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Zeppilli D, Madabeni A, Nogara PA, Rocha JBT, Orian L. Reactivity of Zinc Fingers in Oxidizing Environments: Insight from Molecular Models Through Activation Strain Analysis. Chempluschem 2024; 89:e202400252. [PMID: 38842473 DOI: 10.1002/cplu.202400252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/07/2024]
Abstract
The reactivity of Zn2+ tetrahedral complexes with H2O2 was investigated in silico, as a first step in their disruption process. The substrates were chosen to represent the cores of three different zinc finger protein motifs, i. e., a Zn2+ ion coordinated to four cysteines (CCCC), to three cysteines and one histidine (CCCH), and to two cysteines and two histidines (CCHH). The cysteine and histidine ligands were further simplified to methyl thiolate and imidazole, respectively. H2O2 was chosen as an oxidizing agent due to its biological role as a metabolic product and species involved in signaling processes. The mechanism of oxidation of a coordinated cysteinate to sulfenate-κS and the trends for the different substrates were rationalized through activation strain analysis and energy decomposition analysis in the framework of scalar relativistic Density Functional Theory (DFT) calculations at ZORA-M06/TZ2P ae // ZORA-BLYP-D3(BJ)/TZ2P. CCCC is oxidized most easily, an outcome explained considering both electrostatic and orbital interactions. The isomerization to sulfenate-κO was attempted to assess whether this step may affect the ligand dissociation; however, it was found to introduce a kinetic barrier without improving the energetics of the dissociation. Lastly, ligand exchange with free thiolates and selenolates was investigated as a trigger for ligand dissociation, possibly leading to metal ejection; molecular docking simulations also support this hypothesis.
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Affiliation(s)
- Davide Zeppilli
- Dipartimento di Scienze Chimiche Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Andrea Madabeni
- Dipartimento di Scienze Chimiche Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Pablo A Nogara
- Departamento de Bioquímica e Biologia Molecolar, Universidade Federal de Santa Maria (UFSM), 97105-900, Santa Maria, RS, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia Sul-rio-grandense (IFSul), Av. Leonel de Moura Brizola, 2501, 96418-400, Bagé, RS, Brasil
| | - João B T Rocha
- Departamento de Bioquímica e Biologia Molecolar, Universidade Federal de Santa Maria (UFSM), 97105-900, Santa Maria, RS, Brazil
| | - Laura Orian
- Dipartimento di Scienze Chimiche Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
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2
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Alhasan R, Martins GM, de Castro PP, Saleem RSZ, Zaiter A, Fries-Raeth I, Kleinclauss A, Perrin-Sarrado C, Chaimbault P, da Silva Júnior EN, Gaucher C, Jacob C. Selenoneine-inspired selenohydantoins with glutathione peroxidase-like activity. Bioorg Med Chem 2023; 94:117479. [PMID: 37769443 DOI: 10.1016/j.bmc.2023.117479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/27/2023] [Accepted: 09/17/2023] [Indexed: 09/30/2023]
Abstract
Chronic diseases such as cystic fibrosis, inflammatory bowel diseases, rheumatoid arthritis, and cardiovascular illness have been linked to a decrease in selenium levels and an increase in oxidative stress. Selenium is an essential trace element that exhibits antioxidant properties, with selenocysteine enzymes like glutathione peroxidase being particularly effective at reducing peroxides. In this study, a series of synthetic organoselenium compounds were synthesized and evaluated for their potential antioxidant activities. The new selenohydantoin molecules were inspired by selenoneine and synthesized using straightforward methods. Their antioxidant potential was evaluated and proven using classical radical scavenging and metal-reducing methods. The selenohydantoin derivatives exhibited glutathione peroxidase-like activity, reducing hydroperoxides. Theoretical calculations using Density Functional Theory (DFT) revealed the selenone isomer to be the only one occurring in solution, with selenolate as a possible tautomeric form in the presence of a basic species. Cytocompatibility assays indicated that the selenohydantoin derivatives were non-toxic to primary human aortic smooth muscle cells, paving the way for further biological evaluations of their antioxidant activity. The results suggest that selenohydantoin derivatives with trifluoro-methyl (-CF3) and chlorine (-Cl) substituents have significant activities and could be potential candidates for further biological trials. These compounds may contribute to the development of effective therapies for chronic diseases such cardiovascular diseases.
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Affiliation(s)
- Rama Alhasan
- Université de Lorraine, CITHEFOR, F-54000 Nancy, France; Division of Bioorganic Chemistry, School of Pharmacy, Saarland University, 66123 Saarbruecken, Germany
| | - Guilherme M Martins
- Department of Chemistry, Federal University of Sao Carlos, UFSCar, 13565-905 São Carlos, SP, Brazil; Institute of Exact Sciences, Department of Chemistry, Federal University of Minas Gerais, UFMG, 31270-901 Belo Horizonte, MG, Brazil
| | - Pedro P de Castro
- Department of Chemistry, Federal University of Sao Carlos, UFSCar, 13565-905 São Carlos, SP, Brazil
| | - Rahman Shah Zaib Saleem
- Department of Chemistry and Chemical Engineering, SBA School of Sciences and Engineering, Lahore University of Management Sciences, Lahore 54792, Pakistan
| | - Ali Zaiter
- Université de Lorraine, LCP-A2MC, F-57000 Metz, France
| | | | | | | | | | - Eufrânio N da Silva Júnior
- Institute of Exact Sciences, Department of Chemistry, Federal University of Minas Gerais, UFMG, 31270-901 Belo Horizonte, MG, Brazil.
| | - Caroline Gaucher
- Université de Lorraine, CITHEFOR, F-54000 Nancy, France; Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France.
| | - Claus Jacob
- Division of Bioorganic Chemistry, School of Pharmacy, Saarland University, 66123 Saarbruecken, Germany
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Madabeni A, Orian L. The Key Role of Chalcogenurane Intermediates in the Reduction Mechanism of Sulfoxides and Selenoxides by Thiols Explored In Silico. Int J Mol Sci 2023; 24:ijms24097754. [PMID: 37175462 PMCID: PMC10178455 DOI: 10.3390/ijms24097754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Sulfoxides and selenoxides oxidize thiols to disulfides while being reduced back to sulfides and selenides. While the reduction mechanism of sulfoxides to sulfides has been thoroughly explored experimentally as well as computationally, less attention has been devoted to the heavier selenoxides. In this work, we explore the reductive mechanism of dimethyl selenoxide, as an archetypal selenoxide and, for the sake of comparison, the reductive mechanism of dimethyl sulfoxide to gain insight into the role of the chalcogen on the reaction substrate. Particular attention is devoted to the key role of sulfurane and selenurane intermediates. Moreover, the capacity of these system to oxidize selenols rather than thiols, leading to the formation of selenyl sulfide bridges, is explored in silico. Notably, this analysis provides molecular insight into the role of selenocysteine in methionine sulfoxide reductase selenoenzyme. The activation strain model of chemical reactivity is employed in the studied reactions as an intuitive tool to bridge the computationally predicted effect of the chalcogen on the chalcogenoxide as well as on the chalcogenol.
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Affiliation(s)
- Andrea Madabeni
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Laura Orian
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
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Reactive Human Plasma Glutathione Peroxidase Mutant with Diselenide Bond Succeeds in Tetramer Formation. Antioxidants (Basel) 2022; 11:antiox11061083. [PMID: 35739980 PMCID: PMC9220127 DOI: 10.3390/antiox11061083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 12/05/2022] Open
Abstract
Plasma glutathione peroxidase (GPx3) belongs to the GPx superfamily, and it is the only known secreted selenocysteine (Sec)−containing GPx in humans. It exists as a glycosylated homotetramer and catalyzes the reduction of hydrogen peroxide and lipid peroxides, depending on the Sec in its active center. In this study, a previously reported chimeric tRNAUTuT6 was used for the incorporation of Sec at the UAG amber codon, and the mature form of human GPx3 (hGPx3) without the signal peptide was expressed in amber−less E. coli C321.ΔA.exp. Reactive Sec−hGPx3, able to reduce H2O2 and tert−butyl hydroperoxide (t−BuOOH), was produced with high purity and yield. Study of the quaternary structure suggested that the recombinant Sec−hGPx3 contained an intra−molecular disulfide bridge but failed to form tetramer. Mutational and structural analysis of the mutants with three Cys residues, individually or jointly replaced with Ser, indicated that the formation of intra−molecular disulfide bridges involved structure conformational changes. The secondary structure containing Cys77 and Cys132 was flexible and could form a disulfide bond, or form a sulfhydryl–selenyl bond with Sec49 in relative mutants. Mutation of Cys8 and Cys132 to Sec8 and Sec132 could fix the oligomerization loop through the formation of diselenide bond, which, in turn, facilitated tetramer formation and noticeably improved the GPx activity. This research provides an important foundation for the further catalysis and functional study of hGPx3.
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Nair AG, Perumalla DS, Anjukandi P. Towards solvent regulated self-activation of N-terminal disulfide bond oxidoreductase-D. Phys Chem Chem Phys 2022; 24:7691-7699. [PMID: 35311864 DOI: 10.1039/d1cp05819c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
N-terminal disulfide bond oxidoreductase-D (nDsbD), an essential redox enzyme in Gram-negative bacteria, consists of a single disulfide bond (Cys103-Cys109) in its active site. The enzymatic functions are believed to be regulated by an electron transfer mediated redox switching of the disulfide bond, which is vital in controlling bacterial virulence factors. In light of the disulfide bond's inclination towards nucleophilic cleavage, it is also plausible that an internal nucleophile could second the existing electron transfer mechanism in nDsbD. Using QM/MM MD metadynamics simulations, we explore different possibilities of generating an internal nucleophile near the nDsbD active site, which could serve as a fail-over mechanism in cleaving the disulfide bond. The simulations show the formation of the internal nucleophile Tyr42O- (F ≈ 9 kcal mol-1) and its stabilization through the solvent medium. The static gas-phase calculations show that Tyr42O- could be a potential nucleophile for cleaving the S-S bond. Most strikingly, it is also seen that Tyr42O- and Asp68OH communicate with each other through a proton-hole like water wire (F ≈ 12 kcal mol-1), thus modulating the nucleophile formation. Accordingly, we propose the role of a solvent in regulating the internal nucleophilic reactions and the subsequent self-activation of nDsbD. We believe that this could be deterministic while designing enzyme-targeted inhibitor compounds.
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Affiliation(s)
- Aparna G Nair
- Department of Chemistry, Indian Institute of Technology, Palakkad-678557, Kerala, India.
| | | | - Padmesh Anjukandi
- Department of Chemistry, Indian Institute of Technology, Palakkad-678557, Kerala, India.
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Barchielli G, Capperucci A, Tanini D. The Role of Selenium in Pathologies: An Updated Review. Antioxidants (Basel) 2022; 11:antiox11020251. [PMID: 35204134 PMCID: PMC8868242 DOI: 10.3390/antiox11020251] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/09/2022] [Accepted: 01/25/2022] [Indexed: 12/10/2022] Open
Abstract
Selenium is an essential microelement required for a number of biological functions. Selenium—and more specifically the amino acid selenocysteine—is present in at least 25 human selenoproteins involved in a wide variety of essential biological functions, ranging from the regulation of reactive oxygen species (ROS) concentration to the biosynthesis of hormones. These processes also play a central role in preventing and modulating the clinical outcome of several diseases, including cancer, diabetes, Alzheimer’s disease, mental disorders, cardiovascular disorders, fertility impairments, inflammation, and infections (including SARS-CoV-2). Over the past years, a number of studies focusing on the relationship between selenium and such pathologies have been reported. Generally, an adequate selenium nutritional state—and in some cases selenium supplementation—have been related to improved prognostic outcome and reduced risk of developing several diseases. On the other hand, supra-nutritional levels might have adverse effects. The results of recent studies focusing on these topics are summarized and discussed in this review, with particular emphasis on advances achieved in the last decade.
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Affiliation(s)
- Damiano Tanini
- University of Florence Department of Chemistry ‘‘Ugo Schiff'' Via della Lastruccia 3–13 I-50019 Sesto Fiorentino Italy
| | - Antonella Capperucci
- University of Florence Department of Chemistry ‘‘Ugo Schiff'' Via della Lastruccia 3–13 I-50019 Sesto Fiorentino Italy
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Orian L, Flohé L. Selenium-Catalyzed Reduction of Hydroperoxides in Chemistry and Biology. Antioxidants (Basel) 2021; 10:1560. [PMID: 34679695 PMCID: PMC8533274 DOI: 10.3390/antiox10101560] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/06/2021] [Accepted: 09/28/2021] [Indexed: 01/23/2023] Open
Abstract
Among the chalcogens, selenium is the key element for catalyzed H2O2 reduction. In organic synthesis, catalytic amounts of organo mono- and di-selenides are largely used in different classes of oxidations, in which H2O2 alone is poorly efficient. Biological hydroperoxide metabolism is dominated by peroxidases and thioredoxin reductases, which balance hydroperoxide challenge and contribute to redox regulation. When their selenocysteine is replaced by cysteine, the cellular antioxidant defense system is impaired. Finally, classes of organoselenides have been synthesized with the aim of mimicking the biological strategy of glutathione peroxidases, but their therapeutic application has so far been limited. Moreover, their therapeutic use may be doubted, because H2O2 is not only toxic but also serves as an important messenger. Therefore, over-optimization of H2O2 reduction may lead to unexpected disturbances of metabolic regulation. Common to all these systems is the nucleophilic attack of selenium to one oxygen of the peroxide bond promoting its disruption. In this contribution, we revisit selected examples from chemistry and biology, and, by using results from accurate quantum mechanical modelling, we provide an accurate unified picture of selenium's capacity of reducing hydroperoxides. There is clear evidence that the selenoenzymes remain superior in terms of catalytic efficiency.
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Affiliation(s)
- Laura Orian
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, 35131 Padova, Italy
| | - Leopold Flohé
- Dipartimento di Medicina Molecolare, Università degli Studi di Padova, 35121 Padova, Italy
- Departamento de Bioquimica, Universidad de la Republica, Montevideo 11800, Uruguay
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Mechanistic Insight into SARS-CoV-2 Mpro Inhibition by Organoselenides: The Ebselen Case Study. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11146291] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The main protease (Mpro) of SARS-CoV-2 is a current target for the inhibition of viral replication. Through a combined Docking and Density Functional Theory (DFT) approach, we investigated in-silico the molecular mechanism by which ebselen (IUPAC: 2-phenyl-1,2-benzoselenazol-3-one), the most famous and pharmacologically active organoselenide, inhibits Mpro. For the first time, we report on a mechanistic investigation in an enzyme for the formation of the covalent -S-Se- bond between ebselen and a key enzymatic cysteine. The results highlight the strengths and weaknesses of ebselen and provide hints for a rational drug design of bioorganic selenium-based inhibitors.
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Madabeni A, Nogara PA, Bortoli M, Rocha JB, Orian L. Effect of Methylmercury Binding on the Peroxide-Reducing Potential of Cysteine and Selenocysteine. Inorg Chem 2021; 60:4646-4656. [PMID: 33587617 PMCID: PMC8763373 DOI: 10.1021/acs.inorgchem.0c03619] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Indexed: 01/09/2023]
Abstract
Methylmercury (CH3Hg+) binding to catalytically fundamental cysteine and selenocysteine of peroxide-reducing enzymes has long been postulated as the origin of its toxicological activity. Only very recently, CH3Hg+ binding to the selenocysteine of thioredoxin reductase has been directly observed [Pickering, I. J. Inorg. Chem., 2020, 59, 2711-2718], but the precise influence of the toxicant on the peroxide-reducing potential of such a residue has never been investigated. In this work, we employ state-of-the-art density functional theory calculations to study the reactivity of molecular models of the free and toxified enzymes. Trends in activation energies are discussed with attention to the biological consequences and are rationalized within the chemically intuitive framework provided by the activation strain model. With respect to the free, protonated amino acids, CH3Hg+ binding promotes oxidation of the S or Se nucleus, suggesting that chalcogenoxide formation might occur in the toxified enzyme, even if the actual rate of peroxide reduction is almost certainly lowered as suggested by comparison with fully deprotonated amino acids models.
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Affiliation(s)
- Andrea Madabeni
- Dipartimento
di Scienze Chimiche, Università degli
Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Pablo A. Nogara
- Dipartimento
di Scienze Chimiche, Università degli
Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
- Departamento
de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), 97105-900 Santa
Maria, RS, Brazil
| | - Marco Bortoli
- Dipartimento
di Scienze Chimiche, Università degli
Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - João B.
T. Rocha
- Departamento
de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), 97105-900 Santa
Maria, RS, Brazil
| | - Laura Orian
- Dipartimento
di Scienze Chimiche, Università degli
Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
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