1
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Katoch A, Mandal D. Impact of carboxylate ligation on the C-H activation reactivity of a non-heme Fe(IV)O complex: a computational investigation. Dalton Trans 2024; 53:15264-15272. [PMID: 39222036 DOI: 10.1039/d4dt02139h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
A comprehensive DFT investigation has been presented to predict how a carboxylate-rich macrocycle would affect the reactivity of a non-heme Fe(IV)O complex towards C-H activation. The popular non-heme iron oxo complex [FeIV(O)(N4Py)]2+, (N4Py = N,N-(bis(2-pyridyl)methyl)N-bis(2-pyridylmethyl)amine) (1), has been selected here as the primary compound. It is transformed to the compound [FeIV(O)(nBu-P2DA)], where nBu-P2DA = N-(1',1'-bis(2-pyridyl)pentyl)iminodiacetate (2) after the replacement of two pyridine donors of N4Py with carboxylate groups. Two other complexes, namely 3 and 4, have been predicted sequentially substituting nitrogen with the carboxylate groups. Ethylbenzene and dihydrotoluene were chosen as substrates. In terms of C-H activation reactivity, an interesting pattern emerges: as the carboxylate group becomes more equatorially enriched, the reactivity increases, following the trend 1 < 2 < 3 < 4. This also aligns with available experimental reports related to complexes 1 and 2. Fe(IV)O complexes exhibit two-state reactivity (triplet and quintet), whereas the quintet state is more favourable due to the stabilization of the transition states through exchange interactions involving a greater number of unpaired electrons. A detailed analysis of the factors influencing reactivity has been performed, including distortion energy (which decreases for the transition state with the addition of carboxylate groups), the triplet-quintet oxidant energy gap (which consistently decreases as carboxylate group enrichment increases), steric factors, and quantum mechanical tunneling. This investigation provides a detailed explanation of the observed outcomes and predicts the higher reactivity of carboxylate-enriched Fe(IV)O complexes. After potential experimental verification, this could lead to the development of new, optimal catalysts for C-H activation.
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Affiliation(s)
- Akanksha Katoch
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala-147001, Punjab, India.
| | - Debasish Mandal
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala-147001, Punjab, India.
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2
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Krishnan A, Waheed SO, Melayikandy S, LaRouche C, Paik M, Schofield CJ, Karabencheva-Christova TG. Effects of Clinical Mutations in the Second Coordination Sphere and Remote Regions on the Catalytic Mechanism of Non-Heme Fe(II)/2-Oxoglutarate-Dependent Aspartyl Hydroxylase AspH. Chemphyschem 2024; 25:e202400303. [PMID: 38839574 DOI: 10.1002/cphc.202400303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/07/2024]
Abstract
Aspartyl/asparaginyl hydroxylase (AspH) catalyzes the post-translational hydroxylations of vital human proteins, playing an essential role in maintaining their biological functions. Single-point mutations in the Second Coordination Sphere (SCS) and long-range (LR) residues of AspH have been linked to pathological conditions such as the ophthalmologic condition Traboulsi syndrome and chronic kidney disease (CKD). Although the clinical impacts of these mutations are established, there is a critical knowledge gap regarding their specific atomistic effects on the catalytic mechanism of AspH. In this study, we report integrated computational investigations on the potential mechanistic implications of four mutant forms of human AspH with clinical importance: R735W, R735Q, R688Q, and G434V. All the mutant forms exhibited altered binding interactions with the co-substrate 2-oxoglutarate (2OG) and the main substrate in the ferric-superoxo and ferryl complexes, which are critical for catalysis, compared to the wild-type (WT). Importantly, the mutations strongly influence the energetics of the frontier molecular orbitals (FMOs) and, thereby, the activation energies for the hydrogen atom transfer (HAT) step compared to the WT AspH. Insights from our study can contribute to enzyme engineering and the development of selective modulators for WT and mutants of AspH, ultimately aiding in treating cancers, Traboulsi syndrome and, CKD.
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Affiliation(s)
- Anandhu Krishnan
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Sreerag Melayikandy
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Ciara LaRouche
- Department of Chemical Engineering, Michigan Techno, Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Meredith Paik
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, OX1 3TA, United Kingdom
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3
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Wenger ES, Martinie RJ, Ushimaru R, Pollock CJ, Sil D, Li A, Hoang N, Palowitch GM, Graham BP, Schaperdoth I, Burke EJ, Maggiolo AO, Chang WC, Allen BD, Krebs C, Silakov A, Boal AK, Bollinger JM. Optimized Substrate Positioning Enables Switches in the C-H Cleavage Site and Reaction Outcome in the Hydroxylation-Epoxidation Sequence Catalyzed by Hyoscyamine 6β-Hydroxylase. J Am Chem Soc 2024; 146:24271-24287. [PMID: 39172701 PMCID: PMC11374477 DOI: 10.1021/jacs.4c04406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Hyoscyamine 6β-hydroxylase (H6H) is an iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenase that produces the prolifically administered antinausea drug, scopolamine. After its namesake hydroxylation reaction, H6H then couples the newly installed C6 oxygen to C7 to produce the drug's epoxide functionality. Oxoiron(IV) (ferryl) intermediates initiate both reactions by cleaving C-H bonds, but it remains unclear how the enzyme switches the target site and promotes (C6)O-C7 coupling in preference to C7 hydroxylation in the second step. In one possible epoxidation mechanism, the C6 oxygen would─analogously to mechanisms proposed for the Fe/2OG halogenases and, in our more recent study, N-acetylnorloline synthase (LolO)─coordinate as alkoxide to the C7-H-cleaving ferryl intermediate to enable alkoxyl coupling to the ensuing C7 radical. Here, we provide structural and kinetic evidence that H6H does not employ substrate coordination or repositioning for the epoxidation step but instead exploits the distinct spatial dependencies of competitive C-H cleavage (C6 vs C7) and C-O-coupling (oxygen rebound vs cyclization) steps to promote the two-step sequence. Structural comparisons of ferryl-mimicking vanadyl complexes of wild-type H6H and a variant that preferentially 7-hydroxylates instead of epoxidizing 6β-hydroxyhyoscyamine suggest that a modest (∼10°) shift in the Fe-O-H(C7) approach angle is sufficient to change the outcome. The 7-hydroxylation:epoxidation partition ratios of both proteins increase more than 5-fold in 2H2O, reflecting an epoxidation-specific requirement for cleavage of the alcohol O-H bond, which, unlike in the LolO oxacyclization, is not accomplished by iron coordination in advance of C-H cleavage.
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Affiliation(s)
- Eliott S Wenger
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | - Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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4
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Hardy FJ, Quesne MG, Gérard EF, Zhao J, Ortmayer M, Taylor CJ, Ali HS, Slater JW, Levy CW, Heyes DJ, Bollinger JM, de Visser SP, Green AP. Probing Ferryl Reactivity in a Nonheme Iron Oxygenase Using an Expanded Genetic Code. ACS Catal 2024; 14:11584-11590. [PMID: 39114090 PMCID: PMC11301626 DOI: 10.1021/acscatal.4c02365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024]
Abstract
The ability to introduce noncanonical amino acids as axial ligands in heme enzymes has provided a powerful experimental tool for studying the structure and reactivity of their FeIV=O ("ferryl") intermediates. Here, we show that a similar approach can be used to perturb the conserved Fe coordination environment of 2-oxoglutarate (2OG) dependent oxygenases, a versatile class of enzymes that employ highly-reactive ferryl intermediates to mediate challenging C-H functionalizations. Replacement of one of the cis-disposed histidine ligands in the oxygenase VioC with a less electron donating N δ-methyl-histidine (MeHis) preserves both catalytic function and reaction selectivity. Significantly, the key ferryl intermediate responsible for C-H activation can be accumulated in both the wildtype and the modified protein. In contrast to heme enzymes, where metal-oxo reactivity is extremely sensitive to the nature of the proximal ligand, the rates of C-H activation and the observed large kinetic isotope effects are only minimally affected by axial ligand replacement in VioC. This study showcases a powerful tool for modulating the coordination sphere of nonheme iron enzymes that will enhance our understanding of the factors governing their divergent activities.
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Affiliation(s)
- Florence J. Hardy
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Matthew G. Quesne
- Research
Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Oxford, Didcot, Oxon OX11
0FA, U.K.
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K.
| | - Emilie F. Gérard
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Jingming Zhao
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Mary Ortmayer
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Christopher J. Taylor
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Hafiz S. Ali
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Jeffrey W. Slater
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Colin W. Levy
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Derren J. Heyes
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - J. Martin Bollinger
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sam P. de Visser
- Department
of Chemical Engineering & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Anthony P. Green
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
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5
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Kim S, Lee Y, Tripodi GL, Roithová J, Lee S, Cho J. Controlling Reactivity through Spin Manipulation: Steric Bulkiness of Peroxocobalt(III) Complexes. J Am Chem Soc 2024. [PMID: 39031334 DOI: 10.1021/jacs.4c03211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2024]
Abstract
The intrinsic relationship between spin states and reactivity in peroxocobalt(III) complexes was investigated, specifically focusing on the influence of steric modulation on supporting ligands. Together with the previously reported [CoIII(TBDAP)(O2)]+ (2Tb), which exhibits spin crossover characteristics, two peroxocobalt(III) complexes, [CoIII(MDAP)(O2)]+ (2Me) and [CoIII(ADDAP)(O2)]+ (2Ad), bearing pyridinophane ligands with distinct N-substituents such as methyl and adamantyl groups, were synthesized and characterized. By manipulating the steric bulkiness of the N-substituents, control of spin states in peroxocobalt(III) complexes was demonstrated through various physicochemical analyses. Notably, 2Ad oxidized the nitriles to generate hydroximatocobalt(III) complexes, while 2Me displayed an inability for such oxidation reactions. Furthermore, both 2Ad and 2Tb exhibited similarities in spectroscopic and geometric features, demonstrating spin crossover behavior between S = 0 and S = 1. The steric bulkiness of the adamantyl and tert-butyl group on the axial amines was attributed to inducing a weak ligand field on the cobalt(III) center. Thus, 2Ad and 2Tb are an S = 1 state under the reaction conditions. In contrast, the less bulky methyl group on the amines of 2Me resulted in an S = 0 state. The redox potential of the peroxocobalt(III) complexes was also influenced by the ligand field arising from the steric bulkiness of the N-substituents in the order of 2Me (-0.01 V) < 2Tb (0.29 V) = 2Ad (0.29 V). Theoretical calculations using DFT supported the experimental observations, providing insights into the electronic structure and emphasizing the importance of the spin state of peroxocobalt(III) complexes in nitrile activation.
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Affiliation(s)
- Seonghan Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Department of Emerging Materials Science, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Yuri Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Guilherme L Tripodi
- Department of Spectroscopy and Catalysis, Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen 6525 AJ, The Netherlands
| | - Jana Roithová
- Department of Spectroscopy and Catalysis, Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen 6525 AJ, The Netherlands
| | - Sunggi Lee
- Department of Emerging Materials Science, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Jaeheung Cho
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
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6
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Wen X, Ma Y, Chen J, Wang B. A synthetically useful catalytic system for aliphatic C-H oxidation with a nonheme cobalt complex and m-CPBA. Org Biomol Chem 2024; 22:5729-5733. [PMID: 38932595 DOI: 10.1039/d4ob00807c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
We report herein a synthetically useful catalytic system for aliphatic C-H oxidation with a mononuclear nonheme cobalt(II) complex and m-chloroperbenzoic acid (m-CPBA). Preliminary mechanistic studies suggest that a high-valent cobalt-oxygen species (e.g., cobalt(IV)-oxo or cobalt(III)-oxyl) is the oxidant that effects C-H oxidation via a rate-determining hydrogen atom abstraction (HAA) step.
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Affiliation(s)
- Xiang Wen
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China.
| | - Yidong Ma
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China.
| | - Jie Chen
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China.
| | - Bin Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China.
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7
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Pan J, Wenger ES, Lin CY, Zhang B, Sil D, Schaperdoth I, Saryazdi S, Grossman RB, Krebs C, Bollinger JM. An Unusual Ferryl Intermediate and Its Implications for the Mechanism of Oxacyclization by the Loline-Producing Iron(II)- and 2-Oxoglutarate-Dependent Oxygenase, LolO. Biochemistry 2024; 63:1674-1683. [PMID: 38898603 PMCID: PMC11219260 DOI: 10.1021/acs.biochem.4c00166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
N-Acetylnorloline synthase (LolO) is one of several iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases that catalyze sequential reactions of different types in the biosynthesis of valuable natural products. LolO hydroxylates C2 of 1-exo-acetamidopyrrolizidine before coupling the C2-bonded oxygen to C7 to form the tricyclic loline core. Each reaction requires cleavage of a C-H bond by an oxoiron(IV) (ferryl) intermediate; however, different carbons are targeted, and the carbon radicals have different fates. Prior studies indicated that the substrate-cofactor disposition (SCD) controls the site of H· abstraction and can affect the reaction outcome. These indications led us to determine whether a change in SCD from the first to the second LolO reaction might contribute to the observed reactivity switch. Whereas the single ferryl complex in the C2 hydroxylation reaction was previously shown to have typical Mössbauer parameters, one of two ferryl complexes to accumulate during the oxacyclization reaction has the highest isomer shift seen to date for such a complex and abstracts H· from C7 ∼ 20 times faster than does the first ferryl complex in its previously reported off-pathway hydroxylation of C7. The detectable hydroxylation of C7 in competition with cyclization by the second ferryl complex is not enhanced in 2H2O solvent, suggesting that the C2 hydroxyl is deprotonated prior to C7-H cleavage. These observations are consistent with the coordination of the C2 oxygen to the ferryl complex, which may reorient its oxo ligand, the substrate, or both to positions more favorable for C7-H cleavage and oxacyclization.
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Affiliation(s)
- Juan Pan
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: New England Biolabs, Ipswich, Massachusetts 01938, United States
| | - Eliott S. Wenger
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chi-Yun Lin
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Bo Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Debangsu Sil
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
| | - Irene Schaperdoth
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Engineering, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Setareh Saryazdi
- Department of Chemistry, The University of Kentucky, Lexington, Kentucky 40506, United States
- Present address: College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Robert B. Grossman
- Department of Chemistry, The University of Kentucky, Lexington, Kentucky 40506, United States
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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8
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Josephy T, Kumar R, Bleher K, Röhs F, Glaser T, Rajaraman G, Comba P. Synthesis, Characterization, and Reactivity of Bispidine-Iron(IV)-Tosylimido Species. Inorg Chem 2024; 63:12109-12119. [PMID: 38875304 DOI: 10.1021/acs.inorgchem.4c01237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
Reported are the synthesis and detailed studies of the iron(IV)-tosylimido complexes of two isomeric pentadentate bispidine ligands (bispidines are 3,7-diazabicyclo[3.3.1]nonane derivatives). This completes a series of five tosylimido complexes with comparable pentadentate amine/pyridine ligands, where the corresponding [(L)FeIV═O]2+ oxidants have been studied in detail. The characterization of the two new complexes in solution (UV-vis-NIR, Mössbauer, HR-ESI-MS) shows that these oxidants have an intermediate spin (S = 1) electronic ground state. The reactivities have been studied as oxidants in C-H activation at 1,3-cyclohexadiene and nitrogen atom transfer to thioanisole. For the latter substrate, the entire set of data for the five ligands and for both nitrogen and oxygen atom transfer is now available and the interesting observation is that oxygen atom transfer is, as expected, generally faster than nitrogen atom transfer, with the exception of the two ligands that have four and three pyridine groups oriented parallel to the Fe-O and Fe-N axes. A thorough DFT analysis indicates that this is due to steric effects in the case of the [(L)FeIV═O]2+ species, which are less important in the [(L)FeIV═NTs]2+ compounds due to partial electron transfer from the thioanisole substrate to the iron(IV)-tosylimido oxidant.
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Affiliation(s)
- Thomas Josephy
- Anorganisch-Chemisches Institut, Universität Heidelberg, INF 270,Heidelberg D-69120, Germany
| | - Ravi Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Katharina Bleher
- Anorganisch-Chemisches Institut, Universität Heidelberg, INF 270,Heidelberg D-69120, Germany
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen 76344, Germany
| | - Fridolin Röhs
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, Bielefeld D-33615, Germany
| | - Thorsten Glaser
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, Bielefeld D-33615, Germany
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Peter Comba
- Anorganisch-Chemisches Institut, Universität Heidelberg, INF 270,Heidelberg D-69120, Germany
- Interdisziplinäres Zentrum für Wissenschaftliches Rechnen (IWR), Universität Heidelberg, Heidelberg 69120, Germany
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9
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Xue S, Tang Y, Kurnikov IV, Liao HJ, Li J, Chan NL, Kurnikova MG, Chang WC, Guo Y. Spectroscopic and computational studies of a bifunctional iron- and 2-oxoglutarate dependent enzyme, AsqJ. Methods Enzymol 2024; 704:199-232. [PMID: 39300648 PMCID: PMC11415609 DOI: 10.1016/bs.mie.2024.05.023] [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] [Indexed: 09/22/2024]
Abstract
Iron and 2-oxoglutarate dependent (Fe/2OG) enzymes exhibit an exceedingly broad reaction repertoire. The most prevalent reactivity is hydroxylation, but many other reactivities have also been discovered in recent years, including halogenation, desaturation, epoxidation, endoperoxidation, epimerization, and cyclization. To fully explore the reaction mechanisms that support such a diverse reactivities in Fe/2OG enzyme, it is necessary to utilize a multi-faceted research methodology, consisting of molecular probe design and synthesis, in vitro enzyme assay development, enzyme kinetics, spectroscopy, protein crystallography, and theoretical calculations. By using such a multi-faceted research approach, we have explored reaction mechanisms of desaturation and epoxidation catalyzed by a bi-functional Fe/2OG enzyme, AsqJ. Herein, we describe the experimental protocols and computational workflows used in our studies.
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Affiliation(s)
- Shan Xue
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Yijie Tang
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Igor V Kurnikov
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Hsuan-Jen Liao
- Institute of Biochemistry and Molecular Biology, College of Medicine, National (Taiwan) University, Taipei, Taiwan
| | - Jikun Li
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Nei-Li Chan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National (Taiwan) University, Taipei, Taiwan.
| | - Maria G Kurnikova
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, United States.
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, NC, United States.
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, United States.
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10
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Rice DB, Wong D, Weyhermüller T, Neese F, DeBeer S. The spin-forbidden transition in iron(IV)-oxo catalysts relevant to two-state reactivity. SCIENCE ADVANCES 2024; 10:eado1603. [PMID: 38941457 PMCID: PMC11212722 DOI: 10.1126/sciadv.ado1603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/23/2024] [Indexed: 06/30/2024]
Abstract
Quintet oxoiron(IV) intermediates are often invoked in nonheme iron enzymes capable of performing selective oxidation, while most well-characterized synthetic model oxoiron(IV) complexes have a triplet ground state. These differing spin states lead to the proposal of a two-state reactivity model, where the complexes cross from the triplet to an excited quintet state. However, the energy of this quintet state has never been measured experimentally. Here, magnetic circular dichroism is used to assign the singlet and triplet excited states in a series of triplet oxoiron(IV) complexes. These transition energies are used to determine the energies of the quintet state via constrained fitting of 2p3d resonant inelastic x-ray scattering. This allowed for a direct correlation between the quintet energies and substrate C─H oxidation rates.
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Affiliation(s)
- Derek B. Rice
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
| | - Deniz Wong
- Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany
| | - Thomas Weyhermüller
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
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11
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Paris JC, Hei Cheung Y, Zhang T, Chang WC, Liu P, Guo Y. New Frontiers in Nonheme Enzymatic Oxyferryl Species. Chembiochem 2024:e202400307. [PMID: 38900645 DOI: 10.1002/cbic.202400307] [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: 04/04/2024] [Revised: 06/13/2024] [Accepted: 06/20/2024] [Indexed: 06/22/2024]
Abstract
Non-heme mononuclear iron dependent (NHM-Fe) enzymes exhibit exceedingly diverse catalytic reactivities. Despite their catalytic versatilities, the mononuclear iron centers in these enzymes show a relatively simple architecture, in which an iron atom is ligated with 2-4 amino acid residues, including histidine, aspartic or glutamic acid. In the past two decades, a common high-valent reactive iron intermediate, the S=2 oxyferryl (Fe(IV)-oxo or Fe(IV)=O) species, has been repeatedly discovered in NHM-Fe enzymes containing a 2-His-Fe or 2-His-1-carboxylate-Fe center. However, for 3-His/4-His-Fe enzymes, no common reactive intermediate has been identified. Recently, we have spectroscopically characterized the first S=1 Fe(IV) intermediate in a 3-His-Fe containing enzyme, OvoA, which catalyzes a novel oxidative carbon-sulfur bond formation. In this review, we summarize the broad reactivities demonstrated by S=2 Fe(IV)-oxo intermediates, the discovery of the first S=1 Fe(IV) intermediate in OvoA and the mechanistic implication of such a discovery, and the intrinsic reactivity differences of the S=2 and the S=1 Fe(IV)-oxo species. Finally, we postulate the possible reasons to utilize an S=1 Fe(IV) species in OvoA and their implications to other 3-His/4-His-Fe enzymes.
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Affiliation(s)
- Jared C Paris
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA, 15213, USA
| | - Yuk Hei Cheung
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA, 02215, USA
| | - Tao Zhang
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA, 02215, USA
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC, 27695, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA, 02215, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA, 15213, USA
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12
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Smithwick ER, Bhagi-Damodaran A, Damodaran AR. Equilibrium dialysis with HPLC detection to measure substrate binding affinity of a non-heme iron halogenase. Methods Enzymol 2024; 703:51-63. [PMID: 39261003 DOI: 10.1016/bs.mie.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Determination of substrate binding affinity (Kd) is critical to understanding enzyme function. An extensive number of methods have been developed and employed to study ligand/substrate binding, but the best approach depends greatly on the substrate and the enzyme in question. Below we describe how to measure the Kd of BesD, a non-heme iron halogenase, for its native substrate lysine using equilibrium dialysis coupled with High Performance Liquid Chromatography (HPLC) for subsequent detection. This method can be performed in anaerobic glove bag settings. It requires readily available HPLC instrumentation for ligand quantitation and is adaptable to meet the needs of a variety of substrate affinity measurements.
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Affiliation(s)
- Elizabeth R Smithwick
- Department of Chemistry, University of Minnesota - Twin Cities, Minneapolis, MN, United States
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota - Twin Cities, Minneapolis, MN, United States.
| | - Anoop Rama Damodaran
- Department of Chemistry, University of Minnesota - Twin Cities, Minneapolis, MN, United States.
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13
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Xu J, Hao J, Bu C, Meng Y, Xiao H, Zhang M, Li C. XMECP: Reaching State-of-the-Art MECP Optimization in Multiscale Complex Systems. J Chem Theory Comput 2024; 20:3590-3600. [PMID: 38651739 DOI: 10.1021/acs.jctc.4c00033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The Python-based program, XMECP, is developed for realizing robust, efficient, and state-of-the-art minimum energy crossing point (MECP) optimization in multiscale complex systems. This article introduces the basic capabilities of the XMECP program by theoretically investigating the MECP mechanism of several example systems including (1) the photosensitization mechanism of benzophenone, (2) photoinduced proton-coupled electron transfer in the cytosine-guanine base pair in DNA, (3) the spin-flip process in oxygen activation catalyzed by an iron-containing 2-oxoglutarate-dependent oxygenase (Fe/2OGX), and (4) the photochemical pathway of flavoprotein adjusted by the intensity of an external electric field. MECPs related to multistate reaction and multistate reactivity in large-scale complex biochemical systems can be well-treated by workflows suggested by the XMECP program. The branching plane updating the MECP optimization algorithm is strongly recommended as it provides derivative coupling vector (DCV) with explicit calculation and can equivalently evaluate contributions from non-QM residues to DCV, which can be nonadiabatic coupling or spin-orbit coupling in different cases. In the discussed QM/MM examples, we also found that the influence on the QM region by DCV can occur through noncovalent interactions and decay with distance. In the example of DNA base pairs, the nonadiabatic coupling occurs across the π-π stacking structure formed in the double-helix system. In contrast to general intuition, in the example of Fe/2OGX, the central ferrous and oxygen part contribute little to the spin-orbit coupling; however, a nearby arginine residue, which is treated by molecular mechanics in the QM/MM method, contributes significantly via two hydrogen bonds formed with α-ketoglutarate (α-KG). This indicates that the arginine residue plays a significant role in oxygen activation, driving the initial triplet state toward the productive quintet state, which is more than the previous knowledge that the arginine residue can bind α-KG at the reaction site by hydrogen bonds.
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Affiliation(s)
- Jiawei Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jian Hao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Caijie Bu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350117, Fujian, P. R. China
| | - Yajie Meng
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Han Xiao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
| | - Minyi Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
| | - Chunsen Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, Fujian, P. R. China
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14
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Cao Y, Hay S, de Visser SP. An Active Site Tyr Residue Guides the Regioselectivity of Lysine Hydroxylation by Nonheme Iron Lysine-4-hydroxylase Enzymes through Proton-Coupled Electron Transfer. J Am Chem Soc 2024; 146:11726-11739. [PMID: 38636166 PMCID: PMC11066847 DOI: 10.1021/jacs.3c14574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024]
Abstract
Lysine dioxygenase (KDO) is an important enzyme in human physiology involved in bioprocesses that trigger collagen cross-linking and blood pressure control. There are several KDOs in nature; however, little is known about the factors that govern the regio- and stereoselectivity of these enzymes. To understand how KDOs can selectively hydroxylate their substrate, we did a comprehensive computational study into the mechanisms and features of 4-lysine dioxygenase. In particular, we selected a snapshot from the MD simulation on KDO5 and created large QM cluster models (A, B, and C) containing 297, 312, and 407 atoms, respectively. The largest model predicts regioselectivity that matches experimental observation with rate-determining hydrogen atom abstraction from the C4-H position, followed by fast OH rebound to form 4-hydroxylysine products. The calculations show that in model C, the dipole moment is positioned along the C4-H bond of the substrate and, therefore, the electrostatic and electric field perturbations of the protein assist the enzyme in creating C4-H hydroxylation selectivity. Furthermore, an active site Tyr233 residue is identified that reacts through proton-coupled electron transfer akin to the axial Trp residue in cytochrome c peroxidase. Thus, upon formation of the iron(IV)-oxo species in the catalytic cycle, the Tyr233 phenol loses a proton to the nearby Asp179 residue, while at the same time, an electron is transferred to the iron to create an iron(III)-oxo active species. This charged tyrosyl residue directs the dipole moment along the C4-H bond of the substrate and guides the selectivity to the C4-hydroxylation of the substrate.
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Affiliation(s)
- Yuanxin Cao
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Sam Hay
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Chemical Engineering, The University
of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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15
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Hardy FG, Wong HPH, de Visser SP. Computational Study Into the Oxidative Ring-Closure Mechanism During the Biosynthesis of Deoxypodophyllotoxin. Chemistry 2024; 30:e202400019. [PMID: 38323740 DOI: 10.1002/chem.202400019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/08/2024]
Abstract
The nonheme iron dioxygenase deoxypodophyllotoxin synthase performs an oxidative ring-closure reaction as part of natural product synthesis in plants. How the enzyme enables the oxidative ring-closure reaction of (-)-yatein and avoids substrate hydroxylation remains unknown. To gain insight into the reaction mechanism and understand the details of the pathways leading to products and by-products we performed a comprehensive computational study. The work shows that substrate is bound tightly into the substrate binding pocket with the C7'-H bond closest to the iron(IV)-oxo species. The reaction proceeds through a radical mechanism starting with hydrogen atom abstraction from the C7'-H position followed by ring-closure and a final hydrogen transfer to form iron(II)-water and deoxypodophyllotoxin. Alternative mechanisms including substrate hydroxylation and an electron transfer pathway were explored but found to be higher in energy. The mechanism is guided by electrostatic perturbations of charged residues in the second-coordination sphere that prevent alternative pathways.
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Affiliation(s)
- Fintan G Hardy
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Henrik P H Wong
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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16
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Smithwick ER, Bhagi-Damodaran A, Damodaran AR. Equilibrium dialysis with HPLC detection to measure substrate binding affinity of a non-heme iron halogenase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.588023. [PMID: 38617253 PMCID: PMC11014511 DOI: 10.1101/2024.04.03.588023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Determination of substrate binding affinity (Kd) is critical to understanding enzyme function. An extensive number of methods have been developed and employed to study ligand/substrate binding, but the best approach depends greatly on the substrate and the enzyme in question. Below we describe how to measure the Kd of BesD, a non-heme iron halogenase, for its native substrate lysine using equilibrium dialysis with subsequent detection with High Performance Liquid Chromatography (HPLC). This method can be performed in anaerobic glove bag settings, requires readily available HPLC instrumentation for subsequent detection, and is adaptable to meet the needs of a variety of substrate affinity measurements.
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Affiliation(s)
- Elizabeth R. Smithwick
- Department of Chemistry, University of Minnesota -Twin Cities, 207 Pleasant St. SE. Minneapolis, MN 55455
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota -Twin Cities, 207 Pleasant St. SE. Minneapolis, MN 55455
| | - Anoop Rama Damodaran
- Department of Chemistry, University of Minnesota -Twin Cities, 207 Pleasant St. SE. Minneapolis, MN 55455
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17
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Cheung-Lee WL, Kolev JN, McIntosh JA, Gil AA, Pan W, Xiao L, Velásquez JE, Gangam R, Winston MS, Li S, Abe K, Alwedi E, Dance ZEX, Fan H, Hiraga K, Kim J, Kosjek B, Le DN, Marzijarani NS, Mattern K, McMullen JP, Narsimhan K, Vikram A, Wang W, Yan JX, Yang RS, Zhang V, Zhong W, DiRocco DA, Morris WJ, Murphy GS, Maloney KM. Engineering Hydroxylase Activity, Selectivity, and Stability for a Scalable Concise Synthesis of a Key Intermediate to Belzutifan. Angew Chem Int Ed Engl 2024; 63:e202316133. [PMID: 38279624 DOI: 10.1002/anie.202316133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
Biocatalytic oxidations are an emerging technology for selective C-H bond activation. While promising for a range of selective oxidations, practical use of enzymes catalyzing aerobic hydroxylation is presently limited by their substrate scope and stability under industrially relevant conditions. Here, we report the engineering and practical application of a non-heme iron and α-ketoglutarate-dependent dioxygenase for the direct stereo- and regio-selective hydroxylation of a non-native fluoroindanone en route to the oncology treatment belzutifan, replacing a five-step chemical synthesis with a direct enantioselective hydroxylation. Mechanistic studies indicated that formation of the desired product was limited by enzyme stability and product overoxidation, with these properties subsequently improved by directed evolution, yielding a biocatalyst capable of >15,000 total turnovers. Highlighting the industrial utility of this biocatalyst, the high-yielding, green, and efficient oxidation was demonstrated at kilogram scale for the synthesis of belzutifan.
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Affiliation(s)
| | - Joshua N Kolev
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - John A McIntosh
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Agnieszka A Gil
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Weilan Pan
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Li Xiao
- Modeling & Informatics, Discovery Chemistry, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Juan E Velásquez
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Rekha Gangam
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Matthew S Winston
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Shasha Li
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Kotoe Abe
- Chemical Commercialization Technologies, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Embarek Alwedi
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Zachary E X Dance
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Haiyang Fan
- API Process Research & Development (Biocatalysis), Shanghai STA Pharmaceutical Co., Ltd., Shanghai, 201507, China
| | - Kaori Hiraga
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Jungchul Kim
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Birgit Kosjek
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Diane N Le
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Keith Mattern
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Karthik Narsimhan
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Ajit Vikram
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Wei Wang
- API Process Research & Development (Biocatalysis), Shanghai STA Pharmaceutical Co., Ltd., Shanghai, 201507, China
| | - Jia-Xuan Yan
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Rong-Sheng Yang
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Victoria Zhang
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Wendy Zhong
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Daniel A DiRocco
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - William J Morris
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Grant S Murphy
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Kevin M Maloney
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
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18
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Vennelakanti V, Jeon M, Kulik HJ. How Do Differences in Electronic Structure Affect the Use of Vanadium Intermediates as Mimics in Nonheme Iron Hydroxylases? Inorg Chem 2024; 63:4997-5011. [PMID: 38428015 DOI: 10.1021/acs.inorgchem.3c04421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
We study active-site models of nonheme iron hydroxylases and their vanadium-based mimics using density functional theory to determine if vanadyl is a faithful structural mimic. We identify crucial structural and energetic differences between ferryl and vanadyl isomers owing to the differences in their ground electronic states, i.e., high spin (HS) for Fe and low spin (LS) for V. For the succinate cofactor bound to the ferryl intermediate, we predict facile interconversion between monodentate and bidentate coordination isomers for ferryl species but difficult rearrangement for vanadyl mimics. We study isomerization of the oxo intermediate between axial and equatorial positions and find the ferryl potential energy surface to be characterized by a large barrier of ca. 10 kcal/mol that is completely absent for the vanadyl mimic. This analysis reveals even starker contrasts between Fe and V in hydroxylases than those observed for this metal substitution in nonheme halogenases. Analysis of the relative bond strengths of coordinating carboxylate ligands for Fe and V reveals that all of the ligands show stronger binding to V than Fe owing to the LS ground state of V in contrast to the HS ground state of Fe, highlighting the limitations of vanadyl mimics of native nonheme iron hydroxylases.
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Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mugyeom Jeon
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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19
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Krishnan A, Waheed SO, Varghese A, Cherilakkudy FH, Schofield CJ, Karabencheva-Christova TG. Unusual catalytic strategy by non-heme Fe(ii)/2-oxoglutarate-dependent aspartyl hydroxylase AspH. Chem Sci 2024; 15:3466-3484. [PMID: 38455014 PMCID: PMC10915816 DOI: 10.1039/d3sc05974j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
Biocatalytic C-H oxidation reactions are of important synthetic utility, provide a sustainable route for selective synthesis of important organic molecules, and are an integral part of fundamental cell processes. The multidomain non-heme Fe(ii)/2-oxoglutarate (2OG) dependent oxygenase AspH catalyzes stereoselective (3R)-hydroxylation of aspartyl- and asparaginyl-residues. Unusually, compared to other 2OG hydroxylases, crystallography has shown that AspH lacks the carboxylate residue of the characteristic two-His-one-Asp/Glu Fe-binding triad. Instead, AspH has a water molecule that coordinates Fe(ii) in the coordination position usually occupied by the Asp/Glu carboxylate. Molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) studies reveal that the iron coordinating water is stabilized by hydrogen bonding with a second coordination sphere (SCS) carboxylate residue Asp721, an arrangement that helps maintain the six coordinated Fe(ii) distorted octahedral coordination geometry and enable catalysis. AspH catalysis follows a dioxygen activation-hydrogen atom transfer (HAT)-rebound hydroxylation mechanism, unusually exhibiting higher activation energy for rebound hydroxylation than for HAT, indicating that the rebound step may be rate-limiting. The HAT step, along with substrate positioning modulated by the non-covalent interactions with SCS residues (Arg688, Arg686, Lys666, Asp721, and Gln664), are essential in determining stereoselectivity, which likely proceeds with retention of configuration. The tetratricopeptide repeat (TPR) domain of AspH influences substrate binding and manifests dynamic motions during catalysis, an observation of interest with respect to other 2OG oxygenases with TPR domains. The results provide unique insights into how non-heme Fe(ii) oxygenases can effectively catalyze stereoselective hydroxylation using only two enzyme-derived Fe-ligating residues, potentially guiding enzyme engineering for stereoselective biocatalysis, thus advancing the development of non-heme Fe(ii) based biomimetic C-H oxidation catalysts, and supporting the proposal that the 2OG oxygenase superfamily may be larger than once perceived.
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Affiliation(s)
- Anandhu Krishnan
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Ann Varghese
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | | | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford OX1 3TA Oxford UK
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20
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Amaya JA, Manley OM, Bian JC, Rutland CD, Leschinsky N, Ratigan SC, Makris TM. Enhancing ferryl accumulation in H 2O 2-dependent cytochrome P450s. J Inorg Biochem 2024; 252:112458. [PMID: 38141432 DOI: 10.1016/j.jinorgbio.2023.112458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/08/2023] [Accepted: 12/16/2023] [Indexed: 12/25/2023]
Abstract
A facile strategy is presented to enhance the accumulation of ferryl (iron(IV)-oxo) species in H2O2 dependent cytochrome P450s (CYPs) of the CYP152 family. We report the characterization of a highly chemoselective CYP decarboxylase from Staphylococcus aureus (OleTSA) that is soluble at high concentrations. Examination of OleTSA Compound I (CpdI) accumulation with a variety of fatty acid substrates reveals a dependence on resting spin-state equilibrium. Alteration of this equilibrium through targeted mutagenesis of the proximal pocket favors the high-spin form, and as a result, enhances Cpd-I accumulation to nearly stoichiometric yields.
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Affiliation(s)
- Jose A Amaya
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America
| | - Olivia M Manley
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America; Department of Structural and Molecular Biochemistry, North Carolina State University, Raleigh, NC 27695, United States of America
| | - Julia C Bian
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America
| | - Cooper D Rutland
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America
| | - Nicholas Leschinsky
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America
| | - Steven C Ratigan
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America
| | - Thomas M Makris
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America; Department of Structural and Molecular Biochemistry, North Carolina State University, Raleigh, NC 27695, United States of America; Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States of America.
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21
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Lionetti D, Suseno S, Shiau AA, de Ruiter G, Agapie T. Redox Processes Involving Oxygen: The Surprising Influence of Redox-Inactive Lewis Acids. JACS AU 2024; 4:344-368. [PMID: 38425928 PMCID: PMC10900226 DOI: 10.1021/jacsau.3c00675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 03/02/2024]
Abstract
Metalloenzymes with heteromultimetallic active sites perform chemical reactions that control several biogeochemical cycles. Transformations catalyzed by such enzymes include dioxygen generation and reduction, dinitrogen reduction, and carbon dioxide reduction-instrumental transformations for progress in the context of artificial photosynthesis and sustainable fertilizer production. While the roles of the respective metals are of interest in all these enzymatic transformations, they share a common factor in the transfer of one or multiple redox equivalents. In light of this feature, it is surprising to find that incorporation of redox-inactive metals into the active site of such an enzyme is critical to its function. To illustrate, the presence of a redox-inactive Ca2+ center is crucial in the Oxygen Evolving Complex, and yet particularly intriguing given that the transformation catalyzed by this cluster is a redox process involving four electrons. Therefore, the effects of redox inactive metals on redox processes-electron transfer, oxygen- and hydrogen-atom transfer, and O-O bond cleavage and formation reactions-mediated by transition metals have been studied extensively. Significant effects of redox inactive metals have been observed on these redox transformations; linear free energy correlations between Lewis acidity and the redox properties of synthetic model complexes are observed for several reactions. In this Perspective, these effects and their relevance to multielectron processes will be discussed.
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Affiliation(s)
| | - Sandy Suseno
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, 1200 East California Boulevard, MC 127-72, Pasadena, California 91125, United States
| | - Angela A. Shiau
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, 1200 East California Boulevard, MC 127-72, Pasadena, California 91125, United States
| | - Graham de Ruiter
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, 1200 East California Boulevard, MC 127-72, Pasadena, California 91125, United States
| | - Theodor Agapie
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, 1200 East California Boulevard, MC 127-72, Pasadena, California 91125, United States
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22
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Monkcom EC, Gómez L, Lutz M, Ye S, Bill E, Costas M, Klein Gebbink RJM. Synthesis, Structure and Reactivity of a Mononuclear N,N,O-Bound Fe(II) α-Keto-Acid Complex. Chemistry 2024; 30:e202302710. [PMID: 37882223 DOI: 10.1002/chem.202302710] [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: 08/18/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 10/27/2023]
Abstract
A bulky, tridentate phenolate ligand (ImPh2 NNOtBu ) was used to synthesise the first example of a mononuclear, facial, N,N,O-bound iron(II) benzoylformate complex, [Fe(ImPh2 NNOtBu )(BF)] (2). The X-ray crystal structure of 2 reveals that the iron centre is pentacoordinate (τ=0.5), with a vacant site located cis to the bidentate BF ligand. The Mössbauer parameters of 2 are consistent with high-spin iron(II), and are very close to those reported for α-ketoglutarate-bound non-heme iron enzyme active sites. According to NMR and UV-vis spectroscopies, the structural integrity of 2 is retained in both coordinating and non-coordinating solvents. Cyclic voltammetry studies show that the iron centre has a very low oxidation potential and is more prone to electrochemical oxidation than the redox-active phenolate ligand. Complex 2 reacts with NO to form a S=3 /2 {FeNO}7 adduct in which NO binds directly to the iron centre, according to EPR, UV-vis, IR spectroscopies and DFT analysis. Upon O2 exposure, 2 undergoes oxidative decarboxylation to form a diiron(III) benzoate complex, [Fe2 (ImPh2 NNOtBu )2 (μ2 -OBz)(μ2 -OH)2 ]+ (3). A small amount of hydroxylated ligand was also observed by ESI-MS, hinting at the formation of a high-valent iron(IV)-oxo intermediate. Initial reactivity studies show that 2 is capable of oxygen atom transfer reactivity with O2 , converting methyl(p-tolyl)sulfide to sulfoxide.
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Affiliation(s)
- Emily C Monkcom
- Organic Chemistry and Catalysis, Institute for Sustainable and Circular Chemistry, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Laura Gómez
- Serveis Tècnics de Recerca, Universitat de Girona, Pic de Peguera 15, Parc Cientific, 17003, Girona, Spain
| | - Martin Lutz
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Shengfa Ye
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, 45470, Mülheim an der Ruhr, Germany
| | - Miquel Costas
- Institut de Química Computacional i Catàlisi, Universitat de Girona, Pic de Peguera 15, Parc Cientific, 17003, Girona, Spain
| | - Robertus J M Klein Gebbink
- Organic Chemistry and Catalysis, Institute for Sustainable and Circular Chemistry, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
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23
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Toubiana LA, Valaydon-Pillay A, Elinburg JK, Bacon JW, Ozarowski A, Doerrer LH, Stoian SA. Spectroscopic and Theoretical Investigation of High-Spin Square-Planar and Trigonal Fe(II) Complexes Supported by Fluorinated Alkoxides. Inorg Chem 2024; 63:2370-2387. [PMID: 38259134 DOI: 10.1021/acs.inorgchem.3c03236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The electronic structures and spectroscopic behavior of three high-spin FeII complexes of fluorinated alkoxides were studied: square-planar {K(DME)2}2[Fe(pinF)2] (S) and quasi square-planar {K(C222)}2[Fe(pinF)2] (S') and trigonal-planar {K(18C6)}[Fe(OC4F9)3] (T) where pinF = perfluoropinacolate and OC4F9 = tris-perfluoro-t-butoxide. The zero-field splitting (ZFS) and hyperfine structure parameters of the S = 2 ground states were determined using field-dependent 57Fe Mössbauer and high-field and -frequency electron paramagnetic resonance (HFEPR) spectroscopies. The spin Hamiltonian parameters were analyzed with crystal field theory and corroborated by density functional theory (DFT) and ab initio complete active space self-consistent field (CASSCF) calculations. Whereas the ZFS tensor of S has a small rhombicity, E/D = 0.082, and a positive D = 15.17 cm-1, T exhibits a negative D = -9.16 cm-1 and a large rhombicity, E/D = 0.246. Computational investigation of the structural factors suggests that the ground-state electronic configuration and geometry of T's Fe site are determined by the interaction of [Fe(OC4F9)3]- with {K(18C6)}+. In contrast, two distinct countercations of S/S' have a negligible influence on their [Fe(pinF)2]2- moieties. Instead, the distortions in S' are likely induced by the chelate ring conformation change from δλ, observed for S, to the δδ conformation, determined for S'.
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Affiliation(s)
- Léa A Toubiana
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Adam Valaydon-Pillay
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844, United States
| | - Jessica K Elinburg
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Jeffrey W Bacon
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Andrew Ozarowski
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Linda H Doerrer
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Sebastian A Stoian
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844, United States
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24
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Kumar R, Ansari A, Comba P, Rajaraman G. Rebound or Cage Escape? The Role of the Rebound Barrier for the Reactivity of Non-Heme High-Valent Fe IV =O Species. Chemistry 2024; 30:e202303300. [PMID: 37929771 DOI: 10.1002/chem.202303300] [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: 10/09/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/07/2023]
Abstract
Owing to their high reactivity and selectivity, variations in the spin ground state and a range of possible pathways, high-valent FeIV =O species are popular models with potential bioinspired applications. An interesting example of a structure-reactivity pattern is the detailed study with five nonheme amine-pyridine pentadentate ligand FeIV =O species, including N4py: [(L1 )FeIV =O]2+ (1), bntpen: [(L2 )FeIV =O]2+ (2), py2 tacn: [(L3 )FeIV =O]2+ (3), and two isomeric bispidine derivatives: [(L4 )FeIV =O]2+ (4) and [(L5 )FeIV =O]2+ (5). In this set, the order of increasing reactivity in the hydroxylation of cyclohexane differs from that with cyclohexadiene as substrate. A comprehensive DFT, ab initio CASSCF/NEVPT2 and DLPNO-CCSD(T) study is presented to untangle the observed patterns. These are well reproduced when both activation barriers for the C-H abstraction and the OH rebound are taken into account. An MO, NBO and deformation energy analysis reveals the importance of π(pyr) → π*xz (FeIII -OH) electron donation for weakening the FeIII -OH bond and thus reducing the rebound barrier. This requires that pyridine rings are oriented perpendicularly to the FeIII -OH bond and this is a subtle but crucial point in ligand design for non-heme iron alkane hydroxylation.
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Affiliation(s)
- Ravi Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Powai, 400076, India
| | - Azaj Ansari
- Department of Chemistry, Central University of Haryana, Haryana, 123031, India
| | - Peter Comba
- Institute of Inorganic Chemistry &, Interdisciplinary Center for Scientific Computing, Heidelberg University, 69120, Heidelberg, Germany
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Powai, 400076, India
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25
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Jeong D, Kim K, Lee Y, Cho J. Synthetic Advances for Mechanistic Insights: Metal-Oxygen Intermediates with a Macrocyclic Pyridinophane System. Acc Chem Res 2024; 57:120-130. [PMID: 38110355 DOI: 10.1021/acs.accounts.3c00582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
ConspectusMetalloenzymes, which are proteins containing earth-abundant transition-metal ions as cofactors in the active site, generate various metal-oxygen intermediates via activating a dioxygen molecule (O2) to mediate vital metabolic functions, such as the oxidative metabolism of xenobiotics and the biotransformation of naturally occurring molecules. By replicating the active sites of metalloenzymes, many bioinorganic chemists have studied the geometric and electronic properties and reactivities of model complexes to understand the nature of enzymatic intermediates and develop bioinspired metal catalysts. Among the reported model complexes, nonporphyrinic macrocyclic ligands are the predominant coordination system widely used in stabilizing and isolating diverse metal-oxygen intermediates, which allows us to extensively investigate the physicochemical characteristics of the analogs of reactive intermediates of metalloenzymes. In particular, it has been reported that the ring size of the macrocyclic ligands, defined by the number of atoms in the macrocyclic ring, drastically affects the identity of the metal-oxygen intermediate. Thus, systematic modification of the macrocyclic ligands has been a great subject being examined in various inorganic fields.In this Account, we describe synthetic advances of a macrocyclic ligand system by introducing pyridine donors into a 12-membered tetraazamacrocyclic ligand (12-TMC) that initially has 4 amine donors. Interestingly, the backbone of the pyridinophane ligand with 2 pyridine and 2 amine donors in a 12-membered ring is shown to be much more folded than in other macrocyclic ligands, thereby allowing the axial and equatorial donors to separately control the electronic structure of metal complexes. Then, we looked over independent electronic and steric effects on metal-oxygen species with thorough physicochemical analysis. The NiIII-peroxo complexes exhibit nucleophilic reactivity dependent on the steric hindrance of the second coordination sphere. Furthermore, the C-H bond strength of the second coordination sphere has also been an important factor in determining the stability of MnIV-bis(hydroxo) intermediates. Electronic tuning on CoIII-hydroperoxo intermediates results in a trend between the electron-donating abilities of para-substituents on pyridine in the pyridinophane ligand and electrophilic reactivities, from which mechanistic insights into the metal-hydroperoxo species have been gained. Importantly, the metal-oxygen intermediates supported by the pyridinophane ligand system have revealed quite challenging chemical reactions, including dioxygenase-like nitrile activation by CoIII-peroxo intermediates and the oxidation of aldehyde and aromatic compounds by manganese-oxygen intermediates. Based on the fine substitution of donors, we have addressed that those novel reactions originated from the unique framework of the pyridinophane system incorporating spin-crossover behavior and high redox potentials of the metal-oxygen intermediates. These results will be valuable for the structure-activity relationship of metal-oxygen intermediates, giving a better understanding on the enzymatic coordination system where amino acid ligands vary for specific chemical reactions.
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Affiliation(s)
- Donghyun Jeong
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Kyungmin Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yujeong Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jaeheung Cho
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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26
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Vennelakanti V, Li GL, Kulik HJ. Why Nonheme Iron Halogenases Do Not Fluorinate C-H Bonds: A Computational Investigation. Inorg Chem 2023; 62:19758-19770. [PMID: 37972340 DOI: 10.1021/acs.inorgchem.3c03215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Selective halogenation is necessary for a range of fine chemical applications, including the development of therapeutic drugs. While synthetic processes to achieve C-H halogenation require harsh conditions, enzymes such as nonheme iron halogenases carry out some types of C-H halogenation, i.e., chlorination or bromination, with ease, while others, i.e., fluorination, have never been observed in natural or engineered nonheme iron enzymes. Using density functional theory and correlated wave function theory, we investigate the differences in structural and energetic preferences of the smaller fluoride and the larger chloride or bromide intermediates throughout the catalytic cycle. Although we find that the energetics of rate-limiting hydrogen atom transfer are not strongly impacted by fluoride substitution, the higher barriers observed during the radical rebound reaction for fluoride relative to chloride and bromide contribute to the difficulty of C-H fluorination. We also investigate the possibility of isomerization playing a role in differences in reaction selectivity, and our calculations reveal crucial differences in terms of isomer energetics of the key ferryl intermediate between fluoride and chloride/bromide intermediates. While formation of monodentate isomers believed to be involved in selective catalysis is shown for chloride and bromide intermediates, we find that formation of the fluoride monodentate intermediate is not possible in our calculations, which lack additional stabilizing interactions with the greater protein environment. Furthermore, the shorter Fe-F bonds are found to increase isomerization reaction barriers, suggesting that incorporation of residues that form a halogen bond with F and elongate Fe-F bonds could make selective C-H fluorination possible in nonheme iron halogenases. Our work highlights the differences between the fluoride and chloride/bromide intermediates and suggests potential steps toward engineering nonheme iron halogenases to enable selective C-H fluorination.
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Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Grace L Li
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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27
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Rao J, Dong S, Yang C, Liu Q, Leng X, Wang D, Zhu J, Deng L. A Triplet Iron Carbyne Complex. J Am Chem Soc 2023; 145:25766-25775. [PMID: 37971755 DOI: 10.1021/jacs.3c09280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Tuning the spin state of metal carbynes, which have broad applications in organic synthesis and material science, presents a formidable challenge for modern chemists as the strong field nature of carbyne ligands dictates low-spin ground spin states (S = 0 or 1/2) for known metal carbynes. Through the oxidative addition reaction of a low-coordinate iron(0) N-heterocyclic carbene complex with the C-S bond of a thioazole-2-ylidene, we synthesized the first triplet (S = 1) metal terminal carbyne, an iron cyclic carbyne complex. Different from the classical metal carbynes, the triplet complex features an LXZ-type carbyne ligand and a weak Fe≡C triple bond, which endow it with the unique reactivity pattern of facile carbyne coupling, weak affinity toward nucleophiles, and facial addition reactions with electrophiles.
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Affiliation(s)
- Jiahao Rao
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Shicheng Dong
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chengbo Yang
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Qing Liu
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xuebing Leng
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Dongyang Wang
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Jun Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Liang Deng
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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28
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Antolini C, Jacoby DJ, Tiano SM, Otolski CJ, Doumy G, March AM, Walko DA, Goodwill JE, Hayes D. Ten-Fold Solvent Kinetic Isotope Effect for the Nonradiative Relaxation of the Aqueous Ferrate(VI) Ion. J Phys Chem A 2023. [PMID: 38029389 DOI: 10.1021/acs.jpca.3c06042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Hypervalent iron intermediates have been invoked in the catalytic cycles of many metalloproteins, and thus, it is crucial to understand how the coupling between such species and their environment can impact their chemical and physical properties in such contexts. In this work, we take advantage of the solvent kinetic isotope effect (SKIE) to gain insight into the nonradiative deactivation of electronic excited states of the aqueous ferrate(VI) ion. We observe an exceptionally large SKIE of 9.7 for the nanosecond-scale relaxation of the lowest energy triplet ligand field state to the ground state. Proton inventory studies demonstrate that a single solvent O-H bond is coupled to the ion during deactivation, likely due to the sparse vibrational structure of ferrate(VI). Such a mechanism is consistent with that reported for the deactivation of f-f excited states of aqueous trivalent lanthanides, which exhibit comparably large SKIE values. This phenomenon is ascribed entirely to dissipation of energy into a higher overtone of a solvent acceptor mode, as any impact on the apparent relaxation rate due to a change in solvent viscosity is negligible.
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Affiliation(s)
- Cali Antolini
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Danielle J Jacoby
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Sophia M Tiano
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Christopher J Otolski
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Gilles Doumy
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Anne Marie March
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Donald A Walko
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Joseph E Goodwill
- Department of Civil and Environmental Engineering, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Dugan Hayes
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
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29
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Ushimaru R, Cha L, Shimo S, Li X, Paris JC, Mori T, Miyamoto K, Coffer L, Uchiyama M, Guo Y, Chang WC, Abe I. Mechanistic Analysis of Stereodivergent Nitroalkane Cyclopropanation Catalyzed by Nonheme Iron Enzymes. J Am Chem Soc 2023; 145:24210-24217. [PMID: 37874539 PMCID: PMC10725191 DOI: 10.1021/jacs.3c08413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
BelL and HrmJ are α-ketoglutarate-dependent nonheme iron enzymes that catalyze the oxidative cyclization of 6-nitronorleucine, resulting in the formation of two diastereomeric 3-(2-nitrocyclopropyl)alanine (Ncpa) products containing trans-cyclopropane rings with (1'R,2'R) and (1'S,2'S) configurations, respectively. Herein, we investigate the catalytic mechanism and stereodivergency of the cyclopropanases. The results suggest that the nitroalkane moiety of the substrate is first deprotonated to produce the nitronate form. Spectroscopic analyses and biochemical assays with substrates and analogues indicate that an iron(IV)-oxo species abstracts proS-H from C4 to initiate intramolecular C-C bond formation. A hydroxylation intermediate is unlikely to be involved in the cyclopropanation reaction. Additionally, a genome mining approach is employed to discover new homologues that perform the cyclopropanation of 6-nitronorleucine to generate cis-configured Ncpa products with (1'R,2'S) or (1'S,2'R) stereochemistries. Sequence and structure comparisons of these cyclopropanases enable us to determine the amino acid residues critical for controlling the stereoselectivity of cyclopropanation.
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Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Lide Cha
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Shotaro Shimo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Xiaojun Li
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Jared C Paris
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Kazunori Miyamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Lindsay Coffer
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Research Initiative for Supra-Materials, Shinshu University, Nagano 380-8553, Japan
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
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30
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Hou K, Börgel J, Jiang HZH, SantaLucia DJ, Kwon H, Zhuang H, Chakarawet K, Rohde RC, Taylor JW, Dun C, Paley MV, Turkiewicz AB, Park JG, Mao H, Zhu Z, Alp EE, Zhao J, Hu MY, Lavina B, Peredkov S, Lv X, Oktawiec J, Meihaus KR, Pantazis DA, Vandone M, Colombo V, Bill E, Urban JJ, Britt RD, Grandjean F, Long GJ, DeBeer S, Neese F, Reimer JA, Long JR. Reactive high-spin iron(IV)-oxo sites through dioxygen activation in a metal-organic framework. Science 2023; 382:547-553. [PMID: 37917685 DOI: 10.1126/science.add7417] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/24/2023] [Indexed: 11/04/2023]
Abstract
In nature, nonheme iron enzymes use dioxygen to generate high-spin iron(IV)=O species for a variety of oxygenation reactions. Although synthetic chemists have long sought to mimic this reactivity, the enzyme-like activation of O2 to form high-spin iron(IV) = O species remains an unrealized goal. Here, we report a metal-organic framework featuring iron(II) sites with a local structure similar to that in α-ketoglutarate-dependent dioxygenases. The framework reacts with O2 at low temperatures to form high-spin iron(IV) = O species that are characterized using in situ diffuse reflectance infrared Fourier transform, in situ and variable-field Mössbauer, Fe Kβ x-ray emission, and nuclear resonance vibrational spectroscopies. In the presence of O2, the framework is competent for catalytic oxygenation of cyclohexane and the stoichiometric conversion of ethane to ethanol.
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Affiliation(s)
- Kaipeng Hou
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jonas Börgel
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Henry Z H Jiang
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Daniel J SantaLucia
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
| | - Hyunchul Kwon
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Hao Zhuang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA
| | | | - Rachel C Rohde
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Jordan W Taylor
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Chaochao Dun
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Maria V Paley
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ari B Turkiewicz
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Jesse G Park
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Haiyan Mao
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Ziting Zhu
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA
| | - E Ercan Alp
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Barbara Lavina
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA
| | - Sergey Peredkov
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
| | - Xudong Lv
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Julia Oktawiec
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Katie R Meihaus
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | | | - Marco Vandone
- Department of Chemistry, University of Milan, 20133 Milan, Italy
| | - Valentina Colombo
- Department of Chemistry, University of Milan, 20133 Milan, Italy
- Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), UdR Milano, Via Golgi 19, 20133 Milano, Italy
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
| | - Jeffrey J Urban
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - R David Britt
- Department of Chemistry, University of California, Davis, CA 95616, USA
- Miller Institute for Basic Research in Science, University of California, Berkeley CA 94720, USA
| | - Fernande Grandjean
- Department of Chemistry, Missouri University of Science and Technology, University of Missouri, Rolla, MO 65409, USA
| | - Gary J Long
- Department of Chemistry, Missouri University of Science and Technology, University of Missouri, Rolla, MO 65409, USA
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
| | - Jeffrey A Reimer
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Jeffrey R Long
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
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31
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Paris JC, Hu S, Wen A, Weitz AC, Cheng R, Gee LB, Tang Y, Kim H, Vegas A, Chang WC, Elliott SJ, Liu P, Guo Y. An S=1 Iron(IV) Intermediate Revealed in a Non-Heme Iron Enzyme-Catalyzed Oxidative C-S Bond Formation. Angew Chem Int Ed Engl 2023; 62:e202309362. [PMID: 37640689 PMCID: PMC10592081 DOI: 10.1002/anie.202309362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/11/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
Ergothioneine (ESH) and ovothiol A (OSHA) are two natural thiol-histidine derivatives. ESH has been implicated as a longevity vitamin and OSHA inhibits the proliferation of hepatocarcinoma. The key biosynthetic step of ESH and OSHA in the aerobic pathways is the O2 -dependent C-S bond formation catalyzed by non-heme iron enzymes (e.g., OvoA in ovothiol biosynthesis), but due to the lack of identification of key reactive intermediate the mechanism of this novel reaction is unresolved. In this study, we report the identification and characterization of a kinetically competent S=1 iron(IV) intermediate supported by a four-histidine ligand environment (three from the protein residues and one from the substrate) in enabling C-S bond formation in OvoA from Methyloversatilis thermotoleran, which represents the first experimentally observed intermediate spin iron(IV) species in non-heme iron enzymes. Results reported in this study thus set the stage to further dissect the mechanism of enzymatic oxidative C-S bond formation in the OSHA biosynthesis pathway. They also afford new opportunities to study the structure-function relationship of high-valent iron intermediates supported by a histidine rich ligand environment.
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Affiliation(s)
- Jared C Paris
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA 15213, USA
| | - Sha Hu
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Aiwen Wen
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Andrew C Weitz
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Ronghai Cheng
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Leland B Gee
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA
| | - Yijie Tang
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA 15213, USA
| | - Hyomin Kim
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Arturo Vegas
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Sean J Elliott
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA 15213, USA
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32
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Yamaguchi K, Isobe H, Shoji M, Kawakami T, Miyagawa K. The Nature of the Chemical Bonds of High-Valent Transition-Metal Oxo (M=O) and Peroxo (MOO) Compounds: A Historical Perspective of the Metal Oxyl-Radical Character by the Classical to Quantum Computations. Molecules 2023; 28:7119. [PMID: 37894598 PMCID: PMC10609222 DOI: 10.3390/molecules28207119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
This review article describes a historical perspective of elucidation of the nature of the chemical bonds of the high-valent transition metal oxo (M=O) and peroxo (M-O-O) compounds in chemistry and biology. The basic concepts and theoretical backgrounds of the broken-symmetry (BS) method are revisited to explain orbital symmetry conservation and orbital symmetry breaking for the theoretical characterization of four different mechanisms of chemical reactions. Beyond BS methods using the natural orbitals (UNO) of the BS solutions, such as UNO CI (CC), are also revisited for the elucidation of the scope and applicability of the BS methods. Several chemical indices have been derived as the conceptual bridges between the BS and beyond BS methods. The BS molecular orbital models have been employed to explain the metal oxyl-radical character of the M=O and M-O-O bonds, which respond to their radical reactivity. The isolobal and isospin analogy between carbonyl oxide R2C-O-O and metal peroxide LFe-O-O has been applied to understand and explain the chameleonic chemical reactivity of these compounds. The isolobal and isospin analogy among Fe=O, O=O, and O have also provided the triplet atomic oxygen (3O) model for non-heme Fe(IV)=O species with strong radical reactivity. The chameleonic reactivity of the compounds I (Cpd I) and II (Cpd II) is also explained by this analogy. The early proposals obtained by these theoretical models have been examined based on recent computational results by hybrid DFT (UHDFT), DLPNO CCSD(T0), CASPT2, and UNO CI (CC) methods and quantum computing (QC).
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Affiliation(s)
- Kizashi Yamaguchi
- SANKEN, Osaka University, Ibaraki 567-0047, Osaka, Japan
- Center for Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka 560-0043, Osaka, Japan
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Okayama, Japan;
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan; (M.S.); (K.M.)
| | - Takashi Kawakami
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka 560-0043, Osaka, Japan;
| | - Koichi Miyagawa
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan; (M.S.); (K.M.)
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33
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Sen A, Ansari A, Swain A, Pandey B, Rajaraman G. Probing the Origins of Puzzling Reactivity in Fe/Mn-Oxo/Hydroxo Species toward C-H Bonds: A DFT and Ab Initio Perspective. Inorg Chem 2023; 62:14931-14941. [PMID: 37650771 DOI: 10.1021/acs.inorgchem.3c01632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Activation of C-H bonds using an earth-abundant metal catalyst is one of the top challenges of chemistry, where high-valent Mn/Fe-oxo(hydroxo) biomimic species play an important role. There are several open questions related to the comparative oxidative abilities of these species, and a unifying concept that could accommodate various factors influencing reactivity is lacking. To shed light on these open questions, here, we have used a combination of density functional theory (DFT) (B3LYP-D3/def2-TZVP) and ab initio (CASSCF/NEVPT2) calculations to study a series of high-valent metal-oxo species [Mn+H3buea(O/OH)] (M = Mn and Fe, n = II to V; H3buea = tris[(N'-tert-butylureaylato)-N-ethylene)]aminato towards the activation of dihydroanthracene (DHA). The H-bonding network in the ligand architecture influences the ground state-excited state gap and brings several excited states of the same spin multiplicity closer in energy, which triggers reactivity via one of those excited states, reducing the kinetic barriers for the C-H bond activation and rationalizing several puzzling reactivity trends observed in various high-valent Mn/Fe-oxo(hydroxo) species.
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Affiliation(s)
- Asmita Sen
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai400076, India
| | - Azaj Ansari
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai400076, India
| | - Abinash Swain
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai400076, India
| | - Bhawana Pandey
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai400076, India
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai400076, India
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34
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Braun A, Gee LB, Mara MW, Hill EA, Kroll T, Nordlund D, Sokaras D, Glatzel P, Hedman B, Hodgson KO, Borovik AS, Baker ML, Solomon EI. X-ray Spectroscopic Study of the Electronic Structure of a Trigonal High-Spin Fe(IV)═O Complex Modeling Non-Heme Enzyme Intermediates and Their Reactivity. J Am Chem Soc 2023; 145:18977-18991. [PMID: 37590931 PMCID: PMC10631461 DOI: 10.1021/jacs.3c06181] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Fe K-edge X-ray absorption spectroscopy (XAS) has long been used for the study of high-valent iron intermediates in biological and artificial catalysts. 4p-mixing into the 3d orbitals complicates the pre-edge analysis but when correctly understood via 1s2p resonant inelastic X-ray scattering and Fe L-edge XAS, it enables deeper insight into the geometric structure and correlates with the electronic structure and reactivity. This study shows that in addition to the 4p-mixing into the 3dz2 orbital due to the short iron-oxo bond, the loss of inversion in the equatorial plane leads to 4p mixing into the 3dx2-y2,xy, providing structural insight and allowing the distinction of 6- vs 5-coordinate active sites as shown through application to the Fe(IV)═O intermediate of taurine dioxygenase. Combined with O K-edge XAS, this study gives an unprecedented experimental insight into the electronic structure of Fe(IV)═O active sites and their selectivity for reactivity enabled by the π-pathway involving the 3dxz/yz orbitals. Finally, the large effect of spin polarization is experimentally assigned in the pre-edge (i.e., the α/β splitting) and found to be better modeled by multiplet simulations rather than by commonly used time-dependent density functional theory.
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Affiliation(s)
- Augustin Braun
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Leland B Gee
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Michael W Mara
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Ethan A Hill
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Dennis Nordlund
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Pieter Glatzel
- ESRF-The European Synchrotron Radiation Facility, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Keith O Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - A S Borovik
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Michael L Baker
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
- Department of Chemistry, The University of Manchester, Manchester M13 9PL, U.K
- The University of Manchester at Harwell, Diamond Light Source, Harwell Campus, Didcot OX11 0DE, U.K
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
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35
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Slater JW, Lin CY, Neugebauer ME, McBride MJ, Sil D, Nair M, Katch BJ, Boal AK, Chang MC, Silakov A, Krebs C, Bollinger JM. Synergistic Binding of the Halide and Cationic Prime Substrate of l-Lysine 4-Chlorinase, BesD, in Both Ferrous and Ferryl States. Biochemistry 2023; 62:2480-2491. [PMID: 37542461 PMCID: PMC10829012 DOI: 10.1021/acs.biochem.3c00248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2023]
Abstract
An aliphatic halogenase requires four substrates: 2-oxoglutarate (2OG), halide (Cl- or Br-), the halogenation target ("prime substrate"), and dioxygen. In well-studied cases, the three nongaseous substrates must bind to activate the enzyme's Fe(II) cofactor for efficient capture of O2. Halide, 2OG, and (lastly) O2 all coordinate directly to the cofactor to initiate its conversion to a cis-halo-oxo-iron(IV) (haloferryl) complex, which abstracts hydrogen (H•) from the non-coordinating prime substrate to enable radicaloid carbon-halogen coupling. We dissected the kinetic pathway and thermodynamic linkage in binding of the first three substrates of the l-lysine 4-chlorinase, BesD. After addition of 2OG, subsequent coordination of the halide to the cofactor and binding of cationic l-Lys near the cofactor are associated with strong heterotropic cooperativity. Progression to the haloferryl intermediate upon the addition of O2 does not trap the substrates in the active site and, in fact, markedly diminishes cooperativity between halide and l-Lys. The surprising lability of the BesD•[Fe(IV)=O]•Cl•succinate•l-Lys complex engenders pathways for decay of the haloferryl intermediate that do not result in l-Lys chlorination, especially at low chloride concentrations; one identified pathway involves oxidation of glycerol. The mechanistic data imply (i) that BesD may have evolved from a hydroxylase ancestor either relatively recently or under weak selective pressure for efficient chlorination and (ii) that acquisition of its activity may have involved the emergence of linkage between l-Lys binding and chloride coordination following the loss of the anionic protein-carboxylate iron ligand present in extant hydroxylases.
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Affiliation(s)
- Jeffrey W. Slater
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Chi-Yun Lin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Monica E. Neugebauer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, United States
- Present address: Department of Systems Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Molly J. McBride
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Present address: Alliance Pharma, New York, NY 10065, United States
| | - Debangsu Sil
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Present address: Department of Chemistry, Indian Institute of Science Education & Research (IISER)-Pune, Pune-411008, India
| | - Mrutyunjay Nair
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Bryce J. Katch
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Present address: Tri-Institutional MD-PhD Program, Weill Cornell Medical College and Cornell University, New York, NY 10065, United States
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Michelle C.Y. Chang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, United States
- Departments of Chemistry and of Molecular and Cell Biology, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Alexey Silakov
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
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36
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Martin CB, Taabazuing CY, Knapp MJ. Dynamic Domain Links Substrate Binding and Catalysis in the Factor-Inhibiting-HIF-1. Biochemistry 2023; 62:2442-2449. [PMID: 37526986 DOI: 10.1021/acs.biochem.3c00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
The interplay between active-site chemistry and functionally relevant enzyme motions can provide useful insights into selective enzyme modulation. Modulation of the hypoxia-sensing function of factor-inhibiting-HIF-1 (FIH) enzyme is a potential therapeutic strategy in disease states such as ischemia and cancer. The hypoxia-sensing function of FIH relies in major part on the tight coupling of the first half of the catalytic mechanism which involves O2 activation and eventual succinate production to the second half which involves HIF-1α/CTAD substrate hydroxylation. In this study, we demonstrate the role of a loop hinge domain in FIH (FIH102-118) called the 100s loop in maintaining this particular tight coupling. Molecular dynamics patterns from Gaussian Network Model (iGNM) database analysis of FIH identified the 100s loop as one dynamic domain containing a hinge residue (Tyr102) with a potential substrate positioning role. Enzymological and biophysical studies of the 100s loop point mutants revealed altered enzyme kinetics with the exception of the conservative FIH mutant Y102F, which suggests a sterics-related role for this residue. Removal of the bulk of Tyr102 (Y102A) resulted in succinate production, autohydroxylation, and an O2 binding environment comparable to wild-type FIH. However, the HIF-1α/CTAD substrate hydroxylation of this mutant was significantly reduced which implies that (1) the FIH loop hinge residue Tyr102 does not affect O2 activation, (2) the stacking steric interaction of Tyr102 is important in substrate positioning for productive hydroxylation, and (3) Tyr102 is important for the synchronization of O2 activation and substrate hydroxylation.
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Affiliation(s)
- Cristina B Martin
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Cornelius Y Taabazuing
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Michael J Knapp
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
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37
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Smithwick ER, Wilson RH, Chatterjee S, Pu Y, Dalluge JJ, Damodaran AR, Bhagi-Damodaran A. Electrostatically regulated active site assembly governs reactivity in non-heme iron halogenases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542349. [PMID: 37292651 PMCID: PMC10245910 DOI: 10.1101/2023.05.25.542349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Non-heme iron halogenases (NHFe-Hals) catalyze the direct insertion of a chloride/bromide ion at an unactivated carbon position using a high-valent haloferryl intermediate. Despite more than a decade of structural and mechanistic characterization, how NHFe-Hals preferentially bind specific anions and substrates for C-H functionalization remains unknown. Herein, using lysine halogenating BesD and HalB enzymes as model systems, we demonstrate strong positive cooperativity between anion and substrate binding to the catalytic pocket. Detailed computational investigations indicate that a negatively charged glutamate hydrogen-bonded to iron's equatorial-aqua ligand acts as an electrostatic lock preventing both lysine and anion binding in the absence of the other. Using a combination of UV-Vis spectroscopy, binding affinity studies, stopped-flow kinetics investigations, and biochemical assays, we explore the implication of such active site assembly towards chlorination, bromination, and azidation reactivities. Overall, our work highlights previously unknown features regarding how anion-substrate pair binding govern reactivity of iron halogenases that are crucial for engineering next-generation C-H functionalization biocatalysts.
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Affiliation(s)
- Elizabeth R. Smithwick
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - R. Hunter Wilson
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Sourav Chatterjee
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Yu Pu
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Joseph J. Dalluge
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Anoop Rama Damodaran
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
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38
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Slater JW, Neugebauer ME, McBride MJ, Sil D, Lin CY, Katch BJ, Boal AK, Chang MC, Silakov A, Krebs C, Bollinger JM. Synergistic Binding of the Halide and Cationic Prime Substrate of the l-Lysine 4-Chlorinase, BesD, in Both Ferrous and Ferryl States. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539147. [PMID: 37205437 PMCID: PMC10187165 DOI: 10.1101/2023.05.02.539147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
An aliphatic halogenase requires four substrates: 2-oxoglutarate (2OG), halide (Cl - or Br - ), the halogenation target ("prime substrate"), and dioxygen. In well-studied cases, the three non-gaseous substrates must bind to activate the enzyme's Fe(II) cofactor for efficient capture of O 2 . Halide, 2OG, and (lastly) O 2 all coordinate directly to the cofactor to initiate its conversion to a cis -halo-oxo-iron(IV) (haloferryl) complex, which abstracts hydrogen (H•) from the non-coordinating prime substrate to enable radicaloid carbon-halogen coupling. We dissected the kinetic pathway and thermodynamic linkage in binding of the first three substrates of the l -lysine 4-chlorinase, BesD. After 2OG adds, subsequent coordination of the halide to the cofactor and binding of cationic l -Lys near the cofactor are associated with strong heterotropic cooperativity. Progression to the haloferryl intermediate upon addition of O 2 does not trap the substrates in the active site and, in fact, markedly diminishes cooperativity between halide and l -Lys. The surprising lability of the BesD•[Fe(IV)=O]•Cl•succinate• l -Lys complex engenders pathways for decay of the haloferryl intermediate that do not result in l -Lys chlorination, especially at low chloride concentrations; one identified pathway involves oxidation of glycerol. The mechanistic data imply that (i) BesD may have evolved from a hydroxylase ancestor either relatively recently or under weak selective pressure for efficient chlorination and (ii) that acquisition of its activity may have involved the emergence of linkage between l -Lys binding and chloride coordination following loss of the anionic protein-carboxylate iron ligand present in extant hydroxylases.
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Affiliation(s)
- Jeffrey W. Slater
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Monica E. Neugebauer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Present address: Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Molly J. McBride
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Debangsu Sil
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Chi-Yun Lin
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Bryce J. Katch
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Michelle C.Y. Chang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Departments of Chemistry and of Molecular and Cell Biology, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alexey Silakov
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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39
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Bleher K, Comba P, Kass D, Ray K, Wadepohl H. Reactivities of iron(IV)-oxido compounds with pentadentate bispidine ligands. J Inorg Biochem 2023; 241:112123. [PMID: 36701984 DOI: 10.1016/j.jinorgbio.2023.112123] [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: 08/30/2022] [Revised: 01/05/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
The FeIVO complexes of bispidines (3,7-diazabicyclo[3.3.1]nonane derivatives) are known to be highly reactive oxidants - with the tetradentate bispidine, the so far most reactive ferryl complex has been reported and two isomeric pentadentate ligands also lead to very reactive high-valent oxidants. With a series of 4 new bispidine derivatives we now try to address the question why the bispidine scaffold in general leads to very reactive oxidants and how this can be tuned by ligand modifications. The study is based on a full structural, spectroscopic and electrochemical analysis of the iron(II) precursors, spectroscopic data of the iron(IV)-oxido complexes, a kinetic analysis of the stoichiometric oxidation of thioanisole by five different bispidine‑iron(IV)-oxido complexes and on product analyses of reactions by the five ferryl oxidants with thioanisole, β-methylstyrene and cis-stilbene as substrates.
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Affiliation(s)
- Katharina Bleher
- Universität Heidelberg, Anorganisch-Chemisches Institut, INF 270, D-69120 Heidelberg, Germany
| | - Peter Comba
- Universität Heidelberg, Anorganisch-Chemisches Institut, INF 270, D-69120 Heidelberg, Germany; Universität Heidelberg, Interdisziplinäres Zentrum für Wissenschaftliches Rechnen (IWR), Germany.
| | - Dustin Kass
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor Strasse 2, D-12489 Berlin, Germany
| | - Kallol Ray
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor Strasse 2, D-12489 Berlin, Germany
| | - Hubert Wadepohl
- Universität Heidelberg, Anorganisch-Chemisches Institut, INF 270, D-69120 Heidelberg, Germany
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40
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Hausinger RP. Five decades of metalloenzymology. Enzymes 2023; 54:71-105. [PMID: 37945178 DOI: 10.1016/bs.enz.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Metalloenzymes have been detailed in The Enzymes since its inception over half a century ago. Here, I review selected metal-containing enzyme highlights from early chapters in this series and I describe advances made since those contributions. Three topics are emphasized: nickel-containing enzymes, Fe(II)/2-oxoglutarate-dependent oxygenases, and enzymes containing non-canonical iron-sulfur clusters.
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Affiliation(s)
- Robert P Hausinger
- Departments of Microbiology & Molecular Genetics and Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States.
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41
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Cha L, Paris JC, Zanella B, Spletzer M, Yao A, Guo Y, Chang WC. Mechanistic Studies of Aziridine Formation Catalyzed by Mononuclear Non-Heme Iron Enzymes. J Am Chem Soc 2023; 145:6240-6246. [PMID: 36913534 DOI: 10.1021/jacs.2c12664] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Aziridines are compounds with a nitrogen-containing three-membered ring. When it is incorporated into natural products, the reactivity of the strained ring often drives the biological activities of aziridines. Despite its importance, the enzymes and biosynthetic strategies deployed to install this reactive moiety remain understudied. Herein, we report the use of in silico methods to identify enzymes with potential aziridine-installing (aziridinase) functionality. To validate candidates, we reconstitute enzymatic activity in vitro and demonstrate that an iron(IV)-oxo species initiates aziridine ring closure by the C-H bond cleavage. Furthermore, we divert the reaction pathway from aziridination to hydroxylation using mechanistic probes. This observation, isotope tracing experiments using H218O and 18O2, and quantitative product analysis, provide evidence for the polar capture of a carbocation species by the amine in the pathway to aziridine installation.
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Affiliation(s)
- Lide Cha
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Jared C Paris
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Brady Zanella
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Martha Spletzer
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Angela Yao
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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42
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Jana S, Pattanayak S, Das S, Ghosh M, Velasco L, Moonshiram D, Sen Gupta S. Comparing the reactivity of an oxoiron(IV) cation radical and its oxoiron(V) tautomer towards C-H bonds. Chem Commun (Camb) 2023; 59:2755-2758. [PMID: 36779358 DOI: 10.1039/d2cc07005g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
An oxoiron(IV) cation radical is generated upon two-electron oxidation of an iron(III) complex bearing an electron-rich methoxy substituted bTAML framework and thoroughly characterized via multiple spectroscopic techniques and density functional theory (DFT). Reactivity studies demonstrate faster rates for oxidation of strong aliphatic sp3 C-H bonds than for its corresponding oxoiron(V) valence tautomer.
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Affiliation(s)
- Sandipan Jana
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India.
| | - Santanu Pattanayak
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India.
| | - Soumadip Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India.
| | - Munmun Ghosh
- Department of Chemistry, Ashoka University, Rajiv Gandhi Education City, Sonepat, Haryana 131029, India.
| | - Lucia Velasco
- Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas, Sor Juana Inés de la Cruz, 3, 28049, Madrid, Spain.
| | - Dooshaye Moonshiram
- Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas, Sor Juana Inés de la Cruz, 3, 28049, Madrid, Spain.
| | - Sayam Sen Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India.
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43
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Guan J, Lu Y, Dai Z, Zhao S, Xu Y, Nie Y. R97 at "Handlebar" Binding Mode in Active Pocket Plays an Important Role in Fe(II)/α-Ketoglutaric Acid-Dependent Dioxygenase cis-P3H-Mediated Selective Synthesis of (2S,3R)-3-Hydroxypipecolic Acid. Molecules 2023; 28:molecules28041854. [PMID: 36838840 PMCID: PMC9968057 DOI: 10.3390/molecules28041854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Pipecolic acid (Pip) and its derivative hydroxypipecolic acids, such as (2S,3R)-3-hydroxypipecolic acid (cis-3-L-HyPip), are components of many natural and synthetic bioactive molecules. Fe(II)/α-ketoglutaric acid (Fe(II)/2-OG)-dependent dioxygenases can catalyze the hydroxylation of pipecolic acid. However, the available enzymes with desired activity and selectivity are limited. Herein, we compare the possible candidates in the Fe(II)/2-OG-dependent dioxygenase family, and cis-P3H is selected for potentially catalyzing selective hydroxylation of L-Pip. cis-P3H was further engineered to increase its catalytic efficiency toward L-Pip. By analyzing the structural confirmation and residue composition in substrate-binding pocket, a "handlebar" mode of molecular interactions is proposed. Using molecular docking, virtual mutation analysis, and dynamic simulations, R97, E112, L57, and G282 were identified as the key residues for subsequent site-directed saturation mutagenesis of cis-P3H. Consequently, the variant R97M showed an increased catalytic efficiency toward L-Pip. In this study, the kcat/Km value of the positive mutant R97M was about 1.83-fold that of the wild type. The mutation R97M would break the salt bridge between R97 and L-Pip and weaken the positive-positive interaction between R97 and R95. Therefore, the force on the amino and carboxyl groups of L-Pip was lightly balanced, allowing the molecule to be stabilized in the active pocket. These results provide a potential way of improving cis-P3H catalytic activity through rational protein engineering.
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Affiliation(s)
- Jiaojiao Guan
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yilei Lu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Zixuan Dai
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Songyin Zhao
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yao Nie
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
- Suqian Industrial Technology Research Institute of Jiangnan University, Suqian 223814, China
- Correspondence:
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44
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Kastner DW, Nandy A, Mehmood R, Kulik HJ. Mechanistic Insights into Substrate Positioning That Distinguish Non-heme Fe(II)/α-Ketoglutarate-Dependent Halogenases and Hydroxylases. ACS Catal 2023. [DOI: 10.1021/acscatal.2c06241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- David W. Kastner
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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45
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Bera A, Sheet D, Paine TK. Iron(II)-α-keto acid complexes of tridentate ligands on gold nanoparticles: the effect of ligand geometry and immobilization on their dioxygen-dependent reactivity. Dalton Trans 2023; 52:1062-1073. [PMID: 36602242 DOI: 10.1039/d2dt02433k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two mononuclear nonheme iron(II)-benzoylformate (BF) complexes [(6Me2-Me-BPA)Fe(BF)](ClO4) (1a) and [(6Me3-TPMM)Fe(BF)](ClO4) (1b) of tridentate nitrogen donor ligands, bis((6-methylpyridin-2-yl)methyl)(N-methyl)amine (6Me2-Me-BPA) and tris(2-(6-methyl)pyridyl)methoxymethane (6Me3-TPMM), were isolated and characterized. The structural characterization of iron(II)-chloro complexes indicates that the ligand 6Me2-Me-BPA binds to the iron(II) centre in a meridional fashion, whereas 6Me3-TPMM behaves as a facial ligand. Both the ligands were functionalized with terminal thiol for immobilization on gold nanoparticles (AuNPs), and the corresponding iron(II) complexes [(6Me2-BPASH)Fe(BF)(ClO4)]@C8Au (2a) and [(6Me3-TPMSH)Fe(BF)(ClO4)]@C8Au (2b) were prepared to probe the effect of immobilization on their ability to perform bioinspired oxidation reactions. All the complexes react with dioxygen to display the oxidative decarboxylation of the coordinated benzoylformate, but the complexes supported by 6Me3-TPMM and its thiol-appended ligand display faster reactivity compared to their analogues with the 6Me2-Me-BPA-derived ligands. In each case, an electrophilic iron-oxygen oxidant was intercepted as the active oxidant generated from dioxygen. The immobilized complexes (2a and 2b) display enhanced O2-dependent reactivity in oxygen-atom transfer reactions (OAT) and hydrogen-atom transfer (HAT) reactions compared to their homogeneous congeners (1a and 1b). Furthermore, the immobilized complex 2b displays catalytic OAT reactions. This study supports that the ligand geometry and immobilization on AuNPs influence the dioxygen-dependent reactivity of the complexes.
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Affiliation(s)
- Abhijit Bera
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Debobrata Sheet
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Tapan Kanti Paine
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
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46
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Dantignana V, Pérez‐Segura MC, Besalú‐Sala P, Delgado‐Pinar E, Martínez‐Camarena Á, Serrano‐Plana J, Álvarez‐Núñez A, Castillo CE, García‐España E, Luis JM, Basallote MG, Costas M, Company A. Characterization of a Ferryl Flip in Electronically Tuned Nonheme Complexes. Consequences in Hydrogen Atom Transfer Reactivity. Angew Chem Int Ed Engl 2023; 62:e202211361. [PMID: 36305539 PMCID: PMC10107328 DOI: 10.1002/anie.202211361] [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: 08/02/2022] [Indexed: 12/04/2022]
Abstract
Two oxoiron(IV) isomers (R 2a and R 2b) of general formula [FeIV (O)(R PyNMe3 )(CH3 CN)]2+ are obtained by reaction of their iron(II) precursor with NBu4 IO4 . The two isomers differ in the position of the oxo ligand, cis and trans to the pyridine donor. The mechanism of isomerization between R 2a and R 2b has been determined by kinetic and computational analyses uncovering an unprecedented path for interconversion of geometrical oxoiron(IV) isomers. The activity of the two oxoiron(IV) isomers in hydrogen atom transfer (HAT) reactions shows that R 2a reacts one order of magnitude faster than R 2b, which is explained by a repulsive noncovalent interaction between the ligand and the substrate in R 2b. Interestingly, the electronic properties of the R substituent in the ligand pyridine ring do not have a significant effect on reaction rates. Overall, the intrinsic structural aspects of each isomer define their relative HAT reactivity, overcoming changes in electronic properties of the ligand.
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Affiliation(s)
- Valeria Dantignana
- Institut de Química Computacional i Catàlisi (IQCC)Departament de Química, Universitat de GironaC/Mª Aurèlia Capmany 6917003GironaCataloniaSpain
| | - M. Carmen Pérez‐Segura
- Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química InorgánicaFacultad de Ciencias, Instituto de Biomoléculas (INBIO)Universidad de CádizPuerto Real11510CádizSpain
| | - Pau Besalú‐Sala
- Institut de Química Computacional i Catàlisi (IQCC)Departament de Química, Universitat de GironaC/Mª Aurèlia Capmany 6917003GironaCataloniaSpain
| | - Estefanía Delgado‐Pinar
- Departamento de Química InorgánicaInstituto de Ciencia Molecular (ICMol)Universidad de ValenciaC/Catedrático José Beltrán, Paterna46980Valencia 2Spain
| | - Álvaro Martínez‐Camarena
- Departamento de Química InorgánicaInstituto de Ciencia Molecular (ICMol)Universidad de ValenciaC/Catedrático José Beltrán, Paterna46980Valencia 2Spain
| | - Joan Serrano‐Plana
- Institut de Química Computacional i Catàlisi (IQCC)Departament de Química, Universitat de GironaC/Mª Aurèlia Capmany 6917003GironaCataloniaSpain
| | - Andrea Álvarez‐Núñez
- Institut de Química Computacional i Catàlisi (IQCC)Departament de Química, Universitat de GironaC/Mª Aurèlia Capmany 6917003GironaCataloniaSpain
| | - Carmen E. Castillo
- Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química InorgánicaFacultad de Ciencias, Instituto de Biomoléculas (INBIO)Universidad de CádizPuerto Real11510CádizSpain
| | - Enrique García‐España
- Departamento de Química InorgánicaInstituto de Ciencia Molecular (ICMol)Universidad de ValenciaC/Catedrático José Beltrán, Paterna46980Valencia 2Spain
| | - Josep M. Luis
- Institut de Química Computacional i Catàlisi (IQCC)Departament de Química, Universitat de GironaC/Mª Aurèlia Capmany 6917003GironaCataloniaSpain
| | - Manuel G. Basallote
- Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química InorgánicaFacultad de Ciencias, Instituto de Biomoléculas (INBIO)Universidad de CádizPuerto Real11510CádizSpain
| | - Miquel Costas
- Institut de Química Computacional i Catàlisi (IQCC)Departament de Química, Universitat de GironaC/Mª Aurèlia Capmany 6917003GironaCataloniaSpain
| | - Anna Company
- Institut de Química Computacional i Catàlisi (IQCC)Departament de Química, Universitat de GironaC/Mª Aurèlia Capmany 6917003GironaCataloniaSpain
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47
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Kim W, Chen TY, Cha L, Zhou G, Xing K, Canty NK, Zhang Y, Chang WC. Elucidation of divergent desaturation pathways in the formation of vinyl isonitrile and isocyanoacrylate. Nat Commun 2022; 13:5343. [PMID: 36097268 PMCID: PMC9467999 DOI: 10.1038/s41467-022-32870-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 08/19/2022] [Indexed: 11/10/2022] Open
Abstract
Two different types of desaturations are employed by iron- and 2-oxoglutarate-dependent (Fe/2OG) enzymes to construct vinyl isonitrile and isocyanoacrylate moieties found in isonitrile-containing natural products. A substrate-bound protein structure reveals a plausible strategy to affect desaturation and hints at substrate promiscuity of these enzymes. Analogs are synthesized and used as mechanistic probes to validate structural observations. Instead of proceeding through hydroxylated intermediate as previously proposed, a plausible carbocation species is utilized to trigger C=C bond installation. These Fe/2OG enzymes can also accommodate analogs with opposite chirality and different functional groups including isonitrile-(D)-tyrosine, N-formyl tyrosine, and phloretic acid, while maintaining the reaction selectivity.
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Affiliation(s)
- Wantae Kim
- McKetta Department of Chemical Engineering, University of Texas, Austin, TX, USA
| | - Tzu-Yu Chen
- Department of Chemistry, NC State University, Raleigh, NC, USA
| | - Lide Cha
- Department of Chemistry, NC State University, Raleigh, NC, USA
| | - Grace Zhou
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Kristi Xing
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | | | - Yan Zhang
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, USA.
| | - Wei-Chen Chang
- Department of Chemistry, NC State University, Raleigh, NC, USA.
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48
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Fernandez RL, Juntunen ND, Brunold TC. Differences in the Second Coordination Sphere Tailor the Substrate Specificity and Reactivity of Thiol Dioxygenases. Acc Chem Res 2022; 55:2480-2490. [PMID: 35994511 PMCID: PMC9583696 DOI: 10.1021/acs.accounts.2c00359] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In recent years, considerable progress has been made toward elucidating the geometric and electronic structures of thiol dioxygenases (TDOs). TDOs catalyze the conversion of substrates with a sulfhydryl group to their sulfinic acid derivatives via the addition of both oxygen atoms from molecular oxygen. All TDOs discovered to date belong to the family of cupin-type mononuclear nonheme Fe(II)-dependent metalloenzymes. While most members of this enzyme family bind the Fe cofactor by two histidines and one carboxylate side chain (2-His-1-carboxylate) to provide a monoanionic binding motif, TDOs feature a neutral three histidine (3-His) facial triad. In this Account, we present a bioinformatics analysis and multiple sequence alignment that highlight the significance of the secondary coordination sphere in tailoring the substrate specificity and reactivity among the different TDOs. These insights provide the framework within which important structural and functional features of the distinct TDOs are discussed.The best studied TDO is cysteine dioxygenase (CDO), which catalyzes the conversion of cysteine to cysteine sulfinic acid in both eukaryotes and prokaryotes. Crystal structures of resting and substrate-bound mammalian CDOs revealed two surprising structural motifs in the first- and second coordination spheres of the Fe center. The first is the presence of the abovementioned neutral 3-His facial triad that coordinates the Fe ion. The second is the existence of a covalent cross-link between the sulfur of Cys93 and an ortho carbon of Tyr157 (mouse CDO numbering scheme). While the exact role of this cross-link remains incompletely understood, various studies established that it is needed for proper substrate Cys positioning and gating solvent access to the active site. Intriguingly, bacterial CDOs lack the Cys-Tyr cross-link; yet, they are as active as cross-linked eukaryotic CDOs.The other known mammalian TDO is cysteamine dioxygenase (ADO). Initially, it was believed that ADO solely catalyzes the oxidation of cysteamine to hypotaurine. However, it has recently been shown that ADO additionally oxidizes N-terminal cysteine (Nt-Cys) peptides, which indicates that ADO may play a much more significant role in mammalian physiology than was originally anticipated. Though predicted on the basis of sequence alignment, site-directed mutagenesis, and spectroscopic studies, it was not until last year that two crystal structures, one of wild-type mouse ADO (solved by us) and the other of a variant of nickel-substituted human ADO, finally provided direct evidence that this enzyme also features a 3-His facial triad. These structures additionally revealed several features that are unique to ADO, including a putative cosubstrate O2 access tunnel that is lined by two Cys residues. Disulfide formation under conditions of high O2 levels may serve as a gating mechanism to prevent ADO from depleting organisms of Nt-Cys-containing molecules.The combination of kinetic and spectroscopic studies in conjunction with structural characterizations of TDOs has furthered our understanding of enzymatic sulfhydryl substrate regulation. In this article, we take advantage of the fact that the ADO X-ray crystal structures provided the final piece needed to compare and contrast key features of TDOs, an essential family of metalloenzymes found across all kingdoms of life.
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Affiliation(s)
- Rebeca L. Fernandez
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Nicholas D. Juntunen
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Thomas C. Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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49
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Li L, Lai S, Lin H, Zhao X, Li X, Chen X, Liu J, Yang G, Zhan C. QM/MM study on the O2 activation reaction of 4-hydroxylphenyl pyruvate dioxygenase reveals a common mechanism for α-ketoglutarate dependent dioxygenase. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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50
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Wilson RH, Chatterjee S, Smithwick ER, Dalluge JJ, Bhagi-Damodaran A. Role of Secondary Coordination Sphere Residues in Halogenation Catalysis of Non-heme Iron Enzymes. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- R. Hunter Wilson
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Sourav Chatterjee
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Elizabeth R. Smithwick
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Joseph J. Dalluge
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, United States
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