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Geeraerts Z, Ishigami I, Lewis-Ballester A, Pham KN, Kozlova A, Mathieu C, Frédérick R, Yeh SR. Structural Insights into Protein-Inhibitor Interactions in Human Tryptophan Dioxygenase. J Med Chem 2024; 67:14543-14552. [PMID: 39106326 DOI: 10.1021/acs.jmedchem.4c01360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2024]
Abstract
Human tryptophan dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) are two important targets in cancer immunotherapy. Extensive research has led to a large number of potent IDO inhibitors; in addition, 52 structures of IDO in complex with inhibitors with a wide array of chemical scaffolds have been documented. In contrast, progress in the development of TDO inhibitors has been limited. Only four structures of TDO in complex with competitive inhibitors that compete with the substrate L-tryptophan for binding to the active site have been reported to date. Here we systematically evaluated the structures of TDO in complex with competitive inhibitors with three types of pharmacophores, imidazo-isoindole, indole-tetrazole, and indole-benzotriazole. The comparative assessment of the protein-inhibitor interactions sheds new light into the structure-based design of enzyme-selective inhibitors.
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Affiliation(s)
- Zachary Geeraerts
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Izumi Ishigami
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Ariel Lewis-Ballester
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Khoa N Pham
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Arina Kozlova
- Medicinal Chemistry Research Group (CMFA), Louvain Drug Research Institute (LDRI), Université Catholique de Louvain (UCLouvain), 73 avenue Mounier, Brussels B-1200, Belgium
| | - Caroline Mathieu
- Medicinal Chemistry Research Group (CMFA), Louvain Drug Research Institute (LDRI), Université Catholique de Louvain (UCLouvain), 73 avenue Mounier, Brussels B-1200, Belgium
| | - Raphaël Frédérick
- Medicinal Chemistry Research Group (CMFA), Louvain Drug Research Institute (LDRI), Université Catholique de Louvain (UCLouvain), 73 avenue Mounier, Brussels B-1200, Belgium
| | - Syun-Ru Yeh
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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Borović Šunjić S, Jaganjac M, Vlainić J, Halasz M, Žarković N. Lipid Peroxidation-Related Redox Signaling in Osteosarcoma. Int J Mol Sci 2024; 25:4559. [PMID: 38674143 PMCID: PMC11050283 DOI: 10.3390/ijms25084559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Oxidative stress and lipid peroxidation play important roles in numerous physiological and pathological processes, while the bioactive products of lipid peroxidation, lipid hydroperoxides and reactive aldehydes, act as important mediators of redox signaling in normal and malignant cells. Many types of cancer, including osteosarcoma, express altered redox signaling pathways. Such redox signaling pathways protect cancer cells from the cytotoxic effects of oxidative stress, thus supporting malignant transformation, and eventually from cytotoxic anticancer therapies associated with oxidative stress. In this review, we aim to explore the status of lipid peroxidation in osteosarcoma and highlight the involvement of lipid peroxidation products in redox signaling pathways, including the involvement of lipid peroxidation in osteosarcoma therapies.
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Affiliation(s)
- Suzana Borović Šunjić
- Laboratory for Oxidative Stress, Division of Molecular Medicine, Ruder Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia; (M.J.); (J.V.); (M.H.)
| | | | | | | | - Neven Žarković
- Laboratory for Oxidative Stress, Division of Molecular Medicine, Ruder Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia; (M.J.); (J.V.); (M.H.)
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Samanta S, Sengupta S, Biswas S, Ghosh S, Barman S, Dey A. Iron Dioxygen Adduct Formed during Electrochemical Oxygen Reduction by Iron Porphyrins Shows Catalytic Heme Dioxygenase Reactivity. J Am Chem Soc 2023; 145:26477-26486. [PMID: 37993986 DOI: 10.1021/jacs.3c10980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Heme dioxygenases oxidize the indole ring of tryptophan to kynurenine which is the first step in the biosynthesis of several important biomolecules like NAD, xanthurenic acid, and picolinic acid. A ferrous heme dioxygen adduct (or FeIII-O2•-) is the oxidant, and both the atoms of O2 are inserted in the product and its catalytic function has been difficult to emulate as it is complicated by competing rapid reactions like auto-oxidation and/or formation of the μ-oxo dimer. In situ resonance Raman spectroscopy technique, SERRS-RDE, is used to probe the species accumulated during electrochemical ORR catalyzed by site-isolated imidazole-bound iron porphyrin installed on a self-assembled monolayer covered electrode. These in situ SERRS-RDE data using labeled O2 show that indeed a FeIII-O2•- species accumulate on the electrode during ORR between -0.05 and -0.30 V versus Ag/AgCl (satd. KCl) and is reduced by proton coupled electron transfer to a FeIII-OOH species which, on the other hand, builds up on the electrode between -0.20 and -0.40 V versus Ag/AgCl (satd. KCl). This FeIII-OOH species then gives way to a FeIV═O species, which accumulates at -0.50 V versus Ag/AgCl (satd. KCl). When 2,3-dimethylindole is present in the solution and the applied potential is held in the range where FeIII-O2•- species accumulate, it gets oxidized to N-(2-acetylphenyl)acetamide retaining both the oxygens from O2 mimicking the reaction of heme dioxygenases. Turnover numbers more than 104 are recorded, establishing this imidazole-bound ferrous porphyrin as a functional model of heme dioxygenases.
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Affiliation(s)
- Soumya Samanta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Srijan Sengupta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Saptarshi Biswas
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Sucheta Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Sudip Barman
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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Delen E, Kucukali CI, Karaaslan Z, Yuceer H, Punar S, Hakan MT, Yaylim I, Ozkok E. Investigation of the effects of oxidative stress, inflammation on the pathway of tryptophan/kynurenine in OCD. Acta Neuropsychiatr 2023:1-11. [PMID: 38012854 DOI: 10.1017/neu.2023.55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
OBJECTIVES Recent studies have shown that the distribution of the tryptophan/kynurenine pathway (KP) plays a role in the development of obsessive-compulsive disorder (OCD). We aimed to reveal the relationship between CYP1A1 rs464903 and aryl hydrocarbon receptor (AhR) rs10249788 associated with the KP and interferon gamma (IFN γ) and oxidative stress in OCD. METHODS In our study, the serum and DNAs of 150 samples, including 100 OCD patients and 50 controls, were used. The activity of glutathione peroxidase (GSH-Px), and the levels of IFN γ, thiobarbituric acid reactive substances (TBARS), tryptophan, and kynurenine were determined by biochemical methods. AhR rs10249788 and cytochrome P450 family CYP1A1 rs4646903, which interact directly with the KP, were analysed by polymerase chain reaction followed by restriction fragment length polymorphism. P < 0.05 was considered statistically significant. RESULT There were no significant differences between groups in CYP1A1 rs4646903 and AhR rs10249788 while tryptophan and IFN γ were found to be higher in controls (p < 0.001, for both), and TBARS and indolamine-2,3-dioxygenase were found to be higher in OCD (p < 0.001, for both). There were significant correlations between IFN γ and TBARS and GSH-Px (p = 0.028, p = 0.020, respectively) in the OCD group. CONCLUSIONS For the first time studied in OCD, it has been shown that IFN γ, tryptophan, oxidative stress parameters, and gene variants of CYP1A1 rs4646903 anAhR rs10249788 are shown effective on the KP.
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Affiliation(s)
- Elif Delen
- Department of Neuroscience, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Cem Ismail Kucukali
- Department of Neuroscience, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Zerrin Karaaslan
- Department of Neuroscience, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Hande Yuceer
- Department of Neuroscience, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Seyma Punar
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Mehmet Tolgahan Hakan
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Ilhan Yaylim
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Elif Ozkok
- Department of Neuroscience, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
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Balasubramanian R, Shutta KH, Guasch-Ferre M, Huang T, Jha SC, Zhu Y, Shadyab AH, Manson JE, Corella D, Fitó M, Hu FB, Rexrode KM, Clish CB, Hankinson SE, Kubzansky LD. Metabolomic profiles of chronic distress are associated with cardiovascular disease risk and inflammation-related risk factors. Brain Behav Immun 2023; 114:262-274. [PMID: 37557964 DOI: 10.1016/j.bbi.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 08/01/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND Chronic psychological distress is associated with increased risk of cardiovascular disease (CVD) and investigators have posited inflammatory factors may be centrally involved in these relationships. However, mechanistic evidence and molecular underpinnings of these processes remain unclear, and data are particularly sparse among women. This study examined if a metabolite profile linked with distress was associated with increased CVD risk and inflammation-related risk factors. METHODS A plasma metabolite-based distress score (MDS) of twenty chronic psychological distress-related metabolites was developed in cross-sectional, 1:1 matched case-control data comprised of 558 women from the Nurses' Health Study (NHS; 279 women with distress, 279 controls). This MDS was then evaluated in two other cohorts: the Women's Health Initiative Observational Cohort (WHI-OS) and the Prevención con Dieta Mediterránea (PREDIMED) trial. We tested the MDS's association with risk of future CVD in each sample and with levels of C-reactive protein (CRP) in the WHI-OS. The WHI-OS subsample included 944 postmenopausal women (472 CHD cases; mean time to event = 5.8 years); the PREDIMED subsample included 980 men and women (224 CVD cases, mean time to event = 3.1 years). RESULTS In the WHI-OS, a 1-SD increase in the plasma MDS was associated with a 20% increased incident CHD risk (odds ratio [OR] = 1.20, 95% CI: 1.04 - 1.38), adjusting for known CVD risk factors excluding total and HDL cholesterol. This association was attenuated after including total and HDL cholesterol. CRP mediated an average 12.9% (95% CI: 4.9% - 28%, p < 10-15) of the total effect of MDS on CHD risk when adjusting for matching factors. This effect was attenuated after adjusting for known CVD risk factors. Of the metabolites in the MDS, tryptophan and threonine were inversely associated with incident CHD risk in univariate models. In PREDIMED, each one SD increase in the MDS was associated with an OR of 1.19 (95% CI: 1.00 - 1.41) for incident CVD risk, after adjusting all risk factors. Similar associations were observed in men and women. Four metabolites in the MDS were associated with incident CVD risk in PREDIMED in univariate models. Biliverdin and C36:5 phosphatidylcholine (PC) plasmalogen had inverse associations; C16:0 ceramide and C18:0 lysophosphatidylethanolamine(LPE) each had positive associations with CVD risk. CONCLUSIONS Our study points to molecular alterations that may underlie the association between chronic distress and subsequent risk of cardiovascular disease in adults.
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Affiliation(s)
- Raji Balasubramanian
- Department of Biostatistics and Epidemiology, University of Massachusetts Amherst, Amherst, MA, United States of America
| | - Katherine H Shutta
- Department of Biostatistics and Epidemiology, University of Massachusetts Amherst, Amherst, MA, United States of America; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Marta Guasch-Ferre
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Tianyi Huang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America; Harvard Medical School, Boston, MA, United States of America
| | - Shaili C Jha
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Yiwen Zhu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Aladdin H Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, United States of America
| | - JoAnn E Manson
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America; Harvard Medical School, Boston, MA, United States of America; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America; Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, United States of America
| | - Dolores Corella
- Department of Preventive Medicine and Public Health. University of Valencia, Valencia Spain and CIBEROBN, Madrid, Spain
| | - Montserrat Fitó
- Epidemiology and Public Health program. Hospital del Mar Research Institute, Barcelona, Spain and CIBEROBN, Madrid, Spain
| | - Frank B Hu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America; Harvard Medical School, Boston, MA, United States of America; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Kathryn M Rexrode
- Harvard Medical School, Boston, MA, United States of America; Division of Women's Health, Department of Medicine, Brigham and Women's Hospital, Boston, MA, the United States of America
| | - Clary B Clish
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, United States of America
| | - Susan E Hankinson
- Department of Biostatistics and Epidemiology, University of Massachusetts Amherst, Amherst, MA, United States of America
| | - Laura D Kubzansky
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
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Zuberi A, Huang Y, Dotts AJ, Wei H, Coon JS, Liu S, Iizuka T, Wu O, Sotos O, Saini P, Chakravarti D, Boyer TG, Dai Y, Bulun SE, Yin P. MED12 mutation activates the tryptophan/kynurenine/AHR pathway to promote growth of uterine leiomyomas. JCI Insight 2023; 8:e171305. [PMID: 37607000 PMCID: PMC10561729 DOI: 10.1172/jci.insight.171305] [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: 04/13/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023] Open
Abstract
Uterine leiomyomas cause heavy menstrual bleeding, anemia, and pregnancy loss in millions of women worldwide. Driver mutations in the transcriptional mediator complex subunit 12 (MED12) gene in uterine myometrial cells initiate 70% of leiomyomas that grow in a progesterone-dependent manner. We showed a distinct chromatin occupancy landscape of MED12 in mutant MED12 (mut-MED12) versus WT-MED12 leiomyomas. Integration of cistromic and transcriptomics data identified tryptophan 2,3-dioxygenase (TDO2) as the top mut-MED12 target gene that was significantly upregulated in mut-MED12 leiomyomas when compared with adjacent myometrium and WT-MED12 leiomyomas. TDO2 catalyzes the conversion of tryptophan to kynurenine, an aryl hydrocarbon receptor (AHR) ligand that we confirmed to be significantly elevated in mut-MED12 leiomyomas. Treatment of primary mut-MED12 leiomyoma cells with tryptophan or kynurenine stimulated AHR nuclear translocation, increased proliferation, inhibited apoptosis, and induced AHR-target gene expression, whereas blocking the TDO2/kynurenine/AHR pathway by siRNA or pharmacological treatment abolished these effects. Progesterone receptors regulated the expression of AHR and its target genes. In vivo, TDO2 expression positively correlated with the expression of genes crucial for leiomyoma growth. In summary, activation of the TDO2/kynurenine/AHR pathway selectively in mut-MED12 leiomyomas promoted tumor growth and may inform the future development of targeted treatments and precision medicine.
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Affiliation(s)
- Azna Zuberi
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Yongchao Huang
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Ariel J. Dotts
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Helen Wei
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - John S. Coon
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Shimeng Liu
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Takashi Iizuka
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Olivia Wu
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Olivia Sotos
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Priyanka Saini
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Debabrata Chakravarti
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Thomas G. Boyer
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Yang Dai
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Serdar E. Bulun
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Ping Yin
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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Gering HE, Li X, Tang H, Swartz PD, Chang WC, Makris TM. A Ferric-Superoxide Intermediate Initiates P450-Catalyzed Cyclic Dipeptide Dimerization. J Am Chem Soc 2023; 145:19256-19264. [PMID: 37611404 DOI: 10.1021/jacs.3c04542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
The cytochrome P450 (CYP) AspB is involved in the biosynthesis of the diketopiperazine (DKP) aspergilazine A. Tryptophan-linked dimeric DKP alkaloids are a large family of natural products that are found in numerous species and exhibit broad and often potent bioactivity. The proposed mechanisms for C-N bond formation by AspB, and similar C-C bond formations by related CYPs, have invoked the use of a ferryl-intermediate as an oxidant to promote substrate dimerization. Here, the parallel application of steady-state and transient kinetic approaches reveals a very different mechanism that involves a ferric-superoxide species as a primary oxidant to initiate DKP-assembly. Single turnover kinetic isotope effects and a substrate analog suggest the probable nature and site for abstraction. The direct observation of CYP-superoxide reactivity rationalizes the atypical outcome of AspB and reveals a new reaction manifold in heme enzymes.
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Affiliation(s)
- Hannah E Gering
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Xiaojun Li
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Haoyu Tang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Paul D Swartz
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Thomas M Makris
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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8
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Biswas P, Stuehr DJ. Indoleamine dioxygenase and tryptophan dioxygenase activities are regulated through control of cell heme allocation by nitric oxide. J Biol Chem 2023; 299:104753. [PMID: 37116709 PMCID: PMC10220489 DOI: 10.1016/j.jbc.2023.104753] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/06/2023] [Accepted: 04/20/2023] [Indexed: 04/30/2023] Open
Abstract
Indoleamine-2, 3-dioxygenase (IDO1) and Tryptophan-2, 3-dioxygenase (TDO) catalyze the conversion of L-tryptophan to N-formyl-kynurenine and thus play primary roles in metabolism, inflammation, and tumor immune surveillance. Because their activities depend on their heme contents, which vary in biological settings and go up or down in a dynamic manner, we studied how their heme levels may be impacted by nitric oxide (NO) in mammalian cells. We utilized cells expressing TDO or IDO1 either naturally or via transfection and determined their activities, heme contents, and expression levels as a function of NO exposure. We found NO has a bimodal effect: a narrow range of low NO exposure promoted cells to allocate heme into the heme-free TDO and IDO1 populations and consequently boosted their heme contents and activities 4- to 6-fold, while beyond this range the NO exposure transitioned to have a negative impact on their heme contents and activities. NO did not alter dioxygenase protein expression levels, and its bimodal impact was observed when NO was released by a chemical donor or was generated naturally by immune-stimulated macrophage cells. NO-driven heme allocations to IDO1 and TDO required participation of a GAPDH-heme complex and for IDO1 required chaperone Hsp90 activity. Thus, cells can up- or downregulate their IDO1 and TDO activities through a bimodal control of heme allocation by NO. This mechanism has important biomedical implications and helps explain why the IDO1 and TDO activities in animals go up and down in response to immune stimulation.
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Affiliation(s)
- Pranjal Biswas
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio, USA
| | - Dennis J Stuehr
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio, USA.
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9
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Mondal P, Ishigami I, Yeh SR, Wijeratne GB. The Role of Heme Peroxo Oxidants in the Rational Mechanistic Modeling of Nitric Oxide Synthase: Characterization of Key Intermediates and Elucidation of the Mechanism. Angew Chem Int Ed Engl 2022; 61:e202211521. [PMID: 36169890 PMCID: PMC9675724 DOI: 10.1002/anie.202211521] [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: 08/04/2022] [Indexed: 11/08/2022]
Abstract
Mammalian nitric oxide synthase (NOS) mediates the two-step O2 -dependent oxidative degradation of arginine, and has been linked to a medley of disease situations in humans. Nonetheless, its exact mechanism of action still remains unclear. This work presents the first NOS model system where biologically proposed heme superoxo and peroxo intermediates are assessed as active oxidants against oxime substrates. Markedly, heme peroxo intermediates engaged in a bioinspired oxime oxidation reaction pathway, converting oximes to ketones and nitroxyl anions (NO- ). Detailed thermodynamic, kinetic, and mechanistic interrogations all evince a rate-limiting step primarily driven by the nucleophilicity of the heme peroxo moiety. Coherent with other findings, 18 O and 15 N isotope substitution experiments herein suffice compelling evidence toward a detailed mechanism, which draw close parallels to one of the enzymatic proposals. Intriguingly, recent enzymatic studies also lend credence to these findings, and several relevant reaction intermediates have been observed during NOS turnover.
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Affiliation(s)
- Pritam Mondal
- Department of Chemistry and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35205, USA
| | - Izumi Ishigami
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, The Bronx, NY 10461, USA
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, The Bronx, NY 10461, USA
| | - Gayan B Wijeratne
- Department of Chemistry and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35205, USA
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10
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Yuasa HJ. Inhibitory effect of ascorbate on tryptophan 2,3-dioxygenase. J Biochem 2022; 171:653-661. [PMID: 35244712 DOI: 10.1093/jb/mvac024] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/02/2022] [Indexed: 11/13/2022] Open
Abstract
Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) catalyze the same reaction, oxidative cleavage of L-tryptophan (L-Trp) to N-formyl-kynurenine. In both enzymes, the ferric (FeIII) form is inactive, and ascorbate (Asc) is frequently used as a reductant in in vitro assays to activate the enzymes by reducing the heme iron. Recently, it has been reported that Asc activates IDO2 by acting as a reductant, however, it is also a competitive inhibitor of the enzyme. Here, the effect of Asc on human TDO (hTDO) is investigated. Similar to its interaction with IDO2, Asc acts as both a reductant and a competitive inhibitor of hTDO in the absence of catalase, and its inhibitory effect was enhanced by the addition of H2O2. Interestingly, however, no inhibitory effect of Asc was observed in the presence of catalase. TDO is known to be activated by H2O2 and a ferryl-oxo (FeIV=O) intermediate (Compound II) is generated during the activation process. The observation that Asc acts as a competitive inhibitor of hTDO only in the absence of catalase can be explained by assuming that the target of Asc is Compound II. Asc seems to compete with L-Trp in an unusual manner.
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Affiliation(s)
- Hajime Julie Yuasa
- Laboratory of Biochemistry, Department of Chemistry and Biotechnology, Faculty of Science and Technology, National University Corporation Kochi University, Kochi 780-8520, Japan
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11
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Biswas P, Dai Y, Stuehr DJ. Indoleamine dioxygenase and tryptophan dioxygenase activities are regulated through GAPDH- and Hsp90-dependent control of their heme levels. Free Radic Biol Med 2022; 180:179-190. [PMID: 35051612 DOI: 10.1016/j.freeradbiomed.2022.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/08/2021] [Accepted: 01/11/2022] [Indexed: 01/15/2023]
Abstract
Indoleamine-2, 3-dioxygenase (IDO1) and Tryptophan-2, 3-dioxygense (TDO) are heme-containing dioxygenases that catalyze the conversion of tryptophan to N-formyl-kynurenine and thus enable generation of l-kynurenine and related metabolites that govern the immune response and broadly impact human biology. Given that TDO and IDO1 activities are directly proportional to their heme contents, it is important to understand their heme delivery and insertion processes. Early studies established that TDO and IDO1 heme levels are sub-saturating in vivo and subject to change but did not identify the cellular mechanisms that provide their heme or enable dynamic changes in their heme contents. We investigated the potential involvement of GAPDH and chaperone Hsp90, based on our previous studies linking these proteins to intracellular heme allocation. We studied heme delivery and insertion into IDO1 and TDO expressed in both normal and heme-deficient HEK293T cells and into IDO1 naturally expressed in HeLa cells in response to IFN-γ, and also investigated the interactions of TDO and IDO1 with GAPDH and Hsp90 in cells and among their purified forms. We found that GAPDH delivered both mitochondrially-generated and exogenous heme to apo-IDO1 and apo-TDO in cells, potentially through a direct interaction with either enzyme. In contrast, we found Hsp90 interacted with apo-IDO1 but not with apo-TDO, and was only needed to drive heme insertion into apo-IDO1. By uncovering the cellular processes that allocate heme to IDO1 and TDO, our study provides new insight on how their activities and l-kynurenine production may be controlled in health and disease.
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Affiliation(s)
- Pranjal Biswas
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, OH, USA
| | - Yue Dai
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, OH, USA
| | - Dennis J Stuehr
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, OH, USA.
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12
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A new regime of heme-dependent aromatic oxygenase superfamily. Proc Natl Acad Sci U S A 2021; 118:2106561118. [PMID: 34667125 DOI: 10.1073/pnas.2106561118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2021] [Indexed: 12/14/2022] Open
Abstract
Two histidine-ligated heme-dependent monooxygenase proteins, TyrH and SfmD, have recently been found to resemble enzymes from the dioxygenase superfamily currently named after tryptophan 2,3-dioxygenase (TDO), that is, the TDO superfamily. These latest findings prompted us to revisit the structure and function of the superfamily. The enzymes in this superfamily share a similar core architecture and a histidine-ligated heme. Their primary functions are to promote O-atom transfer to an aromatic metabolite. TDO and indoleamine 2,3-dioxygenase (IDO), the founding members, promote dioxygenation through a two-step monooxygenation pathway. However, the new members of the superfamily, including PrnB, SfmD, TyrH, and MarE, expand its boundaries and mediate monooxygenation on a broader set of aromatic substrates. We found that the enlarged superfamily contains eight clades of proteins. Overall, this protein group is a more sizeable, structure-based, histidine-ligated heme-dependent, and functionally diverse superfamily for aromatics oxidation. The concept of TDO superfamily or heme-dependent dioxygenase superfamily is no longer appropriate for defining this growing superfamily. Hence, there is a pressing need to redefine it as a heme-dependent aromatic oxygenase (HDAO) superfamily. The revised concept puts HDAO in the context of thiol-ligated heme-based enzymes alongside cytochrome P450 and peroxygenase. It will update what we understand about the choice of heme axial ligand. Hemoproteins may not be as stringent about the type of axial ligand for oxygenation, although thiolate-ligated hemes (P450s and peroxygenases) more frequently catalyze oxygenation reactions. Histidine-ligated hemes found in HDAO enzymes can likewise mediate oxygenation when confronted with a proper substrate.
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13
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Gallio A, Fung SSP, Cammack-Najera A, Hudson AJ, Raven EL. Understanding the Logistics for the Distribution of Heme in Cells. JACS AU 2021; 1:1541-1555. [PMID: 34723258 PMCID: PMC8549057 DOI: 10.1021/jacsau.1c00288] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Indexed: 05/03/2023]
Abstract
Heme is essential for the survival of virtually all living systems-from bacteria, fungi, and yeast, through plants to animals. No eukaryote has been identified that can survive without heme. There are thousands of different proteins that require heme in order to function properly, and these are responsible for processes such as oxygen transport, electron transfer, oxidative stress response, respiration, and catalysis. Further to this, in the past few years, heme has been shown to have an important regulatory role in cells, in processes such as transcription, regulation of the circadian clock, and the gating of ion channels. To act in a regulatory capacity, heme needs to move from its place of synthesis (in mitochondria) to other locations in cells. But while there is detailed information on how the heme lifecycle begins (heme synthesis), and how it ends (heme degradation), what happens in between is largely a mystery. Here we summarize recent information on the quantification of heme in cells, and we present a discussion of a mechanistic framework that could meet the logistical challenge of heme distribution.
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Affiliation(s)
- Andrea
E. Gallio
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Simon S.-P. Fung
- Department
of Chemistry and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Ana Cammack-Najera
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Andrew J. Hudson
- Department
of Chemistry and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Emma L. Raven
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
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14
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Basran J, Booth ES, Campbell LP, Thackray SJ, Jesani MH, Clayden J, Moody PCE, Mowat CG, Kwon H, Raven EL. Binding of l-kynurenine to X. campestris tryptophan 2,3-dioxygenase. J Inorg Biochem 2021; 225:111604. [PMID: 34571402 DOI: 10.1016/j.jinorgbio.2021.111604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/31/2021] [Accepted: 09/10/2021] [Indexed: 11/18/2022]
Abstract
The kynurenine pathway is the major route of tryptophan metabolism. The first step of this pathway is catalysed by one of two heme-dependent dioxygenase enzymes - tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) - leading initially to the formation of N-formylkynurenine (NFK). In this paper, we present a crystal structure of a bacterial TDO from X. campestris in complex with l-kynurenine, the hydrolysed product of NFK. l-kynurenine is bound at the active site in a similar location to the substrate (l-Trp). Hydrogen bonding interactions with Arg117 and the heme 7-propionate anchor the l-kynurenine molecule into the pocket. A mechanism for the hydrolysis of NFK in the active site is presented.
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Affiliation(s)
- Jaswir Basran
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 9HN, UK
| | - Elizabeth S Booth
- Department of Chemistry, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Laura P Campbell
- EastChem School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Sarah J Thackray
- EastChem School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Mehul H Jesani
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Jonathan Clayden
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Peter C E Moody
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 9HN, UK
| | - Christopher G Mowat
- EastChem School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Hanna Kwon
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | - Emma L Raven
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
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15
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Yuasa HJ, Stocker R. Methylene blue and ascorbate interfere with the accurate determination of the kinetic properties of IDO2. FEBS J 2021; 288:4892-4904. [PMID: 33686747 DOI: 10.1111/febs.15806] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/16/2021] [Accepted: 03/08/2021] [Indexed: 11/30/2022]
Abstract
Indoleamine 2,3-dioxygenases (IDOs) catalyze the oxidative cleavage of L-tryptophan (Trp) to N-formylkynurenine. Two IDOs, IDO1 and IDO2, are present in vertebrates. IDO1 is a high-affinity Trp-degrading enzyme involved in several physiological processes. By comparison, IDO2 generally has been reported to have low affinity (high Km -value) for Trp, and the enzyme's in vivo function remains unclear. Using IDOs from different species, we show that compared with ferrous-oxy (Fe2+ -O2 ) IDO1, Fe2+ -O2 IDO2 is substantially more stable and engages in multiple turnovers of the reaction in the absence of a reductant. Without reductant, Fe2+ -O2 IDO2 showed Km -values in the range of 80-356 μM, that is, values substantially lower than reported previously and close to the physiological concentrations of Trp. Methylene blue and ascorbate (Asc), used commonly as the reducing system for IDO activity determination, significantly affected the enzymatic activity of IDO2: In combination, the two reductants increased the apparent Km - and kcat -values 8- to 117-fold and 2-fold, respectively. Asc alone both activated and inhibited IDO2 by acting as a source of electrons and as a weak competitive inhibitor, respectively. In addition, ferric (Fe3+ ) IDO1 and IDO2 exhibited weak dioxygenase activity, similar to tryptophan 2,3-dioxygenase. Our results shed new light in the enzymatic activity of IDO2, and they support the view that this isoform of IDO also participates in the metabolism of Trp in vivo.
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Affiliation(s)
- Hajime J Yuasa
- Laboratory of Biochemistry, Department of Chemistry and Biotechnology, Faculty of Science and Technology, National University Corporation Kochi University, Japan
| | - Roland Stocker
- Arterial Inflammation and Redox Biology Group, Heart Research Institute, Newtown, NSW, Australia
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16
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Shin I, Davis I, Nieves-Merced K, Wang Y, McHardy S, Liu A. A novel catalytic heme cofactor in SfmD with a single thioether bond and a bis-His ligand set revealed by a de novo crystal structural and spectroscopic study. Chem Sci 2021; 12:3984-3998. [PMID: 34163669 PMCID: PMC8179489 DOI: 10.1039/d0sc06369j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/21/2021] [Indexed: 12/13/2022] Open
Abstract
SfmD is a heme-dependent enzyme in the biosynthetic pathway of saframycin A. Here, we present a 1.78 Å resolution de novo crystal structure of SfmD, which unveils a novel heme cofactor attached to the protein with an unusual Hx n HxxxC motif (n ∼ 38). This heme cofactor is unique in two respects. It contains a single thioether bond in a cysteine-vinyl link with Cys317, and the ferric heme has two axial protein ligands, i.e., His274 and His313. We demonstrated that SfmD heme is catalytically active and can utilize dioxygen and ascorbate for a single-oxygen insertion into 3-methyl-l-tyrosine. Catalytic assays using ascorbate derivatives revealed the functional groups of ascorbate essential to its function as a cosubstrate. Abolishing the thioether linkage through mutation of Cys317 resulted in catalytically inactive SfmD variants. EPR and optical data revealed that the heme center undergoes a substantial conformational change with one axial histidine ligand dissociating from the iron ion in response to substrate 3-methyl-l-tyrosine binding or chemical reduction by a reducing agent, such as the cosubstrate ascorbate. The labile axial ligand was identified as His274 through redox-linked structural determinations. Together, identifying an unusual heme cofactor with a previously unknown heme-binding motif for a monooxygenase activity and the structural similarity of SfmD to the members of the heme-based tryptophan dioxygenase superfamily will broaden understanding of heme chemistry.
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Affiliation(s)
- Inchul Shin
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle Texas 78249 USA
| | - Ian Davis
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle Texas 78249 USA
| | - Karinel Nieves-Merced
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle Texas 78249 USA
- Center for Innovative Drug Discovery, The University of Texas at San Antonio One UTSA Circle Texas 78249 USA
| | - Yifan Wang
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle Texas 78249 USA
| | - Stanton McHardy
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle Texas 78249 USA
- Center for Innovative Drug Discovery, The University of Texas at San Antonio One UTSA Circle Texas 78249 USA
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle Texas 78249 USA
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17
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Pham KN, Lewis-Ballester A, Yeh SR. Conformational Plasticity in Human Heme-Based Dioxygenases. J Am Chem Soc 2020; 143:1836-1845. [PMID: 33373218 DOI: 10.1021/jacs.0c09970] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Human indoleamine 2,3-dioxygenase 1 (hIDO1) and human tryptophan dioxygenase (hTDO) are two important heme proteins that degrade the essential amino acid, l-tryptophan (Trp), along the kynurenine pathway. The two enzymes share a similar active site structure and an analogous catalytic mechanism, but they exhibit a variety of distinct functional properties. Here we used carbon monoxide (CO) as a structural probe to interrogate how the functionalities of the two enzymes are encoded in their structures. With X-ray crystallography, we detected an unexpected photochemical intermediate trapped in a crystal of the hIDO1-CO-Trp complex, where CO is photolyzed from the heme iron by X-rays at cryogenic temperatures (100 K). The CO photolysis triggers a large-scale migration of the substrate Trp, as well as the photolyzed CO, from the active site to a temporary binding site, Sa*. It is accompanied by a large conformational change to an active site loop, JK-LoopC, despite the severely restricted protein motion under the frozen conditions, which highlights the remarkable conformational plasticity of the hIDO1 protein. Comparative studies of a crystal of the hTDO-CO-Trp complex show that CO and Trp remain bound in the active site under comparable X-ray illumination, indicating a much more rigid protein architecture. The data offer important new insights into the structure and function relationships of the heme-based dioxygenases and provide new guidelines for structure-based design of inhibitors targeting them.
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Affiliation(s)
- Khoa N Pham
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, The Bronx, New York 10461, United States
| | - Ariel Lewis-Ballester
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, The Bronx, New York 10461, United States
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, The Bronx, New York 10461, United States
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18
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Peoc'h K, Puy V, Fournier T. Haem oxygenases play a pivotal role in placental physiology and pathology. Hum Reprod Update 2020; 26:634-649. [PMID: 32347305 DOI: 10.1093/humupd/dmaa014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 02/20/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Haem oxygenases (HO) catabolise haem, which is the prosthetic group of numerous haemoproteins. Thus, multiple primary cellular pathways and functions rely on haem availability. HO exists in two isoforms, both expressed in the placenta, namely HO-1 and HO-2, the first being inducible. Haem oxygenases, particularly HO-1, have garnered specific interest in the field of physiological and pathological placental function. These enzymes mediate haem degradation by cleaving the alpha methene bridge to produce biliverdin, which is subsequently converted to bilirubin, carbon monoxide and iron. HO-1 has anti-inflammatory and antioxidant activities. SEARCH METHODS An initial literature analysis was performed using PubMed on 3 October 2018 using key terms such as 'haem oxygenase and pregnancy', 'haem oxygenase and placenta', 'HO-1 and pregnancy', 'HO-1 and placenta', 'HO and placenta', 'HO and pregnancy', 'genetic variant and HO', 'CO and pregnancy', 'CO and placenta', 'Bilirubin and pregnancy', 'Iron and pregnancy' and 'PPAR and Haem', selecting consensus conferences, recommendations, meta-analyses, practical recommendations and reviews. A second literature analysis was performed, including notable miscarriages, foetal loss and diabetes mellitus, on 20 December 2019. The three authors studied the publications independently to decipher whether they should be included in the manuscript. OBJECTIVE AND RATIONALE This review aimed to summarise current pieces of knowledge of haem oxygenase location, function and regulation in the placenta, either in healthy pregnancies or those associated with miscarriages and foetal loss, pre-eclampsia, foetal growth restriction and diabetes mellitus. OUTCOMES HO-1 exerts some protective effects on the placentation, probably by a combination of factors, including its interrelation with the PGC-1α/PPAR pathway and the sFlt1/PlGF balance, and through its primary metabolites, notably carbon monoxide and bilirubin. Its protective role has been highlighted in numerous pregnancy conditions, including pre-eclampsia, foetal growth restriction, gestational diabetes mellitus and miscarriages. WIDER IMPLICATIONS HO-1 is a crucial enzyme in physiological and pathological placentation. This protective enzyme is currently considered a potential therapeutic target in various pregnancy diseases.
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Affiliation(s)
- Katell Peoc'h
- Université de Paris, Laboratory of Excellence GR-Ex, Centre de Recherche sur l'Inflammation, INSERM U1149, UFR de Médecine Bichat, 75018 Paris, France
- Assistance Publique des Hôpitaux de Paris, APHP Nord, Paris, France
| | - Vincent Puy
- Reproductive Biology Unit CECOS, Paris-Saclay University, Antoine Béclère Hospital, APHP, Clamart 92140, France
- Laboratoire de Développement des Gonades, UMRE008 Stabilité Génétique Cellules Souches et Radiations, Université de Paris, Université Paris-Saclay, CEA, F-92265 Fontenay-aux-Roses, France
| | - Thierry Fournier
- Université de Paris, INSERM, UMR-S 1139, 3PHM, F-75006, Paris, France
- Fondation PremUp, F-75014, Paris, France
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19
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Geng J, Weitz AC, Dornevil K, Hendrich MP, Liu A. Kinetic and Spectroscopic Characterization of the Catalytic Ternary Complex of Tryptophan 2,3-Dioxygenase. Biochemistry 2020; 59:2813-2822. [PMID: 32659080 DOI: 10.1021/acs.biochem.0c00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The first step of the kynurenine pathway for l-tryptophan (l-Trp) degradation is catalyzed by heme-dependent dioxygenases, tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase. In this work, we employed stopped-flow optical absorption spectroscopy to study the kinetic behavior of the Michaelis complex of Cupriavidus metallidurans TDO (cmTDO) to improve our understanding of oxygen activation and initial oxidation of l-Trp. On the basis of the stopped-flow results, rapid freeze-quench (RFQ) experiments were performed to capture and characterize this intermediate by Mössbauer spectroscopy. By incorporating the chlorite dismutase-chlorite system to produce high concentrations of solubilized O2, we were able to capture the Michaelis complex of cmTDO in a nearly quantitative yield. The RFQ-Mössbauer results confirmed the identity of the Michaelis complex as an O2-bound ferrous species. They revealed remarkable similarities between the electronic properties of the Michaelis complex and those of the O2 adduct of myoglobin. We also found that the decay of this reactive intermediate is the rate-limiting step of the catalytic reaction. An inverse α-secondary substrate kinetic isotope effect was observed with a kH/kD of 0.87 ± 0.03 when (indole-d5)-l-Trp was employed as the substrate. This work provides an important piece of spectroscopic evidence of the chemical identity of the Michaelis complex of bacterial TDO.
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Affiliation(s)
- Jiafeng Geng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Andrew C Weitz
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Kednerlin Dornevil
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States.,Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Michael P Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Aimin Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States.,Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
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20
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Effect of congenital adrenal hyperplasia treated by glucocorticoids on plasma metabolome: a machine-learning-based analysis. Sci Rep 2020; 10:8859. [PMID: 32483270 PMCID: PMC7264133 DOI: 10.1038/s41598-020-65897-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/11/2020] [Indexed: 12/30/2022] Open
Abstract
Background. Congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency leads to impaired cortisol biosynthesis. Treatment includes glucocorticoid supplementation. We studied the specific metabolomics signatures in CAH patients using two different algorithms. Methods. In a case-control study of CAH patients matched on sex and age with healthy control subjects, two metabolomic analyses were performed: one using MetaboDiff, a validated differential metabolomic analysis tool and the other, using Predomics, a novel machine-learning algorithm. Results. 168 participants were included (84 CAH patients). There was no correlation between plasma cortisol levels during glucocorticoid supplementation and metabolites in CAH patients. Indoleamine 2,3-dioxygenase enzyme activity was correlated with ACTH (rho coefficient = −0.25, p-value = 0.02), in CAH patients but not in controls subjects. Overall, 33 metabolites were significantly altered in CAH patients. Main changes came from: purine and pyrimidine metabolites, branched aminoacids, tricarboxylic acid cycle metabolites and associated pathways (urea, glucose, pentose phosphates). MetaboDiff identified 2 modules that were significantly different between both groups: aminosugar metabolism and purine metabolism. Predomics found several interpretable models which accurately discriminated the two groups (accuracy of 0.86 and AUROC of 0.9). Conclusion. CAH patients and healthy control subjects exhibit significant differences in plasma metabolomes, which may be explained by glucocorticoid supplementation.
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21
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Mondal P, Wijeratne GB. Modeling Tryptophan/Indoleamine 2,3-Dioxygenase with Heme Superoxide Mimics: Is Ferryl the Key Intermediate? J Am Chem Soc 2020; 142:1846-1856. [PMID: 31870154 DOI: 10.1021/jacs.9b10498] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Tryptophan oxidation in biology has been recently implicated in a vast array of paramount pathogenic conditions in humans, including multiple sclerosis, rheumatoid arthritis, type-I diabetes, and cancer. This 2,3-dioxygenative cleavage of the indole ring of tryptophan with dioxygen is mediated by two heme enzymes, tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO), during its conversion to N-formylkynurenine in the first and rate-limiting step of kynurenine pathway. Despite the pivotal significance of this enzymatic transformation, a vivid viewpoint of the precise mechanistic events is far from complete. A heme superoxide adduct is thought to be the active oxidant in both TDO and IDO, which, following O-O bond cleavage, presumably generates a key ferryl (FeIV=O) reaction intermediate. This study, for the first time in model chemistry, demonstrates the potential of synthetic heme superoxide adducts to mimic the bioinorganic chemistry of indole dioxygenation by TDO and IDO, challenging the widely accepted categorization of these metal adducts as weak oxidants. Herein, an electronically divergent series of ferric heme superoxo oxidants mediates the facile conversion of an array of indole substrates into their corresponding 2,3-dioxygenated products, while shedding light on an unequivocally occurring, putative ferryl intermediate. The oxygenated indole products have been isolated in ∼31% yield, and characterized by LC-MS, 1H and 13C NMR, and FT-IR methodologies, as well as by 18O2(g) labeling experiments. Distinctly, the most electron-deficient superoxo adduct is observed to react the fastest, specifically with the most electron-rich indole substrate, underscoring the cruciality of electrophilicity of the heme superoxide moiety in facilitating the initial indole activation step. Comprehensive understanding of such mechanistic subtleties will benefit future attempts in the rational design of salient therapeutic agents, including next generation anticancer drug targets with amplified effectivity.
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Affiliation(s)
- Pritam Mondal
- Department of Chemistry , University of Alabama at Birmingham , Birmingham , Alabama 35205 , United States
| | - Gayan B Wijeratne
- Department of Chemistry , University of Alabama at Birmingham , Birmingham , Alabama 35205 , United States
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22
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Chu CE, Porten SP, Grossfeld GD, Meng MV. Role of Indoleamine-2,3-Dioxygenase Inhibitors in Salvage Therapy for Non-Muscle Invasive Bladder Cancer. Urol Clin North Am 2019; 47:111-118. [PMID: 31757294 DOI: 10.1016/j.ucl.2019.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Due to significant risks of cancer recurrence and progression, and limited options after intravesical Bacillus Calmette Guerin (BCG) therapy, there is a critical unmet need to identify novel treatments for those patients with BCG-unresponsive bladder cancer. There is active investigation of immunotherapies which provide both biologic and clinical rationales for indoleamine-2,3- dioxygenase inhibitors in salvage therapy for non-muscle invasive bladder cancer.
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Affiliation(s)
- Carissa E Chu
- Department of Urology, University of California, San Francisco, 550 16th Street, 6th Floor, San Francisco, CA 94143, USA
| | - Sima P Porten
- Department of Urology, University of California, San Francisco, 550 16th Street, 6th Floor, San Francisco, CA 94143, USA
| | - Gary D Grossfeld
- Bristol-Myers Squibb, 3401 Princeton Pike, Lawrenceville, New Jersey 08648, USA
| | - Maxwell V Meng
- Department of Urology, University of California, San Francisco, 550 16th Street, 6th Floor, San Francisco, CA 94143, USA.
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23
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Pham KN, Lewis-Ballester A, Yeh SR. Structural Basis of Inhibitor Selectivity in Human Indoleamine 2,3-Dioxygenase 1 and Tryptophan Dioxygenase. J Am Chem Soc 2019; 141:18771-18779. [PMID: 31682426 DOI: 10.1021/jacs.9b08871] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Indoleamine 2,3-dioxygenase 1 (hIDO1) and tryptophan dioxygenase (hTDO) are two of the only three heme-based dioxygenases in humans. They have recently been identified as key cancer immunotherapeutic drug targets. While structures of hIDO1 in complex with inhibitors have been documented, so far there are no structures of hTDO-inhibitor complexes available. Here we use PF-06840003 (IPD), a hIDO1-selective inhibitor in clinical trials, as a structural probe to elucidate inhibitor-selectivity in hIDO1 versus hTDO. Spectroscopic studies show that IPD exhibits 400-fold higher inhibition activity toward hIDO1 with respect to hTDO. Crystallographic structures reveal that the binding pocket of IPD in the active site in hIDO1 is much more flexible as compared to that in hTDO, which offers a molecular explanation for the superior inhibition activity of IPD in hIDO1 with respect to hTDO. In addition to the IPD bound in the active site, a second IPD molecule was identified in an inhibitory site on the proximal side of the heme in hIDO1 and in an exosite that is ∼40 Å away from the active site in hTDO. Taken together the data provide new insights into structure-based design of mono and dual inhibitors targeting hIDO1 and/or hTDO.
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Affiliation(s)
- Khoa N Pham
- Department of Physiology and Biophysics , Albert Einstein College of Medicine , The Bronx , New York 10461 , United States
| | - Ariel Lewis-Ballester
- Department of Physiology and Biophysics , Albert Einstein College of Medicine , The Bronx , New York 10461 , United States
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics , Albert Einstein College of Medicine , The Bronx , New York 10461 , United States
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24
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Banerjee G, Ghosh I, Kim CJ, Debus RJ, Brudvig GW. Bicarbonate rescues damaged proton-transfer pathway in photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:611-617. [DOI: 10.1016/j.bbabio.2019.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 01/04/2023]
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25
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Audrito V, Managò A, Gaudino F, Sorci L, Messana VG, Raffaelli N, Deaglio S. NAD-Biosynthetic and Consuming Enzymes as Central Players of Metabolic Regulation of Innate and Adaptive Immune Responses in Cancer. Front Immunol 2019; 10:1720. [PMID: 31402913 PMCID: PMC6671870 DOI: 10.3389/fimmu.2019.01720] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/09/2019] [Indexed: 12/15/2022] Open
Abstract
Cancer cells, particularly in solid tumors, are surrounded by non-neoplastic elements, including endothelial and stromal cells, as well as cells of immune origin, which can support tumor growth by providing the right conditions. On the other hand, local hypoxia, and lack of nutrients induce tumor cells to reprogram their metabolism in order to survive, proliferate, and disseminate: the same conditions are also responsible for building a tumor-suppressive microenvironment. In addition to tumor cells, it is now well-recognized that metabolic rewiring occurs in all cellular components of the tumor microenvironment, affecting epigenetic regulation of gene expression and influencing differentiation/proliferation decisions of these cells. Nicotinamide adenine dinucleotide (NAD) is an essential co-factor for energy transduction in metabolic processes. It is also a key component of signaling pathways, through the regulation of NAD-consuming enzymes, including sirtuins and PARPs, which can affect DNA plasticity and accessibility. In addition, both NAD-biosynthetic and NAD-consuming enzymes can be present in the extracellular environment, adding a new layer of complexity to the system. In this review we will discuss the role of the “NADome” in the metabolic cross-talk between cancer and infiltrating immune cells, contributing to cancer growth and immune evasion, with an eye to therapeutic implications.
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Affiliation(s)
- Valentina Audrito
- Department of Medical Sciences, University of Turin, Turin, Italy.,Italian Institute for Genomic Medicine, Turin, Italy
| | - Antonella Managò
- Department of Medical Sciences, University of Turin, Turin, Italy.,Italian Institute for Genomic Medicine, Turin, Italy
| | - Federica Gaudino
- Department of Medical Sciences, University of Turin, Turin, Italy.,Italian Institute for Genomic Medicine, Turin, Italy
| | - Leonardo Sorci
- Division of Bioinformatics and Biochemistry, Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, Italy
| | - Vincenzo Gianluca Messana
- Department of Medical Sciences, University of Turin, Turin, Italy.,Italian Institute for Genomic Medicine, Turin, Italy
| | - Nadia Raffaelli
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Silvia Deaglio
- Department of Medical Sciences, University of Turin, Turin, Italy.,Italian Institute for Genomic Medicine, Turin, Italy
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26
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Yuasa HJ. A comprehensive comparison of the metazoan tryptophan degrading enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140247. [PMID: 31276825 DOI: 10.1016/j.bbapap.2019.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/28/2019] [Accepted: 06/30/2019] [Indexed: 01/15/2023]
Abstract
Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) have an independent origin; however, they have distinctly evolved to catalyze the same reaction. In general, TDO is a single-copy gene in each metazoan species, and TDO enzymes demonstrate similar enzyme activity regardless of their biological origin. In contrast, multiple IDO paralogues are observed in many species, and they display various enzymatic properties. Similar to vertebrate IDO2, invertebrate IDOs generally show low affinity/catalytic efficiency for L-Trp. Meanwhile, two IDO isoforms from scallop (IDO-I and -III) and sponge IDOs show high L-Trp catalytic activity, which is comparable to vertebrate IDO1. Site-directed mutagenesis experiments have revealed that primarily two residues, Tyr located at the 2nd residue on the F-helix (F2nd) and His located at the 9th residue on the G-helix (G9th), are crucial for the high affinity/catalytic efficiency of these 'high performance' invertebrate IDOs. Conversely, those two amino acid substitutions (F2nd/Tyr and G9th/His) resulted in high affinity and catalytic activity in other molluscan 'low performance' IDOs. In human IDO1, G9th is Ser167, whereas the counterpart residue of G9th in human TDO is His76. Previous studies have shown that Ser167 could not be substituted by His because the human IDO1 Ser167His variant showed significantly low catalytic activity. However, this may be specific for human IDO1 because G9th/His was demonstrated to be very effective in increasing the L-Trp affinity even in vertebrate IDOs. Therefore, these findings indicate that the active sites of TDO and IDO are more similar to each other than previously expected.
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Affiliation(s)
- Hajime Julie Yuasa
- Laboratory of Biochemistry, Department of Applied Science, Faculty of Science and Technology, National University Corporation Kochi University, Kochi 780-8520, Japan.
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27
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Maróti P. Chemical rescue of H + delivery in proton transfer mutants of reaction center of photosynthetic bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:317-324. [PMID: 30707884 DOI: 10.1016/j.bbabio.2019.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 12/05/2018] [Accepted: 01/25/2019] [Indexed: 11/27/2022]
Abstract
In the native and most mutant reaction centers of bacterial photosynthesis, the electron transfer is coupled to proton transfer and is rate limiting for the second reduction of QB- → QBH2. In the presence of divalent metal ions (e.g. Cd2+) or in some ("proton transfer") mutants (L210DN/M17DN or L213DN), the proton delivery to QB- is made rate limiting and the properties of the proton pathway can be directly examined. We found that small weak acids and buffers in large concentrations (up to 1 M) were able to rescue the severely impaired proton transfer capability differently depending on the location of the defects: lesions at the protein surface (proton gate H126H/H128H + Cd2+), beneath the surface (M17DN + Cd2+, L210DN/M17DN) or deep inside the protein (L213DN) could be completely, partially or to very small extent recovered, respectively. Small zwitterionic acids (azide/hydrazoic acid) and buffers (tricine) proved to be highly effective rescuers consistent with their enhanced binding affinity and access to any of the proton acceptors (including QB- itself) in the pathway. As a consequence, back titration of the protons at L212Glu could be observed as a pH-dependence of the rate constant of the charge recombination in the presence of azide or formate. Model calculations support the collective influence of the acid cluster on the change of the protonation states upon extension of the cluster with the bound small acid. In proton transfer mutants, the rescuing agents decreased the free energy of activation together with their enthalpic and entropic components. This is in agreement with the hypothesis that they function as protein-penetrating protonophores delivering protons into the chain and select dominating paths out of many alternate routes. We estimate that the proton delivery will be accelerated in one pathway out of 100-200 alternate pathways. The implications for design of the chemical recovery of impaired intra-protein proton transfer pathways in proton transfer mutants are discussed.
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Affiliation(s)
- Péter Maróti
- Institute of Medical Physics, University of Szeged, Hungary.
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28
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Abstract
Iron-containing enzymes such as heme enzymes play crucial roles in biological systems. Three distinct heme-containing dioxygenase enzymes, tryptophan 2,3-dioxygenase (TDO), indoleamine 2,3-dioxygenase 1 (IDO1) and indoleamine 2,3-dioxygenase 2 (IDO2) catalyze the initial and rate-limiting step of l-tryptophan catabolism through the kynurenine pathway in mammals. Overexpression of these enzymes causes depletion of tryptophan and the accumulation of metabolic products, which contributes to tumor immune tolerance and immune dysregulation in a variety of disease pathologies. In the past few decades, IDO1 has garnered the most attention as a therapeutic target with great potential in cancer immunotherapy. Many potential inhibitors of IDO1 have been designed, synthesized and evaluated, among which indoximod (d-1-MT), INCB024360, GDC-0919 (formerly NLG-919), and an IDO1 peptide-based vaccine have advanced to the clinical trial stage. However, recently, the roles of TDO and IDO2 have been elucidated in immune suppression. In this review, the current drug discovery landscape for targeting TDO, IDO1 and IDO2 is highlighted, with particular attention to the recent use of drugs in clinical trials. Moreover, the crystal structures of these enzymes, in complex with inhibitors, and the mechanisms of Trp catabolism in the first step, are summarized to provide information for facilitating the discovery of new enzyme inhibitors.
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Affiliation(s)
- Daojing Yan
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.
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29
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Affiliation(s)
- Yujie Liang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Jialiang Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Xu Qiu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Ning Jiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
- State Key Laboratory of Organometallic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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30
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Shin I, Ambler BR, Wherritt D, Griffith WP, Maldonado AC, Altman RA, Liu A. Stepwise O-Atom Transfer in Heme-Based Tryptophan Dioxygenase: Role of Substrate Ammonium in Epoxide Ring Opening. J Am Chem Soc 2018; 140:4372-4379. [PMID: 29506384 PMCID: PMC5874177 DOI: 10.1021/jacs.8b00262] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Heme-based tryptophan dioxygenases are established immunosuppressive metalloproteins with significant biomedical interest. Here, we synthesized two mechanistic probes to specifically test if the α-amino group of the substrate directly participates in a critical step of the O atom transfer during catalysis in human tryptophan 2,3-dioxygenase (TDO). Substitution of the nitrogen atom of the substrate to a carbon (probe 1) or oxygen (probe 2) slowed the catalytic step following the first O atom transfer such that transferring the second O atom becomes less likely to occur, although the dioxygenated products were observed with both probes. A monooxygenated product was also produced from probe 2 in a significant quantity. Analysis of this new product by HPLC coupled UV-vis spectroscopy, high-resolution mass spectrometry, 1H NMR, 13C NMR, HSQC, HMBC, and infrared (IR) spectroscopies concluded that this monooxygenated product is a furoindoline compound derived from an unstable epoxyindole intermediate. These results prove that small molecules can manipulate the stepwise O atom transfer reaction of TDO and provide a showcase for a tunable mechanism by synthetic compounds. The product analysis results corroborate the presence of a substrate-based epoxyindole intermediate during catalysis and provide the first substantial experimental evidence for the involvement of the substrate α-amino group in the epoxide ring-opening step during catalysis. This combined synthetic, biochemical, and biophysical study establishes the catalytic role of the α-amino group of the substrate during the O atom transfer reactions and thus represents a substantial advance to the mechanistic comprehension of the heme-based tryptophan dioxygenases.
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Affiliation(s)
- Inchul Shin
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Brett R. Ambler
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Daniel Wherritt
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Wendell P. Griffith
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Amanda C. Maldonado
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Ryan A. Altman
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
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31
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Huang X, Groves JT. Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins. Chem Rev 2018; 118:2491-2553. [PMID: 29286645 PMCID: PMC5855008 DOI: 10.1021/acs.chemrev.7b00373] [Citation(s) in RCA: 591] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 12/20/2022]
Abstract
As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply of metalloproteins for oxidative metabolism and protection against reactive oxygen species. Despite the diverse structures and functions of these proteins, they share common mechanistic grounds. An open-shell transition metal like iron or copper is employed to interact with O2 and its derived intermediates such as hydrogen peroxide to afford a variety of metal-oxygen intermediates. These reactive intermediates, including metal-superoxo, -(hydro)peroxo, and high-valent metal-oxo species, are the basis for the various biological functions of O2-utilizing metalloproteins. Collectively, these processes are called oxygen activation. Much of our understanding of the reactivity of these reactive intermediates has come from the study of heme-containing proteins and related metalloporphyrin compounds. These studies not only have deepened our understanding of various functions of heme proteins, such as O2 storage and transport, degradation of reactive oxygen species, redox signaling, and biological oxygenation, etc., but also have driven the development of bioinorganic chemistry and biomimetic catalysis. In this review, we survey the range of O2 activation processes mediated by heme proteins and model compounds with a focus on recent progress in the characterization and reactivity of important iron-oxygen intermediates. Representative reactions initiated by these reactive intermediates as well as some context from prior decades will also be presented. We will discuss the fundamental mechanistic features of these transformations and delineate the underlying structural and electronic factors that contribute to the spectrum of reactivities that has been observed in nature as well as those that have been invented using these paradigms. Given the recent developments in biocatalysis for non-natural chemistries and the renaissance of radical chemistry in organic synthesis, we envision that new enzymatic and synthetic transformations will emerge based on the radical processes mediated by metalloproteins and their synthetic analogs.
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Affiliation(s)
- Xiongyi Huang
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Chemistry, California Institute of Technology, Pasadena, California 91125, United States
| | - John T. Groves
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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32
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Nienhaus K, Nienhaus GU. Different Mechanisms of Catalytic Complex Formation in Two L-Tryptophan Processing Dioxygenases. Front Mol Biosci 2018; 4:94. [PMID: 29354636 PMCID: PMC5758539 DOI: 10.3389/fmolb.2017.00094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/18/2017] [Indexed: 01/25/2023] Open
Abstract
The human heme enzymes tryptophan 2,3-dioxygenase (hTDO) and indoleamine 2,3 dioxygenase (hIDO) catalyze the initial step in L-tryptophan (L-Trp) catabolism, the insertion of dioxygen into L-Trp. Overexpression of these enzymes causes depletion of L-Trp and accumulation of metabolic products, and thereby contributes to tumor immune tolerance and immune dysregulation in a variety of disease pathologies. Understanding the assembly of the catalytically active, ternary enzyme-substrate-ligand complexes is not yet fully resolved, but an essential prerequisite for designing efficient and selective de novo inhibitors. Evidence is mounting that the ternary complex forms by sequential binding of ligand and substrate in a specific order. In hTDO, the apolar L-Trp binds first, decreasing active-site solvation and, as a result, reducing non-productive oxidation of the heme iron by the dioxygen ligand, which may leave the substrate bound to a ferric heme iron. In hIDO, by contrast, dioxygen must first coordinate to the heme iron because a bound substrate would occlude ligand access to the heme iron, so the ternary complex can no longer form. Consequently, faster association of L-Trp at high concentrations results in substrate inhibition. Here, we summarize our present knowledge of ternary complex formation in hTDO and hIDO and relate these findings to structural peculiarities of their active sites.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany.,Institute of Nanotechnology and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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33
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A single amino acid residue regulates the substrate affinity and specificity of indoleamine 2,3-dioxygenase. Arch Biochem Biophys 2017; 640:1-9. [PMID: 29288638 DOI: 10.1016/j.abb.2017.12.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/21/2017] [Accepted: 12/23/2017] [Indexed: 11/20/2022]
Abstract
Indoleamine 2,3-dioxygenase (IDO) is a heme-containing enzyme that catalyses the oxidative cleavage of L-Trp. The ciliate Blepharisma stoltei has four IDO genes (IDO-I, -II, -III and -IV), which seem to have evolved via two sequential gene duplication events. Each IDO enzyme has a distinct enzymatic property, where IDO-III has a high affinity for L-Trp, whereas the affinity of the other three isoforms for L-Trp is low. IDO-I also exhibits a significant catalytic activity with another indole compound: 5-hydroxy-l-tryptophan (5-HTP). IDO-I is considered to be an enzyme that is involved in the biosynthesis of the 5-HTP-derived mating pheromone, gamone 2. By analysing a series of chimeric enzymes based on extant and predicted ancestral enzymes, we identified Asn131 in IDO-I and Glu132 in IDO-III as the key residues responsible for their high affinity for each specific substrate. These two residues were aligned in an identical position as the substrate-determining residue (SDR). Thus, the substrate affinity and specificity are regulated mostly by a single amino acid residue in the Blepharisma IDO-I and IDO-III enzymes.
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34
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Lopez S, Rondot L, Leprêtre C, Marchi-Delapierre C, Ménage S, Cavazza C. Cross-Linked Artificial Enzyme Crystals as Heterogeneous Catalysts for Oxidation Reactions. J Am Chem Soc 2017; 139:17994-18002. [PMID: 29148757 DOI: 10.1021/jacs.7b09343] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Designing systems that merge the advantages of heterogeneous catalysis, enzymology, and molecular catalysis represents the next major goal for sustainable chemistry. Cross-linked enzyme crystals display most of these essential assets (well-designed mesoporous support, protein selectivity, and molecular recognition of substrates). Nevertheless, a lack of reaction diversity, particularly in the field of oxidation, remains a constraint for their increased use in the field. Here, thanks to the design of cross-linked artificial nonheme iron oxygenase crystals, we filled this gap by developing biobased heterogeneous catalysts capable of oxidizing carbon-carbon double bonds. First, reductive O2 activation induces selective oxidative cleavage, revealing the indestructible character of the solid catalyst (at least 30 000 turnover numbers without any loss of activity). Second, the use of 2-electron oxidants allows selective and high-efficiency hydroxychlorination with thousands of turnover numbers. This new technology by far outperforms catalysis using the inorganic complexes alone, or even the artificial enzymes in solution. The combination of easy catalyst synthesis, the improvement of "omic" technologies, and automation of protein crystallization makes this strategy a real opportunity for the future of (bio)catalysis.
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Affiliation(s)
- Sarah Lopez
- Université Grenoble-Alpes , Grenoble F-38000, France.,CEA, BIG, Laboratory of Chemistry and Biology of Metals, BioCE and BioCat group , Grenoble F-38054, France.,CNRS, UMR5249 , Grenoble F-38054, France
| | - Laurianne Rondot
- Université Grenoble-Alpes , Grenoble F-38000, France.,CEA, BIG, Laboratory of Chemistry and Biology of Metals, BioCE and BioCat group , Grenoble F-38054, France.,CNRS, UMR5249 , Grenoble F-38054, France
| | - Chloé Leprêtre
- Université Grenoble-Alpes , Grenoble F-38000, France.,CEA, BIG, Laboratory of Chemistry and Biology of Metals, BioCE and BioCat group , Grenoble F-38054, France.,CNRS, UMR5249 , Grenoble F-38054, France
| | - Caroline Marchi-Delapierre
- Université Grenoble-Alpes , Grenoble F-38000, France.,CEA, BIG, Laboratory of Chemistry and Biology of Metals, BioCE and BioCat group , Grenoble F-38054, France.,CNRS, UMR5249 , Grenoble F-38054, France
| | - Stéphane Ménage
- Université Grenoble-Alpes , Grenoble F-38000, France.,CEA, BIG, Laboratory of Chemistry and Biology of Metals, BioCE and BioCat group , Grenoble F-38054, France.,CNRS, UMR5249 , Grenoble F-38054, France
| | - Christine Cavazza
- Université Grenoble-Alpes , Grenoble F-38000, France.,CEA, BIG, Laboratory of Chemistry and Biology of Metals, BioCE and BioCat group , Grenoble F-38054, France.,CNRS, UMR5249 , Grenoble F-38054, France
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35
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Zhang Y, Zou Y, Brock NL, Huang T, Lan Y, Wang X, Deng Z, Tang Y, Lin S. Characterization of 2-Oxindole Forming Heme Enzyme MarE, Expanding the Functional Diversity of the Tryptophan Dioxygenase Superfamily. J Am Chem Soc 2017; 139:11887-11894. [PMID: 28809552 DOI: 10.1021/jacs.7b05517] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
3-Substituted 2-oxindoles are important structural motifs found in many biologically active natural products and pharmaceutical lead compounds. Here, we report an enzymatic formation of the 3-substituted 2-oxindoles catalyzed by MarE in the maremycin biosynthetic pathway in Streptomyces sp. B9173. MarE is a homologue of FeII/heme-dependent tryptophan 2,3-dioxygenases (TDOs). Typical TDOs usually catalyze the insertion of two oxygen atoms from O2 into an indole ring to generate N-formylkynurenine (NFK)-like products. In contrast, MarE catalyzes the insertion of a single oxygen atom from O2 into an indole ring, to probably generate an epoxyindole intermediate that undergoes an unprecedented 2,3-hydride migration to form 2-oxindole structure. MarE shows substrate robustness to catalyze the conversion of a series of 3-substituted indoles into their corresponding 3-substituted 2-oxindoles. Although containing most key amino acid residues conserved in well-known TDO homologues, MarE falls into a separate new subgroup in the phylogenetic tree. The characterization of MarE and its homologue enriches the functional diversities of TDO superfamily and provides a new strategy for discovering novel natural products containing 3-substituted 2-oxindole pharmacophores by genome mining.
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Affiliation(s)
- Yuyang Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, China
| | - Yi Zou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, China.,Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, and Department of Bioengineering, University of California, Los Angeles , 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Nelson L Brock
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, China
| | - Tingting Huang
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, China
| | - Yingxia Lan
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, China
| | - Xiaozheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, China
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, and Department of Bioengineering, University of California, Los Angeles , 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, China
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36
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Nienhaus K, Hahn V, Hüpfel M, Nienhaus GU. Substrate Binding Primes Human Tryptophan 2,3-Dioxygenase for Ligand Binding. J Phys Chem B 2017; 121:7412-7420. [PMID: 28715185 DOI: 10.1021/acs.jpcb.7b03463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human heme enzyme tryptophan 2,3-dioxygenase (hTDO) catalyzes the insertion of dioxygen into its cognate substrate, l-tryptophan (l-Trp). Its active site structure is highly dynamic, and the mechanism of enzyme-substrate-ligand complex formation and the ensuing enzymatic reaction is not yet understood. Here we have studied complex formation in hTDO by using time-resolved optical and infrared spectroscopy with carbon monoxide (CO) as a ligand. We have observed that both substrate-free and substrate-bound hTDO coexist in two discrete conformations with greatly different ligand binding rates. In the fast rebinding hTDO conformation, there is facile ligand access to the heme iron, but it is greatly hindered in the slowly rebinding conformation. Spectroscopic evidence implicates active site solvation as playing a crucial role for the observed kinetic differences. Substrate binding shifts the conformational equilibrium markedly toward the fast species and thus primes the active site for subsequent ligand binding, ensuring that formation of the ternary complex occurs predominantly by first binding l-Trp and then the ligand. Consequently, the efficiency of catalysis is enhanced because O2 binding prior to substrate binding, resulting in nonproductive oxidation of the heme iron, is greatly suppressed.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany
| | - Vincent Hahn
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany
| | - Manuel Hüpfel
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany.,Institute of Nanotechnology (INT) and Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT) , 76344 Eggenstein-Leopoldshafen, Germany.,Department of Physics, University of Illinois at Urbana-Champaign , 1110 W. Green Street, Urbana, Illinois 61801, United States
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Nienhaus K, Nickel E, Nienhaus GU. Substrate binding in human indoleamine 2,3-dioxygenase 1: A spectroscopic analysis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:453-463. [DOI: 10.1016/j.bbapap.2017.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/22/2017] [Accepted: 02/07/2017] [Indexed: 11/27/2022]
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Wang Y, Li J, Liu A. Oxygen activation by mononuclear nonheme iron dioxygenases involved in the degradation of aromatics. J Biol Inorg Chem 2017; 22:395-405. [PMID: 28084551 DOI: 10.1007/s00775-017-1436-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/03/2017] [Indexed: 11/25/2022]
Abstract
Molecular oxygen is utilized in numerous metabolic pathways fundamental for life. Mononuclear nonheme iron-dependent oxygenase enzymes are well known for their involvement in some of these pathways, activating O2 so that oxygen atoms can be incorporated into their primary substrates. These reactions often initiate pathways that allow organisms to use stable organic molecules as sources of carbon and energy for growth. From the myriad of reactions in which these enzymes are involved, this perspective recounts the general mechanisms of aromatic dihydroxylation and oxidative ring cleavage, both of which are ubiquitous chemical reactions found in life-sustaining processes. The organic substrate provides all four electrons required for oxygen activation and insertion in the reactions mediated by extradiol and intradiol ring-cleaving catechol dioxygenases. In contrast, two of the electrons are provided by NADH in the cis-dihydroxylation mechanism of Rieske dioxygenases. The catalytic nonheme Fe center, with the aid of active site residues, facilitates these electron transfers to O2 as key elements of the activation processes. This review discusses some general questions for the catalytic strategies of oxygen activation and insertion into aromatic compounds employed by mononuclear nonheme iron-dependent dioxygenases. These include: (1) how oxygen is activated, (2) whether there are common intermediates before oxygen transfer to the aromatic substrate, and (3) are these key intermediates unique to mononuclear nonheme iron dioxygenases?
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Jiasong Li
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA.
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Fischer AA, Lindeman SV, Fiedler AT. Spectroscopic and computational studies of reversible O2 binding by a cobalt complex of relevance to cysteine dioxygenase. Dalton Trans 2017; 46:13229-13241. [DOI: 10.1039/c7dt01600j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Spectroscopic and computational studies of reversible O2 binding by a cobalt active-site mimic shed light on the catalytic mechanism of cysteine dioxygenases.
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Basran J, Booth ES, Lee M, Handa S, Raven EL. Analysis of Reaction Intermediates in Tryptophan 2,3-Dioxygenase: A Comparison with Indoleamine 2,3-Dioxygenase. Biochemistry 2016; 55:6743-6750. [PMID: 27951658 DOI: 10.1021/acs.biochem.6b01005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) are heme-containing enzymes that catalyze the O2-dependent oxidation of l-tryptophan (l-Trp) in biological systems. Although many decades have passed since their discovery, the mechanism of tryptophan oxidation has not been established. It has been widely assumed that IDO and TDO react using the same mechanism, although there is no evidence that they do. For IDO, a Compound II (ferryl) species accumulates in the steady state and is implicated in the mechanism; in TDO, no such species has ever been observed. In this paper, we examine the kinetics of tryptophan oxidation in TDO. We find no evidence for the accumulation of Compound II during TDO catalysis. Instead, a ternary [Fe(II)-O2, l-Trp] complex is detected under steady state conditions. The absence of a Compound II species in the steady state in TDO is not due to an intrinsic inability of the TDO enzyme to form ferryl heme, because Compound II can be formed directly through a different route in which ferrous heme is reacted with peroxide. We interpret the data to mean that the rate-limiting step in the IDO and TDO mechanisms is not the same.
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Affiliation(s)
- Jaswir Basran
- Department of Molecular and Cellular Biology and Henry Wellcome Laboratories for Structural Biology, Henry Wellcome Building, University of Leicester , Lancaster Road, Leicester LE1 7RH, England, U.K
| | - Elizabeth S Booth
- Department of Chemistry, University of Leicester , University Road, Leicester LE1 7RH, England, U.K
| | - Michael Lee
- Department of Molecular and Cellular Biology and Henry Wellcome Laboratories for Structural Biology, Henry Wellcome Building, University of Leicester , Lancaster Road, Leicester LE1 7RH, England, U.K
| | - Sandeep Handa
- Department of Chemistry, University of Leicester , University Road, Leicester LE1 7RH, England, U.K
| | - Emma L Raven
- Department of Chemistry, University of Leicester , University Road, Leicester LE1 7RH, England, U.K
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Raven EL. A short history of heme dioxygenases: rise, fall and rise again. J Biol Inorg Chem 2016; 22:175-183. [PMID: 27909919 PMCID: PMC5350241 DOI: 10.1007/s00775-016-1412-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/10/2016] [Indexed: 01/20/2023]
Abstract
It is well established that there are two different classes of enzymes—tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO)—that catalyse the O2-dependent oxidation of l-tryptophan to N-formylkynurenine. But it was not always so. This perspective presents a short history of the early TDO and IDO literature, the people that were involved in creating it, and the legacy that this left for the future.
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Affiliation(s)
- Emma L Raven
- Department of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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Yuasa HJ. Highl-Trp affinity of indoleamine 2,3-dioxygenase 1 is attributed to two residues located in the distal heme pocket. FEBS J 2016; 283:3651-3661. [DOI: 10.1111/febs.13834] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 05/31/2016] [Accepted: 08/12/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Hajime J. Yuasa
- Laboratory of Biochemistry; Department of Applied Science; Faculty of Science; National University Corporation Kochi University; Japan
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Davis I, Liu A. What is the tryptophan kynurenine pathway and why is it important to neurotherapeutics? Expert Rev Neurother 2015; 15:719-21. [PMID: 26004930 DOI: 10.1586/14737175.2015.1049999] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The kynurenine pathway has received increasing attention as its connection to inflammation, the immune system and neurological conditions has become more apparent. It is the primary route for tryptophan catabolism in the liver and the starting point for the synthesis of nicotinamide adenine dinucleotide in mammals. Dysregulation or overactivation of this pathway can lead to immune system activation and accumulation of potentially neurotoxic compounds. These aspects make the kynurenine pathway a promising target for therapeutic development to treat inflammation and disease with neurological aspects, especially in cancer patients undergoing chemotherapy.
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Affiliation(s)
- Ian Davis
- Department of Chemistry, Atlanta, GA 30303, USA
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Bis-Fe(IV): nature's sniper for long-range oxidation. J Biol Inorg Chem 2014; 19:1057-67. [PMID: 24722994 DOI: 10.1007/s00775-014-1123-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
Iron-dependent enzymes are prevalent in nature and participate in a wide range of biological redox activities. Frequently, high-valence iron intermediates are involved in the catalytic events of iron-dependent enzymes, especially when the activation of peroxide or molecular oxygen is involved. Building on the fundamental framework of iron-oxygen chemistry, these reactive intermediates constantly attract significant attention from the enzymology community. During the past few decades, tremendous efforts from a number of laboratories have been dedicated to the capture and characterization of these intermediates to improve mechanistic understandings. In 2008, an unprecedented bis-Fe(IV) intermediate was reported in a c-type diheme enzyme, MauG, which is involved in the maturation of a tryptophan tryptophylquinone cofactor of methylamine dehydrogenase. This intermediate, although chemically equivalent to well-characterized high-valence iron intermediates, such as compound I, compound ES, and intermediate Q in methane monooxygenase, as well as the hypothetical Fe(V) species in Rieske non-heme oxygenases, is orders of magnitude more stable than these other high-valence species in the absence of its primary substrate. It has recently been discovered that the bis-Fe(IV) intermediate exhibits a unique near-IR absorption feature which has been attributed to a novel charge-resonance phenomenon. This review compares the properties of MauG with structurally related enzymes, summarizes the current knowledge of this new high-valence iron intermediate, including its chemical origin and structural basis, explores the formation and consequences of charge resonance, and recounts the long-range catalytic mechanism in which bis-Fe(IV) participates. Biological strategies for storing oxidizing equivalents with iron ions are also discussed.
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