Inhibition of Urease by Hydroquinones: A Structural and Kinetic Study

Hydroquinones are a class of organic compounds abundant in nature that result from the full reduction of the corresponding quinones. Quinones are known to efficiently inhibit urease, a Ni^II-containing enzyme that catalyzes the hydrolysis of urea to yield ammonia and carbonate and acts as a virulence factor of several human pathogens, in addition to decreasing the efficiency of soil organic nitrogen fertilization. Here, we report the molecular characterization of the inhibition of urease from Sporosarcina pasteurii (SPU) and Canavalia ensiformis (jack bean, JBU) by 1,4-hydroquinone (HQ) and its methyl and tert-butyl derivatives. The 1.63-Å resolution X-ray crystal structure of the SPU-HQ complex discloses that HQ covalently binds to the thiol group of αCys322, a key residue located on a mobile protein flap directly involved in the catalytic mechanism. Inhibition kinetic data obtained for the three compounds on JBU reveals the occurrence of an irreversible inactivation process that involves a radical-based autocatalytic mechanism.     

Enabling Aromatic Hydroxylation in a Cytochrome P450 Monooxygenase Enzyme through Protein Engineering

The cytochrome P450 (CYP) family of heme monooxygenases catalyse the selective oxidation of C−H bonds under ambient conditions. The CYP199A4 enzyme from Rhodopseudomonas palustris catalyses aliphatic oxidation of 4-cyclohexylbenzoic acid but not the aromatic oxidation of 4-phenylbenzoic acid, due to the distinct mechanisms of aliphatic and aromatic oxidation. The aromatic substrates 4-benzyl-, 4-phenoxy- and 4-benzoyl-benzoic acid and methoxy-substituted phenylbenzoic acids were assessed to see if they could achieve an orientation more amenable to aromatic oxidation. CYP199A4 could catalyse the efficient benzylic oxidation of 4-benzylbenzoic acid. The methoxy-substituted phenylbenzoic acids were oxidatively demethylated with low activity. However, no aromatic oxidation was observed with any of these substrates. Crystal structures of CYP199A4 with 4-(3′-methoxyphenyl)benzoic acid demonstrated that the substrate binding mode was like that of 4-phenylbenzoic acid. 4-Phenoxy- and 4-benzoyl-benzoic acid bound with the ether or ketone oxygen atom hydrogen-bonded to the heme aqua ligand. We also investigated whether the substitution of phenylalanine residues in the active site could permit aromatic hydroxylation. Mutagenesis of the F298 residue to a valine did not significantly alter the substrate binding position or enable the aromatic oxidation of 4-phenylbenzoic acid; however the F182L mutant was able to catalyse 4-phenylbenzoic acid oxidation generating 2′-hydroxy-, 3′-hydroxy- and 4′-hydroxy metabolites in a 83 : 9 : 8 ratio, respectively. Molecular dynamics simulations, in which the distance and angle of attack were considered, demonstrated that in the F182L variant, in contrast to the wild-type enzyme, the phenyl ring of 4-phenylbenzoic acid attained a productive geometry for aromatic oxidation to occur.     

pH-Sensitive Oscillatory Motion of a Urease Motor on the Urea Aqueous Phase

A self-propelled object coupled with an enzyme reaction between urease and urea was investigated at the air/aqueous interface. A plastic object that was fixed to a urease-immobilized filter paper was used as a self-propelled object, termed a urease motor, placed on an aqueous urea solution. The driving force of the urease motor is the difference in the surface tension around the object. Oscillatory motion or no motion was triggered depending on the initial pH of the urea solution. Both the frequency and maximum speed of the oscillatory motion varied depending on the initial pH of the water phase. The mechanisms underlying the oscillatory motion and no motion were discussed in relation to the bell-shaped enzyme activity of urease in the enzyme reaction and the surface tension around the urease motor.     

Development of a Functional cis‐Prolyl Bond Biomimetic and Mechanistic Implications for Nickel Superoxide Dismutase

During recent years several peptide‐based Ni superoxide dismutase (NiSOD) models have been developed. These NiSOD models show an important structural difference compared to the native NiSOD enzyme, which could cause a completely different mechanism of superoxide dismutation. In the native enzyme the peptide bond between Leu4 and Pro5 is cis‐configured, while the NiSOD models exhibit a trans‐configured peptide bond between these two residues. To shed light on how the configuration of this single peptide bond influences the activity of the NiSOD model peptides, a new cis‐prolyl bond surrogate was developed. As surrogate we chose a leucine/alanine‐based disubstituted 1,2,3‐triazole, which was incorporated into the NiSOD model peptide replacing residues Leu4 and Pro5. The yielded 1,5‐disubstituted triazole nickel peptide exhibited high SOD activity, which was approximately the same activity as its parent trans‐configured analogue. Hence, the conformation of the prolyl peptide bond apparently has of minor importance for the catalytic activity of the metallopeptides as postulated in literature. Furthermore, it is shown that the triazole metallopeptide is forming a stable cyanide adduct as a substrate analogue model complex.     

A Calorimetric Study on the Interaction of Zinc and Cadmium Ions with Jack Bean Urease

A thermodynamic study on the interaction of Jack bean urease, JBU, with Zn²⁺ and Cd²⁺ ions was studied by isothermal titration calorimetry (ITC) at 290, 300 and 310 K in 30 mmol/L Tris buffer solution, pH 7.0. The heats of JBU+Zn²⁺ and JBU+ ²⁺ interactions are reported and analyzed in terms of the extended solvation theory. It was indicated that there is a set of 12 identical and non‐interacting binding sites for Zn²⁺ and Cd²⁺ ions. The interactions of Zn²⁺ and Cd²⁺ ions with JBU are exothermic and both enthalpy and entropy driven. The association equilibrium constants for JBU+Zn²⁺ complexes are 4118.20, 3354.70 and 2790.62 L·mol^?1 at 290, 300 and 310 K respectively. The association equilibrium constants for JBU+Cd²⁺ interactions are 2831.6 and 2386.28 L· ^?1 at 300 and 310 K, respectively.     

New Insight into the Mode of Action of Nickel Superoxide Dismutase by Investigating Metallopeptide Substrate Models

For the first time, the existence of a substrate adduct of a nickel superoxide dismutase (NiSOD) model, based on the first nine residues from the N terminus of the active form of Streptomyces coelicolor NiSOD, has been proven and the adduct has been isolated. This adduct is based on the cyanide anion (CN^?), as a substrate analogue of the superoxide anion (O₂^.?), and the nickel metallopeptide H‐HCDLPCGVY‐NH₂‐Ni. Spectroscopic studies, including IR, UV/Vis, and liquid‐ and solid‐state NMR spectroscopy, show a single nickel‐bound cyanide anion, which is embedded in the metallopeptide structure. This complex sheds new light on the question of whether the mode of action of the NiSOD enzyme is an inner‐ or outer‐sphere mechanism. Whereas discussion was previously biased in favor of an outer‐sphere electron‐transfer mechanism due to the fact that binding of cyanide or azide moieties to the nickel active site had never been observed, our results are a clear indication in favor of the inner‐sphere electron‐transfer mechanism for the disproportionation of the O₂^.? ion, whereby the substrate is attached to the Ni atom in the active site of the NiSOD.     

Water Induced Alterations in Self-Assembly of a Bio-Surfactant in Deep Eutectic Solvent for Enhanced Enzyme Activity

Deep eutectic solvents (DESs) meet important requirements for green solvent technology, including non-toxicity, biodegradability, sustainability, and affordability. Despite possessing low cohesive energy density than water, DESs have been found to support the self-assembly of amphiphiles. It is very much pertinent to examine the effect of water on self-assembly of surfactants in DESs as the presence of water alters the inherent structure of DES, which is expected to affect the characteristic properties of self-assembly. Following this, we have investigated the self-assembly of amino-acid based surfactant, Sodium N-lauroyl sarcosinate (SLS), in DES-water mixtures (10, 30 and 50 w/w% of water) and explored the catalytic activity of Cytochrome-c (Cyt-c) in the formed colloidal systems. Investigations using surface tension, fluorescence, dynamic light scattering (DLS), and isothermal titration calorimetry (ITC) have shown that DES-water mixtures promote the aggregation of SLS, resulting in the lower critical aggregation concentration (cac ∼1.5–6-fold) of the surfactant as compared to water. The nanoclustering of DES at low water content and it's complete de-structuring at high water content affects the self-assembly in a contrasting manner governed by different set of interactions. Further, Cyt-c dispersed in DES-water colloidal solutions demonstrated 5-fold higher peroxidase activity than that observed in phosphate buffer.     

Computational Mechanistic Insights on Homogeneous Water Oxidation Versus Catalyst Deactivation: A Case Study with Mononuclear Nickel and Copper Complexes

Water splitting is a potential pathway for hydrogen gas evolution and thereby realization of a carbon-neutral sustainable energy scheme. However, oxidation of water to dioxygen is the major impediment in conversion of solar energy to fuel. Herein, density functional studies are conducted to explore the reactivity conduits of two molecular electro-catalysts consisting of nickel and copper tetra-anionic tetradentate amide ligand complexes of the type [(L1)M^II]²⁻, where L1=o-phenylenebis(oxamidate), and their substitutionally modified analogues. While nickel complexes demonstrate complex borderline chemistry between homogeneous and heterogeneous pathways, showing competition between water oxidation and molecular species degradation, copper complexes display robust and efficient molecular water oxidation behavior. Our analysis predict that this disparity is primarily due to the reversible O−O bond formation in nickel complexes, which provide the platform necessary for a direct attack of OH⁻/H⁺ on the metal and terminally accessible amidate groups of the 2e⁻ oxidized anionic intermediate, [(L1⋅)Ni^III(OH)]¹⁻, respectively. This intermediate streamline ligand deactivation with a comparatively higher driving force for nickel complexes in acidic medium. Contrarily, the copper complexes display radical character on the hydroxyl ligand in the corresponding intermediate, [(L1⋅)Cu^II(OH⋅)]¹⁻, that expedite O−O interaction, leading to predominant homogeneous water oxidation under all conditions.     

An Artificial Enzyme Made by Covalent Grafting of an FeII Complex into β‐Lactoglobulin: Molecular Chemistry,Oxidation Catalysis,and Reaction‐Intermediate Monitoring in a Protein

An artificial metalloenzyme based on the covalent grafting of a nonheme Fe^II polyazadentate complex into bovine β‐lactoglobulin has been prepared and characterized by using various spectroscopic techniques. Attachment of the Fe^II catalyst to the protein scaffold is shown to occur specifically at Cys121. In addition, spectrophotometric titration with cyanide ions based on the spin‐state conversion of the initial high spin (S=2) Fe^II complex into a low spin (S=0) one allows qualitative and quantitative characterization of the metal center’s first coordination sphere. This biohybrid catalyst activates hydrogen peroxide to oxidize thioanisole into phenylmethylsulfoxide as the sole product with an enantiomeric excess of up to 20 %. Investigation of the reaction between the biohybrid system and H₂O₂ reveals the generation of a high spin (S=5/2) Fe^III(η²‐O₂) intermediate, which is proposed to be responsible for the catalytic sulfoxidation of the substrate.     

Asymmetric Stepwise Reductive Amination of Sulfonamides,Sulfamates, and a Phosphinamide by Nickel Catalysis

Asymmetric reductive amination of poorly nucleophilic sulfonamides was realized in the presence of nickel catalysts and titanium alkoxide. A wide range of ketones, including enolizable ketones and some biaryl ones, were converted into sulfonamides in excellent enantiomeric excess. The cyclization of sulfamates and intermolecular reductive amination of a diarylphosphinamide were also successful. Formic acid was used as a safe and economic surrogate of high‐pressure hydrogen gas.     

High Enzyme Activity of a Binuclear Nickel Complex Formed with the Binding Loops of the NiSOD Enzyme**

Detailed equilibrium, spectroscopic and superoxide dismutase (SOD) activity studies are reported on a nickel complex formed with a new metallopeptide bearing two nickel binding loops of NiSOD. The metallopeptide exhibits unique nickel binding ability and the binuclear complex is a major species with 2×(NH₂,N_amide,S⁻,S⁻) donor set even in an equimolar solution of the metal ion and the ligand. Nickel(III) species were generated by oxidizing the Ni^II complexes with KO₂ and the coordination modes were identified by EPR spectroscopy. The binuclear complex formed with the binding motifs exhibits superior SOD activity, in this respect it is an excellent model of the native NiSOD enzyme. A detailed kinetic model is postulated that incorporates spontaneous decomposition of the superoxide ion, the dismutation cycle and fast redox degradation of the binuclear complex. The latter process leads to the elimination of the SOD activity. A unique feature of this system is that the Ni^III form of the catalyst rapidly accumulates in the dismutation cycle and simultaneously the Ni^II form becomes a minor species.     

The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme

Among industrially important pyridoxal-5’-phosphate (PLP)-dependent transaminases of fold type IV D-amino acid transaminases are the least studied. However, the development of cascade enzymatic processes, including the synthesis of D-amino acids, renewed interest in their study. Here, we describe the identification, biochemical and structural characterization of a new D-amino acid transaminase from Haliscomenobacter hydrossis (Halhy). The new enzyme is strictly specific towards D-amino acids and their keto analogs; it demonstrates one of the highest rates of transamination between D-glutamate and pyruvate. We obtained the crystal structure of the Halhy in the holo form with the protonated Schiff base formed by the K143 and the PLP. Structural analysis revealed a novel set of the active site residues that differ from the key residues forming the active sites of the previously studied D-amino acids transaminases. The active site of Halhy includes three arginine residues, one of which is unique among studied transaminases. We identified critical residues for the Halhy catalytic activity and suggested functions of the arginine residues based on the comparative structural analysis, mutagenesis, and molecular modeling simulations. We suggested a strong positive charge in the O-pocket and the unshaped P-pocket as a structural code for the D-amino acid specificity among transaminases of PLP fold type IV. Characteristics of Halhy complement our knowledge of the structural basis of substrate specificity of D-amino acid transaminases and the sequence-structure-function relationships in these enzymes.     

Light-Promoted Nickel Catalysis: Etherification of Aryl Electrophiles with Alcohols Catalyzed by a NiII-Aryl Complex

A highly effective C−O coupling reaction of (hetero)aryl electrophiles with primary and secondary alcohols is reported. Catalyzed by a Ni^II-aryl complex under long-wave UV (390–395 nm) irradiation in the presence of a soluble amine base without any additional photosensitizer, the reaction enables the etherification of aryl bromides and aryl chlorides as well as sulfonates with a wide range of primary and secondary aliphatic alcohols, affording synthetically important ethers. Intramolecular C−O coupling is also possible. The reaction appears to proceed via a Ni^I–Ni^III catalytic cycle.     

Asymmetric Synthesis of Bicyclic Diol Derivatives through Metal and Enzyme Catalysis: Application to the Formal Synthesis of Sertraline

Enzyme‐ and ruthenium‐catalyzed dynamic kinetic asymmetric transformation (DYKAT) of bicyclic diols to their diacetates was highly enantio‐ and diastereoselective to give the corresponding diacetates in high yield with high enantioselectivity (99.9 % ee). The enantiomerically pure diols are accessible by simple hydrolysis (NaOH, MeOH), but an alternative enzyme‐catalyzed ester cleavage was also used to give the trans‐diol (R,R)‐ 1 b in extremely high diastereomeric purity (trans/cis=99.9:0.1, >99.9 % ee). It was demonstrated that the diols can be selectively oxidized to the ketoalcohols in a ruthenium‐catalyzed Oppenauer‐type reaction. A formal enantioselective synthesis of sertraline from a simple racemic cis/trans diol 1 b was demonstrated.     

Nickel on Oxidatively Modified Carbon as a Promising Cost-Efficient Catalyst for Reduction of P-Nitrophenol

The reduction of p-nitrophenol to p-aminophenol has become a benchmark reaction for testing the efficiency of new catalytic systems. In this study, we use oxidatively modified carbon (OMC) as a structural support to develop a new cost-efficient nickel-based catalytic system. The newly developed material comprises single nickel ions, chemically bound to the oxygen functional groups on the OMC surface. The highly oxidized character of OMC ensures the high lateral density of nickel ions on its surface at relatively low nickel content. We demonstrate excellent catalytic properties of the new material by using it as a stationary phase in a prototype of a continuous flow reactor: the reagent fed into the reactor is p-nitrophenol, and the product, exiting the reactor, is the fully converted p-aminophenol. The catalytic properties of the new catalyst are associated with its specific morphology, and with high lateral density of active sites on the surface. The reaction can be considered as an example of single-atom catalysis. The resulting material can be used as an inexpensive but efficient catalyst for industrial wastewater treatment. The study opens the doors for the synthesis of a new series of catalytic systems comprising transition metal atoms on the OMC structural support.     

基于电活性铁氰化镍和金属模拟酶协同催化的蛋白质电化学检测

该文设计了一种基于金属纳米模拟酶协同催化产生不溶性沉淀的"signal-off"型电化学免疫传感器用于超灵敏检测甲胎蛋白(AFP)。通过夹心免疫法将具有辣根过氧化物活性的二抗耦合物空心纳米金-铂钯纳米颗粒(HAuNPs-PtPdNPs-Ab₂)固载在电活性物质铁氰化镍纳米颗粒修饰的电极上。在H₂O₂存在下,以AFP捕获的二抗耦合物中的HAuNPs和PtPdNPs作为辣根过氧化物模拟酶催化4-氯-1-萘酚(4-CN),并在电极界面生成不溶且不导电的沉淀物苯并-4-氯己二烯酮(4-CD),有效阻碍了电子传递,电化学信号显著降低,可用于AFP的定量检测。实验表明,该传感器对0.1 pg/mL～200 ng/mL AFP表现出良好的检测线性,检出限(S/N=3)为33 fg/mL。该传感策略具有协同催化作用,可提供一种新的多重信号放大方法用于改善传感器的灵敏度。     

Hydrolysis of a Lipid Membrane by Single Enzyme Molecules: Accurate Determination of Kinetic Parameters

The accurate determination of the maximum turnover number and Michaelis constant for membrane enzymes remains challenging. Here, this problem has been solved by observing in parallel the hydrolysis of thousands of individual fluorescently labeled immobilized liposomes each processed by a single phospholipase A2 molecule. The release of the reaction product was tracked using total internal reflection fluorescence microscopy. A statistical analysis of the hydrolysis kinetics was shown to provide the Michaelis–Menten parameters with an accuracy better than 20 % without variation of the initial substrate concentration. The combined single‐liposome and single‐enzyme mode of operation made it also possible to unravel a significant nanoscale dependence of these parameters on membrane curvature.     

X-Ray Crystallography: The Past and Present of the Phase Problem

The story of the progress thus far made on the phase problem of X-ray crystallography is briefly reviewed.     

Conformational analysis 29: Preparation and1H and13C NMR,FTIR, MS,and crystallographic conformational and configurational study of 3-Oxo-1,3-oxathiane and its monomethyl derivatives

3-Oxo-1,3-oxathiane (1) and its monomethyl derivatives were prepared by oxidation of the corresponding 1,3-oxathianes. The structural analysis was carried out by¹H and¹³C NMR, FTIR, and mass spectrometry. At 298 K compound1 was a 1 1 (at 173 K a 3 1) mixture of the SO(ax) and SO(eq) chair forms. The major oxidation products of methyl 1,3-oxathianes attained exclusively the SO(ax), Me(eq) chair forms except that of the 5-methyl derivative, which consisted of 7% of the SO(eq), Me(ax) chair conformation in CDCl₃ solution. The minor products of oxidation existed in anancomeric SO(eq), Me(eq) chair conformations. The oxidation of 2-methyl- 1,3-oxathiane, however, led to 3,3-dioxo derivative (6) in addition to thetrans [SO(eq)] monoxide. The crystal structures of6 andtrans-3-oxo-5-methyl-1,3-oxathiane were solved by X-ray diffractometry.