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Terao R, Lee TJ, Colasanti J, Pfeifer CW, Lin JB, Santeford A, Hase K, Yamaguchi S, Du D, Sohn BS, Sasaki Y, Yoshida M, Apte RS. LXR/CD38 activation drives cholesterol-induced macrophage senescence and neurodegeneration via NAD + depletion. Cell Rep 2024; 43:114102. [PMID: 38636518 PMCID: PMC11223747 DOI: 10.1016/j.celrep.2024.114102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 02/23/2024] [Accepted: 03/27/2024] [Indexed: 04/20/2024] Open
Abstract
Although dysregulated cholesterol metabolism predisposes aging tissues to inflammation and a plethora of diseases, the underlying molecular mechanism remains poorly defined. Here, we show that metabolic and genotoxic stresses, convergently acting through liver X nuclear receptor, upregulate CD38 to promote lysosomal cholesterol efflux, leading to nicotinamide adenine dinucleotide (NAD+) depletion in macrophages. Cholesterol-mediated NAD+ depletion induces macrophage senescence, promoting key features of age-related macular degeneration (AMD), including subretinal lipid deposition and neurodegeneration. NAD+ augmentation reverses cellular senescence and macrophage dysfunction, preventing the development of AMD phenotype. Genetic and pharmacological senolysis protect against the development of AMD and neurodegeneration. Subretinal administration of healthy macrophages promotes the clearance of senescent macrophages, reversing the AMD disease burden. Thus, NAD+ deficit induced by excess intracellular cholesterol is the converging mechanism of macrophage senescence and a causal process underlying age-related neurodegeneration.
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Affiliation(s)
- Ryo Terao
- John F. Hardesty, MD Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA; Department of Ophthalmology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Tae Jun Lee
- John F. Hardesty, MD Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason Colasanti
- John F. Hardesty, MD Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Charles W Pfeifer
- John F. Hardesty, MD Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Joseph B Lin
- John F. Hardesty, MD Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrea Santeford
- John F. Hardesty, MD Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Keitaro Hase
- John F. Hardesty, MD Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA; Department of Ophthalmology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Hokkaido, Japan
| | - Shinobu Yamaguchi
- John F. Hardesty, MD Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel Du
- John F. Hardesty, MD Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian S Sohn
- John F. Hardesty, MD Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Yo Sasaki
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Mitsukuni Yoshida
- John F. Hardesty, MD Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Rajendra S Apte
- John F. Hardesty, MD Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
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Paulus A, Malavasi F, Chanan-Khan A. CD38 as a multifaceted immunotherapeutic target in CLL. Leuk Lymphoma 2022; 63:2265-2275. [DOI: 10.1080/10428194.2022.2090551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Aneel Paulus
- Department of Hematology-Oncology, Mayo Clinic Florida, Jacksonville, FL, USA
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Fabio Malavasi
- Dipartimento Scienze Mediche, Università di Torino, Torino, Italy
- Fondazione Ricerca Molinette ONLUS, Università di Torino, Torino, Italy
| | - Asher Chanan-Khan
- Department of Hematology-Oncology, Mayo Clinic Florida, Jacksonville, FL, USA
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
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3
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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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Benton TZ, Mills CM, Turner JM, Francis MJ, Solomon DJ, Burger PB, Peterson YK, Dolloff NG, Bachmann AS, Woster PM. Selective targeting of CD38 hydrolase and cyclase activity as an approach to immunostimulation. RSC Adv 2021; 11:33260-33270. [PMID: 35497564 PMCID: PMC9042253 DOI: 10.1039/d1ra06266b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/03/2021] [Indexed: 11/21/2022] Open
Abstract
The ectoenzyme CD38 is highly expressed on the surface of mature immune cells, where they are a marker for cell activation, and also on the surface of multiple tumor cells such as multiple myeloma (MM). CD38-targeted monoclonal antibodies (MABs) such as daratumumab and isatuximab bind to CD38 and promote cancer cell death by stimulating the antitumor immune response. Although MABs are achieving unprecedented success in a percentage of cases, high rates of resistance limit their efficacy. Formation of the immunosuppressive intermediate adenosine is a major route by which this resistance is mediated. Thus there is an urgent need for small molecule agents that boost the immune response in T-cells. Importantly, CD38 is a dual-function enzyme, serving as a hydrolase and a nicotinamide adenine dinucleotide (NAD+) cyclase, and both of these activities promote immunosuppression. We have employed virtual and physical screening to identify novel compounds that are selective for either the hydrolase or the cyclase activity of CD38, and have demonstrated that these compounds activate T cells in vitro. We are currently optimizing these inhibitors for use in immunotherapy. These small molecule inhibitors of the CD38-hydrolase or cyclase activity can serve as chemical probes to determine the mechanism by which CD38 promotes resistance to MAB therapy, and could become novel and effective therapeutic agents that produce immunostimulatory effects. Our studies have identified the first small molecule inhibitors of CD38 specifically for use as immunostimulants.
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Affiliation(s)
- Thomas Z Benton
- Dept. of Drug Discovery and Biomedical Sciences, Medical University of South Carolina 70 President St Charleston SC 29425 USA
| | - Catherine M Mills
- Dept. of Drug Discovery and Biomedical Sciences, Medical University of South Carolina 70 President St Charleston SC 29425 USA
| | - Jonathan M Turner
- Dept. of Drug Discovery and Biomedical Sciences, Medical University of South Carolina 70 President St Charleston SC 29425 USA
| | - Megan J Francis
- Dept. of Drug Discovery and Biomedical Sciences, Medical University of South Carolina 70 President St Charleston SC 29425 USA
| | - Dalan J Solomon
- Dept. of Drug Discovery and Biomedical Sciences, Medical University of South Carolina 70 President St Charleston SC 29425 USA
| | - Pieter B Burger
- Dept. of Drug Discovery and Biomedical Sciences, Medical University of South Carolina 70 President St Charleston SC 29425 USA
| | - Yuri K Peterson
- Dept. of Drug Discovery and Biomedical Sciences, Medical University of South Carolina 70 President St Charleston SC 29425 USA
| | - Nathan G Dolloff
- Dept of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina 173 Ashley Ave. Charleston SC 29425 USA
| | - André S Bachmann
- Dept of Pediatrics and Human Development, College of Human Medicine, Michigan State University 400 Monroe Ave. NW Grand Rapids MI 49503 USA
| | - Patrick M Woster
- Dept. of Drug Discovery and Biomedical Sciences, Medical University of South Carolina 70 President St Charleston SC 29425 USA
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Jiao Y, Yi M, Xu L, Chu Q, Yan Y, Luo S, Wu K. CD38: targeted therapy in multiple myeloma and therapeutic potential for solid cancers. Expert Opin Investig Drugs 2020; 29:1295-1308. [PMID: 32822558 DOI: 10.1080/13543784.2020.1814253] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION CD38 is expressed by some cells of hematological malignancies and tumor-related immunosuppressive cells, including regulatory T cells, regulatory B cells, and myeloid-derived suppressor cells. CD38 is an effective target in some hematological malignancies such as multiple myeloma (MM). Daratumumab (Dara), a CD38-targeting antibody, can eliminate CD38high immune suppressor cells and is regarded as a standard therapy for MM because of its outstanding clinical efficacy. Other CD38 monospecific antibodies, such as isatuximab, MOR202, and TAK079, showed promising effects in clinical trials. AREA COVERED This review examines the expression, function, and targeting of CD38 in MM and its potential to deplete immunosuppressive cells in solid cancers. We summarize the distribution and biological function of CD38 and discuss the application of anti-CD38 drugs in hematological malignancies. We also analyz the role of CD38+ immune cells in the tumor microenvironment to encourage additional investigations that target CD38 in solid cancers. PubMed and ClinicalTrials were searched to identify relevant literature from the database inception to 30 April 2020. EXPERT OPINION There is convincing evidence that CD38-targeted immunotherapeutics reduce CD38+ immune suppressor cells. This result suggests that CD38 can be exploited to treat solid tumors by regulating the immunosuppressive microenvironment.
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Affiliation(s)
- Ying Jiao
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology , Wuhan, China
| | - Ming Yi
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology , Wuhan, China
| | - Linping Xu
- Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital , Zhengzhou, China
| | - Qian Chu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology , Wuhan, China
| | - Yongxiang Yan
- R & D Department, Wuhan YZY Biopharma Co., Ltd , Wuhan, China
| | - Suxia Luo
- Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital , Zhengzhou, China
| | - Kongming Wu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology , Wuhan, China.,Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital , Zhengzhou, China
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Assessing Molecular Docking Tools to Guide Targeted Drug Discovery of CD38 Inhibitors. Int J Mol Sci 2020; 21:ijms21155183. [PMID: 32707824 PMCID: PMC7432575 DOI: 10.3390/ijms21155183] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 01/08/2023] Open
Abstract
A promising protein target for computational drug development, the human cluster of differentiation 38 (CD38), plays a crucial role in many physiological and pathological processes, primarily through the upstream regulation of factors that control cytoplasmic Ca2+ concentrations. Recently, a small-molecule inhibitor of CD38 was shown to slow down pathways relating to aging and DNA damage. We examined the performance of seven docking programs for their ability to model protein-ligand interactions with CD38. A test set of twelve CD38 crystal structures, containing crystallized biologically relevant substrates, were used to assess pose prediction. The rankings for each program based on the median RMSD between the native and predicted were Vina, AD4 > PLANTS, Gold, Glide, Molegro > rDock. Forty-two compounds with known affinities were docked to assess the accuracy of the programs at affinity/ranking predictions. The rankings based on scoring power were: Vina, PLANTS > Glide, Gold > Molegro >> AutoDock 4 >> rDock. Out of the top four performing programs, Glide had the only scoring function that did not appear to show bias towards overpredicting the affinity of the ligand-based on its size. Factors that affect the reliability of pose prediction and scoring are discussed. General limitations and known biases of scoring functions are examined, aided in part by using molecular fingerprints and Random Forest classifiers. This machine learning approach may be used to systematically diagnose molecular features that are correlated with poor scoring accuracy.
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Vaisitti T, Arruga F, Guerra G, Deaglio S. Ectonucleotidases in Blood Malignancies: A Tale of Surface Markers and Therapeutic Targets. Front Immunol 2019; 10:2301. [PMID: 31636635 PMCID: PMC6788384 DOI: 10.3389/fimmu.2019.02301] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/11/2019] [Indexed: 12/11/2022] Open
Abstract
Leukemia develops as the result of intrinsic features of the transformed cell, such as gene mutations and derived oncogenic signaling, and extrinsic factors, such as a tumor-friendly, immunosuppressed microenvironment, predominantly in the lymph nodes and the bone marrow. There, high extracellular levels of nucleotides, mainly NAD+ and ATP, are catabolized by different ectonucleotidases, which can be divided in two families according to substrate specificity: on one side those that metabolize NAD+, including CD38, CD157, and CD203a; on the other, those that convert ATP, namely CD39 (and other ENTPDases) and CD73. They generate products that modulate intracellular calcium levels and that activate purinergic receptors. They can also converge on adenosine generation with profound effects, both on leukemic cells, enhancing chemoresistance and homing, and on non-malignant immune cells, polarizing them toward tolerance. This review will first provide an overview of ectonucleotidases expression within the immune system, in physiological and pathological conditions. We will then focus on different hematological malignancies, discussing their role as disease markers and possibly pathogenic agents. Lastly, we will describe current efforts aimed at therapeutic targeting of this family of enzymes.
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Affiliation(s)
- Tiziana Vaisitti
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Francesca Arruga
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Giulia Guerra
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Silvia Deaglio
- Department of Medical Sciences, University of Turin, Turin, Italy
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The Essential Role of Ca 2+ Signals in UVB-Induced IL-1β Secretion in Keratinocytes. J Invest Dermatol 2018; 139:1362-1372. [PMID: 30578820 DOI: 10.1016/j.jid.2018.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 12/24/2022]
Abstract
UVB-induced skin damage is attributable to reactive oxygen species, which are triggered by intracellular Ca2+ signals. However, exactly how the reactive oxygen species are triggered by intracellular Ca2+ upon UVB irradiation remains obscure. Here, we show that UVB induces Ca2+ signals via sequential generation of the following Ca2+ messengers: inositol 1,4,5-trisphosphate, nicotinic acid adenine dinucleotide phosphate, and cyclic ADP-ribose. UVB induced H2O2 production through NADPH oxidase 4 activation, which is downstream to inositol 1,4,5-trisphosphate and nicotinic acid adenine dinucleotide phosphate. H2O2 derived from NADPH oxidase 4 activated CD38 to produce cyclic ADP-ribose. UVB first evoked the pannexin channel to release ATP, which acts on P2X7 receptor to generate inositol 1,4,5-trisphosphate. Inhibitors of these messengers, as well as antioxidants, blocked UVB-induced Ca2+ signals and IL-1β secretion in keratinocytes. Furthermore, ablation of CD38 and NADPH oxidase 4 protected against UVB-induced inflammation and IL-1β secretion in the murine epidermis. These results show that UVB induces IL-1β secretion through cross-talk between Ca2+ and reactive oxygen species, providing insight towards potential targets against UVB-induced inflammation.
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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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NAD binding by human CD38 analyzed by Trp189 fluorescence. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1866:1189-1196. [PMID: 30472140 DOI: 10.1016/j.bbamcr.2018.11.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 11/23/2022]
Abstract
The NAD-glycohydrolase/ADP-ribosyl cyclase CD38 catalyzes the metabolism of nicotinamide adenine dinucleotide (NAD) to the Ca2+ mobilizing second messengers ADP-ribose (ADPR), 2'-deoxy-ADPR, and cyclic ADP-ribose (cADPR). In the present study, we investigated binding and metabolism of NAD by a soluble fragment of human CD38, sCD38, and its catalytically inactive mutant by monitoring changes in endogenous tryptophan (Trp) fluorescence. Addition of NAD resulted in a concentration-dependent decrease in sCD38 fluorescence that is mainly caused by the Trp residue W189. Amplitude of the fluorescence decrease was fitted as one-site binding curve revealing a dissociation constant for NAD of 29 μM. A comparable dissociation constant was found with the catalytically inactive sCD38 mutant (KD 37 μM NAD) indicating that binding of NAD is not significantly affected by the mutation. The NAD-induced decrease in Trp fluorescence completely recovered in case of sCD38. Kinetics of recovery was slowed down with decreasing temperature and sCD38 concentration and increasing NAD concentration demonstrating that recovery in fluorescence is proportional to the enzymatic activity of sCD38. Accordingly, recovery in fluorescence was not observed with the catalytically inactive mutant. This article is part of a Special Issue entitled: ECS Meeting edited by Claus Heizmann, Joachim Krebs and Jacques Haiech.
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11
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Brunnbauer P, Leder A, Kamali C, Kamali K, Keshi E, Splith K, Wabitsch S, Haber P, Atanasov G, Feldbrügge L, Sauer IM, Pratschke J, Schmelzle M, Krenzien F. The nanomolar sensing of nicotinamide adenine dinucleotide in human plasma using a cycling assay in albumin modified simulated body fluids. Sci Rep 2018; 8:16110. [PMID: 30382125 PMCID: PMC6208386 DOI: 10.1038/s41598-018-34350-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/15/2018] [Indexed: 01/05/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD), a prominent member of the pyridine nucleotide family, plays a pivotal role in cell-oxidation protection, DNA repair, cell signalling and central metabolic pathways, such as beta oxidation, glycolysis and the citric acid cycle. In particular, extracellular NAD+ has recently been demonstrated to moderate pathogenesis of multiple systemic diseases as well as aging. Herein we present an assaying method, that serves to quantify extracellular NAD+ in human heparinised plasma and exhibits a sensitivity ranging from the low micromolar into the low nanomolar domain. The assay achieves the quantification of extracellular NAD+ by means of a two-step enzymatic cycling reaction, based on alcohol dehydrogenase. An albumin modified revised simulated body fluid was employed as standard matrix in order to optimise enzymatic activity and enhance the linear behaviour and sensitivity of the method. In addition, we evaluated assay linearity, reproducibility and confirmed long-term storage stability of extracellular NAD+ in frozen human heparinised plasma. In summary, our findings pose a novel standardised method suitable for high throughput screenings of extracellular NAD+ levels in human heparinised plasma, paving the way for new clinical discovery studies.
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Affiliation(s)
- Philipp Brunnbauer
- Experimental Surgery and Regenerative Medicine, Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany
| | - Annekatrin Leder
- Experimental Surgery and Regenerative Medicine, Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany
| | - Can Kamali
- Experimental Surgery and Regenerative Medicine, Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany
| | - Kaan Kamali
- Experimental Surgery and Regenerative Medicine, Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany
| | - Eriselda Keshi
- Experimental Surgery and Regenerative Medicine, Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany
| | - Katrin Splith
- Experimental Surgery and Regenerative Medicine, Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany
| | - Simon Wabitsch
- Experimental Surgery and Regenerative Medicine, Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany
| | - Philipp Haber
- Experimental Surgery and Regenerative Medicine, Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany
| | - Georgi Atanasov
- Experimental Surgery and Regenerative Medicine, Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany
| | - Linda Feldbrügge
- Experimental Surgery and Regenerative Medicine, Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany.,Berlin Institute of Health (BIH), Berlin, 10178, Germany
| | - Igor M Sauer
- Experimental Surgery and Regenerative Medicine, Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany
| | - Johann Pratschke
- Experimental Surgery and Regenerative Medicine, Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany
| | - Moritz Schmelzle
- Experimental Surgery and Regenerative Medicine, Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany
| | - Felix Krenzien
- Experimental Surgery and Regenerative Medicine, Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany. .,Berlin Institute of Health (BIH), Berlin, 10178, Germany.
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12
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Saatori SM, Perez TJ, Graham SM. Variable-Temperature NMR Spectroscopy, Conformational Analysis, and Thermodynamic Parameters of Cyclic Adenosine 5'-Diphosphate Ribose Agonists and Antagonists. J Org Chem 2018; 83:2554-2569. [PMID: 29365260 DOI: 10.1021/acs.joc.7b02749] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cyclic adenosine 5'-diphosphate ribose (cADPR) is a ubiquitous Ca2+-releasing second messenger. Knowledge of its conformational landscape is an essential tool for unraveling the structure-activity relationship (SAR) in cADPR. Variable-temperature 1H NMR spectroscopy, in conjunction with PSEUROT and population analyses, allowed us to determine the conformations and thermodynamic parameters of the furanose rings, γ-bonds (C4'-C5'), and β-bonds (C5'-O5') in the cADPR analogues 2'-deoxy-cADPR, 7-deaza-cADPR, and 8-bromo-cADPR. A significant finding was that, although the analogues are similar to each other and to cADPR itself in terms of overall conformation and population (ΔG°), there were subtle yet important differences in some of thermodynamic properties (ΔH°, ΔS°) associated with each of the conformational equilibria. These differences prompted us to propose a model for cADPR in which the interactions between the A2'-N3, A5″-N3, and H2-R5' atoms serve to fine-tune the N-glycosidic torsion angles (χ).
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Affiliation(s)
- Sarah-Marie Saatori
- Department of Chemistry, St. John's University , 8000 Utopia Parkway, Queens, New York 11439, United States
| | - Tanner J Perez
- Department of Chemistry, St. John's University , 8000 Utopia Parkway, Queens, New York 11439, United States
| | - Steven M Graham
- Department of Chemistry, St. John's University , 8000 Utopia Parkway, Queens, New York 11439, United States
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Specific cyclic ADP-ribose phosphohydrolase obtained by mutagenic engineering of Mn 2+-dependent ADP-ribose/CDP-alcohol diphosphatase. Sci Rep 2018; 8:1036. [PMID: 29348648 PMCID: PMC5773619 DOI: 10.1038/s41598-017-18393-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/12/2017] [Indexed: 01/16/2023] Open
Abstract
Cyclic ADP-ribose (cADPR) is a messenger for Ca2+ mobilization. Its turnover is believed to occur by glycohydrolysis to ADP-ribose. However, ADP-ribose/CDP-alcohol diphosphatase (ADPRibase-Mn) acts as cADPR phosphohydrolase with much lower efficiency than on its major substrates. Recently, we showed that mutagenesis of human ADPRibase-Mn at Phe37, Leu196 and Cys253 alters its specificity: the best substrate of the mutant F37A + L196F + C253A is cADPR by a short difference, Cys253 mutation being essential for cADPR preference. Its proximity to the 'northern' ribose of cADPR in docking models indicates Cys253 is a steric constraint for cADPR positioning. Aiming to obtain a specific cADPR phosphohydrolase, new mutations were tested at Asp250, Val252, Cys253 and Thr279, all near the 'northern' ribose. First, the mutant F37A + L196F + C253G, with a smaller residue 253 (Ala > Gly), showed increased cADPR specificity. Then, the mutant F37A + L196F + V252A + C253G, with another residue made smaller (Val > Ala), displayed the desired specificity, with cADPR kcat/KM ≈20-200-fold larger than for any other substrate. When tested in nucleotide mixtures, cADPR was exhausted while others remained unaltered. We suggest that the specific cADPR phosphohydrolase, by cell or organism transgenesis, or the designed mutations, by genome editing, provide opportunities to study the effect of cADPR depletion on the many systems where it intervenes.
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14
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Javornik U, Plavec J, Wang B, Graham SM. A combined variable temperature 600 MHz NMR/MD study of the calcium release agent cyclic adenosine diphosphate ribose (cADPR): Structure, conformational analysis, and thermodynamics of the conformational equilibria. Carbohydr Res 2017; 455:71-80. [PMID: 29175657 DOI: 10.1016/j.carres.2017.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/10/2017] [Accepted: 11/10/2017] [Indexed: 11/17/2022]
Abstract
A combined variable temperature 600 MHz NMR/molecular dynamics study of the Ca2+-release agent cyclic adenosine 5'-diphosphate ribose (cADPR) was conducted. In addition to elucidating the major and minor orientations of the conformationally flexible furanose rings, γ- (C4'-C5'), and β- (C5'-O5') bonds, the thermodynamics (ΔHo, ΔSo) associated with each of these conformational equilibria were determined. Both furanose rings were biased towards a south conformation (64-74%) and both β-bonds heavily favored trans conformations. The R-ring γ-bond was found to exist almost exclusively as the γ+ conformer, whereas the A-ring γ-bond was a mixture of the γ+ and γt conformers, with the trans conformer being slightly favored. Enthalpic factors accounted for most of the observed conformational preferences, although the R-ring furanose exists as its major conformation based solely on entropic factors. There was excellent agreement between the NMR and MD results, particularly with regard to the conformer identities, but the MD showed a bias towards γ+ conformers. The MD results showed that both N-glycosidic χ-bonds are exclusively syn. Collectively the data allowed for the construction of a model for cADPR in which many of the conformationally flexible units in fact effectively adopt single orientations and where most of the conformational diversity resides in its A-ring furanose and γ-bond.
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Affiliation(s)
- Uroš Javornik
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.
| | - Baifan Wang
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.
| | - Steven M Graham
- Department of Chemistry, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA.
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15
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Zhang S, Xue X, Zhang L, Zhang L, Liu Z. Comparative Analysis of Pharmacophore Features and Quantitative Structure-Activity Relationships for CD38 Covalent and Non-covalent Inhibitors. Chem Biol Drug Des 2015; 86:1411-24. [PMID: 26072680 DOI: 10.1111/cbdd.12606] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 05/09/2015] [Accepted: 06/03/2015] [Indexed: 01/19/2023]
Abstract
In the past decade, the discovery, synthesis, and evaluation for hundreds of CD38 covalent and non-covalent inhibitors has been reported sequentially by our group and partners; however, a systematic structure-based guidance is still lacking for rational design of CD38 inhibitor. Here, we carried out a comparative analysis of pharmacophore features and quantitative structure-activity relationships for CD38 inhibitors. The results uncover that the essential interactions between key residues and covalent/non-covalent CD38 inhibitors include (i) hydrogen bond and hydrophobic interactions with residues Glu226 and Trp125, (ii) electrostatic or hydrogen bond interaction with the positively charged residue Arg127 region, and (iii) the hydrophobic interaction with residue Trp189. For covalent inhibitors, besides the covalent effect with residue Glu226, the electrostatic interaction with residue Arg127 is also necessary, while another hydrogen/non-bonded interaction with residues Trp125 and Trp189 can also be detected. By means of the SYBYL multifit alignment function, the best CoMFA and CoMSIA with CD38 covalent inhibitors presented cross-validated correlation coefficient values (q(2)) of 0.564 and 0.571, and non-cross-validated values (r(2)) of 0.967 and 0.971, respectively. The CD38 non-covalent inhibitors can be classified into five groups according to their chemical scaffolds, and the residues Glu226, Trp189, and Trp125 are indispensable for those non-covalent inhibitors binding to CD38, while the residues Ser126, Arg127, Asp155, Thr221, and Phe222 are also important. The best CoMFA and CoMSIA with the F12 analogues presented cross-validated correlation coefficient values (q(2)) of 0.469 and 0.454, and non-cross-validated values (r(2)) of 0.814 and 0.819, respectively.
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Affiliation(s)
- Shuang Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Xiwen Xue
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
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16
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Cabezas A, Ribeiro JM, Rodrigues JR, López-Villamizar I, Fernández A, Canales J, Pinto RM, Costas MJ, Cameselle JC. Molecular bases of catalysis and ADP-ribose preference of human Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase and conversion by mutagenesis to a preferential cyclic ADP-ribose phosphohydrolase. PLoS One 2015; 10:e0118680. [PMID: 25692488 PMCID: PMC4334965 DOI: 10.1371/journal.pone.0118680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/06/2015] [Indexed: 11/19/2022] Open
Abstract
Among metallo-dependent phosphatases, ADP-ribose/CDP-alcohol diphosphatases form a protein family (ADPRibase-Mn-like) mainly restricted, in eukaryotes, to vertebrates and plants, with preferential expression, at least in rodents, in immune cells. Rat and zebrafish ADPRibase-Mn, the only biochemically studied, are phosphohydrolases of ADP-ribose and, somewhat less efficiently, of CDP-alcohols and 2´,3´-cAMP. Furthermore, the rat but not the zebrafish enzyme displays a unique phosphohydrolytic activity on cyclic ADP-ribose. The molecular basis of such specificity is unknown. Human ADPRibase-Mn showed similar activities, including cyclic ADP-ribose phosphohydrolase, which seems thus common to mammalian ADPRibase-Mn. Substrate docking on a homology model of human ADPRibase-Mn suggested possible interactions of ADP-ribose with seven residues located, with one exception (Cys253), either within the metallo-dependent phosphatases signature (Gln27, Asn110, His111), or in unique structural regions of the ADPRibase-Mn family: s2s3 (Phe37 and Arg43) and h7h8 (Phe210), around the active site entrance. Mutants were constructed, and kinetic parameters for ADP-ribose, CDP-choline, 2´,3´-cAMP and cyclic ADP-ribose were determined. Phe37 was needed for ADP-ribose preference without catalytic effect, as indicated by the increased ADP-ribose Km and unchanged kcat of F37A-ADPRibase-Mn, while the Km values for the other substrates were little affected. Arg43 was essential for catalysis as indicated by the drastic efficiency loss shown by R43A-ADPRibase-Mn. Unexpectedly, Cys253 was hindering for cADPR phosphohydrolase, as indicated by the specific tenfold gain of efficiency of C253A-ADPRibase-Mn with cyclic ADP-ribose. This allowed the design of a triple mutant (F37A+L196F+C253A) for which cyclic ADP-ribose was the best substrate, with a catalytic efficiency of 3.5´104 M-1s-1 versus 4´103 M-1s-1 of the wild type.
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Affiliation(s)
- Alicia Cabezas
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
| | - João Meireles Ribeiro
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
| | - Joaquim Rui Rodrigues
- Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Leiria, Leiria, Portugal
| | - Iralis López-Villamizar
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
| | - Ascensión Fernández
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
| | - José Canales
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
| | - Rosa María Pinto
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
| | - María Jesús Costas
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
| | - José Carlos Cameselle
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
- * E-mail:
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17
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Wang S, Zhu W, Wang X, Li J, Zhang K, Zhang L, Zhao YJ, Lee HC, Zhang L. Design, synthesis and SAR studies of NAD analogues as potent inhibitors towards CD38 NADase. Molecules 2014; 19:15754-67. [PMID: 25268725 PMCID: PMC6271716 DOI: 10.3390/molecules191015754] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/22/2014] [Accepted: 09/22/2014] [Indexed: 11/21/2022] Open
Abstract
Nicotinamide adenine dinucleotide (NAD), one of the most important coenzymes in the cells, is a substrate of the signaling enzyme CD38, by which NAD is converted to a second messenger, cyclic ADP-ribose, which releases calcium from intracellular calcium stores. Starting with 2′-deoxy-2′-fluoroarabinosyl-β-nicotinamide adenine dinucleotide (ara-F NAD), a series of NAD analogues were synthesized and their activities to inhibit CD38 NAD glycohydrolase (NADase) were evaluated. The adenosine-modified analogues showed potent inhibitory activities, among which 2′-deoxy-2′-fluoroarabinosyl-β-nicotinamideguanine dinucleotide (ara-F NGD) was the most effective one. The structure-activity relationship of NAD analogues was also discussed.
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Affiliation(s)
- Shengjun Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Wenjie Zhu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518052, China.
| | - Xuan Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Jianguo Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Kehui Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Yong-Juan Zhao
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518052, China.
| | - Hon Cheung Lee
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518052, China.
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
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18
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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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Kuhn I, Kellenberger E, Schuber F, Muller-Steffner H. Schistosoma mansoni NAD(+) catabolizing enzyme: identification of key residues in catalysis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2520-7. [PMID: 24035885 DOI: 10.1016/j.bbapap.2013.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 08/21/2013] [Accepted: 09/05/2013] [Indexed: 10/26/2022]
Abstract
Schistosoma mansoni NAD(+) catabolizing enzyme (SmNACE), a distant homolog of mammalian CD38, shows significant structural and functional analogy to the members of the CD38/ADP-ribosyl cyclase family. The hallmark of SmNACE is the lack of ADP-ribosyl cyclase activity that might be ascribed to subtle changes in its active site. To better characterize the residues of the active site we determined the kinetic parameters of nine mutants encompassing three acidic residues: (i) the putative catalytic residue Glu202 and (ii) two acidic residues within the 'signature' region (the conserved Glu124 and the downstream Asp133), (iii) Ser169, a strictly conserved polar residue and (iv) two aromatic residues (His103 and Trp165). We established the very important role of Glu202 and of the hydrophobic domains overwhelmingly in the efficiency of the nicotinamide-ribosyl bond cleavage step. We also demonstrated that in sharp contrast with mammalian CD38, the 'signature' Glu124 is as critical as Glu202 for catalysis by the parasite enzyme. The different environments of the two Glu residues in the crystal structure of CD38 and in the homology model of SmNACE could explain such functional discrepancies. Mutagenesis data and 3D structures also indicated the importance of aromatic residues, especially His103, in the stabilization of the reaction intermediate as well as in the selection of its conformation suitable for cyclization to cyclic ADP-ribose. Finally, we showed that inhibition of SmNACE by the natural product cyanidin requires the integrity of Glu202 and Glu124, but not of His103 and Trp165, hence suggesting different recognition modes for substrate and inhibitor.
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Affiliation(s)
- Isabelle Kuhn
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199 CNRS-Université de Strasbourg, Faculté de Pharmacie, Medalis Drug Discovery Center, 74 route du Rhin, 67400 Illkirch, France
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20
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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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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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22
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Rodrigues JR, Fernández A, Canales J, Cabezas A, Ribeiro JM, Costas MJ, Cameselle JC. Characterization of Danio rerio Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase, the structural prototype of the ADPRibase-Mn-like protein family. PLoS One 2012; 7:e42249. [PMID: 22848751 PMCID: PMC3407115 DOI: 10.1371/journal.pone.0042249] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 07/04/2012] [Indexed: 11/30/2022] Open
Abstract
The ADPRibase-Mn-like protein family, that belongs to the metallo-dependent phosphatase superfamily, has different functional and structural prototypes. The functional one is the Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase from Rattus norvegicus, which is essentially inactive with Mg2+ and active with low micromolar Mn2+ in the hydrolysis of the phosphoanhydride linkages of ADP-ribose, CDP-alcohols and cyclic ADP-ribose (cADPR) in order of decreasing efficiency. The structural prototype of the family is a Danio rerio protein with a known crystallographic structure but functionally uncharacterized. To estimate the structure-function correlation with the same protein, the activities of zebrafish ADPRibase-Mn were studied. Differences between zebrafish and rat enzymes are highlighted. The former showed a complex activity dependence on Mn2+, significant (≈25%) Mg2+-dependent activity, but was almost inactive on cADPR (150-fold less efficient than the rat counterpart). The low cADPR hydrolase activity agreed with the zebrafish genome lacking genes coding for proteins with significant homology with cADPR-forming enzymes. Substrate-docking to zebrafish wild-type protein, and characterization of the ADPRibase-Mn H97A mutant pointed to a role of His-97 in catalysis by orientation, and to a bidentate water bridging the dinuclear metal center as the potential nucleophile. Finally, three structural elements that delimit the active site entrance in the zebrafish protein were identified as unique to the ADPRibase-Mn-like family within the metallo-dependent phosphatase superfamily.
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Affiliation(s)
- Joaquim Rui Rodrigues
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
- Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Leiria, Leiria, Portugal
| | - Ascensión Fernández
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
| | - José Canales
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
| | - Alicia Cabezas
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
| | - João Meireles Ribeiro
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
| | - María Jesús Costas
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
| | - José Carlos Cameselle
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
- * E-mail:
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23
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Lee HC. Cyclic ADP-ribose and nicotinic acid adenine dinucleotide phosphate (NAADP) as messengers for calcium mobilization. J Biol Chem 2012; 287:31633-40. [PMID: 22822066 DOI: 10.1074/jbc.r112.349464] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyclic ADP-ribose and nicotinic acid adenine dinucleotide phosphate were discovered >2 decades ago. That they are second messengers for mobilizing Ca(2+) stores has since been firmly established. Separate stores and distinct Ca(2+) channels are targeted, with cyclic ADP-ribose acting on the ryanodine receptors in the endoplasmic reticulum, whereas nicotinic acid adenine dinucleotide phosphate mobilizes the endolysosomes via the two-pore channels. Despite the structural and functional differences, both messengers are synthesized by a ubiquitous enzyme, CD38, whose crystal structure and catalytic mechanism have now been well elucidated. How this novel signaling enzyme is regulated remains largely unknown and is the focus of this minireview.
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Affiliation(s)
- Hon Cheung Lee
- Department of Physiology, University of Hong Kong, Hong Kong, China.
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24
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Egea PF, Muller-Steffner H, Kuhn I, Cakir-Kiefer C, Oppenheimer NJ, Stroud RM, Kellenberger E, Schuber F. Insights into the mechanism of bovine CD38/NAD+glycohydrolase from the X-ray structures of its Michaelis complex and covalently-trapped intermediates. PLoS One 2012; 7:e34918. [PMID: 22529956 PMCID: PMC3329556 DOI: 10.1371/journal.pone.0034918] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 03/06/2012] [Indexed: 01/02/2023] Open
Abstract
Bovine CD38/NAD+glycohydrolase (bCD38) catalyses the hydrolysis of NAD+ into nicotinamide and ADP-ribose and the formation of cyclic ADP-ribose (cADPR). We solved the crystal structures of the mono N-glycosylated forms of the ecto-domain of bCD38 or the catalytic residue mutant Glu218Gln in their apo state or bound to aFNAD or rFNAD, two 2′-fluorinated analogs of NAD+. Both compounds behave as mechanism-based inhibitors, allowing the trapping of a reaction intermediate covalently linked to Glu218. Compared to the non-covalent (Michaelis) complex, the ligands adopt a more folded conformation in the covalent complexes. Altogether these crystallographic snapshots along the reaction pathway reveal the drastic conformational rearrangements undergone by the ligand during catalysis with the repositioning of its adenine ring from a solvent-exposed position stacked against Trp168 to a more buried position stacked against Trp181. This adenine flipping between conserved tryptophans is a prerequisite for the proper positioning of the N1 of the adenine ring to perform the nucleophilic attack on the C1′ of the ribofuranoside ring ultimately yielding cADPR. In all structures, however, the adenine ring adopts the most thermodynamically favorable anti conformation, explaining why cyclization, which requires a syn conformation, remains a rare alternate event in the reactions catalyzed by bCD38 (cADPR represents only 1% of the reaction products). In the Michaelis complex, the substrate is bound in a constrained conformation; the enzyme uses this ground-state destabilization, in addition to a hydrophobic environment and desolvation of the nicotinamide-ribosyl bond, to destabilize the scissile bond leading to the formation of a ribooxocarbenium ion intermediate. The Glu218 side chain stabilizes this reaction intermediate and plays another important role during catalysis by polarizing the 2′-OH of the substrate NAD+. Based on our structural analysis and data on active site mutants, we propose a detailed analysis of the catalytic mechanism.
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Affiliation(s)
- Pascal F. Egea
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail: (PFE); (FS)
| | - Hélène Muller-Steffner
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Isabelle Kuhn
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Céline Cakir-Kiefer
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
- Unité de Recherche Animal et Fonctionnalités des Produits Animaux, UR AFPA, Nancy Université, Vandoeuvre-les-Nancy, France
| | - Norman J. Oppenheimer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Robert M. Stroud
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Esther Kellenberger
- Laboratoire d'Innovation Thérapeutique, UMR 7200 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Francis Schuber
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
- * E-mail: (PFE); (FS)
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25
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Ikeda T, Takasawa S, Noguchi N, Nata K, Yamauchi A, Takahashi I, Yoshikawa T, Sugawara A, Yonekura H, Okamoto H. Identification of a major enzyme for the synthesis and hydrolysis of cyclic ADP-ribose in amphibian cells and evolutional conservation of the enzyme from human to invertebrate. Mol Cell Biochem 2012; 366:69-80. [PMID: 22422046 DOI: 10.1007/s11010-012-1284-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 03/02/2012] [Indexed: 11/30/2022]
Abstract
Cyclic ADP-ribose (cADPR), a metabolite of NAD(+), is known to function as a second messenger for intracellular Ca(2+) mobilization in various vertebrate and invertebrate tissues. In this study, we isolated two Xenopus laevis cDNAs (frog cd38 and cd157 cDNAs) homologous to the one encoding the human cADPR-metabolizing enzyme CD38. Frog CD38 and CD157 are 298-amino acid proteins with 35.9 and 27.2 % identity to human CD38 and CD157, respectively. Transfection of expression vectors for frog CD38 and CD157 into COS-7 cells revealed that frog CD38 had NAD(+) glycohydrolase, ADP-ribosyl cyclase (ARC), and cADPR hydrolase activities, and that frog CD157 had no enzymatic activity under physiological conditions. In addition, when recombinant CD38 and frog brain homogenate were electrophoresed on an SDS-polyacrylamide gel, ARC of the brain homogenate migrated to the same position in the gel as that of frog CD38, suggesting that frog CD38 is the major enzyme responsible for cADPR metabolism in amphibian cells. The frog cd38 gene consists of eight exons and is ubiquitously expressed in various tissues. These findings provide evidence for the existence of the CD38-cADPR signaling system in frog cells and suggest that the CD38-cADPR signaling system is conserved during vertebrate evolution.
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Affiliation(s)
- Takayuki Ikeda
- Department of Biochemistry, Kanazawa Medical University School of Medicine, 1-1 Daigaku, Uchinada, Kahoku-gun, Ishikawa 920-0293, Japan.
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26
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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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27
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Kwong AKY, Chen Z, Zhang H, Leung FP, Lam CMC, Ting KY, Zhang L, Hao Q, Zhang LH, Lee HC. Catalysis-based inhibitors of the calcium signaling function of CD38. Biochemistry 2011; 51:555-64. [PMID: 22142305 DOI: 10.1021/bi201509f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
CD38 is a signaling enzyme responsible for catalyzing the synthesis of cyclic ADP ribose (cADPR) and nicotinic acid adenine dinucleotide phosphate; both are universal Ca(2+) messenger molecules. Ablation of the CD38 gene in mice causes multiple physiological defects, including impaired oxytocin release, that result in altered social behavior. A series of catalysis-based inhibitors of CD38 were designed and synthesized, starting with arabinosyl-2'-fluoro-2'-deoxynicotinamide mononucleotide. Structure-function relationships were analyzed to assess the structural determinants important for inhibiting the NADase activity of CD38. X-ray crystallography was used to reveal the covalent intermediates that were formed with the catalytic residue, Glu226. Metabolically stable analogues that were resistant to inactivation by phosphatase and esterase were synthesized and shown to be effective in inhibiting intracellular cADPR production in human HL-60 cells during induction of differentiation by retinoic acid. The inhibition was species-independent, and the analogues were similarly effective in blocking the cyclization reaction of CD38 in rat ventricular tissue extracts, as well as inhibiting the α-agonist-induced constriction in rat mesentery arteries. These compounds thus represent the first generally applicable and catalysis-based inhibitors of the Ca(2+) signaling function of CD38.
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Affiliation(s)
- Anna Ka Yee Kwong
- Department of Physiology, 4/F Lab Block, University of Hong Kong, Hong Kong
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28
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Kotaka M, Graeff R, Chen Z, Zhang LH, Lee HC, Hao Q. Structural studies of intermediates along the cyclization pathway of Aplysia ADP-ribosyl cyclase. J Mol Biol 2011; 415:514-26. [PMID: 22138343 DOI: 10.1016/j.jmb.2011.11.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 11/02/2011] [Accepted: 11/08/2011] [Indexed: 11/19/2022]
Abstract
Cyclic ADP-ribose (cADPR) is a calcium messenger that can mobilize intracellular Ca²⁺ stores and activate Ca²⁺ influx to regulate a wide range of physiological processes. Aplysia cyclase is the first member of the ADP-ribosyl cyclases identified to catalyze the cyclization of NAD⁺ into cADPR. The catalysis involves a two-step reaction, the elimination of the nicotinamide ring and the cyclization of the intermediate resulting in the covalent attachment of the purine ring to the terminal ribose. Aplysia cyclase exhibits a high degree of leniency towards the purine base of its substrate, and the cyclization reaction takes place at either the N1- or the N7-position of the purine ring. To decipher the mechanism of cyclization in Aplysia cyclase, we used a crystallization setup with multiple Aplysia cyclase molecules present in the asymmetric unit. With the use of natural substrates and analogs, not only were we able to capture multiple snapshots during enzyme catalysis resulting in either N1 or N7 linkage of the purine ring to the terminal ribose, we were also able to observe, for the first time, the cyclized products of both N1 and N7 cyclization bound in the active site of Aplysia cyclase.
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Affiliation(s)
- Masayo Kotaka
- Department of Physiology, University of Hong Kong, Hong Kong SAR, China
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29
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Lee HC. Cyclic ADP-ribose and NAADP: fraternal twin messengers for calcium signaling. SCIENCE CHINA-LIFE SCIENCES 2011; 54:699-711. [PMID: 21786193 DOI: 10.1007/s11427-011-4197-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 06/10/2011] [Indexed: 12/17/2022]
Abstract
The concept advanced by Berridge and colleagues that intracellular Ca(2+)-stores can be mobilized in an agonist-dependent and messenger (IP(3))-mediated manner has put Ca(2+)-mobilization at the center stage of signal transduction mechanisms. During the late 1980s, we showed that Ca(2+)-stores can be mobilized by two other messengers unrelated to inositol trisphosphate (IP(3)) and identified them as cyclic ADP-ribose (cADPR), a novel cyclic nucleotide from NAD, and nicotinic acid adenine dinucleotide phosphate (NAADP), a linear metabolite of NADP. Their messenger functions have now been documented in a wide range of systems spanning three biological kingdoms. Accumulated evidence indicates that the target of cADPR is the ryanodine receptor in the sarco/endoplasmic reticulum, while that of NAADP is the two pore channel in endolysosomes.As cADPR and NAADP are structurally and functionally distinct, it is remarkable that they are synthesized by the same enzyme. They are thus fraternal twin messengers. We first identified the Aplysia ADP-ribosyl cyclase as one such enzyme and, through homology, found its mammalian homolog, CD38. Gene knockout in mice confirms the important roles of CD38 in diverse physiological functions from insulin secretion, susceptibility to bacterial infection, to social behavior of mice through modulating neuronal oxytocin secretion. We have elucidated the catalytic mechanisms of the Aplysia cyclase and CD38 to atomic resolution by crystallography and site-directed mutagenesis. This article gives a historical account of the cADPR/NAADP/CD38-signaling pathway and describes current efforts in elucidating the structure and function of its components.
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Affiliation(s)
- Hon Cheung Lee
- Department of Physiology, University of Hong Kong, Hong Kong, China.
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30
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Expression of CD38 with intracellular enzymatic activity: a possible explanation for the insulin release induced by intracellular cADPR. Mol Cell Biochem 2011; 352:293-9. [PMID: 21387169 DOI: 10.1007/s11010-011-0765-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 02/24/2011] [Indexed: 10/18/2022]
Abstract
CD38 is a transmembrane glycoprotein expressed in multiple cell types, including pancreatic β cells. It can serve as an enzyme that catalyzes the metabolism of two different Ca(2+)-mobilizing compounds, cyclic adenosine diphosphoribose (cADPR) and nicotinic acid adenine dinucleotide phosphate. One of these metabolites, cADPR, is known to be involved in glucose-induced insulin secretion from pancreatic β cells. Although the essential role of CD38 for endogenous cADPR synthesis has been established, the relationship between the proposed extracellular enzymatic activity of CD38 and the intracellular Ca(2+) modulation caused by the intracellular cADPR accumulation has not yet been fully explained. For a better understanding of the role of CD38 in the insulin secretion machinery, analysis of the intracellular localization of this molecule in pancreatic β cells is essential. In an attempt to provide a method to probe the N-terminal and C-terminal of CD38 separately, we generated an insulin-secreting MIN6 murine pancreatic β cell line expressing a human CD38 bearing an N-terminal FLAG epitope tag. We found a weak but consistent expression of the FLAG epitope outside of the cells, indicating the presence of a small amount of CD38 with cytoplasmic enzymatic activity. MIN6 cells transfected with human CD38 exhibited increased glucose-induced insulin release. In addition, anti-FLAG cross-linking further enhanced the insulin release, suggesting that the N-terminal of CD38 expressed on the cell surface functions as a receptor for an unknown ligand and triggers positive signals for insulin secretion.
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31
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Zhang H, Graeff R, Chen Z, Zhang L, Zhang L, Lee H, Hao Q. Dynamic conformations of the CD38-mediated NAD cyclization captured in a single crystal. J Mol Biol 2010; 405:1070-8. [PMID: 21134381 DOI: 10.1016/j.jmb.2010.11.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 11/22/2010] [Accepted: 11/23/2010] [Indexed: 10/18/2022]
Abstract
The extracellular domain of human CD38 is a multifunctional enzyme involved in the metabolism of two Ca(2+) messengers: cyclic ADP-ribose and nicotinic acid adenine dinucleotide phosphate. When NAD is used as substrate, CD38 predominantly hydrolyzes it to ADP-ribose, with a trace amount of cyclic ADP-ribose produced through cyclization of the substrate. However, mutation of a key residue at the active site, E146, inhibits the hydrolysis activity of CD38 but greatly increases its cyclization activity. To understand the role of the residue E146 in the catalytic process, we determined the crystal structure of the E146A mutant protein with a substrate analogue, arabinosyl-2'-fluoro-deoxy-nicotinamide adenine dinucleotide. The structure captured the enzymatic reaction intermediates in six different conformations in a crystallographic asymmetric unit. The structural results indicate a folding-back process for the adenine ring of the substrate and provide the first multiple snapshots of the process. Our approach of utilizing multiple molecules in the crystallographic asymmetric unit should be generally applicable for capturing the dynamic nature of enzymatic catalysis.
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Affiliation(s)
- HongMin Zhang
- Department of Physiology, The University of Hong Kong, Hong Kong SAR, China
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32
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Nguyen MH, Dang VU, Luu BV. Computational characterization for catalytic activities of human CD38's wild type, E226 and E146 mutants. Interdiscip Sci 2010; 2:193-204. [PMID: 20640790 DOI: 10.1007/s12539-010-0091-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 02/16/2010] [Accepted: 03/04/2010] [Indexed: 11/26/2022]
Abstract
A series of the complexes of human CD38's wild type, E226 and E146 mutants as well have been simulated. The biosoftwares well simulate the penetration of nicotinamide-adenine-dinucleotide (NAD) into the active site. The nicotinamide end of NAD penetrates deep into the active site consistent with cleavage of the nicotinamide-glycosidic bond which is the first step of catalysis creating a Michaelis complex regarded as the intermediate product of NAD cyclase and hydrolysis reaction. The breaking down hydrogen bond between 2'-3' OH ribosyl and the residues replaced Glu(226) makes NAD to be less constrained in active site and nicotinamide (NA) becomes more difficult to be cleaved and eliminates the mutant catalytic activities. The large majority of the substrate NAD is hydrolyzed to ADPR while the conversion of NAD to cADPR is not the dominant reaction catalyzed by wild-type human CD38. The more strongly kept ribosyl group by hydrogen bonds the more NADase and the less cyclase activity. Breaking hydrogen bonds of ribosyl 2'- and 3'-OH by mutation will loosen it to promote the cyclase. The cyclic adenosine diphosphate-ribose (cADPR) could also penetrate deeply into active site to make some hydrogen bonds with Glu(146) and Glu(226); however, its docking poses are affected by a residue located at the entrance of the catalytic pocket (Lys(129)). These results are in good agreement with the previous crystallographic analysis and the experiments quantified the catalytic activities of human CD38 and its mutants.
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Affiliation(s)
- My H Nguyen
- Faculty of Chemistry, Hanoi University of Natural Science, VNU, 19 Le Thanh Tong, Hanoi, Vietnam
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33
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Liu W, Hou S, Zhao ZK. Synthesis and electrochemical behavior of triazole-containing nicotinamide adenine dinucleotide analogs. CAN J CHEM 2010. [DOI: 10.1139/v09-145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The coupling of 2′,3′-di-O-acetyl nicotinamide mononucleotide with 3-butyn-1-ol in the presence of 2,4,6-triisopropylbenzenesulfonyl chloride quantitatively afforded a terminal alkyne-containing intermediate. Furthermore, copper(I)-mediated Huisgen [3 + 2] cycloaddition with a series of azido compounds in a two-phase solvent system gave eight triazole-containing nicotinamide adenine dinucleotide analogs with yields over 88%. The cyclic voltammetric behaviors of these novel analogs were investigated with a glassy carbon electrode, and structural features of these analogs on their electrochemical properties were briefly discussed.
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Affiliation(s)
- Wujun Liu
- Dalian Institute of Chemical Physics, CAS, Dalian 116023, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
- Dalian National Laboratory of Clean Energy, Dalian 116023, P. R. China
| | - Shuhua Hou
- Dalian Institute of Chemical Physics, CAS, Dalian 116023, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
- Dalian National Laboratory of Clean Energy, Dalian 116023, P. R. China
| | - Zongbao Kent Zhao
- Dalian Institute of Chemical Physics, CAS, Dalian 116023, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
- Dalian National Laboratory of Clean Energy, Dalian 116023, P. R. China
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34
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Covalent and noncovalent intermediates of an NAD utilizing enzyme, human CD38. ACTA ACUST UNITED AC 2008; 15:1068-78. [PMID: 18940667 DOI: 10.1016/j.chembiol.2008.08.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Revised: 08/01/2008] [Accepted: 08/04/2008] [Indexed: 11/22/2022]
Abstract
Enzymatic utilization of nicotinamide adenine dinucleotide (NAD) has increasingly been shown to have fundamental roles in gene regulation, signal transduction, and protein modification. Many of the processes require the cleavage of the nicotinamide moiety from the substrate and the formation of a reactive intermediate. Using X-ray crystallography, we show that human CD38, an NAD-utilizing enzyme, is capable of catalyzing the cleavage reactions through both covalent and noncovalent intermediates, depending on the substrate used. The covalent intermediate is resistant to further attack by nucleophiles, resulting in mechanism-based enzyme inactivation. The noncovalent intermediate is stabilized mainly through H-bond interactions, but appears to remain reactive. Our structural results favor the proposal of a noncovalent intermediate during normal enzymatic utilization of NAD by human CD38 and provide structural insights into the design of covalent and noncovalent inhibitors targeting NAD-utilization pathways.
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35
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Liu Q, Graeff R, Kriksunov IA, Lam CMC, Lee HC, Hao Q. Conformational Closure of the Catalytic Site of Human CD38 Induced by Calcium. Biochemistry 2008; 47:13966-13973. [DOI: 10.1021/bi801642q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Qun Liu
- MacCHESS, Cornell High Energy Synchrotron Source, and School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, and Department of Physiology, University of Hong Kong, Hong Kong, China
| | - Richard Graeff
- MacCHESS, Cornell High Energy Synchrotron Source, and School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, and Department of Physiology, University of Hong Kong, Hong Kong, China
| | - Irina A. Kriksunov
- MacCHESS, Cornell High Energy Synchrotron Source, and School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, and Department of Physiology, University of Hong Kong, Hong Kong, China
| | - Connie M. C. Lam
- MacCHESS, Cornell High Energy Synchrotron Source, and School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, and Department of Physiology, University of Hong Kong, Hong Kong, China
| | - Hon Cheung Lee
- MacCHESS, Cornell High Energy Synchrotron Source, and School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, and Department of Physiology, University of Hong Kong, Hong Kong, China
| | - Quan Hao
- MacCHESS, Cornell High Energy Synchrotron Source, and School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, and Department of Physiology, University of Hong Kong, Hong Kong, China
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36
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Abstract
Cells possess multiple calcium ion (Ca2+) stores and multiple messenger molecules to mobilize them. These include d-myo-inositol 1,4,5-trisphosphate (IP(3)), cyclic adenosine diphosphoribose (cADPR), and the most recently identified Ca2+-mobilizing messenger, nicotinic acid adenine dinucleotide phosphate (NAADP), which acts on a wide spectrum of cells, from plant cells to mammalian cells. Accumulating evidence indicates that NAADP targets both acidic (lysosome-like) Ca2+ stores and endoplasmic reticular stores. Recent studies in invertebrate and mammalian cells suggest that NAADP provides an initiating Ca2+ signal, which is amplified by cADPR- or IP(3)-dependent mechanisms (or both) through Ca2+-induced Ca2+ release. Diverse stimuli activate a rapid rise of endogenous NAADP concentration, resulting in severalfold increases of NAADP over basal values within seconds. The enzyme CD38 can catalyze both the synthesis and hydrolysis of NAADP, making it ideal for effecting the rapid metabolism of NAADP. The crystal structure of CD38 and the structures of its various substrate complexes have now been determined, clarifying the mechanism of its multifunctional catalysis. We anticipate that these advances will lead to the unmasking of all the key components of the Ca2+ signaling pathway mediated by NAADP.
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Affiliation(s)
- Andreas H Guse
- The Calcium Signaling Group, Institute of Biochemistry and Molecular Biology I, Cellular Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20146 Hamburg, Germany.
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37
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Identification of an unusual AT(D)Pase-like activity in multifunctional NAD glycohydrolase from the venom of Agkistrodon acutus. Biochimie 2008; 91:240-51. [PMID: 18952139 DOI: 10.1016/j.biochi.2008.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Accepted: 09/24/2008] [Indexed: 11/22/2022]
Abstract
NAD-glycohydrolases (NADases) are ubiquitous enzymes that possess NAD glycohydrolase, ADPR cyclase or cADPR hydrolase activity. All these activities are attributed to the NADase-catalyzed cleavage of C-N glycosyl bond. AA-NADase purified from the venom of Agkistrodon acutus is different from the known NADases, for it consists of two chains linked with disulfide-bond(s) and contains one Cu(2+) ion. Here, we show that AA-NADase is not only able to cleave the C-N glycosyl bond of NAD to produce ADPR and nicotinamide, but also able to cleave the phosphoanhydride linkages of ATP, ADP and AMP-PNP to yield AMP. AA-NADase selectively cleaves the P-O-P bond of ATP, ADP and AMP-PNP without the cleavage of P-O-P bond of NAD. The hydrolysis reactions of NAD, ATP and ADP catalyzed by AA-NADase are mutually competitive. ATP is the excellent substrate for AA-NADase with the highest specificity constant k(cat)/K(m) of 293+/-7mM(-1)s(-1). AA-NADase catalyzes the hydrolysis of ATP to produce AMP with an intermediate ADP. AA-NADase binds with one AMP with high affinity determined by isothermal titration calorimetry (ITC). AMP is an efficient inhibitor against NAD. AA-NADase has so far been identified as the first unique multicatalytic enzyme with both NADase and AT(D)Pase-like activities.
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38
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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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39
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Liu Q, Kriksunov IA, Moreau C, Graeff R, Potter BVL, Lee HC, Hao Q. Catalysis-associated conformational changes revealed by human CD38 complexed with a non-hydrolyzable substrate analog. J Biol Chem 2007; 282:24825-32. [PMID: 17591784 DOI: 10.1074/jbc.m701653200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyclic ADP-ribose (cADPR) is a calcium mobilization messenger important for mediating a wide range of physiological functions. The endogenous levels of cADPR in mammalian tissues are primarily controlled by CD38, a multifunctional enzyme capable of both synthesizing and hydrolyzing cADPR. In this study, a novel non-hydrolyzable analog of cADPR, N1-cIDPR (N1-cyclic inosine diphosphate ribose), was utilized to elucidate the structural determinants involved in the hydrolysis of cADPR. N1-cIDPR inhibits CD38-catalyzed cADPR hydrolysis with an IC(50) of 0.26 mM. N1-cIDPR forms a complex with CD38 or its inactive mutant in which the catalytic residue Glu-226 is mutated. Both complexes have been determined by x-ray crystallography at 1.7 and 1.76 A resolution, respectively. The results show that N1-cIDPR forms two hydrogen bonds (2.61 and 2.64 A) with Glu-226, confirming our previously proposed model for cADPR catalysis. Structural analyses reveal that both the enzyme and substrate cADPR undergo catalysis-associated conformational changes. From the enzyme side, residues Glu-146, Asp-147, and Trp-125 work collaboratively to facilitate the formation of the Michaelis complex. From the substrate side, cADPR is found to change its conformation to fit into the active site until it reaches the catalytic residue. The binary CD38-cADPR model described here represents the most detailed description of the CD38-catalyzed hydrolysis of cADPR at atomic resolution. Our structural model should provide insights into the design of effective cADPR analogs.
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Affiliation(s)
- Qun Liu
- MacCHESS, Cornell High Energy Synchrotron Source, Cornell University, Ithaca, New York 14853, USA
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Khan JA, Forouhar F, Tao X, Tong L. Nicotinamide adenine dinucleotide metabolism as an attractive target for drug discovery. Expert Opin Ther Targets 2007; 11:695-705. [PMID: 17465726 DOI: 10.1517/14728222.11.5.695] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD(+)) has crucial roles in many cellular processes, both as a coenzyme for redox reactions and as a substrate to donate ADP-ribose units. Enzymes involved in NAD(+) metabolism are attractive targets for drug discovery against a variety of human diseases, including cancer, multiple sclerosis, neurodegeneration and Huntington's disease. A small-molecule inhibitor of nicotinamide phosphoribosyltransferase, an enzyme in the salvage pathway of NAD(+) biosynthesis, is presently in clinical trials against cancer. An analog of a kynurenine pathway intermediate is efficacious against multiple sclerosis in an animal model. Indoleamine 2,3-dioxygenase plays an important role in immune evasion by cancer cells and other disease processes. Inhibitors against kynurenine 3-hydroxylase can reduce the production of neurotoxic metabolites while increasing the production of neuroprotective compounds. This review summarizes the existing knowledge on NAD(+) metabolic enzymes, with emphasis on their relevance for drug discovery.
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Affiliation(s)
- Javed A Khan
- Columbia University, Department of Biological Sciences, New York, NY 10027, USA
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