Unraveling the Crucial Role of Single Active Water Molecule in the Oxidative Cleavage of Aliphatic C–C Bond of 2,4′-Dihydroxyacetophenone Catalyzed by 2,4′-Dihydroxyacetophenone Dioxygenase Enzyme: A Quantum Mechanics/Molecular Mechanics Investigation

What is the Origin of the Regioselective C3-Hydroxylation of L-Arg by the Nonheme Iron Enzyme Capreomycin C?

The nonheme iron dioxygenase capreomycin C (CmnC) hydroxylates a free L-arginine amino acid regio- and stereospecifically at the C3-position as part of the capreomycin antibiotics biosynthesis. Little is known on its structure, catalytic cycle and substrate specificity and, therefore, a comprehensive computational study was performed. A large QM cluster model of CmnC was created of 297 atoms and the mechanisms for C3-H, C4-H and C5-H hydroxylation and C3-C4 desaturation were investigated. All low-energy pathways correspond to radical reaction mechanisms with an initial hydrogen atom abstraction followed by OH rebound to form alcohol product complexes. The work is compared to alternative L-Arg hydroxylating nonheme iron dioxygenases and the differences in active site polarity are compared. We show that a tight hydrogen bonding network in the substrate binding pocket positions the substrate in an ideal orientation for C3-H activation, whereby the polar groups in the substrate binding pocket induce an electric field effect that guides the selectivity.

Tutorial Review on the Set-Up and Running of Quantum Mechanical Cluster Models for Enzymatic Reaction Mechanisms

Enzymes turnover substrates into products with amazing efficiency and selectivity and as such have great potential for use in biotechnology and pharmaceutical applications. However, details of their catalytic cycles and the origins surrounding the regio- and chemoselectivity of enzymatic reaction processes remain unknown, which makes the engineering of enzymes and their use in biotechnology challenging. Computational modelling can assist experimental work in the field and establish the factors that influence the reaction rates and the product distributions. A popular approach in modelling is the use of quantum mechanical cluster models of enzymes that take the first- and second coordination sphere of the enzyme active site into consideration. These QM cluster models are widely applied but often the results obtained are dependent on model choice and model selection. Herein, we show that QM cluster models can give highly accurate results that reproduce experimental product distributions and free energies of activation within several kcal mol-1, regarded that large cluster models with >300 atoms are used that include key hydrogen bonding interactions and charged residues. In this tutorial review, we give general guidelines on the set-up and applications of the QM cluster method and discuss its accuracy and reproducibility. Finally, several representative QM cluster model examples on metal-containing enzymes are presented, which highlight the strength of the approach.

Computational Study Into the Oxidative Ring-Closure Mechanism During the Biosynthesis of Deoxypodophyllotoxin

The nonheme iron dioxygenase deoxypodophyllotoxin synthase performs an oxidative ring-closure reaction as part of natural product synthesis in plants. How the enzyme enables the oxidative ring-closure reaction of (-)-yatein and avoids substrate hydroxylation remains unknown. To gain insight into the reaction mechanism and understand the details of the pathways leading to products and by-products we performed a comprehensive computational study. The work shows that substrate is bound tightly into the substrate binding pocket with the C7'-H bond closest to the iron(IV)-oxo species. The reaction proceeds through a radical mechanism starting with hydrogen atom abstraction from the C7'-H position followed by ring-closure and a final hydrogen transfer to form iron(II)-water and deoxypodophyllotoxin. Alternative mechanisms including substrate hydroxylation and an electron transfer pathway were explored but found to be higher in energy. The mechanism is guided by electrostatic perturbations of charged residues in the second-coordination sphere that prevent alternative pathways.

Divergent Electrochemical Synthesis of Indoles through pKa Regulation of Amides: Synthetic and Mechanistic Insights

A divergent synthetic approach to access highly substituted indole scaffolds is illustrated. By virtue of a tunable electrochemical strategy, distinct control over the C-3 substitution pattern was achieved by employing two analogous 2-styrylaniline precursors. The chemoselectivity is governed by the fine-tuning of the acidity of the amide proton, relying on the appropriate selection of N-protecting groups, and assisted by the reactivity of the electrogenerated intermediates. Detailed mechanistic investigations based on cyclic voltametric experiments and computational studies revealed the crucial role of water additive, which assists the proton-coupled electron transfer event for highly acidic amide precursors, followed by an energetically favorable intramolecular C-N coupling, causing exclusive fabrication of the C-3 unsubstituted indoles. Alternatively, the implementation of an electrogenerated cationic olefin activator delivers the C-3 substituted indoles through the preferential nucleophilic nature of the N-acyl amides. This electrochemical approach of judicious selection of N-protecting groups to regulate pKa/E° provides an expansion in the domain of switchable generation of heterocyclic derivatives in a sustainable fashion, with high regio- and chemoselectivity.

Mechanism for the Halogenation and Azidation of Lysine Catalyzed by Non-heme Iron BesD Enzyme

Selective halogenation is important in synthetic chemistry. BesD, a new member of the non-heme Fe(II)/α-ketoglutarate (αKG)-dependent halogenase family, can activate the sp3 C-H bond and halogenate lysine, in particular without a carrier protein. Using the density functional calculations, a chlorination mechanism in BesD has been proposed, mainly including the formation of Cl-Fe(IV)=O through the αKG decarboxylation, the isomerization of Cl-Fe(IV)=O, the substrate hydrogen abstraction by Fe(IV)=O, and the rebound of chloro to the substrate carbon radical. The hydrogen abstraction is rate-limiting. The isomerization of Cl-Fe(IV)=O is essential for the hydrogen abstraction and the chiral selectivity. The BesD-catalyzed bromination and azidation of lysine adopt the same mechanism as the chlorination. The hardly-changed overall barriers indicate that the introduced ligands (X) do not affect the reaction rate significantly, implying that the X-introduced reactions catalyzed by BesD may be extended to other X anions.

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.

Decoding Regioselective Reaction Mechanism of the Gentisic Acid Catalyzed by Gentisate 1,2-Dioxygenase Enzyme

Gentisate 1,2-dioxygenase (GDO), a ring-fission non-heme dioxygenase enzyme, displays a unique regioselective reaction of gentisic acid (GTQ) in the presence of molecular oxygen. GTQ is an important intermediate in the...

Can the isonitrile biosynthesis enzyme ScoE assist with the biosynthesis of isonitrile groups in drug molecules? A computational study

Computational studies show that the isonitrile synthesizing enzyme ScoE can catalyse the conversion of γ-Gly substituents in substrates to isonitrile. This enables efficient isonitrile substitution into target molecules such as axisonitrile-1.

Biodegradation of herbicides by a plant nonheme iron dioxygenase: mechanism and selectivity of substrate analogues

Aryloxyalkanoate dioxygenases are unique herbicide biodegrading nonheme iron enzymes found in plants and hence, from environmental and agricultural point of view they are important and valuable. However, they often are substrate specific and little is known on the details of the mechanism and the substrate scope. To this end, we created enzyme models and calculate the mechanism for 2,4-dichlorophenoxyacetic acid biodegradation and 2-methyl substituted analogs by density functional theory. The work shows that the substrate binding is tight and positions the aliphatic group close to the metal center to enable a chemoselective reaction mechanism to form the C 2 -hydroxy products, whereas the aromatic hydroxylation barriers are well higher in energy. Subsequently, we investigated the metabolism of R - and S -methyl substituted inhibitors and show that these do not react as efficiently as 2,4-dichlorophenoxyacetic acid substrate due to stereochemical clashes in the active site and particularly for the R -isomer give high rebound barriers.

Structure and Functional Differences of Cysteine and 3-Mercaptopropionate Dioxygenases: A Computational Study

Thiol dioxygenases are important enzymes for human health; they are involved in the detoxification and catabolism of toxic thiol-containing natural products such as cysteine. As such, these enzymes have relevance to the development of Alzheimer's and Parkinson's diseases in the brain. Recent crystal structure coordinates of cysteine and 3-mercaptopropionate dioxygenase (CDO and MDO) showed major differences in the second-coordination spheres of the two enzymes. To understand the difference in activity between these two analogous enzymes, we created large, active-site cluster models. We show that CDO and MDO have different iron(III)-superoxo-bound structures due to differences in ligand coordination. Furthermore, our studies show that the differences in the second-coordination sphere and particularly the position of a positively charged Arg residue results in changes in substrate positioning, mobility and enzymatic turnover. Furthermore, the substrate scope of MDO is explored with cysteinate and 2-mercaptosuccinic acid and their reactivity is predicted.

Density Functional Theory Study into the Reaction Mechanism of Isonitrile Biosynthesis by the Nonheme Iron Enzyme ScoE

The nonheme iron enzyme ScoE catalyzes the biosynthesis of an isonitrile substituent in a peptide chain. To understand details of the reaction mechanism we created a large active site cluster model of 212 atoms that contains substrate, the active oxidant and the first- and second-coordination sphere of the protein and solvent. Several possible reaction mechanisms were tested and it is shown that isonitrile can only be formed through two consecutive catalytic cycles that both use one molecule of dioxygen and α-ketoglutarate. In both cycles the active species is an iron(IV)-oxo species that in the first reaction cycle reacts through two consecutive hydrogen atom abstraction steps: first from the N–H group and thereafter from the C–H group to desaturate the NH-CH2 bond. The alternative ordering of hydrogen atom abstraction steps was also tested but found to be higher in energy. Moreover, the electronic configurations along that pathway implicate an initial hydride transfer followed by proton transfer. We highlight an active site Lys residue that is shown to donate charge in the transition states and influences the relative barrier heights and bifurcation pathways. A second catalytic cycle of the reaction of iron(IV)-oxo with desaturated substrate starts with hydrogen atom abstraction followed by decarboxylation to give isonitrile directly. The catalytic cycle is completed with a proton transfer to iron(II)-hydroxo to generate the iron(II)-water resting state. The work is compared with experimental observation and previous computational studies on this system and put in a larger perspective of nonheme iron chemistry.

Electrostatic Perturbations from the Protein Affect C-H Bond Strengths of the Substrate and Enable Negative Catalysis in the TmpA Biosynthesis Enzyme

The nonheme iron dioxygenase 2-(trimethylammonio)-ethylphosphonate dioxygenase (TmpA) is an enzyme involved in the regio- and chemoselective hydroxylation at the C¹ -position of the substrate as part of the biosynthesis of glycine betaine in bacteria and carnitine in humans. To understand how the enzyme avoids breaking the weak C² -H bond in favor of C¹ -hydroxylation, we set up a cluster model of 242 atoms representing the first and second coordination sphere of the metal center and substrate binding pocket, and investigated possible reaction mechanisms of substrate activation by an iron(IV)-oxo species by density functional theory methods. In agreement with experimental product distributions, the calculations predict a favorable C¹ -hydroxylation pathway. The calculations show that the selectivity is guided through electrostatic perturbations inside the protein from charged residues, external electric fields and electric dipole moments. In particular, charged residues influence and perturb the homolytic bond strength of the C¹ -H and C² -H bonds of the substrate, and strongly strengthens the C² -H bond in the substrate-bound orientation.

Probing the Mechanism for 2,4'-Dihydroxyacetophenone Dioxygenase Using Biomimetic Iron Complexes

In this study, we report the synthesis and characterization of [Fe(T1Et4iPrIP)(2-OH-AP)(OTf)](OTf) (2), [Fe(T1Et4iPrIP)(2-O-AP)](OTf) (3), and [Fe(T1Et4iPrIP)(DMF)₃](OTf)₃ (4) (T1Et4iPrIP = tris(1-ethyl-4-isopropyl-imidazolyl)phosphine; 2-OH-AP = 2-hydroxyacetophenone, and 2-O-AP^- = monodeprotonated 2-hydroxyacetophenone). Both 2 and 3 serve as model complexes for the enzyme-substrate adduct for the nonheme enzyme 2,4'-dihydroacetophenone (DHAP) dioxygenase or DAD, while 4 serves as a model for the ferric form of DAD. Complexes 2-4 have been characterized by X-ray crystallography which reveals T1Et4iPrIP to bind iron in a tridentate fashion. Complex 2 additionally contains a bidentate 2-OH-AP ligand and a monodentate triflate ligand yielding distorted octahedral geometry, while 3 possesses a bidentate 2-O-AP^- ligand and exhibits distorted trigonal bipyramidal geometry (τ = 0.56). Complex 4 displays distorted octahedral geometry with 3 DMF ligands completing the ligand set. The UV-vis spectrum of 2 matches more closely to the DAD-substrate spectrum than 3, and therefore, it is believed that the substrate for DAD is bound in the protonated form. TD-DFT studies indicate that visible absorption bands for 2 and 3 are due to MLCT bands. Complexes 2 and 3 are capable of oxidizing the coordinated substrate mimics in a stoichiometric and catalytic fashion in the presence of O₂. Complex 4 does not convert 2-OH-AP to products under the same catalytic conditions; however, it becomes anaerobically reduced in the presence of 2 equiv 2-OH-AP to 2.

What Determines the Selectivity of Arginine Dihydroxylation by the Nonheme Iron Enzyme OrfP?

The nonheme iron enzyme OrfP reacts with l-Arg selectively to form the 3R,4R-dihydroxyarginine product, which in mammals can inhibit the nitric oxide synthase enzymes involved in blood pressure control. To understand the mechanisms of dioxygen activation of l-Arg by OrfP and how it enables two sequential oxidation cycles on the same substrate, we performed a density functional theory study on a large active site cluster model. We show that substrate binding and positioning in the active site guides a highly selective reaction through C³ -H hydrogen atom abstraction. This happens despite the fact that the C³ -H and C⁴ -H bond strengths of l-Arg are very similar. Electronic differences in the two hydrogen atom abstraction pathways drive the reaction with an initial C³ -H activation to a low-energy ⁵ σ-pathway, while substrate positioning destabilizes the C⁴ -H abstraction and sends it over the higher-lying ⁵ π-pathway. We show that substrate and monohydroxylated products are strongly bound in the substrate binding pocket and hence product release is difficult and consequently its lifetime will be long enough to trigger a second oxygenation cycle.

Computational studies of DNA base repair mechanisms by nonheme iron dioxygenases: selective epoxidation and hydroxylation pathways

DNA base repair mechanisms of alkylated DNA bases is an important reaction in chemical biology and particularly in the human body. It is typically catalyzed by an α-ketoglutarate-dependent nonheme iron dioxygenase named the AlkB repair enzyme. In this work we report a detailed computational study into the structure and reactivity of AlkB repair enzymes with alkylated DNA bases. In particular, we investigate the aliphatic hydroxylation and C[double bond, length as m-dash]C epoxidation mechanisms of alkylated DNA bases by a high-valent iron(iv)-oxo intermediate. Our computational studies use quantum mechanics/molecular mechanics methods on full enzymatic structures as well as cluster models on active site systems. The work shows that the iron(iv)-oxo species is rapidly formed after dioxygen binding to an iron(ii) center and passes a bicyclic ring structure as intermediate. Subsequent cluster models explore the mechanism of substrate hydroxylation and epoxidation of alkylated DNA bases. The work shows low energy barriers for substrate activation and consequently energetically feasible pathways are predicted. Overall, the work shows that a high-valent iron(iv)-oxo species can efficiently dealkylate alkylated DNA bases and return them into their original form.

Role of water in cyclooxygenase catalysis and design of anti-inflammatory agents targeting two sites of the enzyme

While designing the anti-inflammatory agents targeting cyclooxygenase-2 (COX-2), we first identified a water loop around the heme playing critical role in the enzyme catalysis. The results of molecular dynamic studies supported by the strong hydrogen-bonding equilibria of the participating atoms, radical stabilization energies, the pK_a of the H-donor/acceptor sites and the cyclooxygenase activity of pertinent muCOX-2 ravelled the working of the water–peptide channel for coordinating the flow of H·/electron between the heme and Y385. Based on the working of H·/electron transfer channel between the 12.5 Å distant radical generation and the radical disposal sites, a series of molecules was designed and synthesized. Among this category of compounds, an appreciably potent anti-inflammatory agent exhibiting IC₅₀ 0.06 μM against COX-2 and reversing the formalin induced analgesia and carageenan induced inflammation in mice by 90% was identified. Further it was revealed that, justifying its bidentate design, the compound targets water loop (heme bound site) and the arachidonic acid binding pockets of COX-2.

Mechanistic study of the ATP hydrolysis reaction in dynein motor protein

Dynein, a large and complex motor protein, harnesses energy from adenosine triphosphate (ATP) hydrolysis to regulate essential cellular activities. The ATP hydrolysis mechanism for the dynein motor is still shrouded in mystery. Herein, molecular dynamics simulations of a dynein motor disclosed that two water molecules are present close to the γ-phosphate of ATP and Glu1742 at the AAA1 site of dynein. We have proposed three possible mechanisms for the ATP hydrolysis. We divulge by using a quantum mechanics/molecular mechanics (QM/MM) study that two water molecules and Glu1742 are crucial for facilitating the ATP hydrolysis reaction in dynein. Moreover, the ATP hydrolysis step is initiated by the activation of lytic water (W1) by Glu1742 through relay proton transfers with the help of auxiliary water (W2) yielding HPO₄^2- and ADP, as a product. In the next step, a proton is shifted back from Glu1742 to generate inorganic phosphate (H₂PO₄^-) via another relay proton transfer event. The overall activation barrier for the Glu1742 assisted ATP hydrolysis is found to be the most favourable pathway compared to other plausible pathways. We also unearthed that ATP hydrolysis in dynein follows a so-called associative-like pathway in its rate-limiting step. Our study ascertained the important indirect roles of the two amino acids (such as Arg2109, Asn1792) and Mg²⁺ ion in the ATP hydrolysis of dynein. Additionally, multiple sequence alignment of the different organisms of dynein motors has conveyed the evolutionary importance of the Glu1742, Asn1742, and Arg2109 residues, respectively. As similar mechanisms are also prevalent in other motors, and GTPase and ATPase enzymes, the present finding spells out the definitive requirement of a proton relay process through an extended water-chain as one of the key components in an enzymatic ATP hydrolysis reaction.

Selective Hydrogen Atom Abstraction from Dihydroflavonol by a Nonheme Iron Center Is the Key Step in the Enzymatic Flavonol Synthesis and Avoids Byproducts

The plant non-heme iron dioxygenase flavonol synthase performs a regioselective desaturation reaction as part of the biosynthesis of the signaling molecule flavonol that triggers the growing of leaves and flowers. These compounds also have health benefits for humans. Desaturation of aliphatic compounds generally proceeds through two consecutive hydrogen atom abstraction steps from two adjacent carbon atoms and in nature often is performed by a high-valent iron(IV)-oxo species. We show that the order of the hydrogen atom abstraction steps, however, is opposite of those expected from the C-H bond strengths in the substrate and determines the product distributions. As such, flavonol synthase follows a negative catalysis mechanism. Using density functional theory methods on large active-site model complexes, we investigated pathways for desaturation and hydroxylation by an iron(IV)-oxo active-site model. Contrary to thermochemical predictions, we find that the oxidant abstracts the hydrogen atom from the strong C²-H bond rather than the weaker C³-H bond of the substrate first. We analyze the origin of this unexpected selective hydrogen atom abstraction pathway and find that the alternative C³-H hydrogen atom abstraction would be followed by a low-energy and competitive substrate hydroxylation mechanism hence, should give considerable amount of byproducts. Our computational modeling studies show that substrate positioning in flavonol synthase is essential, as it guides the reactivity to a chemo- and regioselective substrate desaturation from the C²-H group, leading to desaturation products efficiently.

Reaction Mechanism of Histone Demethylation in αKG-dependent Non-Heme Iron Enzymes

Histone demethylases (KDMs) catalyze histone lysine demethylation, an important epigenetic process that controls gene expression in eukaryotes, and represent important cancer drug targets for cancer treatment. Demethylation of histone is comprised of sequential reaction steps including oxygen activation, decarboxylation, and demethylation. The initial oxygen binding and activation steps have been studied. However, the information on the complete catalytic reaction cycle is limited, which has impeded the structure-based design of inhibitors targeting KDMs. Here we report the mechanism of the complete reaction steps catalyzed by a representative nonheme iron αKG-dependent KDM, PHF8 using QM/MM approaches. The atomic-level understanding on the complete reaction mechanism of PHF8 would shed light on the structure-based design of selective inhibitors targeting KDMs to intervene in cancer epigenetics.

Mechanistic insights into ring cleavage of hydroquinone by PnpCD from quantum mechanical/molecular mechanical calculations

QM/MM calculations for ring cleavage of hydroquinone by PnpCD show that Asn258 loses coordination to the iron when the reaction begins. The first-sphere Glu262 can act as an acid–base catalyst to lower the rate-limiting barrier.