N9-butyl-cIDPR complex to a 2.05 Å resolution unexpectedly reveals an N1-hydrolyzed ligand in the active site, suggesting that it is the N6-imino form of cADPR that is hydrolyzed by CD38. While HPLC studies confirm ligand cleavage at very high protein concentrations, they indicate that hydrolysis does not occur under physiological concentrations. Taken together, these analogs confirm that the "northern" ribose is critical for CD38 activity and inhibition, provide new insight into the mechanism of cADPR hydrolysis by CD38, and may aid future inhibitor design.
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Affiliation(s)
- Joanna
M. Swarbrick
- Wolfson
Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Richard Graeff
- Department
of Physiology, University of Hong Kong, Hong Kong, China
| | - Hongmin Zhang
- Department
of Physiology, University of Hong Kong, Hong Kong, China
| | - Mark P. Thomas
- Wolfson
Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Quan Hao
- Department
of Physiology, University of Hong Kong, Hong Kong, China
| | - Barry V. L. Potter
- Wolfson
Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom,Phone: ++44-1225-386639. Fax: ++44-1225-386114. E-mail:
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13
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Probing the catalytic mechanism of bovine CD38/NAD+ glycohydrolase by site directed mutagenesis of key active site residues. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1317-31. [PMID: 24721563 DOI: 10.1016/j.bbapap.2014.03.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/28/2014] [Accepted: 03/31/2014] [Indexed: 01/14/2023]
Abstract
Bovine CD38/NAD(+) glycohydrolase catalyzes the hydrolysis of NAD(+) to nicotinamide and ADP-ribose and the formation of cyclic ADP-ribose via a stepwise reaction mechanism. Our recent crystallographic study of its Michaelis complex and covalently-trapped intermediates provided insights into the modalities of substrate binding and the molecular mechanism of bCD38. The aim of the present work was to determine the precise role of key conserved active site residues (Trp118, Glu138, Asp147, Trp181 and Glu218) by focusing mainly on the cleavage of the nicotinamide-ribosyl bond. We analyzed the kinetic parameters of mutants of these residues which reside within the bCD38 subdomain in the vicinity of the scissile bond of bound NAD(+). To address the reaction mechanism we also performed chemical rescue experiments with neutral (methanol) and ionic (azide, formate) nucleophiles. The crucial role of Glu218, which orients the substrate for cleavage by interacting with the N-ribosyl 2'-OH group of NAD(+), was highlighted. This contribution to catalysis accounts for almost half of the reaction energy barrier. Other contributions can be ascribed notably to Glu138 and Asp147 via ground-state destabilization and desolvation in the vicinity of the scissile bond. Key interactions with Trp118 and Trp181 were also proven to stabilize the ribooxocarbenium ion-like transition state. Altogether we propose that, as an alternative to a covalent acylal reaction intermediate with Glu218, catalysis by bCD38 proceeds through the formation of a discrete and transient ribooxocarbenium intermediate which is stabilized within the active site mostly by electrostatic interactions.
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14
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Moreau C, Liu Q, Graeff R, Wagner GK, Thomas MP, Swarbrick JM, Shuto S, Lee HC, Hao Q, Potter BVL. CD38 Structure-Based Inhibitor Design Using the N1-Cyclic Inosine 5'-Diphosphate Ribose Template. PLoS One 2013; 8:e66247. [PMID: 23840430 PMCID: PMC3686795 DOI: 10.1371/journal.pone.0066247] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 05/02/2013] [Indexed: 11/19/2022] Open
Abstract
Few inhibitors exist for CD38, a multifunctional enzyme catalyzing the formation and metabolism of the Ca(2+)-mobilizing second messenger cyclic adenosine 5'-diphosphoribose (cADPR). Synthetic, non-hydrolyzable ligands can facilitate structure-based inhibitor design. Molecular docking was used to reproduce the crystallographic binding mode of cyclic inosine 5'-diphosphoribose (N1-cIDPR) with CD38, revealing an exploitable pocket and predicting the potential to introduce an extra hydrogen bond interaction with Asp-155. The purine C-8 position of N1-cIDPR (IC50 276 µM) was extended with an amino or diaminobutane group and the 8-modified compounds were evaluated against CD38-catalyzed cADPR hydrolysis. Crystallography of an 8-amino N1-cIDPR:CD38 complex confirmed the predicted interaction with Asp-155, together with a second H-bond from a realigned Glu-146, rationalizing the improved inhibition (IC50 56 µM). Crystallography of a complex of cyclic ADP-carbocyclic ribose (cADPcR, IC50 129 µM) with CD38 illustrated that Glu-146 hydrogen bonds with the ligand N6-amino group. Both 8-amino N1-cIDPR and cADPcR bind deep in the active site reaching the catalytic residue Glu-226, and mimicking the likely location of cADPR during catalysis. Substantial overlap of the N1-cIDPR "northern" ribose monophosphate and the cADPcR carbocyclic ribose monophosphate regions suggests that this area is crucial for inhibitor design, leading to a new compound series of N1-inosine 5'-monophosphates (N1-IMPs). These small fragments inhibit hydrolysis of cADPR more efficiently than the parent cyclic compounds, with the best in the series demonstrating potent inhibition (IC50 = 7.6 µM). The lower molecular weight and relative simplicity of these compounds compared to cADPR make them attractive as a starting point for further inhibitor design.
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Affiliation(s)
- Christelle Moreau
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath, United Kingdom
| | - Qun Liu
- Macromolar Diffraction Facility, Cornell High Energy Synchrotron Source, Cornell University, Ithaca, New York, United States of America
| | - Richard Graeff
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Gerd K. Wagner
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath, United Kingdom
| | - Mark P. Thomas
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath, United Kingdom
| | - Joanna M. Swarbrick
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath, United Kingdom
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Hon Cheung Lee
- Department of Physiology, University of Hong Kong, Hong Kong, China
| | - Quan Hao
- Macromolar Diffraction Facility, Cornell High Energy Synchrotron Source, Cornell University, Ithaca, New York, United States of America
| | - Barry V. L. Potter
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath, United Kingdom
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15
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Szczepankiewicz BG, Dai H, Koppetsch KJ, Qian D, Jiang F, Mao C, Perni RB. Synthesis of carba-NAD and the structures of its ternary complexes with SIRT3 and SIRT5. J Org Chem 2012; 77:7319-29. [PMID: 22849721 DOI: 10.1021/jo301067e] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carba-NAD is a synthetic compound identical to NAD except for one substitution, where an oxygen atom adjacent to the anomeric linkage bearing nicotinamide is replaced with a methylene group. Because it is inert in nicotinamide displacement reactions, carba-NAD is an unreactive substrate analogue for NAD-consuming enzymes. SIRT3 and SIRT5 are NAD-consuming enzymes that are potential therapeutic targets for the treatment of metabolic diseases and cancers. We report an improved carba-NAD synthesis, including a pyrophosphate coupling method that proceeds in approximately 60% yield. We also disclose the X-ray crystal structures of the ternary complexes of SIRT3 and SIRT5 bound to a peptide substrate and carba-NAD. These X-ray crystal structures provide critical snapshots of the mechanism by which human sirtuins function as protein deacylation catalysts.
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16
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Zhou Y, Ting KY, Lam CMC, Kwong AKY, Xia J, Jin H, Liu Z, Zhang L, Cheung Lee H, Zhang L. Design, synthesis and biological evaluation of noncovalent inhibitors of human CD38 NADase. ChemMedChem 2012; 7:223-8. [PMID: 22287152 DOI: 10.1002/cmdc.201100487] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 12/06/2011] [Indexed: 11/06/2022]
Affiliation(s)
- Yi Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
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17
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Pergolizzi G, Butt JN, Bowater RP, Wagner GK. A novel fluorescent probe for NAD-consuming enzymes. Chem Commun (Camb) 2011; 47:12655-7. [PMID: 22042207 DOI: 10.1039/c1cc15499k] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel, fluorescent NAD derivative is processed as substrate by three different NAD-consuming enzymes. The new probe has been used to monitor enzymatic activity in a continuous format by changes in fluorescence and, in one case, to directly visualize alternative reaction pathways.
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Affiliation(s)
- Giulia Pergolizzi
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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18
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Dong M, Si YQ, Sun SY, Pu XP, Yang ZJ, Zhang LR, Zhang LH, Leung FP, Lam CMC, Kwong AKY, Yue J, Zhou Y, Kriksunov IA, Hao Q, Lee HC. Design, synthesis and biological characterization of novel inhibitors of CD38. Org Biomol Chem 2011; 9:3246-57. [PMID: 21431168 DOI: 10.1039/c0ob00768d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human CD38 is a novel multi-functional protein that acts not only as an antigen for B-lymphocyte activation, but also as an enzyme catalyzing the synthesis of a Ca(2+) messenger molecule, cyclic ADP-ribose, from NAD(+). It is well established that this novel Ca(2+) signaling enzyme is responsible for regulating a wide range of physiological functions. Based on the crystal structure of the CD38/NAD(+) complex, we synthesized a series of simplified N-substituted nicotinamide derivatives (Compound 1-14). A number of these compounds exhibited moderate inhibition of the NAD(+) utilizing activity of CD38, with Compound 4 showing the highest potency. The crystal structure of CD38/Compound 4 complex and computer simulation of Compound 7 docking to CD38 show a significant role of the nicotinamide moiety and the distal aromatic group of the compounds for substrate recognition by the active site of CD38. Biologically, we showed that both Compounds 4 and 7 effectively relaxed the agonist-induced contraction of muscle preparations from rats and guinea pigs. This study is a rational design of inhibitors for CD38 that exhibit important physiological effects, and can serve as a model for future drug development.
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Affiliation(s)
- Min Dong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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19
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Cen Y. Sirtuins inhibitors: the approach to affinity and selectivity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:1635-44. [PMID: 19931429 DOI: 10.1016/j.bbapap.2009.11.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2009] [Revised: 11/07/2009] [Accepted: 11/10/2009] [Indexed: 10/20/2022]
Abstract
Accumulating evidence has indicated the importance of sirtuins (class III histone deacetylases) in various biological processes. Their potential roles in metabolic and neurodegenerative diseases have encouraged scientists to seek potent and selective sirtuin inhibitors to investigate their biological functions with a view to eventual new therapeutic treatments. This article surveys current knowledge of sirtuin inhibitors including those discovered via high-throughput screening (HST) or via mechanism-based drug design from synthetic or natural sources. Their inhibitory affinity, selectivities, and possible inhibition mechanisms are discussed.
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Affiliation(s)
- Yana Cen
- Department of Pharmacology, Weill Medical College of Cornell University, New York, NY 10065, USA.
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20
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Malavasi F, Deaglio S, Funaro A, Ferrero E, Horenstein AL, Ortolan E, Vaisitti T, Aydin S. Evolution and function of the ADP ribosyl cyclase/CD38 gene family in physiology and pathology. Physiol Rev 2008; 88:841-86. [PMID: 18626062 DOI: 10.1152/physrev.00035.2007] [Citation(s) in RCA: 619] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The membrane proteins CD38 and CD157 belong to an evolutionarily conserved family of enzymes that play crucial roles in human physiology. Expressed in distinct patterns in most tissues, CD38 (and CD157) cleaves NAD(+) and NADP(+), generating cyclic ADP ribose (cADPR), NAADP, and ADPR. These reaction products are essential for the regulation of intracellular Ca(2+), the most ancient and universal cell signaling system. The entire family of enzymes controls complex processes, including egg fertilization, cell activation and proliferation, muscle contraction, hormone secretion, and immune responses. Over the course of evolution, the molecules have developed the ability to interact laterally and frontally with other surface proteins and have acquired receptor-like features. As detailed in this review, the loss of CD38 function is associated with impaired immune responses, metabolic disturbances, and behavioral modifications in mice. CD38 is a powerful disease marker for human leukemias and myelomas, is directly involved in the pathogenesis and outcome of human immunodeficiency virus infection and chronic lymphocytic leukemia, and controls insulin release and the development of diabetes. Here, the data concerning diseases are examined in view of potential clinical applications in diagnosis, prognosis, and therapy. The concluding remarks try to frame all of the currently available information within a unified working model that takes into account both the enzymatic and receptorial functions of the molecules.
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Affiliation(s)
- Fabio Malavasi
- Laboratory of Immunogenetics, Department of Genetics, Biology, and Biochemistry and Centro di Ricerca in Medicina Sperimentale, University of Torino Medical School, Torino, Italy.
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21
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Mort CJW, Migaud ME, Galione A, Potter BVL. Aplysia californica mediated cyclisation of novel 3'-modified NAD+ analogues: a role for hydrogen bonding in the recognition of cyclic adenosine 5'-diphosphate ribose. Bioorg Med Chem 2004; 12:475-87. [PMID: 14723966 DOI: 10.1016/j.bmc.2003.10.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cyclic ADP-ribose mobilizes intracellular Ca2+ in a variety of cells. To elucidate the nature of the interaction between the C3' substituent of cADP-ribose and the cADPR receptor, three analogues of NAD+ modified in the adenosine ribase (xyloNAD+ 3'F-xyloNAD+ and 3'F-NAD+ were chemically synthesised from D-xylose and adenine starting materials. 3'F-NAD+ was readily converted to cyclic 3'F-ADP ribose by the action of the cyclase enzyme derived from the mollusc Aplysia californica. XyloNAD+ and 3'F-xyloNAD+ were cyclised only reluctantly and in poor yield to afford unstable cyclic products. Biological evaluation of cyclic 3'F-ADP ribose for calcium release in sea urchin egg homogenate gave an EC(50) of 1.5+/-0.5 microM. This high value suggests that the ability of the C3' substituent to donate a hydrogen bond is crucial for agonism.
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Affiliation(s)
- Christopher J W Mort
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
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22
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Landry J, Slama JT, Sternglanz R. Role of NAD(+) in the deacetylase activity of the SIR2-like proteins. Biochem Biophys Res Commun 2000; 278:685-90. [PMID: 11095969 DOI: 10.1006/bbrc.2000.3854] [Citation(s) in RCA: 200] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this report we describe the role of NAD(+) in the deacetylation reaction catalyzed by the SIR2 family of enzymes. We first show that the products of the reaction detected by HPLC analysis are ADP-ribose, nicotinamide, and a deacetylated peptide substrate. These products are in a 1:1:1 molar ratio, indicating that deacetylation involves the hydrolysis of one NAD(+) to ADP-ribose and nicotinamide for each acetyl group removed. Three results suggest that deacetylation requires an enzyme-ADP-ribose intermediate. First, the enzyme can promote an NAD(+) if nicotinamide exchange reaction that depends on an acetylated substrate. Second, a non-hydrolyzable NAD(+) analog is a competitive inhibitor of the enzyme, and, third, nicotinamide shows product inhibition of deacetylase activity.
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Affiliation(s)
- J Landry
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, New York, 11794-5215, USA
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