1
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Khatri J, Mari V, Sarkar A, Karmodak N, Dhar BB. C-H bond chlorination and bromination using water soluble nickel(II) guanidine complexes. Dalton Trans 2024. [PMID: 39636087 DOI: 10.1039/d4dt02783c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2024]
Abstract
Water-soluble nickel(II)-guanidine-based complexes successfully catalyzed the C-H chlorination of a series of hydrocarbons in the presence of NaOCl and acetic acid in water-chloroform (7 : 3, biphasic condition) at room temperature. Majorly chlorinated products (TON ∼680 for cyclohexane) were obtained. Furthermore, C-H bond bromination of cyclohexane, n-hexane, and toluene was also carried out using in situ generation of NaOBr. These putative formations of Ni(III) species were characterized by electron paramagnetic resonance (EPR) spectroscopy, and the plausible mechanism for chlorination was confirmed by DFT calculations.
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Affiliation(s)
- Jaipriya Khatri
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence Deemed to be University, Delhi NCR, Gautam Buddha Nagar, Dadri, UP-201314, India.
| | - Vasanthapandiyan Mari
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence Deemed to be University, Delhi NCR, Gautam Buddha Nagar, Dadri, UP-201314, India.
| | - Aniruddha Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India
| | - Naiwrit Karmodak
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence Deemed to be University, Delhi NCR, Gautam Buddha Nagar, Dadri, UP-201314, India.
| | - Basab Bijayi Dhar
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence Deemed to be University, Delhi NCR, Gautam Buddha Nagar, Dadri, UP-201314, India.
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2
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Bohn A, Robinson AL, Sénéchal-David K, Herrero C, Kanoufi F, Anxolabéhère-Mallart E, Banse F. Electrochemical approach of the reductive activation of O 2 by a nonheme Fe II complex. Some clues for the development of catalytic oxidations. Dalton Trans 2024; 53:15491-15500. [PMID: 39246009 DOI: 10.1039/d4dt01870b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
Abstract
We report an in-depth study of the reductive activation of O2 by the nonheme [FeII(L25)(MeCN)]2+ complex carried out by cyclic voltammetry. Experimental evidence is obtained for the slow coordination of dioxygen to the ferrous center yielding an FeII/O2 adduct with a strong FeII-O2 character rather than an FeIII-superoxo one. Electron injection in the FeII-O2 species occurs at a potential of ca. -700 mV vs. SCE, i.e. 200 mV above the O2 to O2˙- reduction, leading to the formation of a FeIII-peroxo intermediate and then FeIII-hydroperoxo upon protonation by residual water. The experimental CVs recorded at variable scan rate or variable FeII concentration are well simulated taking into account a detailed mechanism initiated by the competitive reduction of O2 and the FeII-O2 adduct. Analysis of the concentration of the reaction intermediates generated as a function of the applied potential indicates that the FeIII-peroxo intermediate significantly accumulates at a potential of -650 mV. Oxidative bromination of anisole is assayed under electrolytic conditions at this potential to yield bromoanisole products. The low faradaic yields observed reveal that deleterious reactions such as direct reduction of reaction intermediates likely occur. Based on the detailed mechanism elucidated, a number of improvements to achieve more efficient catalytic reactions can be proposed.
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Affiliation(s)
- Antoine Bohn
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, 91400, Orsay, France.
| | - Amanda Lyn Robinson
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, 91400, Orsay, France.
| | - Katell Sénéchal-David
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, 91400, Orsay, France.
| | - Christian Herrero
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, 91400, Orsay, France.
| | - Frédéric Kanoufi
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université de Paris, CNRS, F-75013 Paris, France
| | | | - Frédéric Banse
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, 91400, Orsay, France.
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3
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Zhao Q, Rui J, Huang X. Radical-relay C(sp 3)-H azidation catalyzed by an engineered nonheme iron enzyme. Methods Enzymol 2024; 703:195-213. [PMID: 39260996 DOI: 10.1016/bs.mie.2024.07.003] [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
Nonheme iron enzymes are versatile biocatalysts for a broad range of unique and powerful transformations, such as hydroxylation, chlorination, and epimerization as well as cyclization/ring-opening of organic molecules. Beyond their native biological functions, these enzymes are robust for engineering due to their structural diversity and high evolvability. Based on enzyme promiscuity and directed evolution as well as inspired by synthetic organic chemistry, nonheme iron enzymes can be repurposed to catalyze reactions previously only accessible with synthetic catalysts. To this end, our group has engineered a series of nonheme iron enzymes to employ non-natural radical-relay mechanisms for new-to-nature radical transformations. In particular, we have demonstrated that a nonheme iron enzyme, (4-hydroxyphenyl)pyruvate dioxygenase from streptomyces avermitilis (SavHppD), can be repurposed to enable abiological radical-relay process to access C(sp3)-H azidation products. This represents the first known instance of enzymatic radical relay azidation reactions. In this chapter, we describe the detailed experimental protocol to convert promiscuous nonheme iron enzymes into efficient and selective biocatalyst for radical relay azidation reactions. One round of directed evolution is described in detail, which includes the generation and handling of site-saturation mutagenesis, protein expression and whole-cell reactions screening in a 96-well plate. These protocol details might be useful to engineer various nonheme iron enzymes for other applications.
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Affiliation(s)
- Qun Zhao
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, P.R. China.
| | - Jinyan Rui
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, United States
| | - Xiongyi Huang
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, United States.
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4
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Andrys-Olek J, Kluza A, Tataruch M, Heider J, Korecki J, Borowski T. Bacteria at Work - Experimental and Theoretical Studies Reveal the Catalytic Mechanism of Ectoine Synthase. Chemistry 2024; 30:e202304163. [PMID: 38258332 DOI: 10.1002/chem.202304163] [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: 12/13/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 01/24/2024]
Abstract
Ectoine synthase (EctC) catalyses the ultimate step of ectoine biosynthesis, a kosmotropic compound produced as compatible solute by many bacteria and some archaea or eukaryotes. EctC is an Fe2+-dependent homodimeric cytoplasmic protein. Using Mössbauer spectroscopy, molecular dynamics simulations and QM/MM calculations, we determined the most likely coordination number and geometry of the Fe2+ ion and proposed a mechanism of the EctC-catalysed reaction. Most notably, we show that apart from the three amino acids binding to the iron ion (Glu57, Tyr84 and His92), one water molecule and one hydroxide ion are required as additional ligands for the reaction to occur. They fill the first coordination sphere of the Fe2+-cofactor and act as critical proton donors and acceptors during the cyclization reaction.
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Affiliation(s)
- Justyna Andrys-Olek
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Anna Kluza
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Mateusz Tataruch
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Johann Heider
- Department of Biology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Józef Korecki
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
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5
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Abstract
Covering: up to July 2023Terpene cyclases (TCs) catalyze some of the most complicated reactions in nature and are responsible for creating the skeletons of more than 95 000 terpenoid natural products. The canonical TCs are divided into two classes according to their structures, functions, and mechanisms. The class II TCs mediate acid-base-initiated cyclization reactions of isoprenoid diphosphates, terpenes without diphosphates (e.g., squalene or oxidosqualene), and prenyl moieties on meroterpenes. The past twenty years witnessed the emergence of many class II TCs, their reactions and their roles in biosynthesis. Class II TCs often act as one of the first steps in the biosynthesis of biologically active natural products including the gibberellin family of phytohormones and fungal meroterpenoids. Due to their mechanisms and biocatalytic potential, TCs elicit fervent attention in the biosynthetic and organic communities and provide great enthusiasm for enzyme engineering to construct novel and bioactive molecules. To engineer and expand the structural diversities of terpenoids, it is imperative to fully understand how these enzymes generate, precisely control, and quench the reactive carbocation intermediates. In this review, we summarize class II TCs from nature, including sesquiterpene, diterpene, triterpene, and meroterpenoid cyclases as well as noncanonical class II TCs and inspect their sequences, structures, mechanisms, and structure-guided engineering studies.
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Affiliation(s)
- Xingming Pan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7011, USA.
| | - Liao-Bin Dong
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
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6
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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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7
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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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8
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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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9
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Yadav V, Wen L, Yadav S, Siegler MA, Goldberg DP. Selective Radical Transfer in a Series of Nonheme Iron(III) Complexes. Inorg Chem 2023; 62:17830-17842. [PMID: 37857315 PMCID: PMC11296666 DOI: 10.1021/acs.inorgchem.3c02617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
A series of nonheme iron complexes, FeIII(BNPAPh2O)(Lax)(Leq) (Lax/eq = N3-, NCS-, NCO-, and Cl-) have been synthesized using the previously reported BNPAPh2O- ligand. The ferrous analogs FeII(BNPAPh2O)(Lax) (Lax = N3-, NCS-, and NCO-) were also prepared. The complexes were structurally characterized using single crystal X-ray diffraction, which shows that all the FeIII complexes are six-coordinate, with one anionic ligand (Lax) in the H-bonding axial site and the other anionic ligand (Leq) in the equatorial plane, cis to the Lax ligand. The reaction of FeIII(BNPAPh2O-)(Lax)(Leq) with Ph3C• shows that one ligand is selectively transferred in each case. A selectivity trend emerges that shows •N3 is the most favored for transfer in each case to the carbon radical, whereas Cl• is the least favored. The NCO and NCS ligands showed an intermediate propensity for radical transfer, with NCS > NCO. The overall order of selectivity is N3 > NCS > NCO > Cl. In addition, we also demonstrated that H-bonding has a small effect on governing product selectivity by using a non-H-bonded ligand (DPAPh2O-). This study demonstrates the inherent radical transfer selectivity of nonhydroxo-ligated nonheme iron(III) complexes, which could be useful for efforts in synthetic and (bio)catalytic C-H functionalization.
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Affiliation(s)
- Vishal Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Lyupeng Wen
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Sudha Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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10
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Zhang Y, Mokkawes T, de Visser SP. Insights into Cytochrome P450 Enzyme Catalyzed Defluorination of Aromatic Fluorides. Angew Chem Int Ed Engl 2023; 62:e202310785. [PMID: 37641517 DOI: 10.1002/anie.202310785] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
Density functional calculations establish a novel mechanism of aromatic defluorination by P450 Compound I. This is achieved via either an initial epoxide intermediate or through a 1,2-fluorine shift in an electrophilic intermediate, which highlights that the P450s can defluorinate fluoroarenes. However, in the absence of a proton donor a strong Fe-F bond can be obtained as shown from the calculations.
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Affiliation(s)
- Yi Zhang
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M17DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Thirakorn Mokkawes
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M17DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M17DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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11
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Kumar R, Ahsan F, Awasthi A, Swart M, Draksharapu A. Generation of Ru(III)-hypochlorite with resemblance to the heme-dependent haloperoxidase enzyme. Dalton Trans 2023; 52:12552-12559. [PMID: 37609762 DOI: 10.1039/d3dt02028b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The reaction of [(Me/BnTPEN)RuII(NCCH3)]2+ (BnTPEN = N1-benzyl-N1,N2,N2-tris(pyridine-2-ylmethyl)ethane-1,2-diamine and MeTPEN = N1-methyl-N1,N2,N2-tris(pyridine-2-ylmethyl)ethane-1,2-diamine) with mCPBA in the presence of chloride ions in CH3CN : H2O generated a novel (Me/BnTPEN)RuIII-OCl species at room temperature. This hypochlorite adduct could also be obtained by the direct reaction of NaOCl and HClO4 with (L)RuII complexes. The current study mimics the synthesis of a metal hypochlorite adduct in a similar fashion as in the heme-dependent haloperoxidase enzyme. As an electrophilic oxidant, the ruthenium hypochlorite adduct catalyzes hydrogen atom abstraction reactions of phenols and their derivatives.
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Affiliation(s)
- Rakesh Kumar
- Southern Laboratories - 208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Faiza Ahsan
- IQCC & Departament de Química, Universitat de Girona, 17003 Girona, Spain
| | - Ayushi Awasthi
- Southern Laboratories - 208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Marcel Swart
- IQCC & Departament de Química, Universitat de Girona, 17003 Girona, Spain
- ICREA, 08010, Barcelona, Spain.
| | - Apparao Draksharapu
- Southern Laboratories - 208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
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12
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Gérard E, Mokkawes T, Johannissen LO, Warwicker J, Spiess RR, Blanford CF, Hay S, Heyes DJ, de Visser SP. How Is Substrate Halogenation Triggered by the Vanadium Haloperoxidase from Curvularia inaequalis? ACS Catal 2023; 13:8247-8261. [PMID: 37342830 PMCID: PMC10278073 DOI: 10.1021/acscatal.3c00761] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/05/2023] [Indexed: 06/23/2023]
Abstract
Vanadium haloperoxidases (VHPOs) are unique enzymes in biology that catalyze a challenging halogen transfer reaction and convert a strong aromatic C-H bond into C-X (X = Cl, Br, I) with the use of a vanadium cofactor and H2O2. The VHPO catalytic cycle starts with the conversion of hydrogen peroxide and halide (X = Cl, Br, I) into hypohalide on the vanadate cofactor, and the hypohalide subsequently reacts with a substrate. However, it is unclear whether the hypohalide is released from the enzyme or otherwise trapped within the enzyme structure for the halogenation of organic substrates. A substrate-binding pocket has never been identified for the VHPO enzyme, which questions the role of the protein in the overall reaction mechanism. Probing its role in the halogenation of small molecules will enable further engineering of the enzyme and expand its substrate scope and selectivity further for use in biotechnological applications as an environmentally benign alternative to current organic chemistry synthesis. Using a combined experimental and computational approach, we elucidate the role of the vanadium haloperoxidase protein in substrate halogenation. Activity studies show that binding of the substrate to the enzyme is essential for the reaction of the hypohalide with substrate. Stopped-flow measurements demonstrate that the rate-determining step is not dependent on substrate binding but partially on hypohalide formation. Using a combination of molecular mechanics (MM) and molecular dynamics (MD) simulations, the substrate binding area in the protein is identified and even though the selected substrates (methylphenylindole and 2-phenylindole) have limited hydrogen-bonding abilities, they are found to bind relatively strongly and remain stable in a binding tunnel. A subsequent analysis of the MD snapshots characterizes two small tunnels leading from the vanadate active site to the surface that could fit small molecules such as hypohalide, halide, and hydrogen peroxide. Density functional theory studies using electric field effects show that a polarized environment in a specific direction can substantially lower barriers for halogen transfer. A further analysis of the protein structure indeed shows a large dipole orientation in the substrate-binding pocket that could enable halogen transfer through an applied local electric field. These findings highlight the importance of the enzyme in catalyzing substrate halogenation by providing an optimal environment to lower the energy barrier for this challenging aromatic halide insertion reaction.
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Affiliation(s)
- Emilie
F. Gérard
- 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
| | - Thirakorn Mokkawes
- 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
| | - Linus O. Johannissen
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jim Warwicker
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- School
of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester 13 9PL, United
Kingdom
| | - Reynard R. Spiess
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Christopher F. Blanford
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Materials, 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
| | - Derren J. Heyes
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, 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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13
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Zwick CR, Renata H. Overview of Amino Acid Modifications by Iron- and α-Ketoglutarate-Dependent Enzymes. ACS Catal 2023. [DOI: 10.1021/acscatal.3c00424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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14
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Yang M, Chen X, Su X, She YB, Yang YF. Mechanistic Study of Chemoselectivity for Carbon Radical Hydroxylation versus Chlorination with Fe III (OH)(Cl) Complexes. Chem Asian J 2023; 18:e202201311. [PMID: 36705485 DOI: 10.1002/asia.202201311] [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: 12/31/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023]
Abstract
The FeIII (OH)(Cl) complex resembles the key intermediate proposed for the non-heme iron halogenases. Goldberg and co-workers reported that the FeIII (OH)(Cl) RC reacts with triphenylmethyl radical 1 to give an exclusive hydroxylation product. To understand the chemoselectivity of the reaction of RC with 1, density functional theory (DFT) calculations have been conducted. From RC, the competing pathways were identified as the OH-transfer, Cl-transfer, and isomerization pathways. The direct Cl-transfer is more favorable than direct OH-transfer by 2.8 kcal/mol. The hydrogen bonding interactions between the hydroxyl group and the pendent amine ligand impede the direct OH-transfer from RC. Compared with the direct Cl-transfer pathway, the isomerization pathways require lower barriers. In isomer RCiso2 , the equatorial hydroxyl group, which has smaller diabatic bond dissociation energy, prefers to transfer to form the hydroxylation product. In FeIII (Cl)2 RC2 and RC2iso , the equatorial chloride group also prefers to transfer to give the chlorination product.
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Affiliation(s)
- Miao Yang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, P. R. China
| | - Xiahe Chen
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, P. R. China
| | - Xingxing Su
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, P. R. China
| | - Yuan-Bin She
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, P. R. China
| | - Yun-Fang Yang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, P. R. China
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15
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Zhou A, Li XX, Sun D, Cao X, Wu Z, Chen H, Zhao Y, Nam W, Wang Y. Theoretical investigation on the elusive structure-activity relationship of bioinspired high-valence nickel-halogen complexes in oxidative fluorination reactions. Dalton Trans 2023; 52:1977-1988. [PMID: 36691931 DOI: 10.1039/d2dt03212k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Very recently, bioinspired high-valence metal-halogen complexes have been proven to be competent oxidants in the C-H bond activation and heteroatom dihalogenation reactions. However, the structure-activity relationship of such active species and the reaction mechanisms of oxidations mediated by these oxidants are still elusive. In this study, density functional theory (DFT) calculations were performed to systematically study the oxidizing ability of the high-valence NiIII-X (X = F and Cl) complexes Et4N[NiIII(Cl/F)(L)], (1Cl/F, Et = ethyl, L = N,N'-(2,6-dimethylphenyl)-2,6-pyridinedicarboxamide), such as the reaction mechanism of fluorination of 1,4-cyclohexadiene (CHD) by 1F in the presence of AgF and the reaction mechanism of difluorination of triphenyl phosphine (PPh3) by 1F. All calculated results fit well with the experiments and present new mechanistic findings. The C-H bond activation by the high-valence nickel(III)-halogen complexes was found to proceed via a hydrogen-atom transfer (HAT) mechanism by analysis of the molecular orbitals of the transition states. C-H bond activation by 1F takes a Ni-F-H angle of ca. 180°, whereas that by 1Cl takes an angle of ca. 120° on the transition states. These results indicate that the exchange-enhanced reactivity is responsible for the dramatic oxidative difference between these two oxidants. The role of AgF in C-H fluorination of CHD by 1F is proposed to act as a Lewis acid adduct, AgF-binding Ni(III)-fluorine complex 1F-Ag-F, which acts both as an oxidant in C-H bond activation and as a fluorine donor in the fluorination step. A cooperative oxidation mechanism involving two 1F oxidants was proposed for the difluorination of PPh3 by 1F. These theoretical findings will enrich the knowledge of high-valence metal-halogen chemistry and play a positive role in the rational design of new catalysts.
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Affiliation(s)
- Anran Zhou
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Xiao-Xi Li
- Institute of Molecular Science and Engineering, Institute of Frontier and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China
| | - Dongru Sun
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Xuanyu Cao
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Zhimin Wu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Huanhuan Chen
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea.
| | - Yong Wang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
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16
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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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17
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Yadav V, Wen L, Rodriguez RJ, Siegler MA, Goldberg DP. Nonheme Iron(III) Azide and Iron(III) Isothiocyanate Complexes: Radical Rebound Reactivity, Selectivity, and Catalysis. J Am Chem Soc 2022; 144:20641-20652. [PMID: 36382466 PMCID: PMC10226418 DOI: 10.1021/jacs.2c07224] [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: 11/06/2022]
Abstract
The new nonheme iron complexes FeII(BNPAPh2O)(N3) (1), FeIII(BNPAPh2O)(OH)(N3) (2), FeII(BNPAPh2O)(OH) (3), FeIII(BNPAPh2O)(OH)(NCS) (4), FeII(BNPAPh2O)(NCS) (5), FeIII(BNPAPh2O)(NCS)2 (6), and FeIII(BNPAPh2O)(N3)2 (7) (BNPAPh2O = 2-(bis((6-(neopentylamino)pyridin-2-yl) methyl)amino)-1,1-diphenylethanolate) were synthesized and characterized by single crystal X-ray diffraction (XRD), as well as by 1H NMR, 57Fe Mössbauer, and ATR-IR spectroscopies. Complex 2 was reacted with a series of carbon radicals, ArX3C· (ArX = p-X-C6H4), analogous to the proposed radical rebound step for nonheme iron hydroxylases and halogenases. The results show that for ArX3C· (X = Cl, H, tBu), only OH· transfer occurs to give ArX3COH. However, when X = OMe, a mixture of alcohol (ArX3COH) (30%) and azide (ArX3CN3) (40%) products was obtained. These data indicate that the rebound selectivity is influenced by the electron-rich nature of the carbon radicals for the azide complex. Reaction of 2 with Ph3C· in the presence of Sc3+ or H+ reverses the selectivity, giving only the azide product. In contrast to the mixed selectivity seen for 2, the reactivity of cis-FeIII(OH)(NCS) with the X = OMe radical derivative leads only to hydroxylation. Catalytic azidation was achieved with 1 as catalyst, λ3-azidoiodane as oxidant and azide source, and Ph3CH as test substrate, giving Ph3CN3 in 84% (TON = 8). These studies show that hydroxylation is favored over azidation for nonheme iron(III) complexes, but the nature of the carbon radical can alter this selectivity. If an OH· transfer pathway can be avoided, the FeIII(N3) complexes are capable of mediating both stoichiometric and catalytic azidation.
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Affiliation(s)
- Vishal Yadav
- Department of Chemistry, The Johns Hopkins
University, 3400 North Charles Street, Baltimore, Maryland, 21218, USA
| | - Lyupeng Wen
- Department of Chemistry, The Johns Hopkins
University, 3400 North Charles Street, Baltimore, Maryland, 21218, USA
| | - Rodolfo J. Rodriguez
- Department of Chemistry, The Johns Hopkins
University, 3400 North Charles Street, Baltimore, Maryland, 21218, USA
| | - Maxime A. Siegler
- Department of Chemistry, The Johns Hopkins
University, 3400 North Charles Street, Baltimore, Maryland, 21218, USA
| | - David P. Goldberg
- Department of Chemistry, The Johns Hopkins
University, 3400 North Charles Street, Baltimore, Maryland, 21218, USA
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18
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Chan NH, Gomez CA, Vennelakanti V, Du Q, Kulik HJ, Lewis JC. Non-Native Anionic Ligand Binding and Reactivity in Engineered Variants of the Fe(II)- and α-Ketoglutarate-Dependent Oxygenase, SadA. Inorg Chem 2022; 61:14477-14485. [PMID: 36044713 PMCID: PMC9789792 DOI: 10.1021/acs.inorgchem.2c02872] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mononuclear non-heme Fe(II)- and α-ketoglutarate-dependent oxygenases (FeDOs) catalyze a site-selective C-H hydroxylation. Variants of these enzymes in which a conserved Asp/Glu residue in the Fe(II)-binding facial triad is replaced by Ala/Gly can, in some cases, bind various anionic ligands and catalyze non-native chlorination and bromination reactions. In this study, we explore the binding of different anions to an FeDO facial triad variant, SadX, and the effects of that binding on HO• vs X• rebound. We establish not only that chloride and bromide enable non-native halogenation reactions but also that all anions investigated, including azide, cyanate, formate, and fluoride, significantly accelerate and influence the site selectivity of SadX hydroxylation catalysis. Azide and cyanate also lead to the formation of products resulting from N3•, NCO•, and OCN• rebound. While fluoride rebound is not observed, the rate acceleration provided by this ligand leads us to calculate barriers for HO• and F• rebound from a putative Fe(III)(OH)(F) intermediate. These calculations suggest that the lack of fluorination is due to the relative barriers of the HO• and F• rebound transition states rather than an inaccessible barrier for F• rebound. Together, these results improve our understanding of the FeDO facial triad variant tolerance of different anionic ligands, their ability to promote rebound involving these ligands, and inherent rebound preferences relative to HO• that will aid efforts to develop non-native catalysis using these enzymes.
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Affiliation(s)
- Natalie H. Chan
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Christian A. Gomez
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Qian Du
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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19
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Omura K, Aiba Y, Suzuki K, Ariyasu S, Sugimoto H, Shoji O. A P450 Harboring Manganese Protoporphyrin IX Generates a Manganese Analogue of Compound I by Activating Dioxygen. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Keita Omura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yuichiro Aiba
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kazuto Suzuki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shinya Ariyasu
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Hiroshi Sugimoto
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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20
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Kumar R, Awasthi A, Gupta S, Eerlapally R, Draksharapu A. Spectroscopic characterization of a Ru(III)-OCl intermediate: a structural mimic of haloperoxidase enzymes. Dalton Trans 2022; 51:12848-12854. [PMID: 35968730 DOI: 10.1039/d2dt01947g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Haloperoxidase enzymes utilize metal hypohalite species to halogenate aliphatic and aromatic C-H bonds to C-X (X = Cl, Br, I) in nature. In this work, we report the synthesis and spectroscopic characterization of a unique RuIII-OCl species as a structural mimic of haloperoxidase enzymes. The reaction of [(BnTPEN)RuII(NCCH3)]2+ (BnTPEN = N1-benzyl-N1,N2,N2-tris(pyridine-2-ylmethyl)ethane-1,2-diamine) with hypochlorite in the presence of an acid in CH3CN : H2O mixtures generated a novel [(BnTPEN)RuIII-OCl]2+ species that persists for 4.5 h at room temperature. This new species was characterized by UV-vis absorption, EPR, and resonance Raman spectroscopic techniques, and ESI-MS. The RuIII-OCl species is capable of performing oxygen atom transfer and hydrogen atom abstraction to various organic substrates.
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Affiliation(s)
- Rakesh Kumar
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Ayushi Awasthi
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Sikha Gupta
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Raju Eerlapally
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Apparao Draksharapu
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
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21
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Zhou TP, Deng WH, Wu Y, Liao RZ. QM/MM Calculations Suggested Concerted O‒O Bond Cleavage and Substrate Oxidation by Nonheme Diiron Toluene/o‐xylene Monooxygenase. Chem Asian J 2022; 17:e202200490. [DOI: 10.1002/asia.202200490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/01/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Tai-Ping Zhou
- Huazhong University of Science and Technology School of chemistry and chemical engineering CHINA
| | - Wen-Hao Deng
- Huazhong University of Science and Technology School of chemistry and chemical engineering CHINA
| | - Yuzhou Wu
- Huazhong University of Science and Technology School of chemistry and chemical engineering CHINA
| | - Rong-Zhen Liao
- Huazhong University of Science and technology College of Chemistry and Chemical Engeneering Luoyulu 1037 430074 Wuhan CHINA
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22
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Gérard EF, Yadav V, Goldberg DP, de Visser SP. What Drives Radical Halogenation versus Hydroxylation in Mononuclear Nonheme Iron Complexes? A Combined Experimental and Computational Study. J Am Chem Soc 2022; 144:10752-10767. [PMID: 35537044 PMCID: PMC9228086 DOI: 10.1021/jacs.2c01375] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Nonheme iron halogenases
are unique enzymes in nature that selectively
activate an aliphatic C–H bond of a substrate to convert it
into C–X (X = Cl/Br, but not F/I). It is proposed that they
generate an FeIII(OH)(X) intermediate in their catalytic
cycle. The analogous FeIII(OH) intermediate in nonheme
iron hydroxylases transfers OH• to give alcohol
product, whereas the halogenases transfer X• to
the carbon radical substrate. There remains significant debate regarding
what factors control their remarkable selectivity of the halogenases.
The reactivity of the complexes FeIII(BNPAPh2O)(OH)(X) (X = Cl, Br) with a secondary carbon radical (R•) is described. It is found that X• transfer occurs
with a secondary carbon radical, as opposed to OH• transfer with tertiary radicals. Comprehensive computational studies
involving density functional theory were carried out to examine the
possible origins of this selectivity. The calculations reproduce the
experimental findings, which indicate that halogen transfer is not
observed for the tertiary radicals because of a nonproductive equilibrium
that results from the endergonic nature of these reactions, despite
a potentially lower reaction barrier for the halogenation pathway.
In contrast, halogen transfer is favored for secondary carbon radicals,
for which the halogenated product complex is thermodynamically more
stable than the reactant complex. These results are rationalized by
considering the relative strengths of the C–X bonds that are
formed for tertiary versus secondary carbon centers. The computational
analysis also shows that the reaction barrier for halogen transfer
is significantly dependent on secondary coordination sphere effects,
including steric and H-bonding interactions.
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Affiliation(s)
- Emilie F Gérard
- 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
| | - Vishal Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - 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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23
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Vennelakanti V, Mehmood R, Kulik HJ. Are Vanadium Intermediates Suitable Mimics in Non-Heme Iron Enzymes? An Electronic Structure Analysis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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
| | - 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
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24
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Structural and Functional Insights into a Nonheme Iron- and α-Ketoglutarate-Dependent Halogenase That Catalyzes Chlorination of Nucleotide Substrates. Appl Environ Microbiol 2022; 88:e0249721. [PMID: 35435717 DOI: 10.1128/aem.02497-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Nonheme iron- and α-ketoglutarate (αKG)-dependent halogenases (NHFeHals), which catalyze the regio- and stereoselective halogenation of the unactivated C(sp3)-H bonds, exhibit tremendous potential in the challenging asymmetric halogenation. AdeV from Actinomadura sp. ATCC 39365 is the first identified carrier protein-free NHFeHal that catalyzes the chlorination of nucleotide 2'-deoxyadenosine-5'-monophosphate (2'-dAMP) to afford 2'-chloro-2'-deoxyadenosine-5'-monophosphate. Here, we determined the complex crystal structures of AdeV/FeII/Cl and AdeV/FeII/Cl/αKG at resolutions of 1.76 and 1.74 Å, respectively. AdeV possesses a typical β-sandwich topology with H194, H252, αKG, chloride, and one water molecule coordinating FeII in the active site. Molecular docking, mutagenesis, and biochemical analyses reveal that the hydrophobic interactions and hydrogen bond network between the substrate-binding pocket and the adenine, deoxyribose, and phosphate moieties of 2'-dAMP are essential for substrate recognition. Residues H111, R177, and H192 might play important roles in the second-sphere interactions that control reaction partitioning. This study provides valuable insights into the catalytic selectivity of AdeV and will facilitate the rational engineering of AdeV and other NHFeHals for synthesis of halogenated nucleotides. IMPORTANCE Halogenated nucleotides are a group of important antibiotics and are clinically used as antiviral and anticancer drugs. AdeV is the first carrier protein-independent nonheme iron- and α-ketoglutarate (αKG)-dependent halogenase (NHFeHal) that can selectively halogenate nucleotides and exhibits restricted substrate specificity toward several 2'-dAMP analogues. Here, we determined the complex crystal structures of AdeV/FeII/Cl and AdeV/FeII/Cl/αKG. Molecular docking, mutagenesis, and biochemical analyses provide important insights into the catalytic selectivity of AdeV. This study will facilitate the rational engineering of AdeV and other carrier protein-independent NHFeHals for synthesis of halogenated nucleotides.
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25
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Wojdyla Z, Borowski T. Properties of the Reactants and Their Interactions within and with the Enzyme Binding Cavity Determine Reaction Selectivities. The Case of Fe(II)/2-Oxoglutarate Dependent Enzymes. Chemistry 2022; 28:e202104106. [PMID: 34986268 DOI: 10.1002/chem.202104106] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 12/12/2022]
Abstract
Fe(II)/2-oxoglutarate dependent dioxygenases (ODDs) share a double stranded beta helix (DSBH) fold and utilise a common reactive intermediate, ferryl species, to catalyse oxidative transformations of substrates. Despite the structural similarities, ODDs accept a variety of substrates and facilitate a wide range of reactions, that is hydroxylations, desaturations, (oxa)cyclisations and ring rearrangements. In this review we present and discuss the factors contributing to the observed (regio)selectivities of ODDs. They span from inherent properties of the reactants, that is, substrate molecule and iron cofactor, to the interactions between the substrate and the enzyme's binding cavity; the latter can counterbalance the effect of the former. Based on results of both experimental and computational studies dedicated to ODDs, we also line out the properties of the reactants which promote reaction outcomes other than the "default" hydroxylation. It turns out that the reaction selectivity depends on a delicate balance of interactions between the components of the investigated system.
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Affiliation(s)
- Zuzanna Wojdyla
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
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26
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Bal M, Østergaard L. Hormonal Influences on Pod-Seed Intercommunication during Pea Fruit Development. Genes (Basel) 2021; 13:49. [PMID: 35052390 PMCID: PMC8774696 DOI: 10.3390/genes13010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/09/2021] [Accepted: 12/16/2021] [Indexed: 11/17/2022] Open
Abstract
Angiosperms (from the Greek "angeion"-vessel, and "sperma"-seed) are defined by the presence of specialised tissue surrounding their developing seeds. This tissue is known as the ovary and once a flower has been fertilised, it gives rise to the fruit. Fruits serve various functions in relation to the seeds they contain: they often form tough physical barriers to prevent mechanical damage, they may form specialised structures that aid in dispersal, and they act as a site of nutrient and signal exchange between the parent plant and its offspring. The close coordination of fruit growth and seed development is essential to successful reproduction. Firstly, fertilisation of the ovules is required in most angiosperm species to initiate fruit growth. Secondly, it is crucial that seed dispersal facilitated by, e.g., fruit opening or ripening occurs only once the seeds have matured. These highly coordinated events suggest that seeds and fruits are in close communication throughout development and represent a classical problem of interorgan signalling and organismic resource allocation. Here, we review the contribution of studies on the edible, unicarpellate legume Pisum sativum to our understanding of seed and fruit growth coregulation, and propose areas of new research in this species which may yield important advances for both pulse agronomy and natural science.
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27
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Pessoa JC, Santos MF, Correia I, Sanna D, Sciortino G, Garribba E. Binding of vanadium ions and complexes to proteins and enzymes in aqueous solution. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214192] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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28
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Farley GW, Siegler MA, Goldberg DP. Halogen Transfer to Carbon Radicals by High-Valent Iron Chloride and Iron Fluoride Corroles. Inorg Chem 2021; 60:17288-17302. [PMID: 34709780 DOI: 10.1021/acs.inorgchem.1c02666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
High-valent iron halide corroles were examined to determine their reactivity with carbon radicals and their ability to undergo radical rebound-like processes. Beginning with Fe(Cl)(ttppc) (1) (ttppc = 5,10,15-tris(2,4,6-triphenylphenyl)corrolato3-), the new iron corroles Fe(OTf)(ttppc) (2), Fe(OTf)(ttppc)(AgOTf) (3), and Fe(F)(ttppc) (4) were synthesized. Complexes 3 and 4 are the first iron triflate and iron fluoride corroles to be structurally characterized by single crystal X-ray diffraction. The structure of 3 reveals an AgI-pyrrole (η2-π) interaction. The Fe(Cl)(ttppc) and Fe(F)(ttppc) complexes undergo halogen transfer to triarylmethyl radicals, and kinetic analysis of the reaction between (p-OMe-C6H4)3C• and 1 gave k = 1.34(3) × 103 M-1 s-1 at 23 °C and 2.2(2) M-1 s-1 at -60 °C, ΔH⧧ = +9.8(3) kcal mol-1, and ΔS⧧ = -14(1) cal mol-1 K-1 through an Eyring analysis. Complex 4 is significantly more reactive, giving k = 1.16(6) × 105 M-1 s-1 at 23 °C. The data point to a concerted mechanism and show the trend X = F- > Cl- > OH- for Fe(X)(ttppc). This study provides mechanistic insights into halogen rebound for an iron porphyrinoid complex.
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Affiliation(s)
- Geoffrey W Farley
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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29
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Mal S, Jana M, Sarkar S. Recent Update on Transition Metal‐Free C(sp
2
)−H Bond Halogenation in (Hetero) Arenes. ChemistrySelect 2021. [DOI: 10.1002/slct.202102956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sourav Mal
- Department of Chemistry University of Kalyani Kalyani 741235 West Bengal India
| | - Manoranjan Jana
- Department of Chemistry University of Kalyani Kalyani 741235 West Bengal India
| | - Satinath Sarkar
- Department of Chemistry University of Kalyani Kalyani 741235 West Bengal India
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30
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Crowe C, Molyneux S, Sharma SV, Zhang Y, Gkotsi DS, Connaris H, Goss RJM. Halogenases: a palette of emerging opportunities for synthetic biology-synthetic chemistry and C-H functionalisation. Chem Soc Rev 2021; 50:9443-9481. [PMID: 34368824 PMCID: PMC8407142 DOI: 10.1039/d0cs01551b] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Indexed: 12/14/2022]
Abstract
The enzymatic generation of carbon-halogen bonds is a powerful strategy used by both nature and synthetic chemists to tune the bioactivity, bioavailability and reactivity of compounds, opening up the opportunity for selective C-H functionalisation. Genes encoding halogenase enzymes have recently been shown to transcend all kingdoms of life. These enzymes install halogen atoms into aromatic and less activated aliphatic substrates, achieving selectivities that are often challenging to accomplish using synthetic methodologies. Significant advances in both halogenase discovery and engineering have provided a toolbox of enzymes, enabling the ready use of these catalysts in biotransformations, synthetic biology, and in combination with chemical catalysis to enable late stage C-H functionalisation. With a focus on substrate scope, this review outlines the mechanisms employed by the major classes of halogenases, while in parallel, it highlights key advances in the utilisation of the combination of enzymatic halogenation and chemical catalysis for C-H activation and diversification.
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Affiliation(s)
- Charlotte Crowe
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Samuel Molyneux
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Sunil V. Sharma
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Ying Zhang
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Danai S. Gkotsi
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Helen Connaris
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Rebecca J. M. Goss
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
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31
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Li C, Bao W, Zhang H, Lyu Z, Chen Y, Guo Z. Discovery of Brominated Alboflavusins With Anti-MRSA Activities. Front Microbiol 2021; 12:641025. [PMID: 33664724 PMCID: PMC7920986 DOI: 10.3389/fmicb.2021.641025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 01/27/2021] [Indexed: 11/17/2022] Open
Abstract
As methicillin-resistant Staphylococcus aureus (MRSA) is becoming a serious pathogenic threaten to human health worldwide, there is an urgent need to discover new antibiotics for the treatment of MRSA infections. Alboflavusins (AFNs) are a group of halogenated cyclohexapeptides with anti-MRSA activities. In this study, two novel brominated AFN congeners (compounds 1 and 2) were isolated from the wild-type strain Streptomyces alboflavus sp. 313 that was fermented in the production medium supplemented with NaBr; two new (compounds 3 and 5) and a known (compound 4) dehelogenated AFN congeners were isolated from S. alboflavus ΔafnX, in which the tryptophan halogenase gene afnX was inactivated. The structures of these compounds were assigned by careful NMR and MS analyses. The anti-MRSA activities of varied AFN congeners were assessed against different MRSA strains, which revealed that compounds 1 and 2 with bromine displayed effective activities against the tested MRSA strains. Especially, compound 2 showed good anti-MRSA activity, while compounds 3, 4, and 5 without halogen exhibited weak anti-MRSA activities, outlining the influence of halogen substitution to the bioactivities of AFNs.
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Affiliation(s)
- Chao Li
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wuyundalai Bao
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Haoyue Zhang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, China
| | - Zhitang Lyu
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhengyan Guo
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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32
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Yadav V, Siegler MA, Goldberg DP. Temperature-Dependent Reactivity of a Non-heme Fe III(OH)(SR) Complex: Relevance to Isopenicillin N Synthase. J Am Chem Soc 2021; 143:46-52. [PMID: 33356198 DOI: 10.1021/jacs.0c09688] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Non-heme iron complexes with cis-FeIII(OH)(SAr/OAr) coordination were isolated and examined for their reactivity with a tertiary carbon radical. The sulfur-ligated complex shows a temperature dependence on •OH versus ArS• transfer, whereas the oxygen-ligated complex does not. These results provide the first working model for C-S bond formation in isopenicillin N synthase and indicate that kinetic control may be a key factor in the selectivity of non-heme iron "rebound" processes.
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Affiliation(s)
- Vishal Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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33
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Kluza A, Wojdyla Z, Mrugala B, Kurpiewska K, Porebski PJ, Niedzialkowska E, Minor W, Weiss MS, Borowski T. Regioselectivity of hyoscyamine 6β-hydroxylase-catalysed hydroxylation as revealed by high-resolution structural information and QM/MM calculations. Dalton Trans 2020; 49:4454-4469. [PMID: 32182320 DOI: 10.1039/d0dt00302f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Hyoscyamine 6β-hydroxylase (H6H) is a bifunctional non-heme 2-oxoglutarate/Fe2+-dependent dioxygenase that catalyzes the two final steps in the biosynthesis of scopolamine. Based on high resolution crystal structures of H6H from Datura metel, detailed information on substrate binding was obtained that provided insights into the onset of the enzymatic process. In particular, the role of two prominent residues was revealed - Glu-116 that interacts with the tertiary amine located on the hyoscyamine tropane moiety and Tyr-326 that forms CH-π hydrogen bonds with the hyoscyamine phenyl ring. The structures were used as the basis for QM/MM calculations that provided an explanation for the regioselectivity of the hydroxylation reaction on the hyoscyamine tropane moiety (C6 vs. C7) and quantified contributions of active site residues to respective barrier heights.
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Affiliation(s)
- Anna Kluza
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.
| | - Zuzanna Wojdyla
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.
| | - Beata Mrugala
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.
| | - Katarzyna Kurpiewska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland. and Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, PL-30387 Krakow, Poland
| | - Przemyslaw J Porebski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland. and Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908, USA
| | - Ewa Niedzialkowska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland. and Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908, USA
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, D-12489, Berlin, Germany
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.
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34
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Mubarak MQE, Gérard EF, Blanford CF, Hay S, de Visser SP. How Do Vanadium Chloroperoxidases Generate Hypochlorite from Hydrogen Peroxide and Chloride? A Computational Study. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03490] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- M. Qadri E. Mubarak
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Emilie F. Gérard
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Christopher F. Blanford
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Materials, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Sam Hay
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Sam P. de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
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35
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It takes two to tango - The case of thebaine 6-O-demethylase. Int J Biol Macromol 2020; 163:718-729. [DOI: 10.1016/j.ijbiomac.2020.07.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 11/21/2022]
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36
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Menon BRK, Richmond D, Menon N. Halogenases for biosynthetic pathway engineering: Toward new routes to naturals and non-naturals. CATALYSIS REVIEWS-SCIENCE AND ENGINEERING 2020. [DOI: 10.1080/01614940.2020.1823788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Binuraj R. K. Menon
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
| | - Daniel Richmond
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
| | - Navya Menon
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
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37
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Minges H, Sewald N. Recent Advances in Synthetic Application and Engineering of Halogenases. ChemCatChem 2020. [DOI: 10.1002/cctc.202000531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hannah Minges
- Organic and Bioorganic Chemistry Department of Chemistry Bielefeld University Universitätsstraße 25 33501 Bielefeld Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry Department of Chemistry Bielefeld University Universitätsstraße 25 33501 Bielefeld Germany
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38
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Exploring the Biocatalytic Potential of Fe/α‐Ketoglutarate‐Dependent Halogenases. Chemistry 2020; 26:7336-7345. [DOI: 10.1002/chem.201905752] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 12/18/2022]
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39
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Aslan‐Üzel AS, Beier A, Kovář D, Cziegler C, Padhi SK, Schuiten ED, Dörr M, Böttcher D, Hollmann F, Rudroff F, Mihovilovic MD, Buryška T, Damborský J, Prokop Z, Badenhorst CPS, Bornscheuer UT. An Ultrasensitive Fluorescence Assay for the Detection of Halides and Enzymatic Dehalogenation. ChemCatChem 2020; 12:2032-2039. [PMID: 32362951 PMCID: PMC7188320 DOI: 10.1002/cctc.201901891] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/16/2019] [Indexed: 12/31/2022]
Abstract
Halide assays are important for the study of enzymatic dehalogenation, a topic of great industrial and scientific importance. Here we describe the development of a very sensitive halide assay that can detect less than a picomole of bromide ions, making it very useful for quantifying enzymatic dehalogenation products. Halides are oxidised under mild conditions using the vanadium-dependent chloroperoxidase from Curvularia inaequalis, forming hypohalous acids that are detected using aminophenyl fluorescein. The assay is up to three orders of magnitude more sensitive than currently available alternatives, with detection limits of 20 nM for bromide and 1 μM for chloride and iodide. We demonstrate that the assay can be used to determine specific activities of dehalogenases and validate this by comparison to a well-established GC-MS method. This new assay will facilitate the identification and characterisation of novel dehalogenases and may also be of interest to those studying other halide-producing enzymes.
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Affiliation(s)
- Aşkın S. Aslan‐Üzel
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Andy Beier
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - David Kovář
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Clemens Cziegler
- Institute of Applied Synthetic ChemistryTU WienVienna1060Austria
| | - Santosh K. Padhi
- Biocatalysis and Enzyme Engineering Laboratory Department of Biochemistry School of Life SciencesUniversity of HyderabadGachibowli500046India
| | - Eva D. Schuiten
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Mark Dörr
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Dominique Böttcher
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Frank Hollmann
- Department of BiotechnologyDelft University of TechnologyDelft2629 HZ (TheNetherlands
| | - Florian Rudroff
- Institute of Applied Synthetic ChemistryTU WienVienna1060Austria
| | | | - Tomáš Buryška
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
| | - Jiří Damborský
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Zbyněk Prokop
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
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40
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Vila MA, Steck V, Rodriguez Giordano S, Carrera I, Fasan R. C-H Amination via Nitrene Transfer Catalyzed by Mononuclear Non-Heme Iron-Dependent Enzymes. Chembiochem 2020; 21:1981-1987. [PMID: 32189465 DOI: 10.1002/cbic.201900783] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/12/2020] [Indexed: 12/18/2022]
Abstract
Expanding the reaction scope of natural metalloenzymes can provide new opportunities for biocatalysis. Mononuclear non-heme iron-dependent enzymes represent a large class of biological catalysts involved in the biosynthesis of natural products and catabolism of xenobiotics, among other processes. Here, we report that several members of this enzyme family, including Rieske dioxygenases as well as α-ketoglutarate-dependent dioxygenases and halogenases, are able to catalyze the intramolecular C-H amination of a sulfonyl azide substrate, thereby exhibiting a promiscuous nitrene transfer reactivity. One of these enzymes, naphthalene dioxygenase (NDO), was further engineered resulting in several active site variants that function as C-H aminases. Furthermore, this enzyme could be applied to execute this non-native transformation on a gram scale in a bioreactor, thus demonstrating its potential for synthetic applications. These studies highlight the functional versatility of non-heme iron-dependent enzymes and pave the way to their further investigation and development as promising biocatalysts for non-native metal-catalyzed transformations.
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Affiliation(s)
- Maria Agustina Vila
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Química Orgánica y Departamento de Biociencias. Facultad de Química, Universidad de la República, Av General Flores 2124, CP 11800, Montevideo, Uruguay
| | - Viktoria Steck
- Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY 14627, USA
| | - Sonia Rodriguez Giordano
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Química Orgánica y Departamento de Biociencias. Facultad de Química, Universidad de la República, Av General Flores 2124, CP 11800, Montevideo, Uruguay
| | - Ignacio Carrera
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Química Orgánica y Departamento de Biociencias. Facultad de Química, Universidad de la República, Av General Flores 2124, CP 11800, Montevideo, Uruguay
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY 14627, USA
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41
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Visser SP. Second‐Coordination Sphere Effects on Selectivity and Specificity of Heme and Nonheme Iron Enzymes. Chemistry 2020; 26:5308-5327. [DOI: 10.1002/chem.201905119] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/04/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Sam P. Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
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42
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Mubarak MQE, Visser SP. Computational Study on the Catalytic Reaction Mechanism of Heme Haloperoxidase Enzymes. Isr J Chem 2019. [DOI: 10.1002/ijch.201900099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- M. Qadri E. Mubarak
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science The University of Manchester 131 Princess Street Manchester M1 7DN United Kingdom
| | - Sam P. Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science The University of Manchester 131 Princess Street Manchester M1 7DN United Kingdom
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43
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Recent Advances in Flavin-Dependent Halogenase Biocatalysis: Sourcing, Engineering, and Application. Catalysts 2019. [DOI: 10.3390/catal9121030] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The introduction of a halogen atom into a small molecule can effectively modulate its properties, yielding bioactive substances of agrochemical and pharmaceutical interest. Consequently, the development of selective halogenation strategies is of high technological value. Besides chemical methodologies, enzymatic halogenations have received increased interest as they allow the selective installation of halogen atoms in molecular scaffolds of varying complexity under mild reaction conditions. Today, a comprehensive library of aromatic halogenases exists, and enzyme as well as reaction engineering approaches are being explored to broaden this enzyme family’s biocatalytic application range. In this review, we highlight recent developments in the sourcing, engineering, and application of flavin-dependent halogenases with a special focus on chemoenzymatic and coupled biosynthetic approaches.
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44
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Yadav V, Gordon JB, Siegler MA, Goldberg DP. Dioxygen-Derived Nonheme Mononuclear Fe III(OH) Complex and Its Reactivity with Carbon Radicals. J Am Chem Soc 2019; 141:10148-10153. [PMID: 31244183 DOI: 10.1021/jacs.9b03329] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A new tetradentate, monoanionic, mixed N/O donor ligand (BNPAPh2O-) with second coordination sphere H-bonding groups has been synthesized for stabilization of a terminal FeIII(OH) complex. The complex FeII(BNPAPh2O)(OTf) (1) reacts with O2 to give a mononuclear terminal FeIII(OH) complex, FeIII(OH)(BNPAPh2O)(OTf) (2), both of which were characterized by X-ray diffraction, electrospray ionization mass spectrometry, UV-vis, 1H and 19F nuclear magnetic resonance, 57Fe Mössbauer, and electron paramagnetic resonance spectroscopies. Treatment of 2 with carbon radicals (Ar3C·) gives Ar3COH and the FeII complex 1, in direct analogy with the elusive radical "rebound" process proposed for nonheme iron enzymes.
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Affiliation(s)
- Vishal Yadav
- Department of Chemistry , The Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Jesse B Gordon
- Department of Chemistry , The Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Maxime A Siegler
- Department of Chemistry , The Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - David P Goldberg
- Department of Chemistry , The Johns Hopkins University , Baltimore , Maryland 21218 , United States
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Mehmood R, Qi HW, Steeves AH, Kulik HJ. The Protein’s Role in Substrate Positioning and Reactivity for Biosynthetic Enzyme Complexes: The Case of SyrB2/SyrB1. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00865] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Nicolaou M, Drouza C, Keramidas AD. Controlled one pot synthesis of polyoxofluorovanadate molecular hybrids exhibiting peroxidase like activity. NEW J CHEM 2019. [DOI: 10.1039/c9nj01999e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
VV/IV mixed-valence polyoxofluorovanadate clusters have been synthesized through one pot preparation process. The trigonal bipyramidal coordinated vanadium atoms mimic the structure of the active site and activity of the vanadium peroxidases.
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Affiliation(s)
- Maria Nicolaou
- Department of Chemistry
- University of Cyprus
- Nicosia 1678
- Cyprus
| | - Chryssoula Drouza
- Cyprus University of Technology
- Department of Agricultural Production
- Biotechnology and Food Science
- Limassol 3036
- Cyprus
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Timmins A, Fowler NJ, Warwicker J, Straganz GD, de Visser SP. Does Substrate Positioning Affect the Selectivity and Reactivity in the Hectochlorin Biosynthesis Halogenase? Front Chem 2018; 6:513. [PMID: 30425979 PMCID: PMC6218459 DOI: 10.3389/fchem.2018.00513] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022] Open
Abstract
In this work we present the first computational study on the hectochlorin biosynthesis enzyme HctB, which is a unique three-domain halogenase that activates non-amino acid moieties tethered to an acyl-carrier, and as such may have biotechnological relevance beyond other halogenases. We use a combination of small cluster models and full enzyme structures calculated with quantum mechanics/molecular mechanics methods. Our work reveals that the reaction is initiated with a rate-determining hydrogen atom abstraction from substrate by an iron (IV)-oxo species, which creates an iron (III)-hydroxo intermediate. In a subsequent step the reaction can bifurcate to either halogenation or hydroxylation of substrate, but substrate binding and positioning drives the reaction to optimal substrate halogenation. Furthermore, several key residues in the protein have been identified for their involvement in charge-dipole interactions and induced electric field effects. In particular, two charged second coordination sphere amino acid residues (Glu223 and Arg245) appear to influence the charge density on the Cl ligand and push the mechanism toward halogenation. Our studies, therefore, conclude that nonheme iron halogenases have a chemical structure that induces an electric field on the active site that affects the halide and iron charge distributions and enable efficient halogenation. As such, HctB is intricately designed for a substrate halogenation and operates distinctly different from other nonheme iron halogenases.
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Affiliation(s)
- Amy Timmins
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
| | - Nicholas J. Fowler
- The Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Jim Warwicker
- The Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Grit D. Straganz
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
- Institute of Molecular Biosciences, Graz University, Graz, Austria
| | - Sam P. de Visser
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
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