1
|
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.
Collapse
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
| |
Collapse
|
2
|
Li S, Liu X, Tung CH, Liu L. Late-Stage Chemo- and Enantioselective Oxidation of Indoles to C3-Monosubstituted Oxindoles. J Am Chem Soc 2023. [PMID: 38038721 DOI: 10.1021/jacs.3c11742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Catalytic asymmetric preparation of chiral 3-monosubstituted oxindoles represents a significant challenge in synthetic chemistry due to the ease of racemization of the tertiary stereocenter through enolization. Here, we describe a general titanium-catalyzed chemo- and enantioselective indole oxidation to produce a diverse set of chiral 3-monosubstituted oxindoles with up to 96% yield, 99% ee, and with a substrate/catalyst ratio of 10,000 by using the combination of a simple titanium(salan) catalyst with green and atom-economic terminal oxidant H2O2. The mild approach tolerates a broad range of functional groups, enabling late-stage asymmetric diversification of a series of commercial drugs and natural products together with late-stage asymmetric construction of a wide set of enzyme antagonists, all of which are difficult to achieve through existing methods.
Collapse
Affiliation(s)
- Song Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Xigong Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Chen-Ho Tung
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Lei Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, China
| |
Collapse
|
3
|
Shi X, Zhao G, Li H, Zhao Z, Li W, Wu M, Du YL. Hydroxytryptophan biosynthesis by a family of heme-dependent enzymes in bacteria. Nat Chem Biol 2023; 19:1415-1422. [PMID: 37653171 DOI: 10.1038/s41589-023-01416-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 08/03/2023] [Indexed: 09/02/2023]
Abstract
Hydroxytryptophan serves as a chemical precursor to a variety of bioactive specialized metabolites, including the human neurotransmitter serotonin and the hormone melatonin. Although the human and animal routes to hydroxytryptophan have been known for decades, how bacteria catalyze tryptophan indole hydroxylation remains a mystery. Here we report a class of tryptophan hydroxylases that are involved in various bacterial metabolic pathways. These enzymes utilize a histidine-ligated heme cofactor and molecular oxygen or hydrogen peroxide to catalyze regioselective hydroxylation on the tryptophan indole moiety, which is mechanistically distinct from their animal counterparts from the nonheme iron enzyme family. Through genome mining, we also identify members that can hydroxylate the tryptophan indole ring at alternative positions. Our results not only reveal a conserved way to synthesize hydroxytryptophans in bacteria but also provide a valuable enzyme toolbox for biocatalysis. As proof of concept, we assemble a highly efficient pathway for melatonin in a bacterial host.
Collapse
Affiliation(s)
- Xinjie Shi
- The Fourth Affiliated Hospital and Department of Microbiology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Guiyun Zhao
- The Fourth Affiliated Hospital and Department of Microbiology, School of Medicine, Zhejiang University, Hangzhou, China
- Department of Pharmacy, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, China
| | - Hu Li
- Polytechnic Institute, Zhejiang University, Hangzhou, China
| | - Zhijie Zhao
- The Fourth Affiliated Hospital and Department of Microbiology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Wei Li
- The Fourth Affiliated Hospital and Department of Microbiology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Miaolian Wu
- Department of Pharmacy, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, China
| | - Yi-Ling Du
- The Fourth Affiliated Hospital and Department of Microbiology, School of Medicine, Zhejiang University, Hangzhou, China.
- Department of Pharmacy, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China.
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, China.
| |
Collapse
|
4
|
Qi H, Mao S, Rabeah J, Qu R, Yang N, Chen Z, Bourriquen F, Yang J, Li J, Junge K, Beller M. Water-Promoted Carbon-Carbon Bond Cleavage Employing a Reusable Fe Single-Atom Catalyst. Angew Chem Int Ed Engl 2023; 62:e202311913. [PMID: 37681485 DOI: 10.1002/anie.202311913] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/09/2023]
Abstract
The development of methods for selective cleavage reactions of thermodynamically stable C-C/C=C bonds in a green manner is a challenging research field which is largely unexplored. Herein, we present a heterogeneous Fe-N-C catalyst with highly dispersed iron centers that allows for the oxidative C-C/C=C bond cleavage of amines, secondary alcohols, ketones, and olefins in the presence of air (O2 ) and water (H2 O). Mechanistic studies reveal the presence of water to be essential for the performance of the Fe-N-C system, boosting the product yield from <1 % to >90 %. Combined spectroscopic characterizations and control experiments suggest the singlet 1 O2 and hydroxide species generated from O2 and H2 O, respectively, take selectively part in the C-C bond cleavage. The broad applicability (>40 examples) even for complex drugs as well as high activity, selectivity, and durability under comparably mild conditions highlight this unique catalytic system.
Collapse
Affiliation(s)
- Haifeng Qi
- Leibniz-Institut für Katalyse, Albert-Einstein-Straße 29a, 18059, Rostock, Germany
| | - Shuxin Mao
- Leibniz-Institut für Katalyse, Albert-Einstein-Straße 29a, 18059, Rostock, Germany
| | - Jabor Rabeah
- Leibniz-Institut für Katalyse, Albert-Einstein-Straße 29a, 18059, Rostock, Germany
| | - Ruiyang Qu
- Leibniz-Institut für Katalyse, Albert-Einstein-Straße 29a, 18059, Rostock, Germany
| | - Na Yang
- School of Materials and Energy, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Zupeng Chen
- Leibniz-Institut für Katalyse, Albert-Einstein-Straße 29a, 18059, Rostock, Germany
- Analytical & Testing Center College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Florian Bourriquen
- Leibniz-Institut für Katalyse, Albert-Einstein-Straße 29a, 18059, Rostock, Germany
| | - Ji Yang
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Jianfeng Li
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Kathrin Junge
- Leibniz-Institut für Katalyse, Albert-Einstein-Straße 29a, 18059, Rostock, Germany
| | - Matthias Beller
- Leibniz-Institut für Katalyse, Albert-Einstein-Straße 29a, 18059, Rostock, Germany
| |
Collapse
|
5
|
Gering HE, Li X, Tang H, Swartz PD, Chang WC, Makris TM. A Ferric-Superoxide Intermediate Initiates P450-Catalyzed Cyclic Dipeptide Dimerization. J Am Chem Soc 2023; 145:19256-19264. [PMID: 37611404 DOI: 10.1021/jacs.3c04542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
The cytochrome P450 (CYP) AspB is involved in the biosynthesis of the diketopiperazine (DKP) aspergilazine A. Tryptophan-linked dimeric DKP alkaloids are a large family of natural products that are found in numerous species and exhibit broad and often potent bioactivity. The proposed mechanisms for C-N bond formation by AspB, and similar C-C bond formations by related CYPs, have invoked the use of a ferryl-intermediate as an oxidant to promote substrate dimerization. Here, the parallel application of steady-state and transient kinetic approaches reveals a very different mechanism that involves a ferric-superoxide species as a primary oxidant to initiate DKP-assembly. Single turnover kinetic isotope effects and a substrate analog suggest the probable nature and site for abstraction. The direct observation of CYP-superoxide reactivity rationalizes the atypical outcome of AspB and reveals a new reaction manifold in heme enzymes.
Collapse
Affiliation(s)
- Hannah E Gering
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Xiaojun Li
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Haoyu Tang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Paul D Swartz
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Thomas M Makris
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| |
Collapse
|
6
|
Savonije K, Meek A, Weaver DF. Indoleamine 2,3-Dioxygenase as a Therapeutic Target for Alzheimer's Disease and Geriatric Depression. Brain Sci 2023; 13:852. [PMID: 37371332 DOI: 10.3390/brainsci13060852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Neuroimmune-triggered neuroinflammation of the central nervous system is emerging as an important aetiopathogenic factor for multiple neurological disorders, including depression, dementia, Alzheimer's disease, multiple sclerosis and others. Tryptophan metabolism via the kynurenic pathway, which is initiated by the indoleamine-2,3-dioxygenase (IDO-1) enzyme, is a key regulator of the neuroimmune system and its associated neuroinflammatory effects. As discussed in this review, targeting the production of immunopathic and potentially neurotoxic kynurenine metabolites by inhibitory downregulation of IDO-1 may prove a viable target against inflammation-induced neurological conditions, particularly depression and dementia.
Collapse
Affiliation(s)
- Karl Savonije
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Autumn Meek
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Donald F Weaver
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Departments of Chemistry and Medicine, University of Toronto, Toronto, ON M5S 3M2, Canada
| |
Collapse
|
7
|
Nolan K, Wang Y. Combined spectroscopic and structural approaches to explore the mechanism of histidine-ligated heme-dependent aromatic oxygenases. Methods Enzymol 2023; 685:405-432. [PMID: 37245909 PMCID: PMC11057917 DOI: 10.1016/bs.mie.2023.03.008] [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] [Indexed: 05/30/2023]
Abstract
The emergence of histidine-ligated heme-dependent aromatic oxygenases (HDAOs) has greatly enriched heme chemistry, and more studies are required to appreciate the diversity found in His-ligated heme proteins. This chapter describes recent methods in probing the HDAO mechanisms in detail, along with the discussion on how they can benefit structure-function studies of other heme systems. The experimental details are centered on studies of TyrHs, followed by explanation of how the results obtained would advance the understanding of the specific enzyme and also HDAOs. Spectroscopic methods, namely, electronic absorption and EPR spectroscopies, and X-ray crystallography are valuable techniques commonly used to characterize the properties of the heme center and the nature of heme-based intermediate. Herein, we show that the combination of these tools are extremely powerful, not only because one can acquire electronic, magnetic, and conformational information from different phases, but also because of the advantages brought by spectroscopic characterization on crystal samples.
Collapse
Affiliation(s)
- Katie Nolan
- Department of Chemistry, University of Georgia, Athens, GA, United States
| | - Yifan Wang
- Department of Chemistry, University of Georgia, Athens, GA, United States.
| |
Collapse
|
8
|
In Vitro Antiglycation Potential of Erva-Baleeira ( Varronia curassavica Jacq.). Antioxidants (Basel) 2023; 12:antiox12020522. [PMID: 36830081 PMCID: PMC9952575 DOI: 10.3390/antiox12020522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Varronia curassavica Jacq. (Boraginaceae) is traditionally used in the treatment of inflammatory processes. The ethanolic extract of its leaves (EEVc) showed anti-inflammatory properties and low toxicity. Medicinal plants have aroused interest for their antiglycation activities. The formation and accumulation of advanced glycation end products (AGEs) are associated with several chronic diseases. The objective of this study was to evaluate the antiglycation potential of EEVc and two isolated compounds. METHODS The compounds brickellin and cordialin A were obtained by chromatographic methods and identified by spectrometric techniques. Analysis of fluorescent AGEs, biomarkers of amino acid residue oxidation, protein carbonyl groups and crosslink formation were performed in samples obtained from an in vitro model system of protein glycation with methylglyoxal. RESULTS EEVc, brickellin and cordialin A significantly reduced the in vitro formation of AGEs, and reduced the damage caused by oxidative damage to the protein. CONCLUSIONS According to the results, EEVc, brickellin and cordialin A are potential candidates against AGEs formation, which opens the way to expand the therapeutic arsenal for many pathologies resulting from glycoxidative stress.
Collapse
|
9
|
Barcherini V, Loureiro JB, Sena A, Madeira C, Leandro P, Saraiva L, Antunes AMM, Santos MMM. Metabolism-Guided Optimization of Tryptophanol-Derived Isoindolinone p53 Activators. Pharmaceuticals (Basel) 2023; 16:146. [PMID: 37259297 PMCID: PMC9967700 DOI: 10.3390/ph16020146] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 11/30/2023] Open
Abstract
For the first time, the pharmacokinetic (PK) profile of tryptophanol-derived isoindolinones, previously reported as p53 activators, was investigated. From the metabolites' identification, performed by liquid chromatography coupled to high resolution tandem mass spectrometry (LC-HRMS/MS), followed by their preparation and structural elucidation, it was possible to identify that the indole C2 and C3 are the main target of the cytochrome P450 (CYP)-promoted oxidative metabolism in the tryptophanol-derived isoindolinone scaffold. Based on these findings, to search for novel p53 activators a series of 16 enantiopure tryptophanol-derived isoindolinones substituted with a bromine in indole C2 was prepared, in yields of 62-89%, and their antiproliferative activity evaluated in human colon adenocarcinoma HCT116 cell lines with and without p53. Structural optimization led to the identification of two (S)-tryptophanol-derived isoindolinones 3.9-fold and 1.9-fold more active than hit SLMP53-1, respectively. Compounds' metabolic stability evaluation revealed that this substitution led to a metabolic switch, with the impact of Phase I oxidative metabolism being minimized. Through differential scanning fluorimetry (DSF) experiments, the most active compound of the series in cell assays led to an increase in the protein melting temperature (Tm) of 10.39 °C, suggesting an effective binding to wild-type p53 core domain.
Collapse
Affiliation(s)
- Valentina Barcherini
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Joana B. Loureiro
- LAQV/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - Ana Sena
- Centro de Química Estrutural (CQE), Institute of Molecular Sciences, Departamento de Engenharia Química, Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Catarina Madeira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Paula Leandro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Lucília Saraiva
- LAQV/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - Alexandra M. M. Antunes
- Centro de Química Estrutural (CQE), Institute of Molecular Sciences, Departamento de Engenharia Química, Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Maria M. M. Santos
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| |
Collapse
|
10
|
Catala A, Stone M, Busch MP, D'Alessandro A. Reprogramming of red blood cell metabolism in Zika virus–infected donors. Transfusion 2022; 62:1045-1064. [PMID: 35285520 PMCID: PMC9086146 DOI: 10.1111/trf.16851] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Diseases caused by arthropod-borne viruses remain a burden to global health; in particular, Zika virus (ZIKV) has been reported in 87 countries and territories. In healthy blood donors, ZIKV RNA can be detected in red blood cells (RBCs) months after infection, clearance of detectable nucleic acid in plasma, and seroconversion. However, little information is available on the impact of ZIKV infection to metabolism. STUDY DESIGN AND METHODS We applied mass spectrometry-based metabolomics and lipidomics approaches to investigate the impact of ZIKV infection on RBCs over the course of infection. ZIKV-infected blood donors (n = 25) were identified through molecular and serologic methods, which included nucleic acid amplification testing and real-time polymerase chain reaction (PCR) for detection of ZIKV RNA and enzyme-linked immunosorbent assay (ELISA) for detection of flavivirus-specific IgM and IgG. RESULTS In ZIKV RNA-positive donors, we observed lower glucose and lactate levels, and higher levels of ribose phosphate, suggestive of the activation of the pentose phosphate pathway. The top pathways altered in RBCs from ZIKV-IgM-positive donors include amino acid metabolism and biosynthesis, fatty acid metabolism and biosynthesis, linoleic acid and arachidonate metabolism and glutathione metabolism. RBCs from ZIKV-infected donors had increased levels of early glycolytic metabolites, and higher levels of metabolites of the pentose phosphate pathway. Alterations in acyl-carnitine and fatty acid metabolism are consistent with impaired membrane lipid homeostasis in RBCs from ZIKV IgM positive donors. CONCLUSION RBC from healthy blood donors who had been infected by ZIKV are characterized by long-lasting metabolic alterations even months after infection has resolved.
Collapse
Affiliation(s)
- Alexis Catala
- Department of Biochemistry and Molecular Genetics University of Colorado Anschutz Medical Campus Aurora Colorado USA
- Program in Structural Biology and Biochemistry University of Colorado Anschutz Medical Campus Aurora Colorado USA
| | - Mars Stone
- Vitalant Research Institute San Francisco California USA
- Department of Laboratory Medicine University of California San Francisco San Francisco California USA
| | - Michael P. Busch
- Vitalant Research Institute San Francisco California USA
- Department of Laboratory Medicine University of California San Francisco San Francisco California USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics University of Colorado Anschutz Medical Campus Aurora Colorado USA
- Program in Structural Biology and Biochemistry University of Colorado Anschutz Medical Campus Aurora Colorado USA
| |
Collapse
|
11
|
A biosynthetic pathway to aromatic amines that uses glycyl-tRNA as nitrogen donor. Nat Chem 2022; 14:71-77. [PMID: 34725492 PMCID: PMC8758506 DOI: 10.1038/s41557-021-00802-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 08/27/2021] [Indexed: 11/12/2022]
Abstract
Aromatic amines in nature are typically installed with Glu or Gln as the nitrogen donor. Here we report a pathway that features glycyl-tRNA instead. During the biosynthesis of pyrroloiminoquinone-type natural products such as ammosamides, peptide-aminoacyl tRNA ligases append amino acids to the C-terminus of a ribosomally synthesized peptide. First, [Formula: see text] adds Trp in a Trp-tRNA-dependent reaction and the flavoprotein AmmC1 then carries out three hydroxylations of the indole ring of Trp. After oxidation to the corresponding ortho-hydroxy para-quinone, [Formula: see text] attaches Gly to the indole ring in a Gly-tRNA dependent fashion. Subsequent decarboxylation and hydrolysis results in an amino-substituted indole. Similar transformations are catalysed by orthologous enzymes from Bacillus halodurans. This pathway features three previously unknown biochemical processes using a ribosomally synthesized peptide as scaffold for non-ribosomal peptide extension and chemical modification to generate an amino acid-derived natural product.
Collapse
|
12
|
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] [Grants] [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 T m-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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
|
14
|
Chauhan J, Maddi SR, Dubey KD, Sen S. Developing C2-Aroyl Indoles as Novel Inhibitors of IDO1 and Understanding Their Mechanism of Inhibition via Mass Spectroscopy, QM/MM Calculations and Molecular Dynamics Simulation. Front Chem 2021; 9:691319. [PMID: 34336787 PMCID: PMC8319603 DOI: 10.3389/fchem.2021.691319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Indoleamine-2,3-dioxygenase (IDO1) and tryptophan dioxygenases are two heme based metalloenzymes that catalyze the tryptophan oxidation reaction by inserting molecular dioxygen to cleave the pyrrole ring. The mechanism of such ring cleavage reaction is of carcinogenic importance as the malignant tumors recruit this mechanism for immune invasion. In the presence study, we have synthesized a Novel C2 aroyl indoles inhibitor, 8d, which shows significant inhibition of 180 nM at IC50 scale. The binding and conformational changes that transpire after inhibitor binding were thoroughly studied by molecular docking and MD simulations. The subsequent QM/MM (Quantum Mechanical/Molecular Mechanical) calculations were used to proposed the mechanism of inhibition. The QM/MM calculations show that the reaction proceeds via multistep processes where the dioxygen insertion to the substrate 8a is the rate determining process. Theoretical mechanism is further supported by mass spectroscopy, and drug metabolism/pharmacokinetics study (DMPK) and metabolic stability of compound 8d was investigated in rat and human liver microsomes.
Collapse
Affiliation(s)
- Jyoti Chauhan
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| | | | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| | - Subhabrata Sen
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| |
Collapse
|
15
|
Wang Y, Davis I, Shin I, Xu H, Liu A. Molecular Rationale for Partitioning between C-H and C-F Bond Activation in Heme-Dependent Tyrosine Hydroxylase. J Am Chem Soc 2021; 143:4680-4693. [PMID: 33734681 DOI: 10.1021/jacs.1c00175] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The heme-dependent l-tyrosine hydroxylases (TyrHs) in natural product biosynthesis constitute a new enzyme family in contrast to the nonheme iron enzymes for DOPA production. A representative TyrH exhibits dual reactivity of C-H and C-F bond cleavage when challenged with 3-fluoro-l-tyrosine (3-F-Tyr) as a substrate. However, little is known about how the enzyme mediates two distinct reactions. Herein, a new TyrH from the thermophilic bacterium Streptomyces sclerotialus (SsTyrH) was functionally and structurally characterized. A de novo crystal structure of the enzyme-substrate complex at 1.89-Å resolution provides the first comprehensive structural study of this hydroxylase. The binding conformation of l-tyrosine indicates that C-H bond hydroxylation is initiated by electron transfer. Mutagenesis studies confirmed that an active site histidine, His88, participates in catalysis. We also obtained a 1.68-Å resolution crystal structure in complex with the monofluorinated substrate, 3-F-Tyr, which shows one binding conformation but two orientations of the fluorine atom with a ratio of 7:3, revealing that the primary factor of product distribution is the substrate orientation. During in crystallo reaction, a ferric-hydroperoxo intermediate (compound 0, Fe3+-OOH) was observed with 3-F-Tyr as a substrate based on characteristic spectroscopic features. We determined the crystal structure of this compound 0-type intermediate and refined it to 1.58-Å resolution. Collectively, this study provided the first molecular details of the heme-dependent TyrH and determined the primary factor that dictates the partitioning between the dual reactivities of C-H and C-F bond activation.
Collapse
Affiliation(s)
- Yifan Wang
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, Texas 78249, United States
| | - Ian Davis
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, Texas 78249, United States
| | - Inchul Shin
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, Texas 78249, United States
| | - Hui Xu
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, Texas 78249, United States
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, Texas 78249, United States
| |
Collapse
|
16
|
Shin I, Davis I, Nieves-Merced K, Wang Y, McHardy S, Liu A. A novel catalytic heme cofactor in SfmD with a single thioether bond and a bis-His ligand set revealed by a de novo crystal structural and spectroscopic study. Chem Sci 2021; 12:3984-3998. [PMID: 34163669 PMCID: PMC8179489 DOI: 10.1039/d0sc06369j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/21/2021] [Indexed: 12/13/2022] Open
Abstract
SfmD is a heme-dependent enzyme in the biosynthetic pathway of saframycin A. Here, we present a 1.78 Å resolution de novo crystal structure of SfmD, which unveils a novel heme cofactor attached to the protein with an unusual Hx n HxxxC motif (n ∼ 38). This heme cofactor is unique in two respects. It contains a single thioether bond in a cysteine-vinyl link with Cys317, and the ferric heme has two axial protein ligands, i.e., His274 and His313. We demonstrated that SfmD heme is catalytically active and can utilize dioxygen and ascorbate for a single-oxygen insertion into 3-methyl-l-tyrosine. Catalytic assays using ascorbate derivatives revealed the functional groups of ascorbate essential to its function as a cosubstrate. Abolishing the thioether linkage through mutation of Cys317 resulted in catalytically inactive SfmD variants. EPR and optical data revealed that the heme center undergoes a substantial conformational change with one axial histidine ligand dissociating from the iron ion in response to substrate 3-methyl-l-tyrosine binding or chemical reduction by a reducing agent, such as the cosubstrate ascorbate. The labile axial ligand was identified as His274 through redox-linked structural determinations. Together, identifying an unusual heme cofactor with a previously unknown heme-binding motif for a monooxygenase activity and the structural similarity of SfmD to the members of the heme-based tryptophan dioxygenase superfamily will broaden understanding of heme chemistry.
Collapse
Affiliation(s)
- Inchul Shin
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle Texas 78249 USA
| | - Ian Davis
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle Texas 78249 USA
| | - Karinel Nieves-Merced
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle Texas 78249 USA
- Center for Innovative Drug Discovery, The University of Texas at San Antonio One UTSA Circle Texas 78249 USA
| | - Yifan Wang
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle Texas 78249 USA
| | - Stanton McHardy
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle Texas 78249 USA
- Center for Innovative Drug Discovery, The University of Texas at San Antonio One UTSA Circle Texas 78249 USA
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle Texas 78249 USA
| |
Collapse
|
17
|
Marshall JW, de Mattos-Shipley KMJ, Ghannam IAY, Munawar A, Killen JC, Lazarus CM, Cox RJ, Willis CL, Simpson TJ. Fusarochromene, a novel tryptophan-derived metabolite from Fusarium sacchari. Org Biomol Chem 2021; 19:182-187. [PMID: 33107888 DOI: 10.1039/d0ob02031a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fusarochromene isolated from the plant pathogenic fungus, Fusarium sacchari is closely related to a group of mycotoxins including fusarochromanone previously isolated from various Fusaria spp. Despite their assumed polyketide biogenesis, incorporation studies with 13C-labelled acetate, glycerol and tryptophans show that fusarochromene is unexpectedly derived via oxidative cleavage of the aromatic amino acid tryptophan. A putative biosynthetic gene cluster has been identified.
Collapse
Affiliation(s)
- James W Marshall
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Zhang S, Liu Y. Mechanical Insights into the Enzymatic Cleavage of Double C-C Bond in Poly( cis-1,4-isoprene) by the Latex Clearing Protein. Inorg Chem 2020; 59:9627-9637. [PMID: 32644783 DOI: 10.1021/acs.inorgchem.0c00726] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The b-type cytochrome LcpK30 is a latex clearing protein (Lcp), which acts as an endotype dioxygenase to catalyze the extracellular cleavage of the chemically inert aliphatic polymer poly(cis-1,4-isoprene), producing oligo-isoprenoids with different terminal carbonyl groups (aldehyde and ketone, -CH2-CHO and -CH2-COCH3). On the basis of the fact that the muteins of E148A, E148Q, and E148H have substantially reduced reactivity, and the E148-initiated reaction mechanism has been previously proposed, in which a cyclic dioxetane intermediate or an epoxide intermediate may be involved, however, open questions still remain. In this paper, on the basis of the crystal structure of LcpK30, the enzyme-substrate reactant model was constructed, and the cleavage mechanism of the central double bond of poly(cis-1,4-isoprene) was elucidated by performing quantum mechanics/molecular mechanics calculations. Our calculation results revealed that the oxidative cleavage reaction is triggered by the addition of the heme-bound dioxygen to the double bond of the polymer, and E148 does not act as the catalytic base to extract the allylic proton to assist the reaction as previously suggested. Of the two considered pathways, the pathway that involves the dioxetane intermediate was calculated to be more favorable. During the catalysis, the distal oxygen first adds to the double bond of the substrate to form a radical intermediate, and then the Fe-O1 (proximal oxygen) bond cleaves to generate the dioxetane intermediate, which can easily collapse affording the final ketone and aldehyde products. In general, the cleavage mechanism of double C-C bond catalyzed by LcpK30 is similar to those of indoleamine 2,3-dioxygenase, tryptophan 2,3-dioxygenase, and the nonheme stilbene cleavage oxygenase NOV1 that all depend on the iron-bound dioxygen to initiate the cleavage reaction.
Collapse
Affiliation(s)
- Shiqing Zhang
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| |
Collapse
|
20
|
Wei Y, Lu C, Jiang S, Zhang Y, Li Q, Bai W, Wang X. Directed Evolution of a Tryptophan 2,3‐Dioxygenase for the Diastereoselective Monooxygenation of Tryptophans. Angew Chem Int Ed Engl 2020; 59:3043-3047. [DOI: 10.1002/anie.201911825] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/20/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Yanxin Wei
- College of Bioscience and BiotechnologyYangzhou University Yangzhou Jiangsu 225009 China
| | - Chen Lu
- College of Bioscience and BiotechnologyYangzhou University Yangzhou Jiangsu 225009 China
| | - Shengsheng Jiang
- College of Bioscience and BiotechnologyYangzhou University Yangzhou Jiangsu 225009 China
| | - Yanyan Zhang
- Testing CenterYangzhou University Yangzhou Jiangsu 225009 China
| | - Qiuchun Li
- College of Bioscience and BiotechnologyYangzhou University Yangzhou Jiangsu 225009 China
| | - Wen‐Ju Bai
- Department of ChemistryStanford University Stanford California 94305 USA
- Present address: Amgen Inc. 1 Amgen Center Drive Thousand Oaks CA 91320 USA
| | - Xiqing Wang
- College of Bioscience and BiotechnologyYangzhou University Yangzhou Jiangsu 225009 China
| |
Collapse
|
21
|
Wei Y, Lu C, Jiang S, Zhang Y, Li Q, Bai W, Wang X. Directed Evolution of a Tryptophan 2,3‐Dioxygenase for the Diastereoselective Monooxygenation of Tryptophans. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201911825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yanxin Wei
- College of Bioscience and Biotechnology Yangzhou University Yangzhou Jiangsu 225009 China
| | - Chen Lu
- College of Bioscience and Biotechnology Yangzhou University Yangzhou Jiangsu 225009 China
| | - Shengsheng Jiang
- College of Bioscience and Biotechnology Yangzhou University Yangzhou Jiangsu 225009 China
| | - Yanyan Zhang
- Testing Center Yangzhou University Yangzhou Jiangsu 225009 China
| | - Qiuchun Li
- College of Bioscience and Biotechnology Yangzhou University Yangzhou Jiangsu 225009 China
| | - Wen‐Ju Bai
- Department of Chemistry Stanford University Stanford California 94305 USA
- Present address: Amgen Inc. 1 Amgen Center Drive Thousand Oaks CA 91320 USA
| | - Xiqing Wang
- College of Bioscience and Biotechnology Yangzhou University Yangzhou Jiangsu 225009 China
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Su Y, Huang G, Ye F, Qiao P, Ye J, Gao Y, Chen H. Facile access to evodiakine enabled by aerobic copper-catalyzed oxidative rearrangement. Org Biomol Chem 2019; 17:8811-8815. [PMID: 31573009 DOI: 10.1039/c9ob01832h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Oxidation as a fundamentally important method for the synthesis of complex structures is difficult to achieve in a selective manner. Evodiakine, a complex natural product possessing an unprecedented ring system (6/5/5/7/6), has a high oxidation state without a practical solution. Herein, we report the first synthesis of evodiakine via aerobic copper-catalyzed late-stage functionalization of evodiamine.
Collapse
Affiliation(s)
- Yiting Su
- Key Laboratory of Molecule Synthesis and Function Discovery (Fuzhou University), Fujian Province University, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China.
| | | | | | | | | | | | | |
Collapse
|
24
|
Nelp MT, Zheng V, Davis KM, Stiefel KJE, Groves JT. Potent Activation of Indoleamine 2,3-Dioxygenase by Polysulfides. J Am Chem Soc 2019; 141:15288-15300. [PMID: 31436417 DOI: 10.1021/jacs.9b07338] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Indoleamine 2,3-dioxygenase (IDO1) is a heme enzyme that catalyzes the oxygenation of the indole ring of tryptophan to afford N-formylkynurenine. This activity significantly suppresses the immune response, mediating inflammation and autoimmune reactions. These consequential effects are regulated through redox changes in the heme cofactor of IDO1, which autoxidizes to the inactive ferric state during turnover. This change in redox status increases the lability of the heme cofactor leading to further suppression of activity. The cell can thus regulate IDO1 activity through the supply of heme and reducing agents. We show here that polysulfides bind to inactive ferric IDO1 and reduce it to the oxygen-binding ferrous state, thus activating IDO1 to maximal turnover even at low, physiologically significant concentrations. The on-rate for hydrogen disulfide binding to ferric IDO1 was found to be >106 M-1 s-1 at pH 7 using stopped-flow spectrometry. Fe K-edge XANES and EPR spectroscopy indicated initial formation of a low-spin ferric sulfur-bound species followed by reduction to the ferrous state. The μM affinity of polysulfides for IDO1 implicates these polysulfides as important signaling factors in immune regulation through the kynurenine pathway. Tryptophan significantly enhanced the relatively lower-affinity binding of hydrogen sulfide to IDO1, inspiring the use of the small molecule 3-mercaptoindole (3MI), which selectively binds to and activates ferric IDO1. 3MI sustains turnover by catalytically transferring reducing equivalents from glutathione to IDO1, representing a novel strategy of upregulating innate immunosuppression for treatment of autoimmune disorders. Reactive sulfur species are thus likely unrecognized immune-mediators with potential as therapeutic agents through these interactions with IDO1.
Collapse
Affiliation(s)
- Micah T Nelp
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - Vincent Zheng
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - Katherine M Davis
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - Katherine J E Stiefel
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - John T Groves
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| |
Collapse
|
25
|
Unger N, Ferraro A, Holzgrabe U. Investigation of tryptophan-related yellowing in parenteral amino acid solution: Development of a stability-indicating method and assessment of degradation products in pharmaceutical formulations. J Pharm Biomed Anal 2019; 177:112839. [PMID: 31505430 DOI: 10.1016/j.jpba.2019.112839] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/20/2019] [Accepted: 08/26/2019] [Indexed: 11/18/2022]
Abstract
Parenteral amino acid solutions containing tryptophan tend to develop a yellow colouration upon storage. Hence, the aim of the present study was to find out whether tryptophan degradation products are the reason for the yellowing. The degree of discolouration and tryptophan degradation was examined by visual examination and UV/Vis measurements with respect to oxygen presence, pH value, and duration of steam sterilization. LC-UV analyses of autoclaved tryptophan solutions indicated eight degradation products, namely R,R/R,S 2-amino-3-(oxoindolin-3-yl)propanoic acid, R,R/R,S 2-amino-3-hydroxy-2-oxoindolin-3-yl)propanoic acids, cis/trans 3a-hydroxy-1,2,3,3a,8,8a-hexahydropyrrolo[2,3-b]indole-2-carboxylic acid, N´-formylkynurenine, and kynurenine. The proposed degradation products were confirmed by spiking of synthesized degradation products and LC-UV/MS analyses. The LC-UV analysis method was optimized and validated according to the ICH guideline Q2 (R1). Tryptophan stability in commercially available parenteral amino acid formulations was evaluated over a storing period of 12 months in two common types of primary packaging after autoclave procedure.
Collapse
Affiliation(s)
- Nina Unger
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Antonio Ferraro
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Ulrike Holzgrabe
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
| |
Collapse
|
26
|
Li W, Liu W, Leonard DK, Rabeah J, Junge K, Brückner A, Beller M. Practical Catalytic Cleavage of C(sp 3 )-C(sp 3 ) Bonds in Amines. Angew Chem Int Ed Engl 2019; 58:10693-10697. [PMID: 31125156 PMCID: PMC6771714 DOI: 10.1002/anie.201903019] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/16/2019] [Indexed: 12/23/2022]
Abstract
The selective cleavage of thermodynamically stable C(sp3 )-C(sp3 ) single bonds is rare compared to their ubiquitous formation. Herein, we describe a general methodology for such transformations using homogeneous copper-based catalysts in the presence of air. The utility of this novel methodology is demonstrated for Cα -Cβ bond scission in >70 amines with excellent functional group tolerance. This transformation establishes tertiary amines as a general synthon for amides and provides valuable possibilities for their scalable functionalization in, for example, natural products and bioactive molecules.
Collapse
Affiliation(s)
- Wu Li
- Leibniz-Institut für Katalyse e.V. an derUniversität RostockAlbert-Einstein Straße 29a18059RostockGermany
| | - Weiping Liu
- Leibniz-Institut für Katalyse e.V. an derUniversität RostockAlbert-Einstein Straße 29a18059RostockGermany
| | - David K. Leonard
- Leibniz-Institut für Katalyse e.V. an derUniversität RostockAlbert-Einstein Straße 29a18059RostockGermany
| | - Jabor Rabeah
- Leibniz-Institut für Katalyse e.V. an derUniversität RostockAlbert-Einstein Straße 29a18059RostockGermany
| | - Kathrin Junge
- Leibniz-Institut für Katalyse e.V. an derUniversität RostockAlbert-Einstein Straße 29a18059RostockGermany
| | - Angelika Brückner
- Leibniz-Institut für Katalyse e.V. an derUniversität RostockAlbert-Einstein Straße 29a18059RostockGermany
| | - Matthias Beller
- Leibniz-Institut für Katalyse e.V. an derUniversität RostockAlbert-Einstein Straße 29a18059RostockGermany
| |
Collapse
|
27
|
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.
Collapse
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.
| |
Collapse
|
28
|
Li W, Liu W, Leonard DK, Rabeah J, Junge K, Brückner A, Beller M. Practical Catalytic Cleavage of C(sp
3
)−C(sp
3
) Bonds in Amines. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wu Li
- Leibniz-Institut für Katalyse e.V. an derUniversität Rostock Albert-Einstein Straße 29a 18059 Rostock Germany
| | - Weiping Liu
- Leibniz-Institut für Katalyse e.V. an derUniversität Rostock Albert-Einstein Straße 29a 18059 Rostock Germany
| | - David K. Leonard
- Leibniz-Institut für Katalyse e.V. an derUniversität Rostock Albert-Einstein Straße 29a 18059 Rostock Germany
| | - Jabor Rabeah
- Leibniz-Institut für Katalyse e.V. an derUniversität Rostock Albert-Einstein Straße 29a 18059 Rostock Germany
| | - Kathrin Junge
- Leibniz-Institut für Katalyse e.V. an derUniversität Rostock Albert-Einstein Straße 29a 18059 Rostock Germany
| | - Angelika Brückner
- Leibniz-Institut für Katalyse e.V. an derUniversität Rostock Albert-Einstein Straße 29a 18059 Rostock Germany
| | - Matthias Beller
- Leibniz-Institut für Katalyse e.V. an derUniversität Rostock Albert-Einstein Straße 29a 18059 Rostock Germany
| |
Collapse
|
29
|
Ye Q, Huang Y, Grier S, Miller SA. Oxidative degradation pathways of beclabuvir hydrochloride mediated by hydrogen peroxide and UV/Vis light. J Pharm Biomed Anal 2019; 172:388-394. [PMID: 31100536 DOI: 10.1016/j.jpba.2019.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 11/15/2022]
Abstract
Beclabuvir hydrochloride (BCV) is a marketed product for the treatment of hepatitis C viral infection. It contains functional groups such as indole, tertiary amine and amides. Forced degradation studies of BCV revealed different degradation profiles under photo and hydrogen peroxide oxidative conditions. Under the photo-oxidative degradation conditions, the tertiary amine on the piperazine ring was oxidized to form the degradants as the hydroxyl and des-methyl analogs of beclabuvir. However, under the oxidative condition using hydrogen peroxide, the indole ring was oxidized to form a typical kynuric degradant and two unexpected cyclohexyl rearranged diastereomeric degradants. The plausible mechanisms for the photo and hydrogen peroxide mediated oxidative degradation of beclabuvir hydrochloride are proposed.
Collapse
Affiliation(s)
- Qingmei Ye
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, NJ 08903, USA.
| | - Yande Huang
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, NJ 08903, USA
| | - Stephen Grier
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, NJ 08903, USA
| | - Scott A Miller
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, NJ 08903, USA
| |
Collapse
|
30
|
Pavon JA, Xiao L, Li X, Zhao J, Aldredge D, Dank E, Fridman A, Liu YH. Selective Tryptophan Oxidation of Monoclonal Antibodies: Oxidative Stress and Modeling Prediction. Anal Chem 2019; 91:2192-2200. [DOI: 10.1021/acs.analchem.8b04768] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Jorge Alexander Pavon
- Process Research & Development, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Li Xiao
- Modeling and Informatics, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Xiaojuan Li
- Process Research & Development, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Jia Zhao
- Process Research & Development, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Danielle Aldredge
- Process Research & Development, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Eugene Dank
- Process Research & Development, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Alex Fridman
- Process Research & Development, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Yan-Hui Liu
- Process Research & Development, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| |
Collapse
|
31
|
Li Y, Li L, Lu X, Bai Y, Wang Y, Wu Y, Zhong F. Bioinspired radical cyclization of tryptamines: synthesis of peroxypyrroloindolenines as potential anti-cancer agents. Chem Commun (Camb) 2019; 55:63-66. [DOI: 10.1039/c8cc08866g] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Inspired by the heme iron-catalyzed radical insertion of dioxygen to the tryptophan indole ring, herein we utilize alkylperoxy radical species as a coupling partner to trigger a peroxycyclization of readily accessible tryptophan derivatives and enable the first synthesis of peroxypyrroloindolenines.
Collapse
Affiliation(s)
- Yan Li
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology (HUST)
- Wuhan 430074
- China
| | - Longjie Li
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology (HUST)
- Wuhan 430074
- China
| | - Xunbo Lu
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology (HUST)
- Wuhan 430074
- China
| | - Yulong Bai
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology (HUST)
- Wuhan 430074
- China
| | - Yufan Wang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology (HUST)
- Wuhan 430074
- China
| | - Yuzhou Wu
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology (HUST)
- Wuhan 430074
- China
| | - Fangrui Zhong
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology (HUST)
- Wuhan 430074
- China
| |
Collapse
|
32
|
Abstract
Iron-containing enzymes such as heme enzymes play crucial roles in biological systems. Three distinct heme-containing dioxygenase enzymes, tryptophan 2,3-dioxygenase (TDO), indoleamine 2,3-dioxygenase 1 (IDO1) and indoleamine 2,3-dioxygenase 2 (IDO2) catalyze the initial and rate-limiting step of l-tryptophan catabolism through the kynurenine pathway in mammals. Overexpression of these enzymes causes depletion of tryptophan and the accumulation of metabolic products, which contributes to tumor immune tolerance and immune dysregulation in a variety of disease pathologies. In the past few decades, IDO1 has garnered the most attention as a therapeutic target with great potential in cancer immunotherapy. Many potential inhibitors of IDO1 have been designed, synthesized and evaluated, among which indoximod (d-1-MT), INCB024360, GDC-0919 (formerly NLG-919), and an IDO1 peptide-based vaccine have advanced to the clinical trial stage. However, recently, the roles of TDO and IDO2 have been elucidated in immune suppression. In this review, the current drug discovery landscape for targeting TDO, IDO1 and IDO2 is highlighted, with particular attention to the recent use of drugs in clinical trials. Moreover, the crystal structures of these enzymes, in complex with inhibitors, and the mechanisms of Trp catabolism in the first step, are summarized to provide information for facilitating the discovery of new enzyme inhibitors.
Collapse
Affiliation(s)
- Daojing Yan
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.
| | | | | |
Collapse
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
Immune-modulating enzyme indoleamine 2,3-dioxygenase is effectively inhibited by targeting its apo-form. Proc Natl Acad Sci U S A 2018. [PMID: 29531094 PMCID: PMC5879690 DOI: 10.1073/pnas.1719190115] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Indoleamine 2,3-dioxygenase (IDO1) is a heme protein that catalyzes the dioxygenation of tryptophan. Cells expressing this activity are able to profoundly alter their surrounding environment to suppress the immune response. Cancer cells exploit this pathway to avoid immune-mediated destruction. Through a range of kinetic, structural, and cellular assays, we show that two classes of highly selective inhibitors of IDO1 act by competing with heme binding to apo-IDO1. This shows that IDO1 is dynamically bound to its heme cofactor in what is likely a critical step in the regulation of this enzyme. These results have elucidated a previously undiscovered role for the ubiquitous heme cofactor in immune regulation, and it suggests that other heme proteins in biology may be similarly regulated. For cancer cells to survive and proliferate, they must escape normal immune destruction. One mechanism by which this is accomplished is through immune suppression effected by up-regulation of indoleamine 2,3-dioxygenase (IDO1), a heme enzyme that catalyzes the oxidation of tryptophan to N-formylkynurenine. On deformylation, kynurenine and downstream metabolites suppress T cell function. The importance of this immunosuppressive mechanism has spurred intense interest in the development of clinical IDO1 inhibitors. Herein, we describe the mechanism by which a class of compounds effectively and specifically inhibits IDO1 by targeting its apo-form. We show that the in vitro kinetics of inhibition coincide with an unusually high rate of intrinsic enzyme–heme dissociation, especially in the ferric form. X-ray crystal structures of the inhibitor–enzyme complexes show that heme is displaced from the enzyme and blocked from rebinding by these compounds. The results reveal that apo-IDO1 serves as a unique target for inhibition and that heme lability plays an important role in posttranslational regulation.
Collapse
|
35
|
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.
Collapse
|
36
|
Zhang Y, Zou Y, Brock NL, Huang T, Lan Y, Wang X, Deng Z, Tang Y, Lin S. Characterization of 2-Oxindole Forming Heme Enzyme MarE, Expanding the Functional Diversity of the Tryptophan Dioxygenase Superfamily. J Am Chem Soc 2017; 139:11887-11894. [PMID: 28809552 DOI: 10.1021/jacs.7b05517] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
3-Substituted 2-oxindoles are important structural motifs found in many biologically active natural products and pharmaceutical lead compounds. Here, we report an enzymatic formation of the 3-substituted 2-oxindoles catalyzed by MarE in the maremycin biosynthetic pathway in Streptomyces sp. B9173. MarE is a homologue of FeII/heme-dependent tryptophan 2,3-dioxygenases (TDOs). Typical TDOs usually catalyze the insertion of two oxygen atoms from O2 into an indole ring to generate N-formylkynurenine (NFK)-like products. In contrast, MarE catalyzes the insertion of a single oxygen atom from O2 into an indole ring, to probably generate an epoxyindole intermediate that undergoes an unprecedented 2,3-hydride migration to form 2-oxindole structure. MarE shows substrate robustness to catalyze the conversion of a series of 3-substituted indoles into their corresponding 3-substituted 2-oxindoles. Although containing most key amino acid residues conserved in well-known TDO homologues, MarE falls into a separate new subgroup in the phylogenetic tree. The characterization of MarE and its homologue enriches the functional diversities of TDO superfamily and provides a new strategy for discovering novel natural products containing 3-substituted 2-oxindole pharmacophores by genome mining.
Collapse
Affiliation(s)
- Yuyang Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, China
| | - Yi Zou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, China.,Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, and Department of Bioengineering, University of California, Los Angeles , 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Nelson L Brock
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, China
| | - Tingting Huang
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, China
| | - Yingxia Lan
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, China
| | - Xiaozheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, China
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, and Department of Bioengineering, University of California, Los Angeles , 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, China
| |
Collapse
|
37
|
Balti M, Plas A, Meinguet C, Haufroid M, Thémans Q, Efrit ML, Wouters J, Lanners S. Synthesis of 4- and 5-arylthiazolinethiones as inhibitors of indoleamine 2,3-dioxygenase. Bioorg Med Chem Lett 2017; 27:3607-3610. [PMID: 28651980 DOI: 10.1016/j.bmcl.2016.06.052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/16/2016] [Accepted: 06/18/2016] [Indexed: 10/21/2022]
Abstract
Docking studies of 4-phenylthiazolinethione on human IDO1 suggest complexation of the heme iron by the exocyclic sulfur atom further reinforced by hydrophobic interactions of the phenyl ring within pocket A of the enzyme. On this basis, chemical modifications were proposed to increase inhibition activity. Synthetic routes had to be adapted and optimized to yield the desired substituted 4- and 5-arylthiazolinethiones. Their biological evaluation shows that 5-aryl regioisomers are systematically less potent than the corresponding 4-aryl analogs. Substitution on the phenyl ring does not significantly increase inhibition potency, except for 4-Br and 4-Cl derivatives.
Collapse
Affiliation(s)
- Monaem Balti
- NAMEDIC-NARILIS, University of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium; Laboratory of Organic Synthesis and Heterocyclic Chemistry, Department of Chemistry, College of Sciences at Tunis, El Manar University, Campus, 1060 Tunis, Tunisia
| | - Aurélie Plas
- NAMEDIC-NARILIS, University of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium
| | - Céline Meinguet
- NAMEDIC-NARILIS, University of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium
| | - Marie Haufroid
- NAMEDIC-NARILIS, University of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium
| | - Quentin Thémans
- NAMEDIC-NARILIS, University of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium
| | - Mohamed Lotfi Efrit
- Laboratory of Organic Synthesis and Heterocyclic Chemistry, Department of Chemistry, College of Sciences at Tunis, El Manar University, Campus, 1060 Tunis, Tunisia
| | - Johan Wouters
- NAMEDIC-NARILIS, University of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium
| | - Steve Lanners
- NAMEDIC-NARILIS, University of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium.
| |
Collapse
|
38
|
Basran J, Booth ES, Lee M, Handa S, Raven EL. Analysis of Reaction Intermediates in Tryptophan 2,3-Dioxygenase: A Comparison with Indoleamine 2,3-Dioxygenase. Biochemistry 2016; 55:6743-6750. [PMID: 27951658 DOI: 10.1021/acs.biochem.6b01005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) are heme-containing enzymes that catalyze the O2-dependent oxidation of l-tryptophan (l-Trp) in biological systems. Although many decades have passed since their discovery, the mechanism of tryptophan oxidation has not been established. It has been widely assumed that IDO and TDO react using the same mechanism, although there is no evidence that they do. For IDO, a Compound II (ferryl) species accumulates in the steady state and is implicated in the mechanism; in TDO, no such species has ever been observed. In this paper, we examine the kinetics of tryptophan oxidation in TDO. We find no evidence for the accumulation of Compound II during TDO catalysis. Instead, a ternary [Fe(II)-O2, l-Trp] complex is detected under steady state conditions. The absence of a Compound II species in the steady state in TDO is not due to an intrinsic inability of the TDO enzyme to form ferryl heme, because Compound II can be formed directly through a different route in which ferrous heme is reacted with peroxide. We interpret the data to mean that the rate-limiting step in the IDO and TDO mechanisms is not the same.
Collapse
Affiliation(s)
- Jaswir Basran
- Department of Molecular and Cellular Biology and Henry Wellcome Laboratories for Structural Biology, Henry Wellcome Building, University of Leicester , Lancaster Road, Leicester LE1 7RH, England, U.K
| | - Elizabeth S Booth
- Department of Chemistry, University of Leicester , University Road, Leicester LE1 7RH, England, U.K
| | - Michael Lee
- Department of Molecular and Cellular Biology and Henry Wellcome Laboratories for Structural Biology, Henry Wellcome Building, University of Leicester , Lancaster Road, Leicester LE1 7RH, England, U.K
| | - Sandeep Handa
- Department of Chemistry, University of Leicester , University Road, Leicester LE1 7RH, England, U.K
| | - Emma L Raven
- Department of Chemistry, University of Leicester , University Road, Leicester LE1 7RH, England, U.K
| |
Collapse
|
39
|
Raven EL. A short history of heme dioxygenases: rise, fall and rise again. J Biol Inorg Chem 2016; 22:175-183. [PMID: 27909919 PMCID: PMC5350241 DOI: 10.1007/s00775-016-1412-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/10/2016] [Indexed: 01/20/2023]
Abstract
It is well established that there are two different classes of enzymes—tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO)—that catalyse the O2-dependent oxidation of l-tryptophan to N-formylkynurenine. But it was not always so. This perspective presents a short history of the early TDO and IDO literature, the people that were involved in creating it, and the legacy that this left for the future.
Collapse
Affiliation(s)
- Emma L Raven
- Department of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| |
Collapse
|
40
|
Lewis-Ballester A, Forouhar F, Kim SM, Lew S, Wang Y, Karkashon S, Seetharaman J, Batabyal D, Chiang BY, Hussain M, Correia MA, Yeh SR, Tong L. Molecular basis for catalysis and substrate-mediated cellular stabilization of human tryptophan 2,3-dioxygenase. Sci Rep 2016; 6:35169. [PMID: 27762317 PMCID: PMC5071832 DOI: 10.1038/srep35169] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 09/26/2016] [Indexed: 11/09/2022] Open
Abstract
Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) play a central role in tryptophan metabolism and are involved in many cellular and disease processes. Here we report the crystal structure of human TDO (hTDO) in a ternary complex with the substrates L-Trp and O2 and in a binary complex with the product N-formylkynurenine (NFK), defining for the first time the binding modes of both substrates and the product of this enzyme. The structure indicates that the dioxygenation reaction is initiated by a direct attack of O2 on the C2 atom of the L-Trp indole ring. The structure also reveals an exo binding site for L-Trp, located ~42 Å from the active site and formed by residues conserved among tryptophan-auxotrophic TDOs. Biochemical and cellular studies indicate that Trp binding at this exo site does not affect enzyme catalysis but instead it retards the degradation of hTDO through the ubiquitin-dependent proteasomal pathway. This exo site may therefore provide a novel L-Trp-mediated regulation mechanism for cellular degradation of hTDO, which may have important implications in human diseases.
Collapse
Affiliation(s)
- Ariel Lewis-Ballester
- Department of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461, USA
| | - Farhad Forouhar
- Department of Biological Sciences Northeast Structural Genomics Consortium Columbia University New York, NY 10027, USA
| | - Sung-Mi Kim
- Departments of Cellular and Molecular Pharmacology, Pharmaceutical Chemistry, and Bioengineering and Therapeutic Sciences, The Liver Center, University of California at San Francisco San Francisco, CA 94158, USA
| | - Scott Lew
- Department of Biological Sciences Northeast Structural Genomics Consortium Columbia University New York, NY 10027, USA
| | - YongQiang Wang
- Departments of Cellular and Molecular Pharmacology, Pharmaceutical Chemistry, and Bioengineering and Therapeutic Sciences, The Liver Center, University of California at San Francisco San Francisco, CA 94158, USA
| | - Shay Karkashon
- Department of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461, USA
| | - Jayaraman Seetharaman
- Department of Biological Sciences Northeast Structural Genomics Consortium Columbia University New York, NY 10027, USA
| | - Dipanwita Batabyal
- Department of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461, USA
| | - Bing-Yu Chiang
- Department of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461, USA
| | - Munif Hussain
- Department of Biological Sciences Northeast Structural Genomics Consortium Columbia University New York, NY 10027, USA
| | - Maria Almira Correia
- Departments of Cellular and Molecular Pharmacology, Pharmaceutical Chemistry, and Bioengineering and Therapeutic Sciences, The Liver Center, University of California at San Francisco San Francisco, CA 94158, USA
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461, USA
| | - Liang Tong
- Department of Biological Sciences Northeast Structural Genomics Consortium Columbia University New York, NY 10027, USA
| |
Collapse
|
41
|
Scuderi D, Ignasiak MT, Serfaty X, de Oliveira P, Houée Levin C. Tandem mass spectrometry and infrared spectroscopy as a tool to identify peptide oxidized residues. Phys Chem Chem Phys 2016; 17:25998-6007. [PMID: 26292724 DOI: 10.1039/c5cp03223g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The final products obtained by the oxidation of small model peptides containing the thioether function, either methionine or S-methyl cysteine, have been characterized by tandem mass spectrometry and IR Multiple Photon Dissociation (IRMPD) spectroscopy. The modified positions have been clearly identified by the CID-MS(2) fragmentation mass spectra with or without loss of sulfenic acid, as well as by the vibrational signature of the sulfoxide bond at around 1000 cm(-1). The oxidation of the thioether function did not lead to the same products in these model peptides. The sulfoxide and sulfone (to a lesser extent) have been clearly identified as final products of the oxidation of S-methyl-glutathione (GS-Me). Decarboxylation or hydrogen loss are the major oxidation pathways in GS-Me, while they have not been observed in tryptophan-methionine and methionine-tryptophan (Trp-Met and Met-Trp). Interestingly, tryptophan is oxidized in the dipeptide Met-Trp, while that is not the case in the reverse sequence (Trp-Met).
Collapse
Affiliation(s)
- D Scuderi
- Laboratoire de Chimie Physique, Université Paris Sud, 91405 Orsay Cedex, France.
| | | | | | | | | |
Collapse
|
42
|
Yoshimoto FK, Gonzalez E, Auchus RJ, Guengerich FP. Mechanism of 17α,20-Lyase and New Hydroxylation Reactions of Human Cytochrome P450 17A1: 18O LABELING AND OXYGEN SURROGATE EVIDENCE FOR A ROLE OF A PERFERRYL OXYGEN. J Biol Chem 2016; 291:17143-64. [PMID: 27339894 DOI: 10.1074/jbc.m116.732966] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 (P450) reactions can involve C-C bond cleavage, and several of these are critical in steroid and sterol biosynthesis. The mechanisms of P450s 11A1, 17A1, 19A1, and 51A1 have been controversial, in the context of the role of ferric peroxide (FeO2 (-)) versus perferryl (FeO(3+), compound I) chemistry. We reinvestigated the 17α-hydroxyprogesterone and 17α-hydroxypregnenolone 17α,20-lyase reactions of human P450 17A1 and found incorporation of one (18)O atom (from (18)O2) into acetic acid, consonant with proposals for a ferric peroxide mechanism (Akhtar, M., Lee-Robichaud, P., Akhtar, M. E., and Wright, J. N. (1997) J. Steroid Biochem. Mol. Biol. 61, 127-132; Akhtar, M., Wright, J. N., and Lee-Robichaud, P. (2011) J. Steroid Biochem. Mol. Biol. 125, 2-12). However, the reactions were supported by iodosylbenzene (a precursor of the FeO(3+) species) but not by H2O2 We propose three mechanisms that can involve the FeO(3+) entity and that explain the (18)O label in the acetic acid, two involving the intermediacy of an acetyl radical and one a steroid 17,20-dioxetane. P450 17A1 was found to perform 16-hydroxylation reactions on its 17α-hydroxylated products to yield 16,17α-dihydroxypregnenolone and progesterone, suggesting the presence of an active perferryloxo active species of P450 17A1 when its lyase substrate is bound. The 6β-hydroxylation of 16α,17α-dihydroxyprogesterone and the oxidation of both 16α,17α-dihydroxyprogesterone and 16α,17α-dihydroxypregnenolone to 16-hydroxy lyase products were also observed. We provide evidence for the contribution of a compound I mechanism, although contribution of a ferric peroxide pathway in the 17α,20-lyase reaction cannot be excluded.
Collapse
Affiliation(s)
- Francis K Yoshimoto
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146 and the Division of Metabolism, Diabetes and Endocrinology, Departments of Internal Medicine and Pharmacology, University of Michigan, Ann Arbor, Michigan 48019
| | - Eric Gonzalez
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146 and
| | - Richard J Auchus
- the Division of Metabolism, Diabetes and Endocrinology, Departments of Internal Medicine and Pharmacology, University of Michigan, Ann Arbor, Michigan 48019
| | - F Peter Guengerich
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146 and
| |
Collapse
|
43
|
Booth ES, Basran J, Lee M, Handa S, Raven EL. Substrate Oxidation by Indoleamine 2,3-Dioxygenase: EVIDENCE FOR A COMMON REACTION MECHANISM. J Biol Chem 2015; 290:30924-30. [PMID: 26511316 PMCID: PMC4692220 DOI: 10.1074/jbc.m115.695684] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Indexed: 11/06/2022] Open
Abstract
The kynurenine pathway is the major route of l-tryptophan (l-Trp) catabolism in biology, leading ultimately to the formation of NAD+. The initial and rate-limiting step of the kynurenine pathway involves oxidation of l-Trp to N-formylkynurenine. This is an O2-dependent process and catalyzed by indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase. More than 60 years after these dioxygenase enzymes were first isolated (Kotake, Y., and Masayama, I. (1936) Z. Physiol. Chem. 243, 237–244), the mechanism of the reaction is not established. We examined the mechanism of substrate oxidation for a series of substituted tryptophan analogues by indoleamine 2,3-dioxygenase. We observed formation of a transient intermediate, assigned as a Compound II (ferryl) species, during oxidation of l-Trp, 1-methyl-l-Trp, and a number of other substrate analogues. The data are consistent with a common reaction mechanism for indoleamine 2,3-dioxygenase-catalyzed oxidation of tryptophan and other tryptophan analogues.
Collapse
Affiliation(s)
- Elizabeth S Booth
- From the Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, Great Britain, United Kingdom and
| | - Jaswir Basran
- Department of Molecular and Cellular Biology and Henry Wellcome Laboratories for Structural Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, Great Britain, United Kingdom
| | - Michael Lee
- From the Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, Great Britain, United Kingdom and
| | - Sandeep Handa
- From the Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, Great Britain, United Kingdom and
| | - Emma L Raven
- From the Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, Great Britain, United Kingdom and
| |
Collapse
|
44
|
Rivard BS, Rogers MS, Marell DJ, Neibergall MB, Chakrabarty S, Cramer CJ, Lipscomb JD. Rate-Determining Attack on Substrate Precedes Rieske Cluster Oxidation during Cis-Dihydroxylation by Benzoate Dioxygenase. Biochemistry 2015; 54:4652-64. [PMID: 26154836 DOI: 10.1021/acs.biochem.5b00573] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rieske dearomatizing dioxygenases utilize a Rieske iron-sulfur cluster and a mononuclear Fe(II) located 15 Å across a subunit boundary to catalyze O2-dependent formation of cis-dihydrodiol products from aromatic substrates. During catalysis, O2 binds to the Fe(II) while the substrate binds nearby. Single-turnover reactions have shown that one electron from each metal center is required for catalysis. This finding suggested that the reactive intermediate is Fe(III)-(H)peroxo or HO-Fe(V)═O formed by O-O bond scission. Surprisingly, several kinetic phases were observed during the single-turnover Rieske cluster oxidation. Here, the Rieske cluster oxidation and product formation steps of a single turnover of benzoate 1,2-dioxygenase are investigated using benzoate and three fluorinated analogues. It is shown that the rate constant for product formation correlates with the reciprocal relaxation time of only the fastest kinetic phase (RRT-1) for each substrate, suggesting that the slower phases are not mechanistically relevant. RRT-1 is strongly dependent on substrate type, suggesting a role for substrate in electron transfer from the Rieske cluster to the mononuclear iron site. This insight, together with the substrate and O2 concentration dependencies of RRT-1, indicates that a reactive species is formed after substrate and O2 binding but before electron transfer from the Rieske cluster. Computational studies show that RRT-1 is correlated with the electron density at the substrate carbon closest to the Fe(II), consistent with initial electrophilic attack by an Fe(III)-superoxo intermediate. The resulting Fe(III)-peroxo-aryl radical species would then readily accept an electron from the Rieske cluster to complete the cis-dihydroxylation reaction.
Collapse
Affiliation(s)
- Brent S Rivard
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Melanie S Rogers
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Daniel J Marell
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Matthew B Neibergall
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Sarmistha Chakrabarty
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christopher J Cramer
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D Lipscomb
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
45
|
Abstract
IDO1 (indoleamine 2,3-dioxygenase 1) is a member of a unique class of mammalian haem dioxygenases that catalyse the oxidative catabolism of the least-abundant essential amino acid, L-Trp (L-tryptophan), along the kynurenine pathway. Significant increases in knowledge have been recently gained with respect to understanding the fundamental biochemistry of IDO1 including its catalytic reaction mechanism, the scope of enzyme reactions it catalyses, the biochemical mechanisms controlling IDO1 expression and enzyme activity, and the discovery of enzyme inhibitors. Major advances in understanding the roles of IDO1 in physiology and disease have also been realised. IDO1 is recognised as a prominent immune regulatory enzyme capable of modulating immune cell activation status and phenotype via several molecular mechanisms including enzyme-dependent deprivation of L-Trp and its conversion into the aryl hydrocarbon receptor ligand kynurenine and other bioactive kynurenine pathway metabolites, or non-enzymatic cell signalling actions involving tyrosine phosphorylation of IDO1. Through these different modes of biochemical signalling, IDO1 regulates certain physiological functions (e.g. pregnancy) and modulates the pathogenesis and severity of diverse conditions including chronic inflammation, infectious disease, allergic and autoimmune disorders, transplantation, neuropathology and cancer. In the present review, we detail the current understanding of IDO1’s catalytic actions and the biochemical mechanisms regulating IDO1 expression and activity. We also discuss the biological functions of IDO1 with a focus on the enzyme's immune-modulatory function, its medical implications in diverse pathological settings and its utility as a therapeutic target.
Collapse
|
46
|
Makino R, Obayashi E, Hori H, Iizuka T, Mashima K, Shiro Y, Ishimura Y. Initial O2 Insertion Step of the Tryptophan Dioxygenase Reaction Proposed by a Heme-Modification Study. Biochemistry 2015; 54:3604-16. [DOI: 10.1021/acs.biochem.5b00048] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryu Makino
- Department
of Life Science, College of Science, Rikkyo University, Nishi-ikebukuro
3-34-1, Toshima-ku, Tokyo 171-8501, Japan
| | - Eiji Obayashi
- Department
of Biochemistry, Shimane University School of Medicine, Izumo, Shimane 693-8501, Japan
| | - Hiroshi Hori
- Center
for Quantum Science and Technology under Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Tetsutaro Iizuka
- RIKEN Harima Institute/Spring 8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Keisuke Mashima
- Department
of Life Science, College of Science, Rikkyo University, Nishi-ikebukuro
3-34-1, Toshima-ku, Tokyo 171-8501, Japan
| | - Yoshitsugu Shiro
- RIKEN Harima Institute/Spring 8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yuzuru Ishimura
- Department
of Biochemistry, School of Medicine, Keio University, 35 Shinanomachi,
Shinjuku-ku, Tokyo 160-8582, Japan
| |
Collapse
|
47
|
Henrottin J, Zervosen A, Lemaire C, Sapunaric F, Laurent S, Van den Eynde B, Goldman S, Plenevaux A, Luxen A. N (1)-Fluoroalkyltryptophan Analogues: Synthesis and in vitro Study as Potential Substrates for Indoleamine 2,3-Dioxygenase. ACS Med Chem Lett 2015; 6:260-5. [PMID: 25815143 DOI: 10.1021/ml500385d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/25/2015] [Indexed: 12/18/2022] Open
Abstract
Indoleamine 2,3-dioxygenase (hIDO) is an enzyme that catalyzes the oxidative cleavage of the indole ring of l-tryptophan through the kynurenine pathway, thereby exerting immunosuppressive properties in inflammatory and tumoral tissues. The syntheses of 1-(2-fluoroethyl)-tryptophan (1-FETrp) and 1-((1-(2-fluoroethyl)-1H-1,2,3-triazol-4-yl)methyl)-tryptophan, two N (1)-fluoroalkylated tryptophan derivatives, are described here. In vitro enzymatic assays with these two new potential substrates of hIDO show that 1-FETrp is a good and specific substrate of hIDO. Therefore, its radioactive isotopomer, 1-[(18)F]FETrp, should be a molecule of choice to visualize tumoral and inflammatory tissues and/or to validate new potential inhibitors.
Collapse
Affiliation(s)
- Jean Henrottin
- Cyclotron
Research Center, ‡Department of Chemistry, and §Macromolécules Biologiques, Center for Protein
Engineering, Université de Liège, Sart-Tilman, B-4000 Liège, Belgium
| | - Astrid Zervosen
- Cyclotron
Research Center, ‡Department of Chemistry, and §Macromolécules Biologiques, Center for Protein
Engineering, Université de Liège, Sart-Tilman, B-4000 Liège, Belgium
| | - Christian Lemaire
- Cyclotron
Research Center, ‡Department of Chemistry, and §Macromolécules Biologiques, Center for Protein
Engineering, Université de Liège, Sart-Tilman, B-4000 Liège, Belgium
| | | | | | - Benoit Van den Eynde
- Ludwig
Institute for Cancer Research, Brussels Branch and de Duve Institute, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Serge Goldman
- PET/Biomedical
Cyclotron Unit and Department of Nuclear Medicine, Erasme Hospital, Université Libre de Bruxelles, B-1070 Brussels, Belgium
- Center for Microscopy and Molecular Imaging, Rue Adrienne Bolland 8, B-6041 Gosselies, Belgium
| | - Alain Plenevaux
- Cyclotron
Research Center, ‡Department of Chemistry, and §Macromolécules Biologiques, Center for Protein
Engineering, Université de Liège, Sart-Tilman, B-4000 Liège, Belgium
| | - André Luxen
- Cyclotron
Research Center, ‡Department of Chemistry, and §Macromolécules Biologiques, Center for Protein
Engineering, Université de Liège, Sart-Tilman, B-4000 Liège, Belgium
| |
Collapse
|
48
|
Sedlmayr P, Blaschitz A, Stocker R. The role of placental tryptophan catabolism. Front Immunol 2014; 5:230. [PMID: 24904580 PMCID: PMC4032907 DOI: 10.3389/fimmu.2014.00230] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/05/2014] [Indexed: 01/22/2023] Open
Abstract
This review discusses the mechanisms and consequences of degradation of tryptophan (Trp) in the placenta, focusing mainly on the role of indoleamine 2,3-dioxygenase-1 (IDO1), one of three enzymes catalyzing the first step of the kynurenine pathway of Trp degradation. IDO1 has been implicated in regulation of feto-maternal tolerance in the mouse. Local depletion of Trp and/or the presence of metabolites of the kynurenine pathway mediate immunoregulation and exert antimicrobial functions. In addition to the decidual glandular epithelium, IDO1 is localized in the vascular endothelium of the villous chorion and also in the endothelium of spiral arteries of the decidua. Possible consequences of IDO1-mediated catabolism of Trp in the endothelium encompass antimicrobial activity and immunosuppression, as well as relaxation of the placental vasotonus, thereby contributing to placental perfusion and growth of both placenta and fetus. It remains to be evaluated whether other enzymes mediating Trp oxidation, such as indoleamine 2,3-dioxygenase-2, Trp 2,3-dioxygenase, and Trp hydroxylase-1 are of relevance to the biology of the placenta.
Collapse
Affiliation(s)
- Peter Sedlmayr
- Institute of Cell Biology, Histology and Embryology, Medical University of Graz , Graz , Austria
| | - Astrid Blaschitz
- Institute of Cell Biology, Histology and Embryology, Medical University of Graz , Graz , Austria
| | - Roland Stocker
- Victor Chang Cardiac Research Institute , Darlinghurst, NSW , Australia
| |
Collapse
|
49
|
Affiliation(s)
- Thomas L. Poulos
- Departments of Molecular Biology & Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California Irvine, Irvine, California 92697-3900
| |
Collapse
|
50
|
Carvalho C, Siegel D, Inman M, Xiong R, Ross D, Moody CJ. Benzofuranquinones as inhibitors of indoleamine 2,3-dioxygenase (IDO). Synthesis and biological evaluation. Org Biomol Chem 2014; 12:2663-74. [DOI: 10.1039/c3ob42258e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|