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Meng LH, Awakawa T, Li XM, Quan Z, Yang SQ, Wang BG, Abe I. Discovery of (±)-Penindolenes Reveals an Unusual Indole Ring Cleavage Pathway Catalyzed by P450 Monooxygenase. Angew Chem Int Ed Engl 2024; 63:e202403963. [PMID: 38635317 DOI: 10.1002/anie.202403963] [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: 02/27/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 04/19/2024]
Abstract
(±)-Penindolenes A-D (1-4), the first representatives of indole terpenoids featuring a γ-lactam skeleton, were isolated from the mangrove-derived endophytic fungus Penicillium brocae MA-231. Our bioactivity tests revealed their potent antimicrobial and acetylcholinesterase inhibitory activities. The biosynthetic reactions by the five enzymes PbaABCDE leading to γ-lactam ring formation were identified with heterologous expression and in vitro enzymatic assays. Remarkably, the cytochrome P450 monooxygenase PbaB and its homolog in Aspergillus oryzae catalyzed the 2,3-cleavage of the indole ring to generate two keto groups in 1. This is the first example of the oxidative cleavage of indole by a P450 monooxygenase. In addition, rare secondary amide bond formation by the glutamine synthetase-like enzyme PbaD was reported. These findings will contribute to the engineered biosynthesis of unnatural, bioactive indole terpenoids.
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Affiliation(s)
- Ling-Hong Meng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Nanhai Road 7, Qingdao, 266071, China
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- RIKEN Center for Sustainable Resource Science 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Xiao-Ming Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Nanhai Road 7, Qingdao, 266071, China
| | - Zhiyang Quan
- RIKEN Center for Sustainable Resource Science 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Sui-Qun Yang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Nanhai Road 7, Qingdao, 266071, China
| | - Bin-Gui Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Nanhai Road 7, Qingdao, 266071, China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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2
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Devkota L, Xiong J, Fischer AA, Murphy K, Kumar P, Balensiefen EL, Lindeman SV, Popescu CV, Fiedler AT. Observation of oxygenated intermediates in functional mimics of aminophenol dioxygenase. J Inorg Biochem 2024; 259:112632. [PMID: 38950482 DOI: 10.1016/j.jinorgbio.2024.112632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/31/2024] [Accepted: 06/01/2024] [Indexed: 07/03/2024]
Abstract
Aminophenol dioxygenases (APDO) are mononuclear nonheme iron enzymes that utilize dioxygen (O2) to catalyze the conversion of o-aminophenols to 2-picolinic acid derivatives in metabolic pathways. This study describes the synthesis and O2 reactivity of two synthetic models of substrate-bound APDO: [FeII(TpMe2)(tBu2APH)] (1) and [FeII(TpMe2)(tBuAPH)] (2), where TpMe2 = hydrotris(3,5-dimethylpyrazole-1-yl)borate, tBu2APH = 4,6-di-tert-butyl-2-aminophenolate, and tBuAPH2 = 4-tert-butyl-2-aminophenolate. Both Fe(II) complexes behave as functional APDO mimics, as exposure to O2 results in oxidative CC bond cleavage of the o-aminophenolate ligand. The ring-cleaved products undergo spontaneous cyclization to give substituted 2-picolinic acids, as verified by 1H NMR spectroscopy, mass spectrometry, and X-ray crystallography. Reaction of the APDO models with O2 at low temperature reveals multiple intermediates, which were probed with UV-vis absorption, electron paramagnetic resonance (EPR), Mössbauer (MB), and resonance Raman (rRaman) spectroscopies. The most stable intermediate at -70 °C in THF exhibits multiple isotopically-sensitive features in rRaman samples prepared with 16O2 and 18O2, confirming incorporation of O2-derived atom(s) into its molecular structure. Insights into the geometric structures, electronic properties, and spectroscopic features of the observed intermediates were obtained from density functional theory (DFT) calculations. Although functional APDO models have been previously reported, this is the first time that an oxygenated ligand-based radical has been detected and spectroscopically characterized in the ring-cleaving mechanism of a relevant synthetic system.
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Affiliation(s)
- Laxmi Devkota
- Department of Chemistry, Marquette University, 1414 W. Clybourn St., Milwaukee, WI 53233, United States
| | - Jin Xiong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Anne A Fischer
- Department of Chemistry, Marquette University, 1414 W. Clybourn St., Milwaukee, WI 53233, United States
| | - Kate Murphy
- Department of Chemistry, The College of Arts and Sciences, University of St. Thomas, St. Paul, MN 55105, United States
| | - Praveen Kumar
- Department of Chemistry, Marquette University, 1414 W. Clybourn St., Milwaukee, WI 53233, United States
| | - Ellie L Balensiefen
- Department of Chemistry, Marquette University, 1414 W. Clybourn St., Milwaukee, WI 53233, United States
| | - Sergey V Lindeman
- Department of Chemistry, Marquette University, 1414 W. Clybourn St., Milwaukee, WI 53233, United States
| | - Codrina V Popescu
- Department of Chemistry, The College of Arts and Sciences, University of St. Thomas, St. Paul, MN 55105, United States.
| | - Adam T Fiedler
- Department of Chemistry, Marquette University, 1414 W. Clybourn St., Milwaukee, WI 53233, United States.
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Windsor P, Ouyang H, da Costa JAG, Damodaran AR, Chen Y, Bhagi-Damodaran A. Gas tunnel engineering of prolyl hydroxylase reprograms hypoxia signaling in cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.07.552357. [PMID: 37609209 PMCID: PMC10441328 DOI: 10.1101/2023.08.07.552357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Cells have evolved intricate mechanisms for recognizing and responding to changes in oxygen (O2) concentrations. Here, we have reprogrammed cellular hypoxia (low O2) signaling via gas tunnel engineering of prolyl hydroxylase 2 (PHD2), a non-heme iron dependent O2 sensor. Using computational modeling and protein engineering techniques, we identify a gas tunnel and critical residues therein that limit the flow of O2 to PHD2's catalytic core. We show that systematic modification of these residues can open the constriction topology of PHD2's gas tunnel. Using kinetic stopped-flow measurements with NO as a surrogate diatomic gas, we demonstrate up to 3.5-fold enhancement in its association rate to the iron center of tunnel-engineered mutants. Our most effectively designed mutant displays 9-fold enhanced catalytic efficiency (kcat/KM = 830 ± 40 M-1 s-1) in hydroxylating a peptide mimic of hypoxia inducible transcription factor HIF-1α, as compared to WT PHD2 (kcat/KM = 90 ± 9 M-1 s-1). Furthermore, transfection of plasmids that express designed PHD2 mutants in HEK-293T mammalian cells reveal significant reduction of HIF-1α and downstream hypoxia response transcripts under hypoxic conditions of 1% O2. Overall, these studies highlight activation of PHD2 as a new pathway to reprogram hypoxia responses and HIF signaling in cells.
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Affiliation(s)
- Peter Windsor
- Department of Chemistry University of Minnesota, Twin Cities Minneapolis, MN, 55455, United States
| | - Haiping Ouyang
- Department of Biochemistry and Molecular Biology University of Minnesota, Twin Cities Minneapolis, MN, 55455, United States
| | - Joseph A G da Costa
- Department of Chemistry University of Minnesota, Twin Cities Minneapolis, MN, 55455, United States
| | - Anoop Rama Damodaran
- Department of Chemistry University of Minnesota, Twin Cities Minneapolis, MN, 55455, United States
| | - Yue Chen
- Department of Biochemistry and Molecular Biology University of Minnesota, Twin Cities Minneapolis, MN, 55455, United States
| | - Ambika Bhagi-Damodaran
- Department of Chemistry University of Minnesota, Twin Cities Minneapolis, MN, 55455, United States
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4
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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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5
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Li L, Shen S, Bickler P, Jacobson MP, Wu LF, Altschuler SJ. Searching for molecular hypoxia sensors among oxygen-dependent enzymes. eLife 2023; 12:e87705. [PMID: 37494095 PMCID: PMC10371230 DOI: 10.7554/elife.87705] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/09/2023] [Indexed: 07/27/2023] Open
Abstract
The ability to sense and respond to changes in cellular oxygen levels is critical for aerobic organisms and requires a molecular oxygen sensor. The prototypical sensor is the oxygen-dependent enzyme PHD: hypoxia inhibits its ability to hydroxylate the transcription factor HIF, causing HIF to accumulate and trigger the classic HIF-dependent hypoxia response. A small handful of other oxygen sensors are known, all of which are oxygen-dependent enzymes. However, hundreds of oxygen-dependent enzymes exist among aerobic organisms, raising the possibility that additional sensors remain to be discovered. This review summarizes known and potential hypoxia sensors among human O2-dependent enzymes and highlights their possible roles in hypoxia-related adaptation and diseases.
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Affiliation(s)
- Li Li
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Susan Shen
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
- Department of Psychiatry, University of California, San FranciscoSan FranciscoUnited States
| | - Philip Bickler
- Hypoxia Research Laboratory, University of California San Francisco, San FranciscoSan FranciscoUnited States
- Center for Health Equity in Surgery and Anesthesia, University of California San Francisco, San FranciscoSan FranciscoUnited States
- Anesthesia and Perioperative Care, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Lani F Wu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Steven J Altschuler
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
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6
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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 DOI: 10.1016/j.jbc.2023.104753] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [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 down-regulate 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 44195, USA
| | - Dennis J Stuehr
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195, USA.
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7
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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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8
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The Role of Tryptophan Dysmetabolism and Quinolinic Acid in Depressive and Neurodegenerative Diseases. Biomolecules 2022; 12:biom12070998. [PMID: 35883554 PMCID: PMC9313172 DOI: 10.3390/biom12070998] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/04/2022] [Accepted: 07/14/2022] [Indexed: 02/04/2023] Open
Abstract
Emerging evidence suggests that neuroinflammation is involved in both depression and neurodegenerative diseases. The kynurenine pathway, generating metabolites which may play a role in pathogenesis, is one of several competing pathways of tryptophan metabolism. The present article is a narrative review of tryptophan metabolism, neuroinflammation, depression, and neurodegeneration. A disturbed tryptophan metabolism with increased activity of the kynurenine pathway and production of quinolinic acid may result in deficiencies in tryptophan and derived neurotransmitters. Quinolinic acid is an N-methyl-D-aspartate receptor agonist, and raised levels in CSF, together with increased levels of inflammatory cytokines, have been reported in mood disorders. Increased quinolinic acid has also been observed in neurodegenerative diseases, including Parkinson’s disease, Alzheimer’s disease, amyotrophic lateral sclerosis, and HIV-related cognitive decline. Oxidative stress in connection with increased indole-dioxygenase (IDO) activity and kynurenine formation may contribute to inflammatory responses and the production of cytokines. Increased formation of quinolinic acid may occur at the expense of kynurenic acid and neuroprotective picolinic acid. While awaiting ongoing research on potential pharmacological interventions on tryptophan metabolism, adequate protein intake with appropriate amounts of tryptophan and antioxidants may offer protection against oxidative stress and provide a balanced set of physiological receptor ligands.
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9
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Nayek A, Ahmed ME, Samanta S, Dinda S, Patra S, Dey SG, Dey A. Bioinorganic Chemistry on Electrodes: Methods to Functional Modeling. J Am Chem Soc 2022; 144:8402-8429. [PMID: 35503922 DOI: 10.1021/jacs.2c01842] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
One of the major goals of bioinorganic chemistry has been to mimic the function of elegant metalloenzymes. Such functional modeling has been difficult to attain in solution, in particular, for reactions that require multiple protons and multiple electrons (nH+/ne-). Using a combination of heterogeneous electrochemistry, electrode and molecule design one may control both electron transfer (ET) and proton transfer (PT) of these nH+/ne- reactions. Such control can allow functional modeling of hydrogenases (H+ + e- → 1/2 H2), cytochrome c oxidase (O2 + 4 e- + 4 H+ → 2 H2O), monooxygenases (RR'CH2 + O2 + 2 e- + 2 H+ → RR'CHOH + H2O) and dioxygenases (S + O2 → SO2; S = organic substrate) in aqueous medium and at room temperatures. In addition, these heterogeneous constructs allow probing unnatural bioinspired reactions and estimation of the inner- and outer-sphere reorganization energy of small molecules and proteins.
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Affiliation(s)
- Abhijit Nayek
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Md Estak Ahmed
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Soumya Samanta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Souvik Dinda
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Suman Patra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
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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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Mondal P, Rajapakse S, Wijeratne GB. Following Nature's Footprint: Mimicking the High-Valent Heme-Oxo Mediated Indole Monooxygenation Reaction Landscape of Heme Enzymes. J Am Chem Soc 2022; 144:3843-3854. [PMID: 35112858 DOI: 10.1021/jacs.1c11068] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pathways for direct conversion of indoles to oxindoles have accumulated considerable interest in recent years due to their significance in the clear comprehension of various pathogenic processes in humans and the multipotent therapeutic value of oxindole pharmacophores. Heme enzymes are predominantly responsible for this conversion in biology and are thought to proceed with a compound-I active oxidant. These heme-enzyme-mediated indole monooxygenation pathways are rapidly emerging therapeutic targets; however, a clear mechanistic understanding is still lacking. Additionally, such knowledge holds promise in the rational design of highly specific indole monooxygenation synthetic protocols that are also cost-effective and environmentally benign. We herein report the first examples of synthetic compound-I and activated compound-II species that can effectively monooxygenate a diverse array of indoles with varied electronic and steric properties to exclusively produce the corresponding 2-oxindole products in good to excellent yields. Rigorous kinetic, thermodynamic, and mechanistic interrogations clearly illustrate an initial rate-limiting epoxidation step that takes place between the heme oxidant and indole substrate, and the resulting indole epoxide intermediate undergoes rearrangement driven by a 2,3-hydride shift on indole ring to ultimately produce 2-oxindole. The complete elucidation of the indole monooxygenation mechanism of these synthetic heme models will help reveal crucial insights into analogous biological systems, directly reinforcing drug design attempts targeting those heme enzymes. Moreover, these bioinspired model compounds are promising candidates for the future development of better synthetic protocols for the selective, efficient, and sustainable generation of 2-oxindole motifs, which are already known for a plethora of pharmacological benefits.
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Affiliation(s)
- Pritam Mondal
- Department of Chemistry and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35205, United States
| | - Shanuk Rajapakse
- Department of Chemistry and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35205, United States
| | - Gayan B Wijeratne
- Department of Chemistry and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35205, United States
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13
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Sacramento JJD, Albert T, Siegler M, Moënne-Loccoz P, Goldberg DP. An Iron(III) Superoxide Corrole from Iron(II) and Dioxygen. Angew Chem Int Ed Engl 2022; 61:e202111492. [PMID: 34850509 PMCID: PMC8789326 DOI: 10.1002/anie.202111492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/20/2021] [Indexed: 01/12/2023]
Abstract
A new structurally characterized ferrous corrole [FeII (ttppc)]- (1) binds one equivalent of dioxygen to form [FeIII (O2-. )(ttppc)]- (2). This complex exhibits a 16/18 O2 -isotope sensitive ν(O-O) stretch at 1128 cm-1 concomitantly with a single ν(Fe-O2 ) at 555 cm-1 , indicating it is an η1 -superoxo ("end-on") iron(III) complex. Complex 2 is the first well characterized Fe-O2 corrole, and mediates the following biologically relevant oxidation reactions: dioxygenation of an indole derivative, and H-atom abstraction from an activated O-H bond.
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Affiliation(s)
- Jireh Joy D Sacramento
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Therese Albert
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, 97239-3098, USA
| | - Maxime Siegler
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Pierre Moënne-Loccoz
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, 97239-3098, USA
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
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14
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Sacramento JJD, Albert T, Siegler M, Moënne‐Loccoz P, Goldberg DP. An Iron(III) Superoxide Corrole from Iron(II) and Dioxygen. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jireh Joy D. Sacramento
- Department of Chemistry The Johns Hopkins University 3400 North Charles Street Baltimore MD 21218 USA
| | - Therese Albert
- Department of Chemical Physiology and Biochemistry Oregon Health & Science University Portland OR 97239-3098 USA
| | - Maxime Siegler
- Department of Chemistry The Johns Hopkins University 3400 North Charles Street Baltimore MD 21218 USA
| | - Pierre Moënne‐Loccoz
- Department of Chemical Physiology and Biochemistry Oregon Health & Science University Portland OR 97239-3098 USA
| | - David P. Goldberg
- Department of Chemistry The Johns Hopkins University 3400 North Charles Street Baltimore MD 21218 USA
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15
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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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16
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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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17
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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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18
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Mukherjee M, Dey A. Rejigging Electron and Proton Transfer to Transition between Dioxygenase, Monooxygenase, Peroxygenase, and Oxygen Reduction Activity: Insights from Bioinspired Constructs of Heme Enzymes. JACS AU 2021; 1:1296-1311. [PMID: 34604840 PMCID: PMC8479764 DOI: 10.1021/jacsau.1c00100] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Indexed: 05/10/2023]
Abstract
Nature has employed heme proteins to execute a diverse set of vital life processes. Years of research have been devoted to understanding the factors which bias these heme enzymes, with all having a heme cofactor, toward distinct catalytic activity. Among them, axial ligation, distal super structure, and substrate binding pockets are few very vividly recognized ones. Detailed mechanistic investigation of these heme enzymes suggested that several of these enzymes, while functionally divergent, use similar intermediates. Furthermore, the formation and decay of these intermediates depend on proton and electron transfer processes in the enzyme active site. Over the past decade, work in this group, using in situ surface enhanced resonance Raman spectroscopy of synthetic and biosynthetic analogues of heme enzymes, a general idea of how proton and electron transfer rates relate to the lifetime of different O2 derived intermediates has been developed. These findings suggest that the enzymatic activities of all these heme enzymes can be integrated into one general cycle which can be branched out to different catalytic pathways by regulating the lifetime and population of each of these intermediates. This regulation can further be achieved by tuning the electron and proton transfer steps. By strategically populating one of these intermediates during oxygen reduction, one can navigate through different catalytic processes to a desired direction by altering proton and electron transfer steps.
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Affiliation(s)
- Manjistha Mukherjee
- School of Chemical Science, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India, 700032
| | - Abhishek Dey
- School of Chemical Science, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India, 700032
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19
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Characterization of the structural determinants of the ubiquitin-dependent proteasomal degradation of human hepatic tryptophan 2,3-dioxygenase. Biochem J 2021; 478:1999-2017. [PMID: 33960368 DOI: 10.1042/bcj20210213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/17/2022]
Abstract
Human hepatic tryptophan 2,3-dioxygenase (hTDO) is a homotetrameric hemoprotein. It is one of the most rapidly degraded liver proteins with a half-life (t1/2) of ∼2.3 h, relative to an average t1/2 of ∼2-3 days for total liver protein. The molecular mechanism underlying the poor longevity of hTDO remains elusive. Previously, we showed that hTDO could be recognized and ubiquitinated by two E3 ubiquitin (Ub) ligases, gp78/AMFR and CHIP, and subsequently degraded via Ub-dependent proteasomal degradation pathway. Additionally, we identified 15 ubiquitination K-sites and demonstrated that Trp-binding to an exosite impeded its proteolytic degradation. Here, we further established autophagic-lysosomal degradation as an alternative back-up pathway for cellular hTDO degradation. In addition, with protein kinases A and C, we identified 13 phosphorylated Ser/Thr (pS/pT) sites. Mapping these pS/pT sites on the hTDO surface revealed their propinquity to acidic Asp/Glu (D/E) residues engendering negatively charged DEpSpT clusters vicinal to the ubiquitination K-sites over the entire protein surface. Through site-directed mutagenesis of positively charged patches of gp78, previously documented to interact with the DEpSpT clusters in other target proteins, we uncovered the likely role of the DEpSpT clusters in the molecular recognition of hTDO by gp78 and plausibly other E3 Ub-ligases. Furthermore, cycloheximide-chase analyses revealed the critical structural relevance of the disordered N- and C-termini not only in the Ub-ligase recognition, but also in the proteasome engagement. Together, the surface DEpSpT clusters and the N- and C-termini constitute an intrinsic bipartite degron for hTDO physiological turnover.
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20
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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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21
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Cundy NJ, Hare RK, Tang T, Leach AG, Jowitt TA, Qureshi O, Gordon J, Barnes NM, Brady CA, Raven EL, Grainger RS, Butterworth S. Design, synthesis and evaluation of tryptophan analogues as tool compounds to study IDO1 activity. RSC Chem Biol 2021; 2:1651-1660. [PMID: 34977580 PMCID: PMC8637876 DOI: 10.1039/d0cb00209g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 08/20/2021] [Indexed: 11/22/2022] Open
Abstract
The metabolism of l-tryptophan to N-formyl-l-kynurenine by indoleamine-2,3-dioxygenase 1 (IDO1) is thought to play a critical role in tumour-mediated immune suppression. Whilst there has been significant progress in elucidating the overall enzymatic mechanism of IDO1 and related enzymes, key aspects of the catalytic cycle remain poorly understood. Here we report the design, synthesis and biological evaluation of a series of tryptophan analogues which have the potential to intercept putative intermediates in the metabolism of 1 by IDO1. Functionally-relevant binding to IDO1 was demonstrated through enzymatic inhibition, however no IDO1-mediated metabolism of these compounds was observed. Subsequent Tm-shift analysis shows the most active compound, 17, exhibits a distinct profile from known competitive IDO1 inhibitors, with docking studies supporting the hypothesis that 17 may bind at the recently-discovered Si site. These findings provide a start-point for development of further mechanistic probes and more potent tryptophan-based IDO1 inhibitors. We report the rational design, novel syntheses and biophysical and in silico evaluation of tryptophan-inspired tool compounds to probe the illusive MOA of the clinically-relevant heme-dioxygenase protein, IDO1.![]()
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Affiliation(s)
- Nicholas J. Cundy
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Roseanna K. Hare
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Tina Tang
- Celentyx Ltd, Birmingham Research Park, 97 Vincent Drive, Birmingham, B15 2SQ, UK
| | - Andrew G. Leach
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Thomas A. Jowitt
- Wellcome Trust Centre for Cell Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Omar Qureshi
- Celentyx Ltd, Birmingham Research Park, 97 Vincent Drive, Birmingham, B15 2SQ, UK
| | - John Gordon
- Celentyx Ltd, Birmingham Research Park, 97 Vincent Drive, Birmingham, B15 2SQ, UK
| | - Nicholas M. Barnes
- Celentyx Ltd, Birmingham Research Park, 97 Vincent Drive, Birmingham, B15 2SQ, UK
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Catherine A. Brady
- Celentyx Ltd, Birmingham Research Park, 97 Vincent Drive, Birmingham, B15 2SQ, UK
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Emma L. Raven
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Richard S. Grainger
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Sam Butterworth
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
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22
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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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23
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Mirgaux M, Leherte L, Wouters J. Influence of the presence of the heme cofactor on the JK-loop structure in indoleamine 2,3-dioxygenase 1. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:1211-1221. [DOI: 10.1107/s2059798320013510] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/08/2020] [Indexed: 01/13/2023]
Abstract
Indoleamine 2,3-dioxygenase 1 has sparked interest as an immunotherapeutic target in cancer research. Its structure includes a loop, named the JK-loop, that controls the orientation of the substrate or inhibitor within the active site. However, little has been reported about the crystal structure of this loop. In the present work, the conformation of the JK-loop is determined for the first time in the presence of the heme cofactor in the active site through X-ray diffraction experiments (2.44 Å resolution). Molecular-dynamics trajectories were also obtained to provide dynamic information about the loop according to the presence of cofactor. This new structural and dynamic information highlights the importance of the JK-loop in confining the labile heme cofactor to the active site.
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24
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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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25
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Leone L, Chino M, Nastri F, Maglio O, Pavone V, Lombardi A. Mimochrome, a metalloporphyrin‐based catalytic Swiss knife†. Biotechnol Appl Biochem 2020; 67:495-515. [DOI: 10.1002/bab.1985] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/09/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Linda Leone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Marco Chino
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Flavia Nastri
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Ornella Maglio
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
- IBB ‐ National Research Council Napoli Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Angela Lombardi
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
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26
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Mukherjee M, Dey A. Catalytic C–H Bond Oxidation Using Dioxygen by Analogues of Heme Superoxide. Inorg Chem 2020; 59:7415-7425. [DOI: 10.1021/acs.inorgchem.9b03767] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Manjistha Mukherjee
- School of Chemical Science, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata 700032, India
| | - Abhishek Dey
- School of Chemical Science, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata 700032, India
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27
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Liu C, Nan Y, Xia Z, Gu K, Chen C, Dong X, Ju D, Zhao W. Discovery of novel hydroxyamidine derivatives as indoleamine 2,3-dioxygenase 1 inhibitors with in vivo anti-tumor efficacy. Bioorg Med Chem Lett 2020; 30:127038. [PMID: 32088128 DOI: 10.1016/j.bmcl.2020.127038] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/08/2020] [Accepted: 02/14/2020] [Indexed: 01/02/2023]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1) is closely associated with immune escape in many tumor tissues, and is considered to be a valuable therapeutic target in cancer immunotherapy. In this study, the modification of amino sidechain was performed with the hydroxyamidine core kept intact to optimize lead compound Epacadostat. 19 new compounds with hydrazide, thietane or sulfonamide moiety as polar capping group in sidechain were prepared and their IDO1 inhibitory activities were evaluated. Sulfonamide 3a showed potent IDO1 inhibition in both enzymatic and cellular assays with the IC50 value of 71 nM and EC50 value of 11 nM, respectively. Furthermore, in vivo Lewis lung cancer (LLC) allograft studies of 3a indicated that it handicapped the tumor growth with similar efficacy to Epacadostat. Molecular docking demonstrated that the change of polar capping group affords influence on the orientation of amino ethylene side chain and forms new hydrogen bonding.
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Affiliation(s)
- Chang Liu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Yanyang Nan
- Department of Microbiological and Biochemical Pharmacy, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Zhifeng Xia
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Kedan Gu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Cheng Chen
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Xiaochun Dong
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Dianwen Ju
- Department of Microbiological and Biochemical Pharmacy, School of Pharmacy, Fudan University, Shanghai 201203, PR China.
| | - Weili Zhao
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, PR China.
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28
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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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29
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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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30
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Yanagisawa S, Kayama K, Hara M, Sugimoto H, Shiro Y, Ogura T. UV Resonance Raman Characterization of a Substrate Bound to Human Indoleamine 2,3-Dioxygenase 1. Biophys J 2019; 117:706-716. [PMID: 31405517 DOI: 10.1016/j.bpj.2019.07.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/28/2019] [Accepted: 07/08/2019] [Indexed: 01/25/2023] Open
Abstract
Human indoleamine 2,3-dioxygenase 1 (IDO) is a heme enzyme that catalyzes the first reaction of the main metabolic pathway of L-tryptophan (Trp) to produce N-formylkynurenin. The reaction involves cleavage of the C2=C3 bond in the Trp indole ring and insertion of two atomic oxygens from the iron-bound O2 into the indole 2 and 3 position. For establishment of the chemical mechanism of this unique enzymatic reaction, it is necessary to determine the conformation and electronic state of the substrate Trp bound to IDO. In this study, we measured the ultraviolet resonance Raman spectra of IDO in the presence of Trp to detect the vibrational modes of the substrate Trp. We compared the ultraviolet resonace Raman spectra of Trp in a ternary complex (Trp-bound cyanide enzyme) and a binary complex (Trp-bound reduced enzyme) of IDO with that of free Trp in solution and found that binding to IDO influences the conformation of Trp, resulting in similar changes in the two complexes, especially around the C3-Cβ bond. However, the presence of the diatomic ligand at the heme sixth coordination site in the ternary complex significantly alters the mobility and electronic structure of Trp, most likely resulting in the C2=C3 bond cleavage in the enzymatic reaction.
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Affiliation(s)
- Sachiko Yanagisawa
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo, Japan.
| | - Kure'e Kayama
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo, Japan
| | - Masayuki Hara
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo, Japan
| | | | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo, Japan
| | - Takashi Ogura
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo, Japan
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31
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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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32
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Jeon H, Hong S. Peroxide Bond Cleavage of Nonheme Iron-(Hydro/Alkyl)Peroxo Complexes Induced by Endogenous and Exogenous Factors. CHEM LETT 2019. [DOI: 10.1246/cl.180831] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hyeri Jeon
- Department of Chemistry, Sookmyung Women’s University, Seoul 04310, Korea
| | - Seungwoo Hong
- Department of Chemistry, Sookmyung Women’s University, Seoul 04310, Korea
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33
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Adam SM, Wijeratne GB, Rogler PJ, Diaz DE, Quist DA, Liu JJ, Karlin KD. Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function. Chem Rev 2018; 118:10840-11022. [PMID: 30372042 PMCID: PMC6360144 DOI: 10.1021/acs.chemrev.8b00074] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.
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Affiliation(s)
- Suzanne M. Adam
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gayan B. Wijeratne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Patrick J. Rogler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Daniel E. Diaz
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David A. Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jeffrey J. Liu
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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34
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Luo S, Xu K, Xiang S, Chen J, Chen C, Guo C, Tong Y, Tong L. High-resolution structures of inhibitor complexes of human indoleamine 2,3-dioxygenase 1 in a new crystal form. Acta Crystallogr F Struct Biol Commun 2018; 74:717-724. [PMID: 30387777 PMCID: PMC6213978 DOI: 10.1107/s2053230x18012955] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 09/13/2018] [Indexed: 11/11/2022] Open
Abstract
Human indoleamine 2,3-dioxygenase 1 (IDO1) is a heme-dependent enzyme with important roles in many cellular processes and is a potential target for drug discovery against cancer and other diseases. Crystal structures of IDO1 in complex with various inhibitors have been reported. Many of these crystals belong to the same crystal form and most of the reported structures have resolutions in the range 3.2-2.3 Å. Here, three new crystal forms of human IDO1 obtained by introducing a surface mutation, K116A/K117A, distant from the active site are reported. One of these crystal forms diffracted to 1.5 Å resolution and can be readily used for soaking experiments to determine high-resolution structures of IDO1 in complex with the substrate tryptophan or inhibitors that coordinate the heme. In addition, this mutant was used to produce crystals of a complex with an inhibitor that targets the apo form of the enzyme under the same conditions; the structure of this complex was determined at 1.7 Å resolution. Overall, this mutant represents a robust platform for determining the structures of inhibitor and substrate complexes of IDO1 at high resolution.
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Affiliation(s)
- Shukun Luo
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Ke Xu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Shaoyun Xiang
- Suzhou Kintor Pharmaceuticals Inc., Suzhou Industrial Park, Suzhou 215123, People’s Republic of China
| | - Jie Chen
- Suzhou Kintor Pharmaceuticals Inc., Suzhou Industrial Park, Suzhou 215123, People’s Republic of China
| | - Chunyun Chen
- Suzhou Kintor Pharmaceuticals Inc., Suzhou Industrial Park, Suzhou 215123, People’s Republic of China
| | - Chuangxin Guo
- Suzhou Kintor Pharmaceuticals Inc., Suzhou Industrial Park, Suzhou 215123, People’s Republic of China
| | - Youzhi Tong
- Suzhou Kintor Pharmaceuticals Inc., Suzhou Industrial Park, Suzhou 215123, People’s Republic of China
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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35
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Pham KN, Yeh SR. Mapping the Binding Trajectory of a Suicide Inhibitor in Human Indoleamine 2,3-Dioxygenase 1. J Am Chem Soc 2018; 140:14538-14541. [PMID: 30347977 DOI: 10.1021/jacs.8b07994] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Human indoleamine 2,3-dioxygenase 1 (hIDO1) is an important heme-containing enzyme that is a key drug target for cancer immunotherapy. Several hIDO1 inhibitors have entered clinical trials, among which BMS-986205 (BMS) stands out as the only suicide inhibitor. Despite its "best-in-class" activity, the action mechanism of BMS remains elusive. Here, we report three crystal structures of hIDO1-BMS complexes that define the complete binding trajectory of the inhibitor. BMS first binds in a solvent exposed surface cleft near the active site in an extended conformation. The initial binding partially unfolds the active site, which triggers heme release, thereby exposing a new binding pocket. The inhibitor then undergoes a large scale movement to this new binding pocket, where it binds by adopting a high energy kinked conformation. Finally, the inhibitor relaxes to a bent conformation, via an additional large scale rearrangement, culminating in the energy minimum state. The structural data offer a molecular explanation for the remarkable efficacy and suicide inhibition activity of the inhibitor. They also suggest a novel strategy that can be applied for drug development targeting hIDO1 and related enzymes.
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Affiliation(s)
- Khoa N Pham
- Department of Physiology and Biophysics , Albert Einstein College of Medicine , Bronx , New York 10461 , United States
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics , Albert Einstein College of Medicine , Bronx , New York 10461 , United States
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36
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Guengerich FP, Yoshimoto FK. Formation and Cleavage of C-C Bonds by Enzymatic Oxidation-Reduction Reactions. Chem Rev 2018; 118:6573-6655. [PMID: 29932643 DOI: 10.1021/acs.chemrev.8b00031] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Many oxidation-reduction (redox) enzymes, particularly oxygenases, have roles in reactions that make and break C-C bonds. The list includes cytochrome P450 and other heme-based monooxygenases, heme-based dioxygenases, nonheme iron mono- and dioxygenases, flavoproteins, radical S-adenosylmethionine enzymes, copper enzymes, and peroxidases. Reactions involve steroids, intermediary metabolism, secondary natural products, drugs, and industrial and agricultural chemicals. Many C-C bonds are formed via either (i) coupling of diradicals or (ii) generation of unstable products that rearrange. C-C cleavage reactions involve several themes: (i) rearrangement of unstable oxidized products produced by the enzymes, (ii) oxidation and collapse of radicals or cations via rearrangement, (iii) oxygenation to yield products that are readily hydrolyzed by other enzymes, and (iv) activation of O2 in systems in which the binding of a substrate facilitates O2 activation. Many of the enzymes involve metals, but of these, iron is clearly predominant.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States.,Department of Chemistry , University of Texas-San Antonio , San Antonio , Texas 78249-0698 , United States
| | - Francis K Yoshimoto
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States.,Department of Chemistry , University of Texas-San Antonio , San Antonio , Texas 78249-0698 , United States
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37
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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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38
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Alexandre JAC, Swan MK, Latchem MJ, Boyall D, Pollard JR, Hughes SW, Westcott J. New 4-Amino-1,2,3-Triazole Inhibitors of Indoleamine 2,3-Dioxygenase Form a Long-Lived Complex with the Enzyme and Display Exquisite Cellular Potency. Chembiochem 2018; 19:552-561. [PMID: 29240291 DOI: 10.1002/cbic.201700560] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Indexed: 11/09/2022]
Abstract
Indoleamine-2,3 dioxygenase 1 (IDO1) has emerged as a central regulator of immune responses in both normal and disease biology. Due to its established role in promoting tumour immune escape, IDO1 has become an attractive target for cancer treatment. A novel series of highly cell potent IDO1 inhibitors based on a 4-amino-1,2,3-triazole core have been identified. Comprehensive kinetic, biochemical and structural studies demonstrate that compounds from this series have a noncompetitive kinetic mechanism of action with respect to the tryptophan substrate. In co-complex crystal structures, the compounds bind in the tryptophan pocket and make a direct ligand interaction with the haem iron of the porphyrin cofactor. It is proposed that these data can be rationalised by an ordered-binding mechanism, in which the inhibitor binds an apo form of the enzyme that is not competent to bind tryptophan. These inhibitors also form a very tight, long-lived complex with the enzyme, which partially explains their exquisite cellular potency. This novel series represents an attractive starting point for the future development of potent IDO1-targeted drugs.
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Affiliation(s)
| | - Michael Kenneth Swan
- Vertex Pharmaceuticals (Europe) Limited, 86-88 Jubilee Avenue, Abingdon, Oxfordshire, OX14 4RW, UK
| | - Mike John Latchem
- Vertex Pharmaceuticals (Europe) Limited, 86-88 Jubilee Avenue, Abingdon, Oxfordshire, OX14 4RW, UK
| | - Dean Boyall
- Vertex Pharmaceuticals (Europe) Limited, 86-88 Jubilee Avenue, Abingdon, Oxfordshire, OX14 4RW, UK
| | - John Robert Pollard
- Vertex Pharmaceuticals (Europe) Limited, 86-88 Jubilee Avenue, Abingdon, Oxfordshire, OX14 4RW, UK
| | - Stuart Wynn Hughes
- Vertex Pharmaceuticals (Europe) Limited, 86-88 Jubilee Avenue, Abingdon, Oxfordshire, OX14 4RW, UK
| | - James Westcott
- Vertex Pharmaceuticals (Europe) Limited, 86-88 Jubilee Avenue, Abingdon, Oxfordshire, OX14 4RW, UK
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39
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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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40
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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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Lewis-Ballester A, Pham KN, Batabyal D, Karkashon S, Bonanno JB, Poulos TL, Yeh SR. Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1. Nat Commun 2017; 8:1693. [PMID: 29167421 PMCID: PMC5700043 DOI: 10.1038/s41467-017-01725-8] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/11/2017] [Indexed: 12/24/2022] Open
Abstract
Human indoleamine 2,3-dioxygenase 1 (hIDO1) is an attractive cancer immunotherapeutic target owing to its role in promoting tumoral immune escape. However, drug development has been hindered by limited structural information. Here, we report the crystal structures of hIDO1 in complex with its substrate, Trp, an inhibitor, epacadostat, and/or an effector, indole ethanol (IDE). The data reveal structural features of the active site (Sa) critical for substrate activation; in addition, they disclose a new inhibitor-binding mode and a distinct small molecule binding site (Si). Structure-guided mutation of a critical residue, F270, to glycine perturbs the Si site, allowing structural determination of an inhibitory complex, where both the Sa and Si sites are occupied by Trp. The Si site offers a novel target site for allosteric inhibitors and a molecular explanation for the previously baffling substrate-inhibition behavior of the enzyme. Taken together, the data open exciting new avenues for structure-based drug design. Human indoleamine 2,3-dioxygenase 1 (hIDO1) is an immunotherapeutic target for cancer therapy. Here, the authors present the substrate-, inhibitor- and effector-bound hIDO1 crystal structures, which give insights into the mechanism and reveal a second small molecule binding site, which is of interest for drug design.
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Affiliation(s)
- Ariel Lewis-Ballester
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Khoa N Pham
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Dipanwita Batabyal
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA.,Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - Shay Karkashon
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Jeffrey B Bonanno
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Thomas L Poulos
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA.,Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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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: 51] [Impact Index Per Article: 7.3] [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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