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Ferdousian R, Behbahani FK. Organoselenium compounds. Synthesis, application, and biological activity. PHOSPHORUS SULFUR 2022. [DOI: 10.1080/10426507.2022.2119237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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2
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Tupikina EY. Non-covalent interactions in the glutathione peroxidase active center and their influence on the enzyme activity. Org Biomol Chem 2022; 20:5551-5557. [PMID: 35791825 DOI: 10.1039/d2ob00890d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this computational work, the structure of the active center of the enzyme glutathione peroxidase (in three forms -SeH, -SeOH and -Se(O)OH) and the non-covalent interactions in it were investigated using modern quantum chemistry methods. The non-covalent interactions are described in detail. The presence of σ-hole interactions (chalcogen, tetrel and pnictogen bonds) formed mostly by a selenium atom as an electrophile in the glutathione peroxidase active center is confirmed for the first time. It is shown that a number of non-covalent interactions stabilize intermediates along the catalytic cycle and that modelling of the whole enzyme active center is necessary for accurate predictions of thermodynamic parameters, in particular, activation barriers.
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Affiliation(s)
- Elena Yu Tupikina
- Institute of Chemistry, St. Petersburg University, Universitetskaya emb. 7/9, St. Petersburg, Russia.
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3
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Ferrocenylated Chalcogen (Se and Te)-containing N-heterocyclic carbenes: Selenones, silver and palladium complexes. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119531] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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4
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Tiezza MD, Ribaudo G, Orian L. Organodiselenides: Organic Catalysis and Drug Design Learning from Glutathione Peroxidase. CURR ORG CHEM 2019. [DOI: 10.2174/1385272822666180803123137] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Organodiselenides are an important class of compounds characterized by the
presence of two adjacent covalently bonded selenium nuclei. Among them,
diaryldiselenides and their parent compound diphenyl diselenide attract continuing interest
in chemistry as well as in close disciplines like medicinal chemistry, pharmacology and
biochemistry. A search in SCOPUS database has revealed that in the last three years 105
papers have been published on the archetypal diphenyl diselenide and its use in organic
catalysis and drug tests. The reactivity of the Se-Se bond and the redox properties of selenium
make diselenides efficient catalysts for numerous organic reactions, such as Bayer-
Villiger oxidations of aldehydes/ketones, epoxidations of alkenes, oxidations of alcohols
and nitrogen containing compounds. In addition, organodiselenides might find application
as mimics of glutathione peroxidase (GPx), a family of enzymes, which, besides performing other functions,
regulate the peroxide tone in the cells and control the oxidative stress level. In this review, the essential synthetic
and reactivity aspects of organoselenides are collected and rationalized using the results of accurate
computational studies, which have been carried out mainly in the last two decades. The results obtained in
silico provide a clear explanation of the anti-oxidant activity of organodiselenides and more in general of their
ability to reduce hydroperoxides. At the same time, they are useful to gain insight into some aspects of the enzymatic
activity of the GPx, inspiring novel elements for rational catalyst and drug design.
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Affiliation(s)
- Marco Dalla Tiezza
- Dipartimento di Scienze Chimiche, Universita degli Studi di, Via Marzolo 1, 35131 Padova, Italy
| | - Giovanni Ribaudo
- Dipartimento di Scienze del Farmaco, Universita degli Studi di Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Laura Orian
- Dipartimento di Scienze Chimiche, Universita degli Studi di, Via Marzolo 1, 35131 Padova, Italy
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Bayse CA, Pollard DB. Conformation dynamics of cyclic disulfides and selenosulfides in CXXC(U) (X = Gly, Ala) tetrapeptide redox motifs. J Pept Sci 2019; 25:e3160. [PMID: 30873692 DOI: 10.1002/psc.3160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/26/2019] [Accepted: 02/05/2019] [Indexed: 02/01/2023]
Abstract
Thioredoxin fold proteins often contain a Cys-(Xxx)n -Cys(Sec) or CXn C(U) motif, where the active cysteine (C) or selenocysteine (U) is bridged by X residues, which vary with protein function. The effect of the X residues on the conformation space of the oxidized disulfide and selenosulfide forms of the CXXC(U) motif has been investigated using molecular dynamics (MD) and density functional theory. Multi-microsecond-length MD simulations of the CGGC, CGAC, and CAGC cyclic peptides show that CGGC rings readily exchange between several conformations over the course of the simulation, but steric interactions with the methyl group of Ala limit the conformation space available to the cyclic peptide, especially for CGAC. The potential for the motif to be reduced, as measured by the energy of the lowest unoccupied molecular orbitals, is dependent upon the ring conformation. These results suggest that control of available conformations by the bridging residues and the protein tertiary structure may be important for defining the function of the CXXC motif. Theoretical 77 Se chemical shifts of the selenosulfide moiety are dependent upon the conformation and/or intramolecular Se···O interactions with the backbone carbonyl group of the C-terminal U residue.
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Affiliation(s)
- Craig A Bayse
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, 23529
| | - Deanna B Pollard
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, 23529
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Fragoso E, Azpiroz R, Sharma P, Espinosa-Pérez G, Lara-Ochoa F, Toscano A, Gutierrez R, Portillo O. New organoselenium compounds with intramolecular Se⋯O/ Se⋯H interactions: NMR and theoretical studies. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.11.054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Andrei Nogara P, Batista Teixeira Rocha J. In SilicoStudies of Mammalian δ-ALAD Interactions with Selenides and Selenoxides. Mol Inform 2017; 37:e1700091. [DOI: 10.1002/minf.201700091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/18/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Pablo Andrei Nogara
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Naturais e Exatas; Universidade Federal de Santa Maria; Santa Maria, RS Brazil
| | - João Batista Teixeira Rocha
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Naturais e Exatas; Universidade Federal de Santa Maria; Santa Maria, RS Brazil
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Kheirabadi R, Izadyar M. Computational Modeling of the Catalytic Cycle of Glutathione Peroxidase Nanomimic. J Phys Chem A 2016; 120:10108-10115. [PMID: 27983850 DOI: 10.1021/acs.jpca.6b11437] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
To elucidate the role of a derivative of ebselen as a mimic of the antioxidant selenoenzyme glutathione peroxidase, density functional theory and solvent-assisted proton exchange (SAPE) were applied to model the reaction mechanism in a catalytic cycle. This mimic plays the role of glutathione peroxidase through a four-step catalytic cycle. The first step is described as the oxidation of 1 in the presence of hydrogen peroxide, while selenoxide is reduced by methanthiol at the second step. In the third step of the reaction, the reduction of selenenylsulfide occurs by methanthiol, and the selenenic acid is dehydrated at the final step. Based on the kinetic parameters, step 4 is the rate-determining step (RDS) of the reaction. The bond strength of the atoms involved in the RDS is discussed with the quantum theory of atoms in molecules (QTAIM). Low value of electron density, ρ(r), and positive Laplacian values are the evidence for the covalent nature of the hydrogen bonds rupture (O30-H31, O33-H34). A change in the sign of the Laplacian, L(r), from the positive value in the reactant to a negative character at the transition state indicates the depletion of the charge density, confirming the N5-H10 and O11-Se1 bond breaking. The analysis of electron location function (ELF) and localized orbital locator (LOL) of the Se1-N5 and Se1-O11 bonds have been done by multi-WFN program. High values of ELF and LOL at the transition state regions between the Se, N, and O atoms display the bond formation. Finally, the main donor-acceptor interaction energies were analyzed using the natural bond orbital analysis for investigation of their stabilization effects on the critical bonds at the RDS.
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Affiliation(s)
- Ramesh Kheirabadi
- Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, International Campus , Mashhad, Iran
| | - Mohammad Izadyar
- Computational Chemistry Center, Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad , Mashhad, Iran
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Bhabak KP, Bhowmick D. Synthetic strategies of gold(I)-selenolates from ortho-substituted diaryl diselenides via selenol and selenenyl sulfide intermediates. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.06.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Synthesis, Structure and Antioxidant Activity of Cyclohexene-Fused Selenuranes and Related Derivatives. Molecules 2015; 20:12670-85. [PMID: 26184146 PMCID: PMC6332442 DOI: 10.3390/molecules200712670] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/30/2015] [Accepted: 07/06/2015] [Indexed: 01/25/2023] Open
Abstract
Synthesis, structure and antioxidant activity of new cyclohexene-fused spiroselenuranes and a spirotellurane is reported. Oxidation reactions of bis(o-formylcyclohex-1-ene)selenide/bis(2-hydroxymethylcyclohex-1-ene)selenide provide the corresponding spiroselenuranes. The glutathione peroxidase-like activity of the newly synthesized compounds has been evaluated.
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Bayse CA, Shoaf AL. Effect of Methoxy Substituents on the Activation Barriers of the Glutathione Peroxidase-Like Mechanism of an Aromatic Cyclic Seleninate. Molecules 2015; 20:10244-52. [PMID: 26046321 PMCID: PMC6272359 DOI: 10.3390/molecules200610244] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 05/26/2015] [Accepted: 06/01/2015] [Indexed: 01/09/2023] Open
Abstract
Density functional theory (DFT) models including explicit water molecules have been used to model the redox scavenging mechanism of aromatic cyclic seleninates. Experimental studies have shown that methoxy substitutions affect the rate of scavenging of reactive oxygen species differently depending upon the position. Activities are enhanced in the para position, unaffected in the meta, and decreased in the ortho. DFT calculations show that the activation barrier for the oxidation of the selenenyl sulfide, a proposed key intermediate, is higher for the ortho methoxy derivative than for other positions, consistent with the low experimental conversion rate.
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Affiliation(s)
- Craig A Bayse
- Department of Chemistry and Biochemistry, Old Dominion University, Hampton Boulevard, Norfolk, VA 23529, USA.
| | - Ashley L Shoaf
- Department of Chemistry and Biochemistry, Old Dominion University, Hampton Boulevard, Norfolk, VA 23529, USA.
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12
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Wang Z, Wang Y, Li W, Liu Z, Luo Z, Sun Y, Wu R, Huang L, Li X. Computer-assisted designed “selenoxy–chinolin”: a new catalytic mechanism of the GPx-like cycle and inhibition of metal-free and metal-associated Aβ aggregation. Dalton Trans 2015; 44:20913-25. [DOI: 10.1039/c5dt02130h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Using support from rational computer-assisted design, a novel series of hybrids designed by fusing the metal-chelating agent CQ and the antioxidant ebselen were synthesized and evaluated as multitarget-directed ligands.
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Affiliation(s)
- Zhiren Wang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Yali Wang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Wenrui Li
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Zhihong Liu
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Zonghua Luo
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Yang Sun
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Ruibo Wu
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Ling Huang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Xingshu Li
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
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13
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Harper LK, Antony S, Bayse CA. Thiol Reduction of Arsenite and Selenite: DFT Modeling of the Pathways to an As–Se Bond. Chem Res Toxicol 2014; 27:2119-27. [DOI: 10.1021/tx500384h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lenora K. Harper
- Department of Chemistry and
Biochemistry, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Sonia Antony
- Department of Chemistry and
Biochemistry, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Craig A. Bayse
- Department of Chemistry and
Biochemistry, Old Dominion University, Norfolk, Virginia 23529, United States
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14
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Hodage AS, Phadnis PP, Wadawale A, Priyadarsini KI, Jain VK. Synthesis, Characterization, and Structures of α-Substituted Selenenyl-Acetophenones. PHOSPHORUS SULFUR 2014. [DOI: 10.1080/10426507.2013.844144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ananda S. Hodage
- Chemistry Division, Bhabha Atomic Research Centre, Trombay 400085, Mumbai, India
| | - Prasad P. Phadnis
- Chemistry Division, Bhabha Atomic Research Centre, Trombay 400085, Mumbai, India
| | - Amey Wadawale
- Chemistry Division, Bhabha Atomic Research Centre, Trombay 400085, Mumbai, India
| | - K. I. Priyadarsini
- Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Trombay 400085, Mumbai, India
| | - Vimal K. Jain
- Chemistry Division, Bhabha Atomic Research Centre, Trombay 400085, Mumbai, India
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Orian L, Toppo S. Organochalcogen peroxidase mimetics as potential drugs: a long story of a promise still unfulfilled. Free Radic Biol Med 2014; 66:65-74. [PMID: 23499840 DOI: 10.1016/j.freeradbiomed.2013.03.006] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/04/2013] [Accepted: 03/05/2013] [Indexed: 12/14/2022]
Abstract
Organochalcogen compounds have attracted the interest of a multitude of studies to design potential therapeutic agents mimicking the peroxidase activity of selenium-based glutathione peroxidases (GPx's). Starting from the pioneering ebselen, various compounds have been synthesized over the years, which may be traced in three major classes of molecules: cyclic selenenyl amides, diaryl diselenides, and aromatic or aliphatic monoselenides. These compounds share common features and determinants needed to exert an efficient GPx-like activity, such as polarizing groups in close proximity to selenium and steric effects. Nonetheless, the reactivity of selenium, and tellurium as well, poses serious problems for the predictability of the biological effects of these compounds in vivo when used as potential drugs. These molecules, indeed, interfere with thiols of redox-regulated proteins and enzymes, leading to unexpected biological effects. The various chemical aspects of the reaction mechanism of peroxidase mimetics are surveyed here, focusing on experimental evidence and quantum mechanics calculations of organochalcogen representatives of the various classes.
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Affiliation(s)
- Laura Orian
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, 35129 Padova, Italy.
| | - Stefano Toppo
- Dipartimento di Medicina Molecolare, Università degli Studi di Padova, 35121 Padova, Italy.
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McNeil NMR, Matz MC, Back TG. Fluxional Cyclic Seleninate Ester: NMR and Computational Studies, Glutathione Peroxidase-like Behavior, and Unexpected Rearrangement. J Org Chem 2013; 78:10369-82. [DOI: 10.1021/jo401757m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Nicole M. R. McNeil
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Marie C. Matz
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Thomas G. Back
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N 1N4
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Bayse CA, Ortwine KN. Modeling the Glutathione Peroxidase-Like Activity of a Cyclic Seleninate by DFT and Solvent-Assisted Proton Exchange. Eur J Inorg Chem 2013. [DOI: 10.1002/ejic.201300279] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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18
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Antony S, Bayse CA. Modeling the Mechanism of the Glutathione Peroxidase Mimic Ebselen. Inorg Chem 2011; 50:12075-84. [DOI: 10.1021/ic201603v] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sonia Antony
- Department of Chemistry and Biochemistry, Old Dominion University, Hampton Boulevard, Norfolk, Virginia 23529, United States
| | - Craig A. Bayse
- Department of Chemistry and Biochemistry, Old Dominion University, Hampton Boulevard, Norfolk, Virginia 23529, United States
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