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Johnee Britto N, Jaccob M, Comba P, Anandababu K, Mayilmurugan R. DFT insights into the mechanism of O 2 activation catalyzed by a structural and functional model of cysteine dioxygenase with tris(2-pyridyl)methane-based ligand architecture. J Inorg Biochem 2023; 238:112066. [PMID: 36370503 DOI: 10.1016/j.jinorgbio.2022.112066] [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: 07/27/2022] [Revised: 10/26/2022] [Accepted: 11/03/2022] [Indexed: 11/07/2022]
Abstract
Cysteine dioxygenation is an important step in the metabolism of toxic L-cysteine (Cys) in the human body, carried out by cysteine dioxygenase enzyme (CDO). The disruption of this process is found to elicit neurological health issues. This work reports a computational investigation of mechanistic aspects of this reaction, using a recently reported tris(2-pyridyl)methane-based biomimetic model complex of CDO. The computed results indicate that, the initial SO2 bond formation process is the slowest step in the S-dioxygenation process, possessing an activation barrier of 12.7 kcal/mol. The remaining steps were found to be downhill requiring very small activation energies. The transition states were found to undergo spin crossover between triplet and quintet states, while the singlet surface remained unstable throughout the entire reaction. In essence, the mechanistic scheme and multistate reactivity pattern together with the relatively small computed rate-limiting activation barrier as well as the exothermic formation energy demonstrate that the model complex is an efficient biomimetic CDO model. In addition, the study also substantiates the involvement of Fe(IV)oxido intermediates in the mechanism of S-dioxygenation by the chosen model complex. The insights derived from the O2 activation process might pave way for development of more accurate CDO model catalysts that might be capable of even more efficiently mimicking the geometric, spectroscopic and functional features of the CDO enzyme.
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Affiliation(s)
- Neethinathan Johnee Britto
- Department of Chemistry & Computational Chemistry Laboratory, Loyola Institute of Frontier Energy (LIFE), Loyola College, University of Madras, Chennai 600 034, Tamil Nadu, India
| | - Madhavan Jaccob
- Department of Chemistry & Computational Chemistry Laboratory, Loyola Institute of Frontier Energy (LIFE), Loyola College, University of Madras, Chennai 600 034, Tamil Nadu, India.
| | - Peter Comba
- Heidelberg University, Anorganisch-Chemisches Institut and Interdisciplinary Center for Scientific Computing, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany.
| | - Karunanithi Anandababu
- Depatment of Chemistry, Indian Institute of Technology Bhilai, GEC Campus, Sejbahar, Raipur 492015, India
| | - Ramasamy Mayilmurugan
- Depatment of Chemistry, Indian Institute of Technology Bhilai, GEC Campus, Sejbahar, Raipur 492015, India
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Dehydrogenation of Formic Acid to CO2 and H2 by Manganese(I)–Complex: Theoretical Insights for Green and Sustainable Route. Catalysts 2021. [DOI: 10.3390/catal11010141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In this work, a detailed computational study on a recently synthetized Mn(I)-dependent complex [(tBuPNNOP)Mn(CO)2]+ is reported. This species promotes the dehydrogenation of formic acid to carbon dioxide and hydrogen. The here proposed catalytic cycle proceeds through the formation of stabilized adduct between [(tBuPNNOPtBu)Mn(CO)2]+ and formate and the progressive release of CO2 and H2, mediated by the presence of trimethylamine. In order to evaluate the influence of the environment on the catalytic activity, different solvents have been taken into account. The computed barriers and the geometrical parameters account well for the available experimental data, confirming the robustness of the complex and reproducing its good catalytic performance. Outcomes from the present investigation can stimulate further experimental works in the design of new more efficient catalysts devoted to H2 production.
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Prejanò M, Alberto ME, Russo N, Marino T. Hydration of Aromatic Nitriles Catalyzed by Mn-OH Complexes: A Rationalization from Quantum Chemical Investigations. Organometallics 2020. [DOI: 10.1021/acs.organomet.0c00436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via P. Bucci cubo 14 C, Arcavacata di Rende 87036, Italy
| | - Marta Erminia Alberto
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via P. Bucci cubo 14 C, Arcavacata di Rende 87036, Italy
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via P. Bucci cubo 14 C, Arcavacata di Rende 87036, Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via P. Bucci cubo 14 C, Arcavacata di Rende 87036, Italy
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Fischer AA, Stracey N, Lindeman SV, Brunold TC, Fiedler AT. Synthesis, X-ray Structures, Electronic Properties, and O 2/NO Reactivities of Thiol Dioxygenase Active-Site Models. Inorg Chem 2016; 55:11839-11853. [PMID: 27801576 DOI: 10.1021/acs.inorgchem.6b01931] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mononuclear non-heme iron complexes that serve as structural and functional mimics of the thiol dioxygenases (TDOs), cysteine dioxygenase (CDO) and cysteamine dioxygenase (ADO), have been prepared and characterized with crystallographic, spectroscopic, kinetic, and computational methods. The high-spin Fe(II) complexes feature the facially coordinating tris(4,5-diphenyl-1-methylimidazol-2-yl)phosphine (Ph2TIP) ligand that replicates the three histidine (3His) triad of the TDO active sites. Further coordination with bidentate l-cysteine ethyl ester (CysOEt) or cysteamine (CysAm) anions yielded five-coordinate (5C) complexes that resemble the substrate-bound forms of CDO and ADO, respectively. Detailed electronic-structure descriptions of the [Fe(Ph2TIP)(LS,N)]BPh4 complexes, where LS,N = CysOEt (1) or CysAm (2), were generated through a combination of spectroscopic techniques [electronic absorption, magnetic circular dichroism (MCD)] and density functional theory (DFT). Complexes 1 and 2 decompose in the presence of O2 to yield the corresponding sulfinic acid (RSO2H) products, thereby emulating the reactivity of the TDO enzymes and related complexes. Rate constants and activation parameters for the dioxygenation reactions were measured and interpreted with the aid of DFT calculations for O2-bound intermediates. Treatment of the TDO models with nitric oxide (NO)-a well-established surrogate of O2-led to a mixture of high-spin and low-spin {FeNO}7 species at low temperature (-70 °C), as indicated by electron paramagnetic resonance (EPR) spectroscopy. At room temperature, these Fe/NO adducts convert to a common species with EPR and infrared (IR) features typical of cationic dinitrosyl iron complexes (DNICs). To complement these results, parallel spectroscopic, computational, and O2/NO reactivity studies were carried out using previously reported TDO models that feature an anionic hydrotris(3-phenyl-5-methyl-pyrazolyl)borate (Ph,MeTp-) ligand. Though the O2 reactivities of the Ph2TIP- and Ph,MeTp-based complexes are quite similar, the supporting ligand perturbs the energies of Fe 3d-based molecular orbitals and modulates Fe-S bond covalency, suggesting possible rationales for the presence of neutral 3His coordination in CDO and ADO.
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Affiliation(s)
- Anne A Fischer
- Department of Chemistry, Marquette University , Milwaukee, Wisconsin 53201, United States
| | - Nuru Stracey
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Sergey V Lindeman
- Department of Chemistry, Marquette University , Milwaukee, Wisconsin 53201, United States
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Adam T Fiedler
- Department of Chemistry, Marquette University , Milwaukee, Wisconsin 53201, United States
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5
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Safaei E, Hajikhanmirzaei L, Alavi S, Lee YI, Wojtczak A, Jagličić Z. Tetrabromocatecholato Mn(III) complexes of bis(phenol) diamine ligands as models for enzyme–substrate adducts of catechol dioxygenases. Polyhedron 2016. [DOI: 10.1016/j.poly.2016.07.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Driggers CM, Kean KM, Hirschberger LL, Cooley RB, Stipanuk MH, Karplus PA. Structure-Based Insights into the Role of the Cys-Tyr Crosslink and Inhibitor Recognition by Mammalian Cysteine Dioxygenase. J Mol Biol 2016; 428:3999-4012. [PMID: 27477048 DOI: 10.1016/j.jmb.2016.07.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 10/21/2022]
Abstract
In mammals, the non-heme iron enzyme cysteine dioxygenase (CDO) helps regulate Cys levels through converting Cys to Cys sulfinic acid. Its activity is in part modulated by the formation of a Cys93-Tyr157 crosslink that increases its catalytic efficiency over 10-fold. Here, 21 high-resolution mammalian CDO structures are used to gain insight into how the Cys-Tyr crosslink promotes activity and how select competitive inhibitors bind. Crystal structures of crosslink-deficient C93A and Y157F variants reveal similar ~1.0-Å shifts in the side chain of residue 157, and both variant structures have a new chloride ion coordinating the active site iron. Cys binding is also different from wild-type CDO, and no Cys-persulfenate forms in the C93A or Y157F active sites at pH6.2 or 8.0. We conclude that the crosslink enhances activity by positioning the Tyr157 hydroxyl to enable proper Cys binding, proper oxygen binding, and optimal chemistry. In addition, structures are presented for homocysteine (Hcy), D-Cys, thiosulfate, and azide bound as competitive inhibitors. The observed binding modes of Hcy and D-Cys clarify why they are not substrates, and the binding of azide shows that in contrast to what has been proposed, it does not bind in these crystals as a superoxide mimic.
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Affiliation(s)
- Camden M Driggers
- Department of Biochemistry and Biophysics, 2011 Ag & Life Sciences Building, Oregon State University, Corvallis, OR 97331, USA
| | - Kelsey M Kean
- Department of Biochemistry and Biophysics, 2011 Ag & Life Sciences Building, Oregon State University, Corvallis, OR 97331, USA
| | - Lawrence L Hirschberger
- Department of Nutritional Sciences, 227 Savage Hall, Cornell University, Ithaca, NY 14853, USA
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, 2011 Ag & Life Sciences Building, Oregon State University, Corvallis, OR 97331, USA
| | - Martha H Stipanuk
- Department of Nutritional Sciences, 227 Savage Hall, Cornell University, Ithaca, NY 14853, USA.
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, 2011 Ag & Life Sciences Building, Oregon State University, Corvallis, OR 97331, USA.
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Safaei E, Heidari S, Wojtczak A, Cotič P, Kozakiewicz A. 4-Nitrocatecholato iron(III) complexes of 2-aminomethyl pyridine-based bis(phenol) amine as structural models for catechol-bound 3,4-PCD. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.10.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Sallmann M, Limberg C. Utilizing the Trispyrazolyl Borate Ligand for the Mimicking of O2-Activating Mononuclear Nonheme Iron Enzymes. Acc Chem Res 2015; 48:2734-43. [PMID: 26305516 DOI: 10.1021/acs.accounts.5b00148] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mononuclear, O2-activating nonheme iron enzymes are a fascinating class of metalloproteines, capable of realizing the most different reactions, ranging from C-H activation, via O atom transfer to C-C bond cleavage, in the course of O2 activation. They can lead us the way to achieve similar reactions with comparable efficiency and selectivity in chemical laboratories, which would be highly desirable aiming at accessing value-added products or to achieve degradation of unwanted compounds. Hence, these enyzmes motivate attempts to construct artificial low-molecular weight analogues, mimicking structural or functional characteristics. Such models can, for instance, provide insights about which of the features inherent to an active site are essential and guarantee the enzyme function, and from this kind of information the minimal requirements for a biomimetic or bioinspired complex that may be applied in catalysis can be derived. On the other hand, they can contribute to an understanding of the enzyme functioning. In order to create such replicates, it is important to faithfully mimic the surroundings of the iron centers in their active sites. Most of them feature two histidine residues and one carboxylate donor, while a few exhibit a deceptively simple (His)3Fe active site. For the simulation of these, the trispyrazolyl borate ligand (Tp) particularly offers itself, as the facial arrangement of three pyrazole donors is reminiscent of the three histidine-derived imidazole donors. The focus of this Account will be on bioinorganic/biomimetic research from our laboratory utilizing Tp ligands to develop molecular models for (i) two representatives of the (His)3Fe-enzyme family, namely, the cysteine dioxygenase (CDO) and acetyl acetone dioxygenase (Dke1), (ii) a related but less well-explored variant of the CDO-the 2-aminoethanethiol dioxygenase-as well as (iii) the 2-His-1-carboxylate representative 1-aminocyclopropane-1-carboxylic acid oxidase (ACCO). The CDO catalyzes the dioxygenation of cysteine with O2 to give cysteine sulfinic acid, which could be mimicked at TpFe units in a realistic manner. Furthermore, the successful dioxygenation of 2-aminoethanethiol at the same complex metal fragments lends further support to the hypothesis that the active sites of CDO and the one of 2-aminoethanethiol dioxygenase, whose structure is unknown, are quite similar. Dke1 is capable of cleaving diketones and ketoesters to give the corresponding carboxylic acids and α-keto aldehydes, and Tp-based models have achieved comparable C-C bond cleavage reactions. The ACCO develops ethylene from ACC in the course of oxidation, and recently this has been achieved the first time for a TpFe model, too.
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Affiliation(s)
- Madleen Sallmann
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Christian Limberg
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, 12489 Berlin, Germany
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