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VU Research Portal VU Research Portal The Role of Selenium in Glutathione Peroxidase Bortoli, M. 2019 document version Publisher's PDF, also known as Version of record Link to publication in VU Research Portal citation for published version (APA) Bortoli, M. (2019). The Role of Selenium in Glutathione Peroxidase: Insights from Molecular Modeling. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. E-mail address: [email protected] Download date: 23. Sep. 2021 VRIJE UNIVERSITEIT UNIVERSITÀ DEGLI STUDI DI PADOVA THE ROLE OF SELENIUM IN GLUTATHIONE PEROXIDASE: INSIGHTS FROM MOLECULAR MODELING ACADEMISCH PROEFSCHRIFT ter verkrijging van de graad Doctor of Philosophy aan de Vrije Universiteit Amsterdam, op gezag van de rector magnificus prof.dr. V. Subramaniam en Dottore di Ricerca aan de Università degli Studi di Padova op gezag van de rector magnificus prof.dr. Rosario Rizzuto, in het openbaar te verdedigen ten overstaan van de promotiecommissie van de Faculteit der Bètawetenschappen op woensdag 17 april 2019 om 11.45 uur in de aula van de universiteit, De Boelelaan 1105 door Marco Bortoli geboren te Marostica, Italië promotoren: prof.dr. F.M. Bickelhaupt prof.dr. L. Orian Università degli Studi di Padova Vrije Universiteit Amsterdam Department of Chemical Sciences Department of Theoretical Chemistry Administrative seat: University of Padova Vrije Universiteit Amsterdam Doctoral Course in Molecular Sciences Doctoral Programme in Chemistry Curriculum: Chemical Sciences Cycle: XXXI Coordinator: Prof. Dr. Leonard Jan Prins The Role of Selenium in Glutathione Peroxidase: Insights from Molecular Modeling Supervisor: Prof. Dr. F. Matthias Bickelhaupt Co-Supervisor: Prof. Dr. Laura Orian Ph. D. Candidate: Marco Bortoli This manuscript has been presented to jointly opt for the doctoral degree from the University of Padova and the Vrije Universiteit Amsterdam The Role of Selenium in Glutathione Peroxidase: Insights from Molecular Modeling i Alla mia famiglia che mi ha fatto diventare quello che sono ii Contents Preface xv 1 Introduction1 1.1 A brief historical account....................1 1.1.1 Selenium and biology: from poison to prevention..3 1.1.2 Glutathione peroxidase: the non-existing enzyme..6 1.2 Selenocysteine: legacy or novelty?...............7 1.3 Glutathione peroxidase: Not only an antioxidant.......9 1.4 GPx mimics: harnessing the power of glutathione peroxidase 13 2 Theory and methods 17 2.1 Quantum mechanical calculations............... 17 2.1.1 Density functional theory............... 18 2.1.2 Activation strain model and energy decomposition analysis......................... 20 2.1.3 Solvent eects...................... 23 2.2 Classical calculations...................... 25 2.2.1 Molecular dynamics simulations........... 26 2.3 Notation convention and software............... 28 3 The chalcogen-π interaction 29 3.1 Introduction........................... 29 iii iv Contents 3.2 Methods............................. 31 3.3 Results and discussion...................... 33 3.3.1 Geometrical parameters................ 33 3.3.2 Bonding analysis.................... 36 3.4 Conclusions........................... 43 Appendices 45 A Ab initio benchmark 47 B Orbital analysis 51 4 The GPx oxidative phase 53 4.1 Introduction........................... 53 4.2 Methods............................. 57 4.2.1 MD simulations..................... 57 4.2.2 DFT Calculations.................... 58 4.3 Results and discussion...................... 60 4.4 Conclusions........................... 72 Appendices 73 C Parameterization protocol 75 D Benchmarks 81 5 Mimicking the GPx reductive phase 85 5.1 Introduction........................... 85 5.2 Methods............................. 88 5.3 Results and discussion...................... 89 5.3.1 General gas-phase proles............... 90 5.3.2 Trends in gas-phase reactivity............. 96 5.3.3 Eects of solvation................... 98 Contents v 5.3.4 Consequences for undesirable thiol exchange reactions 103 5.4 Conclusions........................... 104 Appendices 107 E Torsional barriers 109 6 Oxidation of organoselenides mimics of GPx by H2O2 113 6.1 Introduction........................... 113 6.2 Methods............................. 114 6.3 Results and discussion...................... 118 6.3.1 Oxidation of diselenides and ditellurides by H2O2 .. 118 6.3.2 Activation strain analysis for the oxidation of RXXR (R=H, CH3, Ph) by H2O2 ................ 121 6.3.2.1 Eect of the chalcogen........... 122 6.3.2.2 Eect of the substituent........... 123 6.3.3 Redox isomerization to anhydride........... 128 6.4 Conclusions........................... 132 Appendices 133 F Alternative mechanism 135 G Energy decomposition analysis 137 7 Conclusions 141 7.1 Summary............................. 141 7.2 Sommario............................ 145 7.3 Concluding remarks....................... 149 7.4 Acknowledgements....................... 151 7.5 List of Publications....................... 152 References 153 vi Contents List of Figures 1.1 Excerpt from the letter from Berzelius to Berthollet, front cover and excerpt from the rst scientic publication where selenium is described and named................4 1.2 Mechanism of organic hydroperoxides reduction catalyzed by Cys/Sec-GPx........................... 11 1.3 Structure of human GPx4 and of the tetramer of human GPx1 with the four monomers in dierent colors........... 11 1.4 Mechanism for the reduction of H2O2 by an organic thiol in the catalytic cycles of ebselen and 2-(N,N-(dimethylamino)- methyl)benzenediselenide.................... 15 2.1 ASM model applied to an SN2 model reaction........ 22 3.1 Examples of the optimized structures of four complexes: F2O···2but, Cl2S···et, Br2Se···et and I2Te···ac................ 34 3.2 HOMOs of the unsaturated substrates............. 40 4.1 Mechanism of organic hydroperoxides reduction catalyzed by Cys/Sec-GPx. Oxidative step highlighted............ 54 4.2 Cluster of amino acids extracted from Cys-GPx and super- position of the optimized geometries of the Cys-, Sec- and Tec-GPx clusters......................... 58 vii viii List of Figures 4.3 MD results: position of the backbone atoms of Cys-GPx, Sec- GPx and Tec- GPx after 500 ns and root mean square uctua- tions for each residue along the 500 ns dynamics....... 61 4.4 Geometries of the optimized adducts E·H2O2·H2O and RMSDs with respect to the initially optimized clusters......... 63 4.5 Mechanism of formation of tellurinic acid via a direct pathway and a hydroxy perhydroxy tellurane intermediate....... 67 4.6 Optimized Tec-cluster in the tellurinic acid form and relevant interatomic distances...................... 68 4.7 Dierent partitioning of the Cys and Sec clusters....... 70 C.1 Atom naming scheme of the parametrized residues: Sec and Tec................................. 76 C.2 Fitting obtained with Paramt of energies of the structures generated with dihedral scans for Sec and Tec......... 78 5.1 Mechanism of organic hydroperoxides reduction catalyzed by Cys/Sec-GPx. Second reductive step highlighted........ 86 5.2 Model reactions scheme..................... 87 5.3 Structures of the stationary points for reactions S–+ SSe and S–+ SeS.............................. 90 5.4 Solvent eect on reaction energy proles in the gas-phase and in water for nucleophilic attack at tellurium selenium and sulfur............................... 100 5.5 Gas phase and condensed phase (water) energy proles for the reactions S–+ SS and S–+ SSe................ 102 5.6 Molecular structures of ebselen and selenenyl sulde as it appears in the ebselen catalytic cycle.............. 104 E.1 Dihedral scans of CH3SSCH3, CH3SeSeCH3 and CH3TeTeCH3 in vacuo at the scalar ZORA-OLYP/TZ2P level of theory... 110 List of Figures ix E.2 Dihedral scan of the TC of the S–+ SS reaction in vacuo at the scalar ZORA-OLYP/TZ2P level of theory............ 111 6.1 Oxidation of 2-(N,N-(dimethylamino)-methyl)benzenediselenide by H2O2 followed by product isomerization to anhydride... 115 6.2 Reaction mechanism for the direct oxidation and subsequent possible redox isomerization of diphenyl diselenides and ditel- lurides............................... 118 6.3 (PhSe)2 optimized structure................... 119 6.4 Reactant complex (RCox), transition state (TSox) and prod- uct complex (PCox) structures for the oxidation of (PhSe)2. 121 6.5 Activation strain analysis along the reaction path for the oxi- dation of (HX)2, without and with empirical correction for dispersion............................. 124 6.6 Activation strain analysis along the reaction path for the oxi- dation of (CH3X)2 and (PhX)2................. 125 6.7 Examples of the “closed” and “open” structures found in aryl dichalcogenides......................... 126 6.8 Stationary points and transition state structures for the iso- merization of (PhSe)2.....................
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