Quinone Reduction Research Articles

Tunneling Mechanisms of Quinones in Photosynthetic Reaction Center–Light Harvesting 1 Supercomplexes

In photosynthesis, light energy is absorbed and transferred to the reaction center, ultimately leading to the reduction of quinone molecules through the electron transfer chain. The oxidation and reduction of quinones generate an electrochemical potential difference used for adenosine triphosphate synthesis. The trafficking of quinone/quinol molecules between electron transport components has been a long‐standing question. Here, an atomic‐level investigation into the molecular mechanism of quinol dissociation in the photosynthetic reaction center–light‐harvesting complex 1 (RC–LH1) supercomplexes from Rhodopseudomonas palustris, using classical molecular dynamics (MD) simulations combined with self‐random acceleration MD‐MD simulations and umbrella sampling methods, is conducted. Results reveal a significant increase in the mobility of quinone molecules upon reduction within RC–LH1, which is accompanied by conformational modifications in the local protein environment. Quinol molecules have a tendency to escape from RC–LH1 in a tail‐first mode, exhibiting channel selectivity, with distinct preferred dissociation pathways in the closed and open LH1 rings. Furthermore, comparative analysis of free energy profiles indicates that alternations in the protein environment accelerate the dissociation of quinol molecules through the open LH1 ring. In particular, aromatic amino acids form π‐stacking interactions with the quinol headgroup, resembling the key components in a conveyor belt system. This study provides insights into the molecular mechanisms that govern quinone/quinol exchange in bacterial photosynthesis and lays the framework for tuning electron flow and energy conversion to improve metabolic performance.

Quinone chemistry in respiratory complex I involves protonation of a conserved aspartic acid residue.

Respiratory complex I is a central metabolic enzyme coupling NADH oxidation and quinone reduction with proton translocation. Despite the knowledge of the structure of the complex, the coupling of both processes is not entirely understood. Here, we use a combination of site-directed mutagenesis, biochemical assays, and redox-induced FTIR spectroscopy to demonstrate that the quinone chemistry includes the protonation and deprotonation of a specific, conserved aspartic acid residue in the quinone binding site (D325 on subunit NuoCD in Escherichia coli). Our experimental data support a proposal derived from theoretical considerations that deprotonation of this residue is involved in triggering proton translocation in respiratory complex I.

Sonochemical Assisted Europium(III) Oxide–Graphitic-Carbon Nitride Nanocomposite for Reversible Electrochemical Detection of Quinol

A new sensor material was constructed to facilitate the reversible detection of Quinol (QL). QL is an isomer of dihydroxybenzene, which poses threats to the environment due to their abundance spillage and wastage from many day-to-day life and healthcare by-products. To recycle the wasted QL from industries, we have prepared a sensor that can oxidize those unwanted QL into less-carcinogenic products and further utilize the same sensor to reduce the benzoquinone into QL. We have successfully prepared the sonochemical assisted nanocomposite of fish scale-like europium(III) oxide (EuO) and graphitic carbon nitride (g-C3N4) (Eu-CN). The proposed material’s structural and morphological characteristics have been proved using various instruments. In addition, the proposed sensor shows exceptional electrocatalytic activity towards QL having wider linear range from 0.01 μM to 681.09 μM with detection limit (LOD) of 4.71 nM. Also, the prepared Eu-CN sensor showed the excellent potential towards reduction of benzoquinone having wide linear range from 1 μM to 870 μM with LOD of 123.46 nM. The sensor also exhibited excellent stability in terms of longer storage and repeatability towards the detection of QL. By facilitating the Eu-CN, the real time detection of QL in tap water and river water showed a promising result.

Redox-Active Carboranyl Diphosphine as an Electron and Proton Transfer Agent.

In this work, we report the first example of the PCET reactivity for a boron cluster compound, the zwitterionic nido-carboranyl diphosphonium derivative 7-P(H)tBu2-10-P(H)iPr2-nido-C2B10H10. This main-group reagent efficiently transfers two electrons and two protons to quinones to yield hydroquinones and regenerate a neutral closo-carboranyl diphosphine, 1-PtBu2-2-PiPr2-closo-C2B10H10. As we have previously reported the conversion of this closo-carboranyl diphosphine into the zwitterionic nido- derivative upon reaction with main group hydrides, the transformation reported herein represents a complete synthetic cycle for the metal-free reduction of quinones, with the redox-active carboranyl diphosphine scaffold acting as a mediator. The proposed mechanism of this reduction, based on pKa determination, electrochemical studies, and kinetic isotope effect determination, involves the electron transfer from the nido- cluster to the quinone coupled with the delivery of protons.

The two alternative NADH:quinone oxidoreductases from Staphylococcus aureus: two players with different molecular and cellular roles.

Staphylococcus aureus is an opportunistic pathogen that has emerged as a major public health threat due to the increased incidence of its drug resistance. S. aureus presents a remarkable capacity to adapt to different niches due to the plasticity of its energy metabolism. In this work, we investigated the energy metabolism of S. aureus, focusing on the alternative NADH:quinone oxidoreductases, NDH-2s. S. aureus presents two genes encoding NDH-2s (NDH-2A and NDH-2B) and lacks genes coding for Complex I, the canonical respiratory NADH:quinone oxidoreductase. This observation makes the action of NDH-2s crucial for the regeneration of NAD+ and, consequently, for the progression of metabolism. Our study involved the comprehensive biochemical characterization of NDH-2B and the exploration of the cellular roles of NDH-2A and NDH-2B, utilizing knockout mutants (Δndh-2a and Δndh-2b). We show that NDH-2B uses NADPH instead of NADH, does not establish a charge-transfer complex in the presence of NADPH, and its reduction by this substrate is the catalytic rate-limiting step. In the case of NDH-2B, the reduction of the flavin is inherently slow, and we suggest the establishment of a charge transfer complex between NADP+ and FADH2, as previously observed for NDH-2A, to slow down quinone reduction and, consequently, prevent the overproduction of reactive oxygen species, which is potentially unnecessary. Furthermore, we observed that the lack of NDH-2A or NDH-2B impacts cell growth, volume, and division differently. The absence of these enzymes results in distinct metabolic phenotypes, emphasizing the unique cellular roles of each NDH-2 in energy metabolism.IMPORTANCEStaphylococcus aureus is an opportunistic pathogen, posing a global challenge in clinical medicine due to the increased incidence of its drug resistance. For this reason, it is essential to explore and understand the mechanisms behind its resistance, as well as the fundamental biological features such as energy metabolism and the respective players that allow S. aureus to live and survive. Despite its prominence as a pathogen, the energy metabolism of S. aureus remains underexplored, with its respiratory enzymes often escaping thorough investigation. S. aureus bioenergetic plasticity is illustrated by its ability to use different respiratory enzymes, two of which are investigated in the present study. Understanding the metabolic adaptation strategies of S. aureus to bioenergetic challenges may pave the way for the design of therapeutic approaches that interfere with the ability of the pathogen to successfully adapt when it invades different niches within its host.

Insights into the Mechanism of Catalytic Activity of Plasmodium Parasite Malate-Quinone Oxidoreductase.

Plasmodium malate-quinone oxidoreductase (MQO) is a membrane flavoprotein catalyzing the oxidation of malate to oxaloacetate and the reduction of quinone to quinol. Recently, using a yeast expression system, we demonstrated that MQO, expressed in place of mitochondrial malate dehydrogenase (MDH), contributes to the TCA cycle and the electron transport chain in mitochondria, making MQO attractive as a promising drug target in Plasmodium malaria parasites, which lack mitochondrial MDH. However, there is little information on the structure of MQO and its catalytic mechanism, information that will be required to develop novel drugs. Here, we investigated the catalytic site of P. falciparum MQO (PfMQO) using our yeast expression system. We generated a model structure for PfMQO with the AI tool AlphaFold and used protein footprinting by acetylation with acetic anhydride to analyze the surface topology of the model, confirming the computational prediction to be reasonably accurate. Moreover, a putative catalytic site, which includes a possible flavin-binding site, was identified by this combination of protein footprinting and structural prediction model. This active site was analyzed by site-directed mutagenesis. By measuring enzyme activity and protein expression levels in the PfMQO mutants, we showed that several residues at the active site are essential for enzyme function. In addition, a single substitution mutation near the catalytic site resulted in enhanced sensitivity to ferulenol, an inhibitor of PfMQO that competes with malate for binding to the enzyme. This strongly supports the notion that the substrate binds to the proposed catalytic site. Then, the location of the catalytic site was demonstrated by structural comparison with a homologous enzyme. Finally, we used our results to propose a mechanism for the catalytic activity of MQO by reference to the mechanism of action of structurally or functionally homologous enzymes.

Heavily Doped Carbon Nitride Nanocrystal Promotes Visible-Near-Infrared Photosynthesis of Hydrogen Peroxide with Near-Unit Photon Utilization.

Direct photosynthesis of hydrogen peroxide (H2O2) from water and oxygen represents an intriguing alternative to the current indirect process involving the reduction and oxidation of quinones. However, limited light utilization and sluggish charge transfer largely impede overall photocatalytic efficiency. Herein, we present a heavily doped carbon nitride (CNKLi) nanocrystal for efficient and selective photoproduction of H2O2 via a two-electron oxygen reduction reaction (ORR) pathway. CNKLi induces metal-to-ligand charge transfer (MLCT) and electron trapping, which broadens the light absorption to the visible-near-infrared (vis-NIR) spectrum and prolongs the photoelectron lifetime to the microsecond time scale with an exceptional charge diffusion length of ∼1200 nm. Near-unit photoutilization with an apparent quantum yield (AQY) of 100% for H2O2 generation is achieved below 420 nm. Impressively, CNKLi exhibits an appreciable AQY of 16% at 700 nm, which reaches the absorption capacity (∼16%), thus suggesting a near-unit photon utilization <700 nm. In situ characterization and theoretical calculations reveal the facilitated charge transfer from K+ to the heptazine ring skeleton. These findings provide an approach to improve the photosynthetic efficiency of direct H2O2 preparation in the vis-NIR region and expand applications for driving kinetically slow and technologically desirable oxidations or high-value chemical generation.

Divergence of Classical and C-Ring-Cleaved Angucyclines: Elucidation of Early Tailoring Steps in Lugdunomycin and Thioangucycline Biosynthesis.

Angucyclines are an important group of microbial natural products that display tremendous chemical diversity. Classical angucyclines are composed of a tetracyclic benz[a]anthracene scaffold with one ring attached at an angular orientation. However, in atypical angucyclines, the polyaromatic aglycone is cleaved at A-, B-, or C-rings, leading to structural rearrangements and enabling further chemical variety. Here, we have elucidated the branching points in angucycline biosynthesis leading toward cleavage of the C-ring in lugdunomycin and thioangucycline biosynthesis. We showed that 12-hydroxylation and 6-ketoreduction of UWM6 are shared steps in classical and C-ring-cleaved angucycline pathways, although the bifunctional 6-ketoreductase LugOIIred harbors additional unique 1-ketoreductase activity. We identified formation of the key intermediate 8-O-methyltetrangomycin by the LugN methyltransferase as the branching point toward C-ring-cleaved angucyclines. The final common step in lugdunomycin and thioangucycline biosynthesis is quinone reduction, catalyzed by the 7-ketoreductases LugG and TacO, respectively. In turn, the committing step toward thioangucyclines is 12-ketoreduction catalyzed by TacA, for which no orthologous protein exists on the lugdunomycin pathway. Our results confirm that quinone reductions are early tailoring steps and, therefore, may be mechanistically important for subsequent C-ring cleavage. Finally, many of the tailoring enzymes harbored broad substrate promiscuity, which we utilized in combinatorial enzymatic syntheses to generate the angucyclines SM 196 A and hydranthomycin. We propose that enzyme promiscuity and the competition of many of the enzymes for the same substrates lead to a branching biosynthetic network and formation of numerous shunt products typical for angucyclines rather than a canonical linear metabolic pathway.

The Catalysis Mechanism of E. coli Nitroreductase A, a Candidate for Gene-Directed Prodrug Therapy: Potentiometric and Substrate Specificity Studies.

E. coli nitroreductase A (NfsA) is a candidate for gene-directed prodrug cancer therapy using bioreductively activated nitroaromatic compounds (ArNO2). In this work, we determined the standard redox potential of FMN of NfsA to be -215 ± 5 mV at pH 7.0. FMN semiquinone was not formed during 5-deazaflavin-sensitized NfsA photoreduction. This determines the two-electron character of the reduction of ArNO2 and quinones (Q). In parallel, we characterized the oxidant specificity of NfsA with an emphasis on its structure. Except for negative outliers nitracrine and SN-36506, the reactivity of ArNO2 increases with their electron affinity (single-electron reduction potential, E17) and is unaffected by their lipophilicity and Van der Waals volume up to 386 Å. The reactivity of quinoidal oxidants is not clearly dependent on E17, but 2-hydroxy-1,4-naphthoquinones were identified as positive outliers and a number of compounds with diverse structures as negative outliers. 2-Hydroxy-1,4-naphthoquinones are characterized by the most positive reaction activation entropy and the negative outlier tetramethyl-1,4-benzoquinone by the most negative. Computer modelling data showed that the formation of H bonds with Arg15, Arg133, and Ser40, plays a major role in the binding of oxidants to reduced NfsA, while the role of the π-π interaction of their aromatic structures is less significant. Typically, the calculated hydride-transfer distances during ArNO2 reduction are smallwer than for Q. This explains the lower reactivity of quinones. Another factor that slows down the reduction is the presence of positively charged aliphatic substituents.

Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations.

The human NQO1 (hNQO1) is a flavin adenine nucleotide (FAD)-dependent oxidoreductase that catalyzes the two-electron reduction of quinones to hydroquinones, being essential for the antioxidant defense system, stabilization of tumor suppressors, and activation of quinone-based chemotherapeutics. Moreover, it is overexpressed in several tumors, which makes it an attractive cancer drug target. To decipher new structural insights into the flavin reductive half-reaction of the catalytic mechanism of hNQO1, we have carried serial crystallography experiments at new ID29 beamline of the ESRF to determine, to the best of our knowledge, the first structure of the hNQO1 in complex with NADH. We have also performed molecular dynamics simulations of free hNQO1 and in complex with NADH. This is the first structural evidence that the hNQO1 functional cooperativity is driven by structural communication between the active sites through long-range propagation of cooperative effects across the hNQO1 structure. Both structural results and MD simulations have supported that the binding of NADH significantly decreases protein dynamics and stabilizes hNQO1 especially at the dimer core and interface. Altogether, these results pave the way for future time-resolved studies, both at x-ray free-electron lasers and synchrotrons, of the dynamics of hNQO1 upon binding to NADH as well as during the FAD cofactor reductive half-reaction. This knowledge will allow us to reveal unprecedented structural information of the relevance of the dynamics during the catalytic function of hNQO1.

Theoretical study on the kinetics and reaction mechanism involved in the reduction of quinone by 1‐benzyl‐1,4‐dihydronicotinamide

AbstractAlthough it is well known that coenzyme NAD(P)H is involved in anabolic and catabolic reactions in the living organism, there is still significant controversy over the reaction mechanism involved in this biochemical transformation. Thus, 1‐benzyl‐1,4‐dihydronicotinamide was used as a NAD(P)H model in the reduction reaction of 1,4‐benzoquinone (Q), 2,3,5,6‐tetrachloro‐1,4‐benzoquinone, and 2,3‐dicyano‐1,4‐benzoquinone in acetonitrile medium. The kinetic calculations support that formal hydride transfer is the main mechanism promoting Q reduction, while the two‐step process dominates 2,3‐dicyano‐1,4‐benzoquinone reduction. Interestingly, only the single‐electron transfer mechanism takes place when 2,3,5,6‐tetrachloro‐1,4‐benzoquinone is used, affording the corresponding semiquinone derivative as the main product. This mechanistic behavior is related to the presence or absence of electron‐withdrawing groups in the quinones used. Furthermore, the kinetic study results showed that calculated reaction rate constants are in close agreement with experimental results. The results support that formal hydride transfer on the reduction reaction of Q by 1‐benzyl‐1,4‐dihydronicotinamide in acetonitrile proceeds through a hydrogen coupled electron transfer mechanism. This theoretical analysis provides valuable knowledge that can be extrapolated to study the reduction of quinones performed by NADH and NADPH in physiological media.

1H-1,2,3-Triazol-5-ylidenes as Catalytic Organic Single-Electron Reductants.

Most of the known single-electron reductants are either metal based reagents, used in a stoichiometric amount, or a combination of an organic species and a photocatalyst. Here we report that 1H-1,2,3-triazol-5-ylidenes act not only as stoichiometric one-electron donors but also as catalytic organic reducing agents, without the need of a photocatalyst. As a proof of concept, we studied the reduction of quinones, which are well-known electron conveyors that are involved in various biological and industrial processes. This work also provides experimental evidence for the formation of a bis(triazolium)carbonate adduct, which acts as the resting state of the catalytic cycle and as the carbene reservoir.

Polymorphisms and Pharmacogenomics of NQO2: The Past and the Future.

The flavoenzyme N-ribosyldihydronicotinamide (NRH):quinone oxidoreductase 2 (NQO2) catalyzes two-electron reductions of quinones. NQO2 contributes to the metabolism of biogenic and xenobiotic quinones, including a wide range of antitumor drugs, with both toxifying and detoxifying functions. Moreover, NQO2 activity can be inhibited by several compounds, including drugs and phytochemicals such as flavonoids. NQO2 may play important roles that go beyond quinone metabolism and include the regulation of oxidative stress, inflammation, and autophagy, with implications in carcinogenesis and neurodegeneration. NQO2 is a highly polymorphic gene with several allelic variants, including insertions (I), deletions (D) and single-nucleotide (SNP) polymorphisms located mainly in the promoter, but also in other regulatory regions and exons. This is the first systematic review of the literature reporting on NQO2 gene variants as risk factors in degenerative diseases or drug adverse effects. In particular, hypomorphic 29 bp I alleles have been linked to breast and other solid cancer susceptibility as well as to interindividual variability in response to chemotherapy. On the other hand, hypermorphic polymorphisms were associated with Parkinson's and Alzheimer's disease. The I and D promoter variants and other NQO2 polymorphisms may impact cognitive decline, alcoholism and toxicity of several nervous system drugs. Future studies are required to fill several gaps in NQO2 research.

Assembled Quantum Dot Porous Clusters for Enhanced Photocatalytic Reduction of Quinone to Hydroquinone

Assembled Quantum Dot Porous Clusters for Enhanced Photocatalytic Reduction of Quinone to Hydroquinone

Voltammetric approach to measuring free acid in anhydride and ester based on benzoquinone electrochemical reduction

AbstractFree acids commonly exist in anhydride and esters because they are unstable and tend to break down into free acids, which affect the quality of subsequent products in industrial production. Phthalic anhydride and ethyl acetate undergo hydrolysis reactions to form phthalic acid and acetic acid. A differential pulse voltammetry method for the determination of phthalic acid and acetic acid was developed with a bare glassy carbon electrode. Phthalic acid and acetic acid caused a new cathodic peak at more positive potential during the reduction of 1,4‐benzoquinone in acetonitrile or aqueous solution. The new peaks are attributed to the drastic increase in pH at the electrode surface caused by the consumption of protons in the benzoquinone reduction reaction. The peak current of the new cathodic peak was dependent on the concentration of phthalic acid and acetic acid but independent of BQ, phthalic anhydride, and ethyl acetate. This method does not cause hydrolysis of anhydride and ester because no external base is introduced. Furthermore, the method is sensitive, rapid, and does not require pretreatment.

Migration-mitigated crossover of organic redox anions across a proton-exchange membrane

We introduce a membrane electrolyzer for the generation of hydrogen peroxide via oxygen reduction and catalyst-free oxidation of quinones. The study reports the effect of the applied coulombic forces on ions, which is the origin of crossover.

The role of an intramolecular hydrogen bond in the redox properties of carboxylic acid naphthoquinones.

A bioinspired naphthoquinone model of the quinones in photosynthetic reaction centers but bearing an intramolecular hydrogen-bonded carboxylic acid has been synthesized and characterized electrochemically, spectroscopically, and computationally to provide mechanistic insight into the role of proton-coupled electron transfer (PCET) of quinone reduction in photosynthesis. The reduction potential of this construct is 370 mV more positive than the unsubstituted naphthoquinone. In addition to the reversible cyclic voltammetry, infrared spectroelectrochemistry confirms that the naphthoquinone/naphthoquinone radical anion couple is fully reversible. Calculated redox potentials agree with the experimental trends arising from the intramolecular hydrogen bond. Molecular electrostatic potentials illustrate the reversible proton transfer driving forces, and analysis of the computed vibrational spectra supports the possibility of a combination of electron transfer and PCET processes. The significance of PCET, reversibility, and redox potential management relevant to the design of artificial photosynthetic assemblies involving PCET processes is discussed.

Mutation at the entrance of the quinone cavity severely disrupts quinone binding in respiratory complex I

In all resolved structures of complex I, there exists a tunnel-like Q-chamber for ubiquinone binding and reduction. The entrance to the Q-chamber in ND1 subunit forms a narrow bottleneck, which is rather tight and requires thermal conformational changes for ubiquinone to get in and out of the binding chamber. The substitution of alanine with threonine at the bottleneck (AlaThr MUT), associated with 3460/ND1 mtDNA mutation in human complex I, is implicated in Leber's Hereditary Optic Neuropathy (LHON). Here, we show the AlaThr MUT further narrows the Q-chamber entrance cross-section area by almost 30%, increasing the activation free energy barrier of quinone passage by approximately 5 kJ mol−1. This severely disrupts quinone binding and reduction as quinone passage through the bottleneck is slowed down almost tenfold. Our estimate of the increase in free energy barrier is entirely due to the bottleneck narrowing, leading to a reduction of the transition state entropy between WT and MUT, and thus more difficult quinone passage. Additionally, we investigate details of possible water exchange between the Q-chamber and membrane. We find water exchange is dynamic in WT but may be severely slowed in MUT. We propose that LHON symptoms caused by 3460/ND1 mtDNA mutation are due to slowed quinone binding. This leads to an increased production of reactive oxidative species due to upstream electron backup at the FMN site of complex I, thus resulting in a mt bioenergetic defect.

Integrated chemical and genetic screens unveil FSP1 mechanisms of ferroptosis regulation.

Ferroptosis, marked by iron-dependent lipid peroxidation, may present an Achilles heel for the treatment of cancers. Ferroptosis suppressor protein-1 (FSP1), as the second ferroptosis mainstay, efficiently prevents lipid peroxidation via NAD(P)H-dependent reduction of quinones. Because its molecular mechanisms have remained obscure, we studied numerous FSP1 mutations present in cancer or identified by untargeted random mutagenesis. This mutational analysis elucidates the FAD/NAD(P)H-binding site and proton-transfer function of FSP1, which emerged to be evolutionarily conserved among different NADH quinone reductases. Using random mutagenesis screens, we uncover the mechanism of action of next-generation FSP1 inhibitors. Our studies identify the binding pocket of the first FSP1 inhibitor, iFSP1, and introduce the first species-independent FSP1 inhibitor, targeting the NAD(P)H-binding pocket. Conclusively, our study provides new insights into the molecular functions of FSP1 and enables the rational design of FSP1 inhibitors targeting cancer cells.

NAD(P)H:Quinone Acceptor Oxidoreductase 1 (NQO1) Activatable Salicylamide H+/Cl- Transporters.

NAD(P)H:quinone acceptor oxidoreductase 1 (NQO1), a detoxifying enzyme overexpressed in tumors, plays a key role in protecting cancer cells against oxidative stress and thus has been considered an attractive candidate for activating prodrug(s). Herein, we report the first use of NQO1 for the selective activation of 'protransporter' systems in cancer cells leading to the induction of apoptosis. Salicylamides, easily synthesizable small molecules, have been effectively used for efficient H+/Cl- symport across lipid membranes. The ion transport activity of salicylamides was efficiently abated by caging the OH group with NQO1 activatable quinones via either ether or ester linkage. The release of active transporters, following the reduction of quinone caged 'protransporters' by NQO1, was verified. Both the transporters and protransporters exhibited significant toxicity towards the MCF-7 breast cancer line, mediated via the induction of oxidative stress, mitochondrial membrane depolarization, and lysosomal deacidification. Induction of cell death via intrinsic apoptotic pathway was verified by monitoring PARP1 cleavage.