Heme Dioxygenases Research Articles

Secondary Sphere Lewis Acid Activated Heme Superoxo Adducts Mimic Crucial Non‐Covalent Interactions in IDO/TDO Heme Dioxygenases

Heme enzymes play a central role in a medley of reactivities within a wide variety of crucial biological systems. Their active sites are highly decorated with pivotal evolutionarily optimized non‐covalent interactions that precisely choreograph their biological functionalities with specific regio‐, stereo‐, and chemo‐selectivities. Gaining a clear comprehension of how such weak interactions within the active sites control reactivity offers powerful information to be implemented into the design of future therapeutic agents that target these heme enzymes. To shed light on such critical details pertaining to tryptophan dioxygenating heme enzymes, this study investigates the indole dioxygenation reactivities of Lewis acid‐activated heme superoxo model systems, wherein an unprecedented kinetic behavior is revealed. In that, the activated heme superoxo adduct is observed to undergo indole dioxygenation with the intermediacy of a non‐covalently organized precursor complex, which forms prior to the rate‐limiting step of the overall reaction landscape. Spectroscopic and theoretical characterization of this precursor complex draws close parallels to the ternary complex of heme dioxygenases, which has been postulated to be of crucial importance for successful 2,3‐dioxygenative cleavage of indole moieties.

Iron Dioxygen Adduct Formed during Electrochemical Oxygen Reduction by Iron Porphyrins Shows Catalytic Heme Dioxygenase Reactivity.

Heme dioxygenases oxidize the indole ring of tryptophan to kynurenine which is the first step in the biosynthesis of several important biomolecules like NAD, xanthurenic acid, and picolinic acid. A ferrous heme dioxygen adduct (or FeIII-O2•-) is the oxidant, and both the atoms of O2 are inserted in the product and its catalytic function has been difficult to emulate as it is complicated by competing rapid reactions like auto-oxidation and/or formation of the μ-oxo dimer. In situ resonance Raman spectroscopy technique, SERRS-RDE, is used to probe the species accumulated during electrochemical ORR catalyzed by site-isolated imidazole-bound iron porphyrin installed on a self-assembled monolayer covered electrode. These in situ SERRS-RDE data using labeled O2 show that indeed a FeIII-O2•- species accumulate on the electrode during ORR between -0.05 and -0.30 V versus Ag/AgCl (satd. KCl) and is reduced by proton coupled electron transfer to a FeIII-OOH species which, on the other hand, builds up on the electrode between -0.20 and -0.40 V versus Ag/AgCl (satd. KCl). This FeIII-OOH species then gives way to a FeIV═O species, which accumulates at -0.50 V versus Ag/AgCl (satd. KCl). When 2,3-dimethylindole is present in the solution and the applied potential is held in the range where FeIII-O2•- species accumulate, it gets oxidized to N-(2-acetylphenyl)acetamide retaining both the oxygens from O2 mimicking the reaction of heme dioxygenases. Turnover numbers more than 104 are recorded, establishing this imidazole-bound ferrous porphyrin as a functional model of heme dioxygenases.

Crystallization of heme dioxygenases IDO and TDO facilitates structure-based design of cancer immunology therapeutics

Crystallization of heme dioxygenases IDO and TDO facilitates structure-based design of cancer immunology therapeutics

Modeling Approaches Reveal New Regulatory Networks in Aspergillus fumigatus Metabolism.

Systems biology approaches are extensively used to model and reverse-engineer gene regulatory networks from experimental data. Indoleamine 2,3-dioxygenases (IDOs)—belonging in the heme dioxygenase family—degrade l-tryptophan to kynurenines. These enzymes are also responsible for the de novo synthesis of nicotinamide adenine dinucleotide (NAD+). As such, they are expressed by a variety of species, including fungi. Interestingly, Aspergillus may degrade l-tryptophan not only via IDO but also via alternative pathways. Deciphering the molecular interactions regulating tryptophan metabolism is particularly critical for novel drug target discovery designed to control pathogen determinants in invasive infections. Using continuous time Bayesian networks over a time-course gene expression dataset, we inferred the global regulatory network controlling l-tryptophan metabolism. The method unravels a possible novel approach to target fungal virulence factors during infection. Furthermore, this study represents the first application of continuous-time Bayesian networks as a gene network reconstruction method in Aspergillus metabolism. The experiment showed that the applied computational approach may improve the understanding of metabolic networks over traditional pathways.

Catalytic C-H Bond Oxidation Using Dioxygen by Analogues of Heme Superoxide.

Heme active sites are capable of oxidizing organic substrates by four electrons using molecular oxygen (heme dioxygenases), where a dioxygen (O2) adduct of heme (FeIII-O2•-) acts as the primary oxidant, in contrast to monooxygenases, where high-valent species are involved. This chemistry, although lucrative, is difficult to access using homogeneous synthetic systems. Over the past few years using a combination of self-assembly and in situ resonance Raman spectroscopy, the distribution of different reactive intermediates formed during the electrochemical reduction of oxygen has been elucidated. An FeIII-O2•- species, which is the reactive species of dioxygenase, is an intermediate in heterogeneous electrochemical O2 reduction by iron porphyrins and its population, under electrochemical conditions, may be controlled by controlling the applied potential. Iron porphyrins having different axial ligands are constructed on a self-assembled monolayer of thiols on an electrode, and these constructs can activate O2 and efficiently catalyze the dioxygenation of 3-methylindole and oxidation of a series of organic compounds having C-H bond energies between 80 and 90 kcal mol-1 at potentials where FeIII-O2•- species are formed on the electrode. Isotope effects suggest that hydrogen-atom transfer from the substrate is likely to be the rate-determining step. Axial thiolate ligands are found to be more efficient than axial imidazoles or phenolates with turnover numbers above 60000 and turnover frequencies over 60 s-1. These results highlight a new reaction engineering approach to harness O2 as a green oxidant for efficient chemical oxidation.

(Invited) Electrochemical Analogues of Dioxygenase and Monooxygenase Activity in Synthetic Iron Porphyrins

Dioxygen adducts of heme proteins are ubiquitous in all O2 activating/reducing heme proteins in nature. While artificial dioxygen adducts of heme are known for six decades, till date these have not been demonstrated to be able to oxidize organic substrates in sharp contrast to their non-heme analogues and naturally occurring enzymes like heme dioxygenases. To address this apparent anomaly an iron porphyrin complex is synthesized which includes a pendant quinol group. The corresponding dioxygen bound iron porphyrin species is demonstrated to perform Hydrogen atom transfer (HAT) from a quinol group appended to the porphyrin ligand. The resultant ferric peroxide, formed by the first HAT, performs a 2nd HAT generating a ferryl species (FeIV=O) and resulting in the 2e-/2H+ oxidation of the pendant hydroquinol to quinone. All the intermediate species are trapped at cryogenic temperatures and spectroscopically characterized using EPR and resonance Raman spectroscopy. DFT calculations reproduce the experimental kinetic parameters and provide insight into the nature of TS involved. These results demonstrate that artificial analogues of both heme ferric superoxide and ferric hydroperoxide species can perform HAT from an organic substrate when appropriately pre-organized to hydrogen bond to the bound superoxide and peroxide species. Siilarly, catalytic oxidation of organic substrates, using a green oxidant like O2, has been a long-term goal of the scientific community. In nature, these oxidations are performed by metalloenzymes which generate highly oxidizing species from O2 which, in turn, can oxidize inert organic substrates e.g. mono/di oxygenases. The same oxidants are produced during O2 reduction during respiration in the mitochondria but are reduced by electron transfer i.e. reductases. Iron porphyrin mimics of the active site of Cytochrome P450 (Cyt P450) are created atop self-assembled monolayer covered electrode. The rate of electron transfer from the electrode to the iron porphyrin site is attenuated to derive monooxygenase reactivity from these constructs which generally show reductase activity and catalytic hydroxylation of inert C-H bonds to alcohol and epoxidation alkenes, using molecular O2, is demonstrated with turnover numbers > 104. Mechanistic investigations suggest that a compound I analogue, formed during O2 reduction, is the primary oxidant and the selectivity is determined by the shape of the distal environment of the catalyst.

Hydrogen atom abstraction by synthetic heme ferric superoxide and hydroperoxide species.

To date, artificial dioxygen adducts of heme have not been demonstrated to be able to oxidize organic substrates in sharp contrast to their non-heme analogues and naturally occurring enzymes like heme dioxygenases. To address this apparent anomaly, an iron porphyrin complex is synthesized which includes a pendant quinol group. The corresponding dioxygen bound iron porphyrin species is demonstrated to perform hydrogen atom transfer (HAT) from the quinol group appended to the porphyrin ligand. The resultant ferric peroxide, formed by the first HAT, performs a 2nd HAT generating a ferryl species (FeIV[double bond, length as m-dash]O) and resulting in the 2e-/2H+ oxidation of the pendant hydroquinone to quinone.

Amino-acid sensing and degrading pathways in immune regulation

Indoleamine 2,3-dioxygenases (IDOs) − belonging in the heme dioxygenase family and degrading tryptophan − are responsible for the de novo synthesis of nicotinamide adenine dinucleotide (NAD+). As such, they are expressed by a variety of invertebrate and vertebrate species. In mammals, IDO1 has remarkably evolved to expand its functions, so to become a prominent homeostatic regulator, capable of modulating infection and immunity in multiple ways, including local tryptophan deprivation, production of biologically active tryptophan catabolites, and non-enzymatic cell-signaling activity. Much like IDO1, arginase 1 (Arg1) is an immunoregulatory enzyme that catalyzes the degradation of arginine. Here, we discuss the possible role of amino-acid degradation as related to the evolution of the immune systems and how the functions of those enzymes are linked by an entwined pathway selected by phylogenesis to meet the newly arising needs imposed by an evolving environment.

Tryptophan 2,3-dioxygenase (TDO)-reactive T cells differ in their functional characteristics in health and cancer

Tryptophan-2,3-dioxygenase (TDO) physiologically regulates systemic tryptophan levels in the liver. However, numerous studies have linked cancer with activation of local and systemic tryptophan metabolism. Indeed, similar to other heme dioxygenases TDO is constitutively expressed in many cancers. In the present study, we detected the presence of both CD8+ and CD4+ T-cell reactivity toward TDO in peripheral blood of patients with malignant melanoma (MM) or breast cancer (BC) as well as healthy subjects. However, TDO-reactive CD4+ T cells constituted distinct functional phenotypes in health and disease. In healthy subjects these cells predominately comprised interferon (IFN)γ and tumor necrosis factor (TNF)-α producing Th1 cells, while in cancer patients TDO-reactive CD4+ T-cells were more differentiated with release of not only IFNγ and TNFα, but also interleukin (IL)-17 and IL-10 in response to TDO-derived MHC-class II restricted peptides. Hence, in healthy donors (HD) a Th1 helper response was predominant, whereas in cancer patients CD4+ T-cell responses were skewed toward a regulatory T cell (Treg) response. Furthermore, MM patients hosting a TDO-specific IL-17 response showed a trend toward an improved overall survival (OS) compared to MM patients with IL-10 producing, TDO-reactive CD4+ T cells. For further characterization, we isolated and expanded both CD8+ and CD4+ TDO-reactive T cells in vitro. TDO-reactive CD8+ T cells were able to kill HLA-matched tumor cells of different origin. Interestingly, the processed and presented TDO-derived epitopes varied between different cancer cells. With respect to CD4+ TDO-reactive T cells, in vitro expanded T-cell cultures comprised a Th1 and/or a Treg phenotype. In summary, our data demonstrate that the immune modulating enzyme TDO is a target for CD8+ and CD4+ T cell responses both in healthy subjects as well as patients with cancer; notably, however, the functional phenotype of these T-cell responses differ depending on the respective conditions of the host.

An Ancient Relative of Cyclooxygenase in Cyanobacteria Is a Linoleate 10S-Dioxygenase That Works in Tandem with a Catalase-related Protein with Specific 10S-Hydroperoxide Lyase Activity

In the course of exploring the scope of catalase-related hemoprotein reactivity toward fatty acid hydroperoxides, we detected a novel candidate in the cyanobacterium Nostoc punctiforme PCC 73102. The immediate neighboring upstream gene, annotated as "cyclooxygenase-2," appeared to be a potential fatty acid heme dioxygenase. We cloned both genes and expressed the cDNAs in Escherichia coli, confirming their hemoprotein character. Oxygen electrode recordings demonstrated a rapid (>100 turnovers/s) reaction of the heme dioxygenase with oleic and linoleic acids. HPLC, including chiral column analysis, UV, and GC-MS of the oxygenated products, identified a novel 10S-dioxygenase activity. The catalase-related hemoprotein reacted rapidly and specifically with linoleate 10S-hydroperoxide (>2,500 turnovers/s) with a hydroperoxide lyase activity specific for the 10S-hydroperoxy enantiomer. The products were identified by NMR as (8E)10-oxo-decenoic acid and the C8 fragments, 1-octen-3-ol and 2Z-octen-1-ol, in ∼3:1 ratio. Chiral HPLC analysis established strict enzymatic control in formation of the 3R alcohol configuration (99% enantiomeric excess) and contrasted with racemic 1-octen-3-ol formed in reaction of linoleate 10S-hydroperoxide with hematin or ferrous ions. The Nostoc linoleate 10S-dioxygenase, the sequence of which contains the signature catalytic sequence of cyclooxygenases and fungal linoleate dioxygenases (YRWH), appears to be a heme dioxygenase ancestor. The novel activity of the lyase expands the known reactions of catalase-related proteins and functions in Nostoc in specific transformation of the 10S-hydroperoxylinoleate.

Heme-containing dioxygenases involved in tryptophan oxidation

Heme iron is often used in biology for activation of oxygen. The mechanisms of oxygen activation by heme-containing monooxygenases (the cytochrome P450s) are well known, and involve formation of a Compound I species, but information on the heme-containing dioxygenase enzymes involved in tryptophan oxidation lags far behind. In this review, we gather together information emerging recently from structural, mechanistic, spectroscopic, and computational approaches on the heme dioxygenase enzymes involved in tryptophan oxidation. We explore the subtleties that differentiate various heme enzymes from each other, and use this to piece together a developing picture for oxygen activation in this particular class of heme-containing dioxygenases.

The mechanism of formation of N-formylkynurenine by heme dioxygenases.

Heme dioxygenases catalyze the oxidation of l-tryptophan to N-formylkynurenine (NFK), the first and rate-limiting step in tryptophan catabolism. Although recent progress has been made on early stages in the mechanism, there is currently no experimental data on the mechanism of product (NFK) formation. In this work, we have used mass spectrometry to examine product formation in a number of dioxygenases. In addition to NFK formation (m/z = 237), the data identify a species (m/z = 221) that is consistent with insertion of a single atom of oxygen into the substrate during O2-driven turnover. The fragmentation pattern for this m/z = 221 species is consistent with a cyclic amino acetal structure; independent chemical synthesis of the 3a-hydroxypyrroloindole-2-carboxylic acid compound is in agreement with this assignment. Labeling experiments with 18O2 confirm the origin of the oxygen atom as arising from O2-dependent turnover. These data suggest that the dioxygenases use a ring-opening mechanism during NFK formation, rather than Criegee or dioxetane mechanisms as previously proposed.

Structure and Reaction Mechanism in the Heme Dioxygenases

As members of the family of heme-dependent enzymes, the heme dioxygenases are differentiated by virtue of their ability to catalyze the oxidation of l-tryptophan to N-formylkynurenine, the first and rate-limiting step in tryptophan catabolism. In the past several years, there have been a number of important developments that have meant that established proposals for the reaction mechanism in the heme dioxygenases have required reassessment. This focused review presents a summary of these recent advances, written from a structural and mechanistic perspective. It attempts to present answers to some of the long-standing questions, to highlight as yet unresolved issues, and to explore the similarities and differences of other well-known catalytic heme enzymes such as the cytochromes P450, NO synthase, and peroxidases.

Reaction Mechanism of Heme-Based Dioxygenases

Indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) are two heme-containing enzymes that catalyze the oxidative cleavage of tryptophan (Trp) to N-formyl kynurenine (NFK), the initial and rate-limiting step of the kynurenine pathway. Until recently it was generally believed that the heme dioxygenase reaction follows a base-catalyzed mechanism. Based on this mechanism, the reaction is initiated by deprotonation of the indoleamine group of Trp by an active site base. It is followed by electrophilic addition of the heme-bound dioxygen to the C2=C3 bond of the indole moiety of Trp, leading to a heme-bound 3-indolenylperoxo intermediate, which subsequently converts to the product NFK, via a dioxetane intermediate or a Criegee type of rearrangement. In this work, we sought to use continuous-flow resonance Raman spectroscopy, combined with stopped-flow UV-Vis spectroscopy, to investigate the dioxygenase reaction carried out by IDO and TDO. Surprisingly, a ferryl intermediate was detected during the IDO reaction at 0.2 s. The presence of this intermediate supports a new mechanism, in which the two atoms of dioxygen are sequentially incorporated into the substrate via a two-step reaction. The ferryl intermediate is not observable during the TDO reaction, highlighting the structural differences between the two types of dioxygenases, as well as the importance of the stereoelectronic factors in modulating the reactions.

Indol-2-yl ethanones as novel indoleamine 2,3-dioxygenase (IDO) inhibitors

Indoleamine 2,3-dioxygenase (IDO) is a heme dioxygenase which has been shown to be involved in the pathological immune escape of diseases such as cancer. The synthesis and structure–activity relationships (SAR) of a novel series of IDO inhibitors based on the indol-2-yl ethanone scaffold is described. In vitro and in vivo biological activities have been evaluated, leading to compounds with IC50 values in the micromolar range in both tests. Introduction of small substituents in the 5- and 6-positions of the indole ring, indole N-methylation and variations of the aromatic side chain are all well tolerated. An iron coordinating group on the linker is a prerequisite for biological activity, thus corroborating the virtual screening results.

ONIOM Study on a Missing Piece in Our Understanding of Heme Chemistry: Bacterial Tryptophan 2,3-Dioxygenase with Dual Oxidants

Unique heme-containing tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) catalyze oxidative cleavage of the pyrrole ring of L-tryptophan (Trp). Although these two heme dioxygenases were discovered more than 40 years ago, their reaction mechanisms were still poorly understood. Encouraged by recent X-ray crystal structures, new mechanistic pathways were proposed. We performed ONIOM(B3LYP:Amber) calculations with explicit consideration of the protein environment to study various possible reaction mechanisms for bacterial TDO. The ONIOM calculations do not support the proposed mechanisms (via either formation of the dioxetane intermediate or Criegee-type rearrangement); a mechanism that is exceptional in the hemes emerges. It starts with (1) direct radical addition of a ferric-superoxide intermediate with C2 of the indole of Trp, followed by (2) ring-closure via homolytic O-O cleavage to give epoxide and ferryl-oxo (Cpd II) intermediates, (3) acid-catalyzed regiospecific ring-opening of the epoxide, (4) oxo-attack, and (5) finally C-C bond cleavage concerted with back proton transfer. The involvement of dual oxidants, ferric-superoxide and ferryl-oxo (Cpd II) intermediates, is proposed to be responsible for the dioxygenase reactivity in bacterial TDO. In particular, the not-well-recognized ferric-superoxide porphyrin intermediate is found to be capable of reacting with pi-systems via direct radical addition, an uncommon dioxygen activation in the hemes. The comparison between Xanthomonas campestris TDO and some heme as well non-heme oxygenases is also discussed.

Reassessment of the Reaction Mechanism in the Heme Dioxygenases

Indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) are heme enzymes that catalyze the O(2)-dependent oxidation of L-tryptophan to N-formyl-kynurenine. Previous proposals for the mechanism of this reaction have suggested that deprotonation of the indole NH group, either by an active-site base or by oxygen bound to the heme iron, as the initial step. In this work, we have examined the activity of 1-Me-L-Trp with three different heme dioxygenases and their site-directed variants. We find, in contrast to previous work, that 1-Me-L-Trp is a substrate for the heme dioxygenase enzymes. These observations suggest that deprotonation of the indole N(1) is not essential for catalysis, and an alternative reaction mechanism, based on the known chemistry of indoles, is presented.

A Kinetic, Spectroscopic, and Redox Study of Human Tryptophan 2,3-Dioxygenase

The family of heme dioxygenases, as exemplified by indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase, catalyzes the oxidative cleavage of L-tryptophan to N-formylkynurenine. Here, we describe a bacterial expression system for human tryptophan 2,3-dioxygenase (rhTDO) together with spectroscopic, kinetic, and redox analyses. We find unexpected differences between human tryptophan 2,3-dioxygenase and human indoleamine 2,3-dioxygenase [Chauhan et al. (2008) Biochemistry 47, 4761-4769 ]. Thus, in contrast to indoleamine 2,3-dioxygenase, the catalytic ferrous-oxy complex of rhTDO is not observed, nor does the enzyme discriminate against substrate binding to the ferric derivative. In addition, we show that the rhTDO is also catalytically active in the ferric form. These new findings illustrate that significant mechanistic differences exist across the heme dioxygenase family, and the data are discussed within this broader framework.

Linoleate diol synthase and pgh synthases — A new gene family of fatty acid heme dioxygenases?

Linoleate diol synthase and pgh synthases — A new gene family of fatty acid heme dioxygenases?

Cloning of Linoleate Diol Synthase Reveals Homology with Prostaglandin H Synthases

Linoleate diol synthase is a homotetrameric ferric hemeprotein, which catalyzes dioxygenation of linoleic acid to (8R)-hydroperoxylinoleate and isomerization of the hydroperoxide to (7S,8S)-dihydroxylinoleate. Ferryl intermediates and a tyrosyl radical are formed in the reaction. Linoleate diol synthase was digested with endoproteinase Lys-C, and internal peptides were sequenced. The sequence information was used for reverse transcription-polymerase chain reaction analysis, and a cDNA probe was obtained. Northern blot analysis of linoleate diol synthase suggested a 3.7-kilobase pair (kb) mRNA. A full-length clone of the linoleate diol synthase gene was obtained by screening of a genomic lambda-ZAP II library of the fungus Gaeumannomyces graminis. The 5'-untranslated region contained CAAT- and TATA-like boxes. The gene contained three short introns and spanned over 3.2-kb. The deduced open reading frame consisted of 2.9-kb, which corresponded to 978 amino acids and a molecular subunit mass of 108,000. Data base analysis with the gapped BLAST algorithm showed that 391 residues of linoleate diol synthase was 23-24% identical and 36-37% positive with the catalytic domain of mammalian prostaglandin H (PGH) synthase-2. Based on homology with PGH synthases, the proximal heme ligand of linoleate diol synthase was tentatively identified as His-379 and the important tyrosine for catalysis as residue 376 (apparent consensus EFNXXXYXWH). The distal heme ligand was tentatively identified as His-203 (apparent consensus THXXFXT). We conclude from catalytic and structural similarities that linoleate diol synthase and PGH synthases likely share common ancestry and may belong to a gene family of fatty acid heme dioxygenases.