Oxoferryl species in mononuclear non-heme iron enzymes: Biosynthesis, properties and reactivity from a theoretical perspective

Dissecting the Mechanism of the Nonheme Iron Endoperoxidase FtmOx1 Using Substrate Analogues

FtmOx1 is a nonheme iron (NHFe) endoperoxidase, catalyzing three disparate reactions, endoperoxidation, alcohol dehydrogenation, and dealkylation, under in vitro conditions; the diversity complicates its mechanistic studies. In this study, we use two substrate analogues to simplify the FtmOx1-catalyzed reaction to either a dealkylation or an alcohol dehydrogenation reaction for structure-function relationship analysis to address two key FtmOx1 mechanistic questions: (1) Y224 flipping in the proposed COX-like model vs α-ketoglutarate (αKG) rotation proposed in the CarC-like mechanistic model and (2) the involvement of a Y224 radical (COX-like model) or a Y68 radical (CarC-like model) in FtmOx1-catalysis. When 13-oxo-fumitremorgin B (7) is used as the substrate, FtmOx1-catalysis changes from the endoperoxidation to a hydroxylation reaction and leads to dealkylation. In addition, consistent with the dealkylation side-reaction in the COX-like model prediction, the X-ray structure of the FtmOx1•Co^II•αKG•7 ternary complex reveals a flip of Y224 to an alternative conformation relative to the FtmOx1•Fe^II•αKG binary complex. Verruculogen (2) was used as a second substrate analogue to study the alcohol dehydrogenation reaction to examine the involvement of the Y224 radical or Y68 radical in FtmOx1-catalysis, and again, the results from the verruculogen reaction are more consistent with the COX-like model.

Multistructural microiteration combined with QM/MM-ONIOM electrostatic embedding

Multistructural microiteration (MSM) is a method to take account of contributions of multiple surrounding structures in a geometrical optimization or reaction path calculation using the quantum mechanics/molecular mechanics (QM/MM) ONIOM method. In this study, we combined MSM with the electrostatic embedding (EE) scheme of the QM/MM-ONIOM method by extending its original formulation for mechanical embedding (ME). MSM-EE takes account of the polarization in the QM region induced by point charges assigned to atoms in the multiple surrounding structures, where the point charges are scaled by the weight factor of each surrounding structure determined through MSM. The performance of MSM-EE was compared with that of the other methods, i.e., ONIOM-ME, ONIOM-EE, and MSM-ME, by applying them to three chemical processes: (1) chorismate-to-prephenate transformation in aqueous solution, (2) the same transformation as (1) in an enzyme, and (3) hydroxylation in p-hydroxybenzoate hydroxylase. These numerical tests of MSM-EE yielded barriers and reaction energies close to experimental values with computational costs comparable to those of the other three methods.

Critical Roles of Exchange and Superexchange Interactions in Dictating Electron Transfer and Reactivity in Metalloenzymes

Electron transfer (ET) is a fundamental process in transition-metal-dependent metalloenzymes. In these enzymes, the spin-spin interactions within the same metal center and/or between different metal sites can play a pivotal role in the catalytic cycle and reactivity. This Perspective highlights that the exchange and/or superexchange interactions can intrinsically modulate the inner-sphere and long-range electron transfer, thus controlling the mechanism and activity of metalloenzymes. For mixed-valence diiron oxygenases, the spin-regulated inner-sphere ET can be dictated by exchange interactions, leading to efficient O-O bond activations. Likewise, the spin-regulated inner-sphere ET can be enhanced by both exchange and superexchange interactions in [Fe4S4]-dependent SAM enzymes, which enable the efficient cleavage of the S─C(γ) or S─C5' bond of SAM. In addition to inner-sphere ET, superexchange interactions may modulate the long-range ET between metalloenzymes. We anticipate that the exchange and superexchange enhanced reactivity could be applicable in other important metalloenzymes, such as Photosystem II and nitrogenases.

Which is the real oxidant in the competitive ligand self-hydroxylation and substrate oxidation, a biomimetic iron(II)-hydroperoxo species or an oxo-iron(IV)-hydroxy one?

Nonheme iron(II)-hydroperoxo species (FeII-(η2-OOH)) 1 and the concomitant oxo-iron(IV)-hydroxyl one 2 are proposed as the key intermediates of a large class of 2-oxoglutarate dependent dioxygenases (e.g., isopenicillin N synthase). Extensive...

Electrostatic perturbations in the substrate-binding pocket of taurine/α-ketoglutarate dioxygenase determine its selectivity

Taurine/α‐ketoglutarate dioxygenase is an important enzyme that takes part in the cysteine catabolism process in the human body and selectively hydroxylates taurine at the C¹‐position. Recent computational studies showed that in the gas‐phase the C²−H bond of taurine is substantially weaker than the C¹−H bond, yet no evidence exists of 2‐hydroxytaurine products. To this end, a detailed computational study on the selectivity patterns in TauD was performed. The calculations show that the second‐coordination sphere and the protonation states of residues play a major role in guiding the enzyme to the right selectivity. Specifically, a single proton on an active site histidine residue can change the regioselectivity of the reaction through its electrostatic perturbations in the active site and effectively changes the C¹−H and C²−H bond strengths of taurine. This is further emphasized by many polar and hydrogen bonding interactions of the protein cage in TauD with the substrate and the oxidant that weaken the pro‐R C¹−H bond and triggers a chemoselective reaction process. The large cluster models reproduce the experimental free energy of activation excellently.

Heterodimeric Non-heme Iron Enzymes in Fungal Meroterpenoid Biosynthesis

Talaromyolides (1-6) are a group of unusual 6/6/6/6/6/6 hexacyclic meroterpenoids with (3R)-6-hydroxymellein and 4,5-seco-drimane substructures, isolated from the marine fungus Talaromyces purpureogenus. We have identified the biosynthetic gene cluster tlxA-J by heterologous expression in Aspergillus, in vitro enzyme assays, and CRISPR-Cas9-based gene inactivation. Remarkably, the heterodimer of non-heme iron (NHI) enzymes, TlxJ-TlxI, catalyzes three steps of oxidation including a key reaction, hydroxylation at C-5 and C-9 of 12, the intermediate with 3-ketohydroxydrimane scaffold, to facilitate a retro-aldol reaction, leading to the construction of the 4,5-secodrimane skeleton and characteristic ketal scaffold of 1-6. The products of TlxJ-TlxI, 1 and 4, were further hydroxylated at C-4'β by another NHI heterodimer, TlxA-TlxC, and acetylated by TlxB to yield the final products, 3 and 6. The X-ray structural analysis coupled with site-directed mutagenesis provided insights into the heterodimer TlxJ-TlxI formation and its catalysis. This is the first report to show that two NHI proteins form a heterodimer for catalysis and utilizes a novel methodology to create functional oxygenase structures in secondary metabolite biosynthesis.

N-Nitrosation Mechanism Catalyzed by Non-heme Iron-Containing Enzyme SznF Involving Intramolecular Oxidative Rearrangement

The non-heme iron-dependent enzyme SznF catalyzes a critical N-nitrosation step during the N-nitrosourea pharmacophore biosynthesis in streptozotocin. The intramolecular oxidative rearrangement process is known to proceed at the Fe^II-containing active site in the cupin domain of SznF, but its mechanism has not been elucidated to date. In this study, based on the density functional theory calculations, a unique mechanism was proposed for the N-nitrosation reaction catalyzed by SznF in which a four-electron oxidation process is accomplished through a series of complicated electron transferring between the iron center and substrate to bypass the high-valent Fe^IV═O species. In the catalytic reaction pathway, the O₂ binds to the iron center and attacks on the substrate to form the peroxo bridge intermediate by obtaining two electrons from the substrate exclusively. Then, instead of cleaving the peroxo bridge, the C^ε-N^ω bond of the substrate is homolytically cleaved first to form a carbocation intermediate, which polarizes the peroxo bridge and promotes its heterolysis. After O-O bond cleavage, the following reaction steps proceed effortlessly so that the N-nitrosation is accomplished without NO exchange among reaction species.

Influence of Varying Functionalization on the Peroxidase Activity of Nickel(II)–Pyridine Macrocycle Catalysts: Mechanistic Insights from Density Functional Theory

Nickel(II) complexes of mono-functionalized pyridine-tetraazamacrocycles (PyMACs) are a new class of catalysts that possess promising activity similar to biological peroxidases. Experimental studies with ABTS (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), substrate) and H2O2 (oxidant) proposed that hydrogen-bonding and proton-transfer reactions facilitated by their pendant arm were responsible for their catalytic activity. In this work, density functional theory calculations were performed to unravel the influence of pendant arm functionalization on the catalytic performance of Ni(II)–PyMACs. Generated frontier orbitals suggested that Ni(II)–PyMACs activate H2O2 by satisfying two requirements: (1) the deprotonation of H2O2 to form the highly nucleophilic HOO−, and (2) the generation of low-spin, singlet state Ni(II)–PyMACs to allow the binding of HOO−. COSMO solvation-based energies revealed that the O–O Ni(II)–hydroperoxo bond, regardless of pendant arm type, ruptures favorably via heterolysis to produce high-spin (S = 1) [(L)Ni3+–O·]2+ and HO−. Aqueous solvation was found crucial in the stabilization of charged species, thereby favoring the heterolytic process over homolytic. The redox reaction of [(L)Ni3+–O·]2+ with ABTS obeyed a 1:2 stoichiometric ratio, followed by proton transfer to produce the final intermediate. The regeneration of Ni(II)–PyMACs at the final step involved the liberation of HO−, which was highly favorable when protons were readily available or when the pKa of the pendant arm was low.

Iron transitions during activation of allosteric heme proteins in cell signaling

Allosteric heme proteins can fulfill a very large number of different functions thanks to the remarkable chemical versatility of heme through the entire living kingdom. Their efficacy resides in the ability of heme to transmit both iron coordination changes and iron redox state changes to the protein structure. Besides the properties of iron, proteins may impose a particular heme geometry leading to distortion, which allows selection or modulation of the electronic properties of heme. This review focusses on the mechanisms of allosteric protein activation triggered by heme coordination changes following diatomic binding to proteins as diverse as the human NO-receptor, cytochromes, NO-transporters and sensors, and a heme-activated potassium channel. It describes at the molecular level the chemical capabilities of heme to achieve very different tasks and emphasizes how the properties of heme are determined by the protein structure. Particularly, this reviews aims at giving an overview of the exquisite adaptability of heme, from bacteria to mammals.

Reactivity patterns of vanadium(iv/v)-oxo complexes with olefins in the presence of peroxides: a computational study

Vanadium porphyrin complexes are naturally occurring substances found in crude oil and have been shown to have medicinal properties as well. Little is known on their activities with substrates; therefore, we decided to perform a detailed density functional theory study on the properties and reactivities of vanadium(iv)- and vanadium(v)-oxo complexes with a TPPCl8 or 2,3,7,8,12,13,17,18-octachloro-meso-tetraphenylporphyrinato ligand system. In particular, we investigated the reactivity of [VV(O)(TPPCl8)]+ and [VIV(O)(TPPCl8)] with cyclohexene in the presence of H2O2 or HCO4-. The work shows that vanadium(iv)-oxo and vanadium(v)-oxo are sluggish oxidants by themselves and react with olefins slowly. However, in the presence of hydrogen peroxide, these metal-oxo species can be transformed into a side-on vanadium-peroxo complex, which reacts with substrates more efficiently. Particularly with anionic axial ligands, the side-on vanadium-peroxo and vanadium-oxo complexes produced epoxides from cyclohexene via small barrier heights. In addition to olefin epoxidation, we investigated aliphatic hydroxylation mechanisms by the same oxidants and some oxidants show efficient and viable cyclohexene hydroxylation mechanisms. The work implies that vanadium-oxo and vanadium-peroxo complexes can react with double bonds through epoxidation, and under certain conditions also undergo hydroxylation, but the overall reactivity is highly dependent on the equatorial ligand, the local environment and the presence or absence of anionic axial ligands.

Non-heme iron enzyme-catalyzed complex transformations: Endoperoxidation, cyclopropanation, orthoester, oxidative C-C and C-S bond formation reactions in natural product biosynthesis

Non-heme iron enzymes catalyze a wide range of chemical transformations, serving as one of the key types of tailoring enzymes in the biosynthesis of natural products. Hydroxylation reaction is the most common type of reactions catalyzed by these enzymes and hydroxylation reactions have been extensively investigated mechanistically. However, the mechanistic details for other types of transformations remain largely unknown or unexplored. In this paper, we present some of the most recently discovered transformations, including endoperoxidation, orthoester formation, cyclopropanation, oxidative C-C and C-S bond formation reactions. In addition, many of them are multi-functional enzymes, which further complicate their mechanistic investigations. In this work, we summarize their biosynthetic pathways, with special emphasis on the mechanistic details available for these newly discovered enzymes.

Recent examples of α-ketoglutarate-dependent mononuclear non-haem iron enzymes in natural product biosyntheses

Covering: up to 2018 α-Ketoglutarate (αKG, also known as 2-oxoglutarate)-dependent mononuclear non-haem iron (αKG-NHFe) enzymes catalyze a wide range of biochemical reactions, including hydroxylation, ring fragmentation, C-C bond cleavage, epimerization, desaturation, endoperoxidation and heterocycle formation. These enzymes utilize iron(ii) as the metallo-cofactor and αKG as the co-substrate. Herein, we summarize several novel αKG-NHFe enzymes involved in natural product biosyntheses discovered in recent years, including halogenation reactions, amino acid modifications and tailoring reactions in the biosynthesis of terpenes, lipids, fatty acids and phosphonates. We also conducted a survey of the currently available structures of αKG-NHFe enzymes, in which αKG binds to the metallo-centre bidentately through either a proximal- or distal-type binding mode. Future structure-function and structure-reactivity relationship investigations will provide crucial information regarding how activities in this large class of enzymes have been fine-tuned in nature.

Assembly of a mononuclear ferrous site using a bulky aldehyde-imidazole ligand

A new iron(II) complex has been prepared and characterized. [Fe(TrImA)2(OTf)2] (1, TrImA = 1-Tritylimidazole-4-carboxaldehyde). The solid state structure of 1 has been determined by X-ray crystallography. Compound 1 crystallizes in monoclinic space group P21/c, with a = 10.8323(18) Å, b = 8.1606(13) Å and c = 24.818(4) Å. The iron center is coordinated to two imidazole groups, two pendant aldehyde-derived carbonyl oxygens and two triflate oxygens. The complex is high spin between 300 and 20 K as indicated by variable field variable temperature magnetic measurements. A fit of the magnetic data yielded g = 2.17 and D = 4.05 cm-1. A large HOMO-LUMO gap energy (4.49 eV) exists for 1 indicating high stability.

Insights into enzymatic halogenation from computational studies

The halogenases are a group of enzymes that have only come to the fore over the last 10 years thanks to the discovery and characterization of several novel representatives. They have revealed the fascinating variety of distinct chemical mechanisms that nature utilizes to activate halogens and introduce them into organic substrates. Computational studies using a range of approaches have already elucidated many details of the mechanisms of these enzymes, often in synergistic combination with experiment. This Review summarizes the main insights gained from these studies. It also seeks to identify open questions that are amenable to computational investigations. The studies discussed herein serve to illustrate some of the limitations of the current computational approaches and the challenges encountered in computational mechanistic enzymology.