De novo design, synthesis, and characterization of quinoproteins

Quinones and quinoproteins are essential redox components and enzymes in biological systems. Here, we report the de novo design, synthesis, and properties of model four-alpha-helix bundle quinoproteins. The proteins were designed and constructed from three different helices with 21 or 22 amino acid residues by chemoselective ligation to a cyclic decapeptide template. A free cysteine unit is placed at the hydrophobic core of the protein for binding of ubiquinone-0 and menaquinone-0 through a thioether bond. The quinoproteins with molecular weights of 11-12 kDa were characterized by electrospray ionization mass spectrometry, UV/Vis spectroscopy, size-exclusion chromatography, circular dichroism measurements, (1)H NMR spectroscopy, cyclic voltammetry, and redox-induced FTIR difference spectroscopy. The midpoint redox potentials at pH 8 in aqueous solution E(m,8) of thioether conjugates with N-acetyl cysteine methyl ester were 89 mV and -63 mV and with a synthetic protein 229 mV and 249 mV versus standard hydrogen electrode (SHE) for ubiquinone-0 and menaquinone-0, respectively. Detailed redox-induced FTIR difference spectroscopic studies of the model compounds and quinoproteins show the special resonance features for C=O bands at 1656-1660 and 1655-1665 cm(-1) due to the sulfur substitution to ubiquinone-0 and menaquinone-0, respectively. The construction of model quinoproteins represents a significant step toward more complex artificial redox systems.     

Preparation and electrochemical properties of palladium(0) complexes coordinated by quinones and 1,5-cyclooctadiene

The complexes Pd(quinone)(COD) (COD = 1,5-cyclooctadiene) are prepared by a ligand substitution reaction of Pd₂(DBA)₃ (DBA = dibenzylideneacetone) in the presence of both quinone and COD. Palladium(0) complexes coordinated by quinones only are formed in the reaction in the absence of COD. The cyclic voltammetric behavior of Pd(quinone)(COD) has been studied. The reduction potentials for quinones shifted toward negative values on coordination to palladium(0). The oxidation potentials for the central palladium(0) in Pd(quinone)(COD) depend on the electron-withdrawing ability of the free quinones, and are in the following series: quinone = p-benzoquinone < 5,8-dihydro-1,4-naphthoquinone ～ 1,4-naphthoquinone < duroquinone. The shift of oxidation potentials for Pd(quinone)(COD) on changing the quinones as ligands is in contrast to that of Pd(quinone)(triphenylphosphine)₂.     

Voltammetric Behavior of 1,4‐Dimethoxypillar[m]arene[n]quinones

The electrochemical properties of a series of 1,4‐dimethoxypillar[m]arene[n]quinones (DMP[m]A[n]Qs) and the interactions between individual quinone units have been investigated on glassy carbon electrode in acetonitrile. All the quinone units showed relative electron uptake behavior except 1,4‐dimethoxypillar[5]quinones (DMP[5]Q). The results have shown that the electrochemical behavior of the DMP[m]A[n]Qs is comparatively different from that of their related linear quinone analogues. The resultant properties were attributed to the close proximity of redox‐active sites as well as the delocalization of electrons on the aromatic rings. Another aspect to be considered responsible for their electronic properties was suggested to be the electrostatic repulsions between adjacent quinone units in these complex structures. Current studies provide a better understanding on the voltammetric behavior of pillararene derivatives with different numbers of quinone units as well as their future scope in certain future electrochemical applications.     

Chemical Modifications of Biopolymers by Quinones and Quinone Methides

Many quinones and their precursors, which are transformed oxidatively into quinones and/or quinone methides, are important natural products. As secondary metabolites, they frequently possess antibiotic and cytotoxic activities, in addition to acting sometimes as pathogens. Several plants and animals, especially insects, use quinonoid substances for defense, often with spectacular results. On the macromolecular level, quinone methides have a key role in the plant kingdom in lignin biosynthesis; the biosynthesis of melanoproteins exemplifies the reactions of o-quinones in the animal kingdom. In insects, cross-linking of structural proteins through quinones and quinone methides results in the construction of the sclerotized exoskeleton. For mankind, the reactivity of quinones in biological systems has far-reaching consequences of pharmaceutical, toxicological, and technical relevance. The examples in this review show that a common principle underlies these reactions, namely, the chemical modification of biopolymers. As demonstrated particularly well in a more detailed discussion of the chemical principles of insect cuticle sclerotization, several major and important new results have emerged from the development and applications of modern methods of sample separation and from solid-state NMR spectroscopy.     

Natural and synthetic quinones and their reduction by the quinone reductase enzyme NQO1: from synthetic organic chemistry to compounds with anticancer potential

The quinone reductase enzyme NAD(P)H: quinone oxidoreductase 1 (NQO1) is a ubiquitous flavoenzyme that catalyzes the two-electron reduction of quinones. This Perspective briefly reviews the structure and mechanism, physiological role, and upregulation and induction of the enzyme, but focuses on the synthesis of new heterocyclic quinones and their metabolism by recombinant human NQO1. Thus a range of indolequinones, some of which are novel analogues of mitomycin C, benzimidazolequinones, benzothiazolequinones and quinolinequinones have been prepared and evaluated, leading to detailed knowledge of the structural requirements for efficient metabolism by the enzyme. Potent mechanism-based inhibitors (suicide substrates) of NQO1 have also been developed. These indolequinones irreversibly alkylate the protein, preventing its function both in standard enzyme assays and also in cells. Some of these quinones are also potent inhibitors of growth of human pancreatic cancer cells, suggesting a potential role for such compounds as therapeutic agents.     

Formation of aromatic radical-cations by oxidation with electronegatively substituted quinones in acid media; kinetics and mechanism

Electronegatively substituted quinones are shown to oxidize electronrich aromatic molecules to the corresponding radical-cations in acid medium via a reversible two step mechanism. The influence of acid strength on the rate of the reaction suggests that a protonated quinone molecule acts as the primary electron acceptor. The rate of formation of the radical cations depends on the one electron oxidation potential of the parent aromatic molecules in a way typical for endothermic outersphere electrontransfer.     

The interaction between polymerization initiators and inhibitors in solutions—VIII. The mechanism of the reaction of azobisisobutyronitrile with p-benzoquinone and chloranil in polar and nonpolar solvents

The reactions of azobisisobutyronitrile (AIBN) with p-benzoquinone (BQ) and chloranil in toluene, chlorobenzene and acetonitrile, have been investigated by isolation and identification of the reaction products. In toluene and chlorobenzene, isobutyroylamino hydroquinone together with tetramethyl dioxazinobenzene are formed in the case of (BQ); the corresponding mono- and dioxazinobenzene derivatives are formed in the case of chloranil. In acetonitrile, however, only polyquinonoid resinous derivatives of the quinones are obtained. The crystalline derivatives as well as the resinous products have no nitrile groups in their structures and the nitrogen atom is directly attached to the parent quinone nucleus. This fact indicates that the radicals from AIBN react with quinones exclusively in the ketenimine form. A mechanism based on the possibility of electron-transfer from the radical to the quinone molecule to form charged species has been suggested. The degree of separation of these species is determined by the polarity of the solvent. Combination of the charged entities produces nuclear-substituted intermediates which may be eventually isolated as hydroquinones or subjected to further radical reactions with the ketenimine substituent to form the oxazinobenzene derivatives. The formation of ether derivatives of hydroquinone and tetrachlorohydroquinone in the reaction of BQ and chloranil with AIBN is accordingly excluded.     

Quinone‐Catalyzed Selective Oxidation of Organic Molecules

Quinones are common stoichiometric reagents in organic chemistry. Para‐quinones with high reduction potentials, such as DDQ and chloranil, are widely used and typically promote hydride abstraction. In recent years, many catalytic applications of these methods have been achieved by using transition metals, electrochemistry, or O₂ to regenerate the oxidized quinone in situ. Complementary studies have led to the development of a different class of quinones that resemble the ortho‐quinone cofactors in copper amine oxidases and mediate the efficient and selective aerobic and/or electrochemical dehydrogenation of amines. The latter reactions typically proceed by electrophilic transamination and/or addition‐elimination reaction mechanisms, rather than hydride abstraction pathways. The collective observations show that the quinone structure has a significant influence on the reaction mechanism and has important implications for the development of new quinone reagents and quinone‐catalyzed transformations.     

Bioactivity Profiles of Cytoprotective Short-Chain Quinones

Short-chain quinones (SCQs) have been investigated as potential therapeutic candidates against mitochondrial dysfunction, which was largely thought to be associated with the reversible redox characteristics of their active quinone core. We recently reported a library of SCQs, some of which showed potent cytoprotective activity against the mitochondrial complex I inhibitor rotenone in the human hepatocarcinoma cell line HepG2. To better characterize the cytoprotection of SCQs at a molecular level, a bioactivity profile for 103 SCQs with different compound chemistries was generated that included metabolism related markers, redox activity, expression of cytoprotective proteins and oxidative damage. Of all the tested endpoints, a positive correlation with cytoprotection by SCQs in the presence of rotenone was only observed for the NAD(P)H:quinone oxidoreductase 1 (NQO1)-dependent reduction of SCQs, which also correlated with an acute rescue of ATP levels. The results of this study suggest an unexpected mode of action for SCQs that appears to involve a modification of NQO1-dependent signaling rather than a protective effect by the reduced quinone itself. This finding presents a new selection strategy to identify and develop the most promising compounds towards their clinical use.     

A computational study of unique properties of pillar[n]quinones: self-assembly to tubular structures and potential applications as electron acceptors and anion recognizers

Density functional theory has been used to calculate the thermodynamic properties and molecular orbitals of pillar[n]quinones. Pillar[n]quinones are expected to be effective electron acceptors and the ability to accept more than one electron increases with the size of the interior cavity. Pillar[5]quinone and pillar[7]quinone show a great intramolecular charge transfer upon the electron excitation from highest occupied molecular orbital (HOMO) to lowest unoccupied molecular orbital (LUMO) as indicated by a large difference of electron distributions between their HOMO and LUMO and a notable dipole moment difference between the ground and first triplet excited state. The aggregation of pillar[n]quinones leads to tubular dimeric structures joined by 2n C? H···O nonclassical hydrogen bonds (HBs) with binding energies about 2 kcal/mol per HB. The longitudinal extension of the supramolecular self‐assembly of pillar[n]quinone may be adjustable through forming and breaking their HBs by controlling the surrounding environment. The tunability of the diameter of the tubular structures can be achieved by changing the number of quinone units in the pillar[n]quinone. The electrostatic potential maps of pillar[n]quinones indicate that the positive charge in the interior cavity decreases as the number of quinone units increases. Chloride and bromide anions are chosen to examine the noncovalent anion‐π interactions between pillar[n]quinones and captured anions. The calculations show that the better compatibility of the effective radius of the anions with the interior dimension of pillar[n]quinone leads to larger stabilization energy. The selectivity of spatial matching and specific interaction of pillar[n]quinone is believed to possibly serve as a candidate for ionic and molecular recognition. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Proximity‐Enabled Protein Crosslinking through Genetically Encoding Haloalkane Unnatural Amino Acids

The selective generation of covalent bonds between and within proteins would provide new avenues for studying protein function and engineering proteins with new properties. New covalent bonds were genetically introduced into proteins by enabling an unnatural amino acid (Uaa) to selectively react with a proximal natural residue. This proximity‐enabled bioreactivity was expanded to a series of haloalkane Uaas. Orthogonal tRNA/synthetase pairs were evolved to incorporate these Uaas, which only form a covalent thioether bond with cysteine when positioned in close proximity. By using the Uaa and cysteine, spontaneous covalent bond formation was demonstrated between an affibody and its substrate Z protein, thereby leading to irreversible binding, and within the affibody to increase its thermostability. This strategy of proximity‐enabled protein crosslinking (PEPC) may be generally expanded to target different natural amino acids, thus providing diversity and flexibility in covalent bond formation for protein research and protein engineering.     

Voltammetric determination of water with inner potential reference and variable linear range based on structure- and redox-controllable hydrogen-bonding interaction between water and quinones

This communication describes a new voltammetric method for the determination of water in nonaqueous solvent by taking advantage of the structure- and redox-controllable hydrogen-bonding interaction between quinone species and water. Three kinds of quinones, i.e., tetrachloro-p-benzoquinone (TCBQ), benzoquinone (BQ), and tetramethyl-p-benzoquinone (TMBQ), are employed in this study in terms of their different structures and thereby different basicities and hydrogen-bonding interaction activities with water. The hydrogen-bonding interaction activities of the quinone species with water actually depend on the structures and the species of quinones, where the interaction activity between quinone dianion and water remains remarkably greater than that between quinone monoanion and water. The former interaction activity eventually leads to the positive shift of the half-wave potential of quinone monoanion/dianion couple, which can be essentially used for the voltammetric determination of water. The structure- and redox-controllable hydrogen-bonding interaction activities of quinones and water substantially make it possible to determine trace amount of water in the nonaqueous solution with inner reference potential and variable dynamic linear range.     

Myoglobin modification by enzyme-generated dopamine reactive species

The generation of reactive quinone species (DAQ) from oxidation of dopamine (DA) is involved in neurodegenerative pathologies like Parkinson's disease (A. Borta, G. U. H?glinger, J. Neurochem. 2007, 100, 587-595). The oxidation of DA to DAQ can occur either in a single two-electron process or in two consecutive one-electron steps, through semiquinone radicals, giving rise to different patterns of reactions. The former type of reaction can be promoted by tyrosinase, the latter by peroxidases in the presence of H(2)O(2), which can be formed under oxidative stress conditions. Both enzymes were employed for the characterization of the thiol-catechol adducts formed by reaction of DA and cysteine or glutathione, and for the identification of specific amino acid residues modified by DAQs in two representative target proteins, human and horse heart myoglobin. Our results indicate that the cysteinyl-DA adducts are formed from the same quinone intermediate independently of the mechanism of DA oxidation, and that the hallmark of a radical mechanism is the formation of the cystine dimer. The reactivity of quinone species also controls the DA-promoted derivatization of histidine residues in proteins. However, for the modification of the cysteine residue in human myoglobin, a radical intramolecular mechanism has been proposed, in which the protein acts both as the catalyst and target of the reaction. Most importantly, the modification of myoglobins through DAQ linkages, and in particular by DA oligomers, has dramatic effects on their stability, as it induces protein unfolding and incorporation into insoluble melanic precipitates.     

Theoretical prediction of the hydride affinities of various p- and o-quinones in DMSO

The hydride affinities of 80 various p- and o-quinones in DMSO solution were predicted by using B3LYP/6-311++G (2df,p)//B3LYP/6-31+G* and MP2/6-311++G**//B3LYP/6-31+G* methods, combined with the PCM cluster continuum model for the first time. The results show that the hydride affinity scale of the 80 quinones in DMSO ranges from -47.4 kcal/mol for 9,10-anthraquinone to -124.5 kcal/mol for 3,4,5,6-tetracyano-1,2-quinone. Such a long scale of the hydride affinities (-47.4 to -124.5 kcal/mol) indicates that the 80 quinones can form a large and useful library of organic oxidants, which can provide various organic hydride acceptors that the hydride affinities are known for chemists to choose in organic syntheses. By examining the effect of substituent on the hydride affinities of quinones, it is found that the hydride affinities of quinones in DMSO are linearly dependent on the sum of the Hammett substituent parameters sigma: DeltaGH-(Q) approximately -16.0Sigmasigmai - 70.5 (kcal/mol) for p-quinones and DeltaGH-(Q) approximately -16.2Sigmasigmai - 81.5 (kcal/mol) for o-quinones only if the substituents have no large electrostatic inductive effect and large ortho-effect. Study of the effect of the aromatic properties of quinone on the hydride affinities showed that the larger the aromatic system of quinone is, the smaller the hydride affinity of the quinone is, and the decrease of the hydride affinities is linearly to take place with the increase of the number of benzene rings in the molecule of quinones, from which the hydride affinities of aromatic quinones with multiple benzene rings can be predicted. By comparing the hydride affinities of p-quinones and the corresponding o-quinones, it is found that the hydride affinities of o-quinones are generally larger than those of the corresponding p-quinones by ca. 11 kcal/mol. Analyzing the effect of solvent on the hydride affinities of quinones showed that the effects of solvent (DMSO) on the hydride affinities of quinones are mainly dependent on the electrostatic interaction of the charged hydroquinone anions (QH-) with solvent (DMSO). All the information disclosed in this work should provide some valuable clues to chemists to choose suitable quinones or hydroquinones as efficient hydride acceptors or donors in organic syntheses and to predict the thermodynamics of hydride exchange between quinones and hydroquinones in DMSO solution.     

Chemistry of pyrrolo[1,2-a]indole- and pyrido[1,2-a]indole-based quinone methides. Mechanistic explanations for differences in cytostatic/cytotoxic properties

In the present study we investigate pyrido[1,2-a]indole- and pyrrolo[1,2-a]indole-based quinones capable of forming quinone methide and vinyl quinone species upon reduction and leaving group elimination. Our goals were to determine the influence of the 6-membered pyrido and the 5-membered pyrrolo fused rings on quinone methide and vinyl quinone formation and fate as well as on cytostatic and cytotoxic activity. We used the technique of Spectral Global Fitting to study the fleeting quinone methide intermediate directly. Conclusions regarding quinone methide reactivity are that carbonyl O-protonation is required for nucleophile trapping and that the pKa value of this protonated species is near neutrality. The abnormally high protonated carbonyl pKa values are due to the formation of an aromatic carbocation species upon protonation. The fused pyrido ring promotes quinone methide and vinyl quinone formation but slows nucleophile trapping compared to the fused pyrrolo ring. These findings are explained by the presence of axial hydrogen atoms in the fused pyrido ring resulting in more steric congestion compared to the relatively flat fused pyrrolo ring. Consequently, pyrrolo[1,2-a]indole-based quinones exhibit more cytostatic activity than the pyrido[1,2-a]indole analogues due to their greater nucleophile trapping capability.     

Structure and Conformation of Photosynthetic Pigments and Related Compounds. 12. A Crystallographic Analysis of Porphyrin-quinones and Their Precursors

Abstract. A comprehensive crystallographic analysis of 10 porphyrin quinone precursors (dimethoxybenzene derivatives), and six porphyrin quinones has been performed. The free bases and zinc(II) complexes of the porphyrin quinones are of the 5,10,15-triaryl/alkyl-20-quinone-porphyrin type and carry various bridging and quinone units. The structural and conformational parameters were determined for all compounds; the donor-acceptor separation distances range from 6.3 to 10.9 Å. Knowledge of these data is a prerequisite for a detailed interpretation of theoretical and spectroscopic studies on such systems. Despite the obvious influence of the type and geometry of the bridging unit and quinone on the spatial arrangement of the donor and acceptor components, a large variety of different packing arrangements in the crystal were observed. These include π stacking, aggregate formation and axial ligation in the zinc(II) porphyrins. The latter often utilized the quinone (or dimethoxy) oxygen atoms for coordination to zinc(II) centers leading to porphyrin quinone dimers and even polymers.     

Electrochemically controlled hydrogen bonding. o-Quinones as simple redox-dependent receptors for arylureas

9,10-Phenanthrenequinone and acenaphthenequinone are shown to act as simple redox-dependent receptors toward aromatic ureas in CH(2)Cl(2) and DMF. Reduction of the o-quinones to their radical anions greatly increases the strength of hydrogen bonding between the quinone carbonyl oxygens and the urea N-hydrogens. This is detected by large positive shifts in the redox potential of the quinones with no change in electrochemical reversibility upon addition of urea guests. Cyclic voltammetric studies with a variety of possible guests show that the effect is quite selective. Only guests with two strong hydrogen donors, such as O-H bonds or amide N-H bonds, that are capable of simultaneously interacting with both carbonyl oxygens give large shifts in the redox potential of the quinones. The electronic character and conformational preference of the guest are also shown to significantly affect the magnitude of the observed potential shift. In the presence of strong proton donors the electrochemistry of the quinone becomes irreversible indicating that proton transfer has taken place. Experiments with compounds of different acidity show that the pK(a) of the protonated quinone radical is about 15 on the DMSO scale, >4 pK(a) units smaller than that of 1,3-diphenylurea. This is further proof that hydrogen bonding and not proton transfer is responsible for the large potential shifts observed with this and similar guests.     

Facile conversion of cysteine and alkyl cysteines to dehydroalanine on protein surfaces: versatile and switchable access to functionalized proteins

An efficient and robust oxidative elimination of cysteine to dehydroalanine has been discovered. The reaction is induced by O-mesitylenesulfonylhydroxylamine (MSH) and is compatible with methionine. The key elimination has been executed on protein surfaces and allows ready access to different post-translationally modified proteins through conjugate addition of sulfur nucleophiles to dehydroalanine. Treatment of the resulting thioether with MSH results in regeneration of dehydroalanine, allowing a "functional switch" by subsequent addition of a different thiol.     

Studies on quinones. Part 40: Synthesis and cytotoxicity evaluation of anthraquinone epoxides and isomerization products

Aerobic oxidation of 1,4,4a,10a-tetrahydro-1,4-alkano-5,10-anthraquinones and thiophene-analogues in dichloromethane-DBU yielded the corresponding dihydroalkanoquinones which, depending on their structures, react with in situ generated hydroperoxide anion to give quinone epoxides and/or hydroperoxides. The calcium hydroxide-induced rearrangement of quinone epoxides yielded furan-containing angular quinones. The cytotoxic activities of quinone epoxides and their isomerization products were evaluated in vitro against normal human lung fibroblasts (MRC-5) and human cancer gastric epithelial cells (AGS).