Theoretical studies of the active-site structure, spectroscopic and thermodynamic properties, and reaction mechanism of multicopper oxidases

Comprehensive Mechanistic View of the Hydrolysis of Oxadiazole-Based Inhibitors by Histone Deacetylase 6 (HDAC6)

Histone deacetylase (HDAC) inhibitors used in the clinic typically contain a hydroxamate zinc-binding group (ZBG). However, more recent work has shown that the use of alternative ZBGs, and, in particular, the heterocyclic oxadiazoles, can confer higher isoenzyme selectivity and more favorable ADMET profiles. Herein, we report on the synthesis and biochemical, crystallographic, and computational characterization of a series of oxadiazole-based inhibitors selectively targeting the HDAC6 isoform. Surprisingly, but in line with a very recent finding reported in the literature, a crystal structure of the HDAC6/inhibitor complex revealed that hydrolysis of the oxadiazole ring transforms the parent oxadiazole into an acylhydrazide through a sequence of two hydrolytic steps. An identical cleavage pattern was also observed both in vitro using the purified HDAC6 enzyme as well as in cellular systems. By employing advanced quantum and molecular mechanics (QM/MM) and QM calculations, we elucidated the mechanistic details of the two hydrolytic steps to obtain a comprehensive mechanistic view of the double hydrolysis of the oxadiazole ring. This was achieved by fully characterizing the reaction coordinate, including identification of the structures of all intermediates and transition states, together with calculations of their respective activation (free) energies. In addition, we ruled out several (intuitively) competing pathways. The computed data (ΔG^‡ ≈ 21 kcal·mol^-1 for the rate-determining step of the overall dual hydrolysis) are in very good agreement with the experimentally determined rate constants, which a posteriori supports the proposed reaction mechanism. We also clearly (and quantitatively) explain the role of the -CF₃ or -CHF₂ substituent on the oxadiazole ring, which is a prerequisite for hydrolysis to occur. Overall, our data provide compelling evidence that the oxadiazole warheads can be efficiently transformed within the active sites of target metallohydrolases to afford reaction products possessing distinct selectivity and inhibition profiles.

Expanding the Promiscuity of a Copper-Dependent Oxidase for Enantioselective Cross-Coupling of Indoles

Herein, we disclose the highly enantioselective oxidative cross-coupling of 3-hydroxyindole esters with various nucleophilic partners as catalyzed by copper efflux oxidase. The biocatalytic transformation delivers functionalized 2,2-disubstituted indolin-3-ones with excellent optical purity (90-99 % ee), which exhibited anticancer activity against MCF-7 cell lines, as shown by preliminary biological evaluation. Mechanistic studies and molecular docking results suggest the formation of a phenoxyl radical and enantiocontrol facilitated by a suited enzyme chiral pocket. This study is significant with regard to expanding the catalytic repertoire of natural multicopper oxidases as well as enlarging the synthetic toolbox for sustainable asymmetric oxidative coupling.

Ionization Energies and Redox Potentials of Hydrated Transition Metal Ions: Evaluation of Domain-Based Local Pair Natural Orbital Coupled Cluster Approaches

Hydrated transition metal ions are prototypical systems that can be used to model properties of transition metals in complex chemical environments. These seemingly simple systems present challenges for computational chemistry and are thus crucial in evaluations of quantum chemical methods for spin-state and redox energetics. In this work, we explore the applicability of the domain-based pair natural orbital implementation of coupled cluster (DLPNO-CC) theory to the calculation of ionization energies and redox potentials for hydrated ions of all first transition row (3d) metals in the 2+/3+ oxidation states, in connection with various solvation approaches. In terms of model definition, we investigate the construction of a minimally explicitly hydrated quantum cluster with a first and second hydration layer. We report on the convergence with respect to the coupled cluster expansion and the PNO space, as well as on the role of perturbative triple excitations. A recent implementation of the conductor-like polarizable continuum model (CPCM) for the DLPNO-CC approach is employed to determine self-consistent redox potentials at the coupled cluster level. Our results establish conditions for the convergence of DLPNO-CCSD(T) energetics and stress the absolute necessity to explicitly consider the second solvation sphere even when CPCM is used. The achievable accuracy for redox potentials of a practical DLPNO-based approach is, on average, 0.13 V. Furthermore, multilayer approaches that combine a higher-level DLPNO-CCSD(T) description of the first solvation sphere with a lower-level description of the second solvation layer are investigated. The present work establishes optimal and transferable methodological choices for employing DLPNO-based coupled cluster theory, the associated CPCM implementation, and cost-efficient multilayer derivatives of the approach for open-shell transition metal systems in complex environments.

Multidimensional redox potential/pKa coupling in multicopper oxidases from molecular dynamics: implications for the proton transfer mechanism

Bilirubin oxidases (BOD) are metalloenzymes that catalyze the conversion of O₂ and bilirubin to biliverdin and water in the metabolism of chlorophyll and porphyrin. In this work we have used the CpHMD method to analyze the effects of the different oxidation states on the BOD trinuclear cluster (TNC). Our results demonstrate that there is a link between the different oxidation states of copper ions and the protonation capacity of nearby titratable residues. Each configuration affects pK_a differently, creating proton gradients within the enzyme that act in an extremely orderly manner. This order is closely linked to the catalytic mechanism and leads us to the conclusion of the entry of the O₂ molecule and its reduction in water molecules is associated with the probability of the release of protons from nearby acid groups. With this information, we deduce that under the initial reaction conditions the acidic side chains of nearby residues can be protonated; this allows the enzyme to reduce the activation energy of the reaction by coupling the proton transfer to oxidation state changes in the metallic center.

A quantum chemical approach for the mechanisms of redox-active metalloenzymes

During the past 20 years, quantum chemistry has grown to be a significant part in the investigation of mechanisms for redox-active enzymes. In our group we have developed an approach that has been applied to a large number of such systems. Hybrid density functional theory (hybrid DFT) has from the start of these investigations been the leading electronic structure tool. An understanding of how the method works in practice has significantly improved the accuracy and applicability. During the past ten years, it has been found that the results for redox enzymes mainly depend on the chosen fraction of exact exchange in the functional, and that a choice of 15% has worked best. The idea has therefore been to vary that fraction over a reasonable range and study the relative energy dependence. For modeling the enzymes, a cluster approach has been developed. In the present review the development of the method we used is described from its start in work on photosystem II, fifteen years ago. Examples from a few recent applications are described, where the metals have been iron, nickel, copper, cobalt or manganese. The results are in excellent agreement with available experiments, and a large number of new predictions have been made.

During the past 20 years, quantum chemistry has grown to be a significant part in the investigation of mechanisms for redox-active enzymes.

Biocathode design with highly-oriented immobilization of multi-copper oxidase from Pyrobaculum aerophilum onto a single-walled carbon nanotube surface via a carbon nanotube-binding peptide

Biofuel cells generate electric energy using an enzyme as a catalyst for an electrode but their stability and low battery output pose problems for practical use. To solve these problems, this study aimed to build a long-lasting and high-output biocathode as a catalyst using a highly stable hyperthermophilic archaeal enzyme, multi-copper oxidase, from Pyrobaculum aerophilum (McoP). To increase output, McoP was oriented and immobilized on single-walled carbon nanotubes (SWCNT) with a high specific surface area, and the electrode interface was designed to achieve highly efficient electron transfer between the enzyme and electrode. Type 1 copper (T1Cu), an electron-accepting site in the McoP molecule, is located near the C-terminus. Therefore, McoP was prepared by genetically engineering a CNT-binding peptide with the sequence LLADTTHHRPWT, at the C-terminus of McoP (McoP-CBP). We then constructed an electrode using a complex in which McoP-CBP was aligned and immobilized on SWCNT, and then clarified the effect of CBP. The amounts of immobilized enzymes on McoP-SWCNT and (McoP-CBP)-SWCNT complexes were almost equal. CV measurement of the electrode modified with both complexes showed 5.4 times greater current density in the catalytic reaction of the (McoP-CBP)-SWCNT/GC electrode than in the McoP-SWCNT/GC electrode. This is probably because CBP fusion immobilize the enzyme on SWCNTs in an orientational manner, and T1Cu, the oxidation-reduction site in McoP, is close to the electrode, which improves electron transfer efficiency.

Site-Directed Mutagenesis of Multicopper Oxidase from Hyperthermophilic Archaea for High-Voltage Biofuel Cells

Enzymes from hyperthermophilic archaea are potential candidates for industrial use because of their superior pH, thermal, and long-term stability, and are expected to improve the long-term stability of biofuel cells (BFCs). However, the reported multicopper oxidase (MCO) from hyperthermophilic archaea has lower redox potential than MCOs from other organisms, which leads to a decrease in the cell voltage of BFCs. In this study, we attempted to positively shift the redox potential of the MCO from hyperthermophilic archaeon Pyrobaculum aerophilum (McoP). Mutations (M470L and M470F) were introduced into the axial ligand of the T1 copper atom of McoP, and the enzymatic chemistry and redox potentials were compared with that of the parent (M470). The redox potentials of M470L and M470F shifted positively by about 0.07 V compared with that of M470. In addition, the catalytic activity of the mutants towards 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) increased 1.2-1.3-fold. The thermal stability of the mutants and the electrocatalytic performance for O₂ reduction of M470F was slightly reduced compared with that of M470. This research provides useful enzymes for application as biocathode catalysts for high-voltage BFCs.

Theoretical Study of O2 Reduction and Water Oxidation in Multicopper Oxidases

Recent electrochemical experiments have shown that the reduction of O₂ can be driven backward to water oxidation, which is the first case that has been successfully demonstrated for an enzyme. To understand this ability of the enzyme, both the forward reduction and backward oxidation have been studied here. For the forward reaction, a mechanism similar to earlier studies was obtained. All steps of the full catalytic cycle were obtained for the first time, and it was shown that the explicit reduction steps contribute significantly to the rate-limiting step of the O–O bond cleavage. For the backward oxidation reaction, it was found that the mechanism of the O–O bond formation is not just the reverse of the reduction step where the O–O bond is cleaved for a protonated peroxide. The formation of two fully deprotonated oxo groups was found to be important, which leads to a large radical character for one of the oxo groups. For this possibility, it is important that the pK_a of the water bound to the cofactor is quite high.

Inhibition in multicopper oxidases: a critical review

This review critiques the literature on inhibition of O₂-reduction catalysis in multicopper oxidases like laccase and bilirubin oxidase and provide recommendations for best practice when carrying out experiments and interpreting published data.

Fast Oxygen Reduction Catalyzed by a Copper(II) Tris(2-pyridylmethyl)amine Complex through a Stepwise Mechanism

Catalytic pathways for the reduction of dioxygen can either lead to the formation of water or peroxide as the reaction product. We demonstrate that the electrocatalytic reduction of O₂ by the pyridylalkylamine copper complex [Cu(tmpa)(L)]²⁺ in a neutral aqueous solution follows a stepwise 4 e^- /4 H⁺ pathway, in which H₂ O₂ is formed as a detectable intermediate and subsequently reduced to H₂ O in two separate catalytic reactions. These homogeneous catalytic reactions are shown to be first order in catalyst. Coordination of O₂ to Cu^I was found to be the rate-determining step in the formation of the peroxide intermediate. Furthermore, electrochemical studies of the reaction kinetics revealed a high turnover frequency of 1.5×10⁵  s^-1 , the highest reported for any molecular copper catalyst.

Contribution of substrate reorganization energies of electron transfer to laccase activity

Laccase substrate reorganization energies computed by DFT show that electronic structure changes of these substrates contribute to enzymatic proficiency.

A structural-chemical explanation of fungal laccase activity

Fungal laccases (EC 1.10.3.2) are multi-copper oxidases that oxidize a wide variety of substrates. Despite extensive studies, the molecular basis for their diverse activity is unclear. Notably, there is no current way to rationally predict the activity of a laccase toward a given substrate. Such knowledge would greatly facilitate the rational design of new laccases for technological purposes. We report a study of three datasets of experimental K_m values and activities for Trametes versicolor and Cerrena unicolor laccase, using a range of protein modeling techniques. We identify diverse binding modes of the various substrates and confirm an important role of Asp-206 and His-458 (T. versicolor laccase numbering) in guiding substrate recognition. Importantly, we demonstrate that experimental K_m values correlate with binding affinities computed by MMGBSA. This confirms the common assumption that the protein-substrate affinity is a major contributor to observed K_m. From quantitative structure-activity relations (QSAR) we identify physicochemical properties that correlate with observed K_m and activities. In particular, the ionization potential, shape, and binding affinity of the substrate largely determine the enzyme’s K_m for the particular substrate. Our results suggest that K_m is not just a binding constant but also contains features of the enzymatic activity. In addition, we identify QSAR models with only a few descriptors showing that phenolic substrates employ optimal hydrophobic packing to reach the T1 site, but then require additional electronic properties to engage in the subsequent electron transfer. Our results advance our ability to model laccase activity and lend promise to future rational optimization of laccases toward phenolic substrates.

Copper(ii) complexes of functionalized 2,2':6',2''-terpyridines and 2,6-di(thiazol-2-yl)pyridine: structure, spectroscopy, cytotoxicity and catalytic activity

Six new copper(ii) complexes with 2,2':6',2''-terpyridine (4'-Rⁿ-terpy) [1 (R¹ = furan-2-yl), 2 (R² = thiophen-2-yl), and 3 (R³ = 1-methyl-1H-pyrrol-2-yl)] and 2,6-di(thiazol-2-yl)pyridine derivatives (Rⁿ-dtpy) [4 (R¹), 5 (R²), and 6 (R³)] have been synthesized by a reaction between copper(ii) chloride and the corresponding ligand. The complexes have been characterized by UV-vis and IR spectroscopy, and their structures have been determined by X-ray analysis. The antiproliferative potential of copper(ii) complexes of 2,2':6',2''-terpyridine and 2,6-di(thiazol-2-yl)pyridine derivatives towards human colorectal (HCT116) and ovarian (A2780) carcinoma as well as towards lung (A549) and breast adenocarcinoma (MCF7) cell lines was examined. Complex 1 and complex 6 were found to have the highest antiproliferative effect on A2780 ovarian carcinoma cells, particularly when compared with complex 2, 3 with no antiproliferative effect. The order of cytotoxicity in this cell line is 6 > 1 > 5 > 4 > 2 ≈ 3. Complex 2 seems to be much more specific towards colorectal carcinoma HCT116 and lung adenocarcinoma A549 cells. The viability loss induced by the complexes agrees with Hoechst 33258 staining and typical morphological apoptotic characteristics like chromatin condensation and nuclear fragmentation. The specificity towards different types of cell lines and the low cytotoxic activity towards healthy cells are of particular interest and are a positive feature for further developments. Complexes 1-6 were also tested in the oxidation of alkanes and alcohols with hydrogen peroxide and tert-butyl-hydroperoxide (TBHP). The most active catalyst 4 gave, after 120 min, 0.105 M of cyclohexanol + cyclohexanone after reduction with PPh₃. This concentration corresponds to a yield of 23% and TON = 210. Oxidation of cis-1,2-dimethylcyclohexane with m-CPBA catalyzed by 4 in the presence of HNO₃ gave a product of a stereoselective reaction (trans/cis = 0.47). Oxidation of secondary alcohols afforded the target ketones in yields up to 98% and TON = 630.

Pinpointing the active species of the Cu(DAT) catalyzed oxygen reduction reaction

Dinuclear CuII complexes bearing two 3,5-diamino-1,2,4-triazole (DAT) ligands have gained considerable attention as a potential model system for laccase due to their low overpotential for the oxygen reduction reaction (ORR). In this study, the active species for the ORR was investigated. The water soluble dinuclear copper complex (Cu(DAT)) was obtained by mixing a 1 : 1 ratio of Cu(OTf)2 and DAT in water. The electron paramagnetic resonance (EPR) spectrum of Cu(DAT) showed a broad axial signal with a g factor of 2.16 as well as a low intensity Ms = ±2 absorption characteristic of the Cu2(μ-DAT)2 moiety. Monitoring the typical 380 nm peak with UV-Vis spectroscopy revealed that the Cu2(μ-DAT)2 core is extremely sensitive to changes in pH, copper to ligand ratios and the presence of anions. Electrochemical quartz crystal microbalance experiments displayed a large decrease in frequency below 0.5 V versus the reversible hydrogen electrode (RHE) in a Cu(DAT) solution implying the formation of deposition. Rotating ring disk electrode experiments showed that this deposition is an active ORR catalyst which reduces O2 all the way to water at pH 5. The activity increased significantly in the course of time. X-ray photoelectron spectroscopy was utilized to analyze the composition of the deposition. Significant shifts in the Cu 2p3/2 and N 1s spectra were observed with respect to Cu(DAT). After ORR catalysis at pH 5, mostly CuI and/or Cu0 species are present and the deposition corresponds to previously reported electrodepositions of copper. This leads us to conclude that the active species is of a heterogeneous nature and lacks any structural similarity with laccase.

Molecular dynamics derived life times of active substrate binding poses explainKMof laccase mutants

Molecular dynamics derived life times of reactive poses and MMGBSA substrate affinities explain trends in experimentalK_Mfor laccases.

Cu(ii) complexes of a tridentate N,N,O-donor Schiff base of pyridoxal: synthesis, X-ray structures, DNA-binding properties and catecholase activity

DNA binding and catecholase activities of two Cu(ii) complexes [Cu(L₁)X] (X = N₃, NCS) of pyridoxal derived ligands are reported.

Mechanism of chloride inhibition of bilirubin oxidases and its dependence on potential and pH

Bilirubin oxidases (BODs) belong to the multi-copper oxidase (MCO) family and efficiently reduce O2 at neutral pH and in physiological conditions where chloride concentrations are over 100 mM. BODs were consequently considered to be Cl- resistant contrary to laccases. However, there has not been a detailed study on the related effect of chloride and pH on the redox state of immobilized BODs. Here, we investigate by electrochemistry the catalytic mechanism of O2 reduction by the thermostable Bacillus pumilus BOD immobilized on carbon nanofibers in the presence of NaCl. The addition of chloride results in the formation of a redox state of the enzyme, previously observed for different BODs and laccases, which is only active after a reductive step. This behavior has not been previously investigated. We show for the first time that the kinetics of formation of this state is strongly dependent on pH, temperature, Cl- concentration and on the applied redox potential. UV-visible spectroscopy allows us to correlate the inhibition process by chloride with the formation of the alternative resting form of the enzyme. We demonstrate that O2 is not required for its formation and show that the application of an oxidative potential is sufficient. In addition, our results suggest that the reactivation may proceed thought the T3 β.

Halide binding and inhibition of laccase copper clusters: the role of reorganization energy

Laccase-like proteins are multicopper oxidases involved in several biological and industrial processes. Their application is commonly limited due to inhibition by fluoride and chloride, and as-isolated proteins are often substantially activated by heat, suggesting that multiple redox states can complicate characterization. Understanding these processes at the molecular level is thus desirable but theoretically unexplored. This paper reports systematic calculations of geometries, reorganization energies, and ionization energies for all partly oxidized states of the trinuclear copper clusters in realistic models with ∼200 atoms. Corrections for scalar-relativistic effects, dispersion, and thermal effects were estimated. Fluoride, chloride, hydroxide, or water was bound to the T2 copper site of the oxidized resting state, and the peroxo intermediate was also computed for reference. Antiferromagnetic coupling, assigned oxidation states, and general structures were consistent with known spectroscopic data. The computations show that (i) ligands bound to the T2 site substantially increase the reorganization energy of the second reduction of the resting state and reduce the redox potentials, providing a possible mechanism for inhibition; (ii) the reorganization energy is particularly large for F(-) but also high for Cl(-), consistent with the experimental tendency of inhibition; (iii) reduction leads to release of Cl(-) from the T2 site, suggesting a mechanism for heat/reduction activation of laccases by dissociation of inhibiting halides or hydroxide from T2.

Reactivity of the binuclear non-heme iron active site of Δ⁹ desaturase studied by large-scale multireference ab initio calculations

The results of density matrix renormalization group complete active space self-consistent field (DMRG-CASSCF) and second-order perturbation theory (DMRG-CASPT2) calculations are presented on various structural alternatives for the O-O and first C-H activating step of the catalytic cycle of the binuclear nonheme iron enzyme Δ(9) desaturase. This enzyme is capable of inserting a double bond into an alkyl chain by double hydrogen (H) atom abstraction using molecular O2. The reaction step studied here is presumably associated with the highest activation barrier along the full pathway; therefore, its quantitative assessment is of key importance to the understanding of the catalysis. The DMRG approach allows unprecedentedly large active spaces for the explicit correlation of electrons in the large part of the chemically important valence space, which is apparently conditio sine qua non for obtaining well-converged reaction energetics. The derived reaction mechanism involves protonation of the previously characterized 1,2-μ peroxy Fe(III)Fe(III) (P) intermediate to a 1,1-μ hydroperoxy species, which abstracts an H atom from the C10 site of the substrate. An Fe(IV)-oxo unit is generated concomitantly, supposedly capable of the second H atom abstraction from C9. In addition, several popular DFT functionals were compared to the computed DMRG-CASPT2 data. Notably, many of these show a preference for heterolytic C-H cleavage, erroneously predicting substrate hydroxylation. This study shows that, despite its limitations, DMRG-CASPT2 is a significant methodological advancement toward the accurate computational treatment of complex bioinorganic systems, such as those with the highly open-shell diiron active sites.

Preparation and properties of a calcium(ii)-based molecular chain decorated with manganese(ii) butterfly-like complexes

The room temperature reaction of [Mn₂O₂(bipy)₄](ClO₄)₃ (bipy = 2,2′-bipyridine) with Ca(CHCl₂COO)₂ in methanol produced a yellow crystalline material.

Density functional theory studies on the structure and electron distribution in the peroxide intermediate of the catalytic cycle of multicopper oxidases

The peroxide intermediate (PI) is obtained in the first step of the reduction of O2 by multicopper oxidases. Earlier density functional theory (DFT) studies as well as spectral and structural comparison to a fully oxidized structural analogue of the PI known as the peroxide adduct (PA) reveal that O2 bridges all three copper atoms of the trinuclear cluster in the PI. This orientation of the oxygen moiety has been discussed as a result of the influence from the second coordination sphere. In the present study, we investigate by DFT and quantum mechanics/molecular mechanics (QM/MM) the potential energy surface (PES) of the PI as a function of the orientation of O2 within the copper cluster to examine the influence of the second coordination sphere on the structure of the PI. We use the second order spin-flip constricted variational DFT method to probe a possible multideterminantal nature of the PI and to devise a computational strategy for its treatment. Our results suggest that the PI can be approximated to a closed shell singlet. Additionally, for the determination of the oxidation states of the three copper atoms in the PI, the electron redistribution upon the formation of the PI has been investigated with the extended transition state–natural orbitals for chemical valence method. We observe a flat PES on which oxygen can easily rotate between the copper atoms. The fully bridged PI structure emerges in the absence of atoms from the second coordination sphere and has been attributed to the coordination unsaturation of the copper atoms in the cluster. The good Cu–O overlap leads to the participation of all copper atoms in the reduction of O2.

Stability mechanisms of a thermophilic laccase probed by molecular dynamics

Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD) was applied to a Trametes versicolor laccase in response to variable ionic strengths, temperatures, and glycosylation status. Near-physiological conditions provided excellent agreement with the crystal structure (average RMSD ∼0.92 Å) and residual agreement with experimental B-factors. The persistence of backbone hydrogen bonds was identified as a key descriptor of structural response to environment, whereas solvent-accessibility, radius of gyration, and fluctuations were only locally relevant. Backbone hydrogen bonds decreased systematically with temperature in all simulations (∼9 per 50 K), probing structural changes associated with enthalpy-entropy compensation. Approaching T_opt (∼350 K) from 300 K, this change correlated with a beginning “unzipping” of critical β-sheets. 0 M ionic strength triggered partial denucleation of the C-terminal (known experimentally to be sensitive) at 400 K, suggesting a general salt stabilization effect. In contrast, F⁻ (but not Cl⁻) specifically impaired secondary structure by formation of strong hydrogen bonds with backbone NH, providing a mechanism for experimentally observed small anion destabilization, potentially remedied by site-directed mutagenesis at critical intrusion sites. N-glycosylation was found to support structural integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F⁻ intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes.