51
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Gu Y, Bloomer BJ, Liu Z, Chen R, Clark DS, Hartwig JF. Directed Evolution of Artificial Metalloenzymes in Whole Cells. Angew Chem Int Ed Engl 2022; 61:e202110519. [PMID: 34766418 PMCID: PMC9707807 DOI: 10.1002/anie.202110519] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/15/2021] [Indexed: 01/28/2023]
Abstract
Artificial metalloenzymes (ArMs), created by introducing synthetic cofactors into protein scaffolds, are an emerging class of catalyst for non-natural reactions. Although many classes of ArMs are known, in vitro reconstitution of cofactors and proteins has been a limiting step in the high-throughput screening and directed evolution of ArMs because purification of individual host proteins is time-consuming. We describe the application of a platform to combine mutants of the P450 enzyme CYP119 and the cofactor Ir(Me)MPIX in vivo, by coexpression of the CYP119 mutants with the heme transporter encoded by the hug operon, to the directed evolution of ArMs containing Ir(Me)MPIX in whole cells. We applied this platform to the development an ArMs catalyzing the insertion of the acyclic carbene from α-diazopropanoate esters (Me-EDA) into the N-H bonds of N-alkyl anilines, a combination of carbene and amine classes for which mutant enzymes of natural hemoproteins previously reacted with low enantioselectivity. The mutants of the artificial metalloenzyme Ir(Me)CYP119 identified by an evolution campaign involving more than 4000 mutants are shown to catalyze the reaction of Me-EDA with N-methyl anilines to form chiral chiral amino esters with high TON and good enantioselectivity, thereby demonstrating that the directed evolution of ArMs can rival that of natural enzymes in vivo.
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Affiliation(s)
- Yang Gu
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Present address: CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Brandon J Bloomer
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Zhennan Liu
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Reichi Chen
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - John F Hartwig
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
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52
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Cammarota RC, Liu W, Bacsa J, Davies HML, Sigman MS. Mechanistically Guided Workflow for Relating Complex Reactive Site Topologies to Catalyst Performance in C–H Functionalization Reactions. J Am Chem Soc 2022; 144:1881-1898. [DOI: 10.1021/jacs.1c12198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ryan C. Cammarota
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Wenbin Liu
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - John Bacsa
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Huw M. L. Davies
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Matthew S. Sigman
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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53
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Lennartz F, Jeoung JH, Ruenger S, Dobbek H, Weiss MS. Determining the oxidation state of elements by X-ray crystallography. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:238-247. [PMID: 35102889 PMCID: PMC8805299 DOI: 10.1107/s2059798321013048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/08/2021] [Indexed: 11/10/2022]
Abstract
Protein-mediated redox reactions play a critical role in many biological processes and often occur at centres that contain metal ions as cofactors. In order to understand the exact mechanisms behind these reactions it is important to not only characterize the three-dimensional structures of these proteins and their cofactors, but also to identify the oxidation states of the cofactors involved and to correlate this knowledge with structural information. The only suitable approach for this based on crystallographic measurements is spatially resolved anomalous dispersion (SpReAD) refinement, a method that has been used previously to determine the redox states of metals in iron–sulfur cluster-containing proteins. In this article, the feasibility of this approach for small, non-iron–sulfur redox centres is demonstrated by employing SpReAD analysis to characterize Sulfolobus tokodaii sulerythrin, a ruberythrin-like protein that contains a binuclear metal centre. Differences in oxidation states between the individual iron ions of the binuclear metal centre are revealed in sulerythrin crystals treated with H2O2. Furthermore, data collection at high X-ray doses leads to photoreduction of this metal centre, showing that careful control of the total absorbed dose is a prerequisite for successfully determining the oxidation state through SpReAD analysis.
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54
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Liu Z, Huang J, Gu Y, Clark DS, Mukhopadhyay A, Keasling JD, Hartwig JF. Assembly and Evolution of Artificial Metalloenzymes within E. coli Nissle 1917 for Enantioselective and Site-Selective Functionalization of C─H and C═C Bonds. J Am Chem Soc 2022; 144:883-890. [PMID: 34985270 DOI: 10.1021/jacs.1c10975] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The potential applications afforded by the generation and reactivity of artificial metalloenzymes (ArMs) in microorganisms are vast. We show that a non-pathogenic E. coli strain, Nissle 1917 (EcN), is a suitable host for the creation of ArMs from cytochrome P450s and artificial heme cofactors. An outer-membrane receptor in EcN transports an iridium porphyrin into the cell, and the Ir-CYP119 (CYP119 containing iridium porphyrin) assembled in vivo catalyzes carbene insertions into benzylic C-H bonds enantioselectively and site-selectively. The application of EcN as a whole-cell screening platform eliminates the need for laborious processing procedures, drastically increases the ease and throughput of screening, and accelerates the development of Ir-CYP119 with improved catalytic properties. Studies to identify the transport machinery suggest that a transporter different from the previously assumed ChuA receptor serves to usher the iridium porphyrin into the cytoplasm.
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Affiliation(s)
- Zhennan Liu
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jing Huang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
| | - Yang Gu
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Aindrila Mukhopadhyay
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States.,Department of Bioengineering, University of California, Berkeley, California 94720, United States.,Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen 518055, China.,Center for Biosustainability, Danish Technical University, Lyngby 2800 Kgs, Denmark
| | - John F Hartwig
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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55
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Stein A, Liang AD, Sahin R, Ward TR. Incorporation of Metal-Chelating Unnatural Amino Acids into HaloTag for Allylic Deamination. J Organomet Chem 2022. [DOI: 10.1016/j.jorganchem.2022.122272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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56
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Ren X, Chandgude AL, Carminati DM, Shen Z, Khare SD, Fasan R. Highly stereoselective and enantiodivergent synthesis of cyclopropylphosphonates with engineered carbene transferases. Chem Sci 2022; 13:8550-8556. [PMID: 35974764 PMCID: PMC9337741 DOI: 10.1039/d2sc01965e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/06/2022] [Indexed: 12/18/2022] Open
Abstract
Organophosphonate compounds have represented a rich source of biologically active compounds, including enzyme inhibitors, antibiotics, and antimalarial agents. Here, we report the development of a highly stereoselective strategy for olefin cyclopropanation in the presence of a phosphonyl diazo reagent as carbene precursor. In combination with a ‘substrate walking’ protein engineering strategy, two sets of efficient and enantiodivergent myoglobin-based biocatalysts were developed for the synthesis of both (1R,2S) and (1S,2R) enantiomeric forms of the desired cyclopropylphosphonate ester products. This methodology enables the efficient transformation of a broad range of vinylarene substrates at a preparative scale (i.e. gram scale) with up to 99% de and ee. Mechanistic studies provide insights into factors that contribute to make this reaction inherently more challenging than hemoprotein-catalyzed olefin cyclopropanation with ethyl diazoacetate investigated previously. This work expands the range of synthetically useful, enzyme-catalyzed transformations and paves the way to the development of metalloprotein catalysts for abiological carbene transfer reactions involving non-canonical carbene donor reagents. Two enantiocomplementary myoglobin-based carbene transfer biocatalysts were developed for the synthesis of cyclopropylphosphonate esters with high diastereo- and enantioselectivity and in high yields.![]()
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Affiliation(s)
- Xinkun Ren
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
| | - Ajay L. Chandgude
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
| | - Daniela M. Carminati
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
| | - Zhuofan Shen
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, USA
| | - Sagar D. Khare
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, USA
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
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57
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Chen X, Cao C, Yang YF, She YB. Computational Insights into Different Regioselectivities in Ir-Porphyrin-Catalyzed C–H Insertion Reaction of Quinoid Carbene. Org Chem Front 2022. [DOI: 10.1039/d1qo01727f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanisms and regioselectivities of Ir-porphyrin-catalyzed C–H insertion reaction of quinoid carbene (QC) were investigated with density functional theory (DFT) calculations. The competing catalytic cycles were identified as the hydrogen-atom...
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58
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Lemon CM, Nissley AJ, Latorraca NR, Wittenborn EC, Marletta MA. Corrole–protein interactions in H-NOX and HasA. RSC Chem Biol 2022; 3:571-581. [PMID: 35656484 PMCID: PMC9092467 DOI: 10.1039/d2cb00004k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/20/2022] [Indexed: 02/04/2023] Open
Abstract
Mutagenesis was utilised to reveal corrole–protein interactions in H-NOX and HasA. The key interaction is a hydrogen bond between the PO unit of the corrole and a protonated histidine residue.
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Affiliation(s)
- Christopher M. Lemon
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA 94720, USA
| | - Amos J. Nissley
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Naomi R. Latorraca
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA 94720, USA
| | - Elizabeth C. Wittenborn
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Michael A. Marletta
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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59
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Zhou Q, Chin M, Fu Y, Liu P, Yang Y. Stereodivergent atom-transfer radical cyclization by engineered cytochromes P450. Science 2021; 374:1612-1616. [PMID: 34941416 PMCID: PMC9309897 DOI: 10.1126/science.abk1603] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Naturally occurring enzymes can be a source of unnatural reactivity that can be molded by directed evolution to generate efficient biocatalysts with valuable activities. Owing to the lack of exploitable stereocontrol elements in synthetic systems, steering the absolute and relative stereochemistry of free-radical processes is notoriously difficult in asymmetric catalysis. Inspired by the innate redox properties of first-row transition-metal cofactors, we repurposed cytochromes P450 to catalyze stereoselective atom-transfer radical cyclization. A set of metalloenzymes was engineered to impose substantial stereocontrol over the radical addition step and the halogen rebound step in these unnatural processes, allowing enantio- and diastereodivergent radical catalysis. This evolvable metalloenzyme platform represents a promising solution to tame fleeting radical intermediates for asymmetric catalysis.
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Affiliation(s)
- Qi Zhou
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Michael Chin
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Yue Fu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, USA.,Biomolecular Science and Engineering Program, University of California Santa Barbara, Santa Barbara, California 93106, USA.,Corresponding author.
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60
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Jeoung JH, Rünger S, Haumann M, Neumann B, Klemke F, Davis V, Fischer A, Dau H, Wollenberger U, Dobbek H. Bimetallic Mn, Fe, Co, and Ni Sites in a Four-Helix Bundle Protein: Metal Binding, Structure, and Peroxide Activation. Inorg Chem 2021; 60:17498-17508. [PMID: 34757735 DOI: 10.1021/acs.inorgchem.1c01919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bimetallic active sites in enzymes catalyze small-molecule conversions that are among the top 10 challenges in chemistry. As different metal cofactors are typically incorporated in varying protein scaffolds, it is demanding to disentangle the individual contributions of the metal and the protein matrix to the activity. Here, we compared the structure, properties, and hydrogen peroxide reactivity of four homobimetallic cofactors (Mn(II)2, Fe(II)2, Co(II)2, Ni(II)2) that were reconstituted into a four-helix bundle protein. Reconstituted proteins were studied in solution and in crystals. All metals bind with high affinity and yield similar cofactor structures. Cofactor variants react with H2O2 but differ in their turnover rates, accumulated oxidation states, and trapped peroxide-bound intermediates. Varying the metal composition thus creates opportunities to tune the reactivity of the bimetallic cofactor and to study and functionalize reactive species.
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Affiliation(s)
- Jae-Hun Jeoung
- Department of Biology, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Stefan Rünger
- Department of Biology, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Bettina Neumann
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Friederike Klemke
- Department of Biology, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Victoria Davis
- Institute for Inorganic and Analytical Chemistry (IAAC), Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany.,Freiburg Material Research Center (FMF), University of Freiburg, 79104 Freiburg, Germany.,Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, 79104 Freiburg, Germany.,Cluster of Excellence livMatS@FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, 79104 Freiburg, Germany
| | - Anna Fischer
- Institute for Inorganic and Analytical Chemistry (IAAC), Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany.,Freiburg Material Research Center (FMF), University of Freiburg, 79104 Freiburg, Germany.,Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, 79104 Freiburg, Germany.,Cluster of Excellence livMatS@FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, 79104 Freiburg, Germany
| | - Holger Dau
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Ulla Wollenberger
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Holger Dobbek
- Department of Biology, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
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61
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Upp DM, Huang R, Li Y, Bultman MJ, Roux B, Lewis JC. Engineering Dirhodium Artificial Metalloenzymes for Diazo Coupling Cascade Reactions**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David M. Upp
- Department of Chemistry Indiana University Bloomington IN 47405 USA
| | - Rui Huang
- Department of Chemistry Indiana University Bloomington IN 47405 USA
| | - Ying Li
- Department of Biochemistry and Molecular Biology University of Chicago Chicago IL 60637 USA
| | - Max J. Bultman
- Department of Chemistry Indiana University Bloomington IN 47405 USA
| | - Benoit Roux
- Department of Biochemistry and Molecular Biology University of Chicago Chicago IL 60637 USA
- Department of Chemistry University of Chicago Chicago IL 60637 USA
| | - Jared C. Lewis
- Department of Chemistry Indiana University Bloomington IN 47405 USA
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62
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Ebensperger P, Jessen-Trefzer C. Artificial metalloenzymes in a nutshell: the quartet for efficient catalysis. Biol Chem 2021; 403:403-412. [PMID: 34653321 DOI: 10.1515/hsz-2021-0329] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/05/2021] [Indexed: 12/22/2022]
Abstract
Artificial metalloenzymes combine the inherent reactivity of transition metal catalysis with the sophisticated reaction control of natural enzymes. By providing new opportunities in bioorthogonal chemistry and biocatalysis, artificial metalloenzymes have the potential to overcome certain limitations in both drug discovery and green chemistry or related research fields. Ongoing advances in organometallic catalysis, directed evolution, and bioinformatics are enabling the design of increasingly powerful systems that outperform conventional catalysis in a growing number of cases. Therefore, this review article collects challenges and opportunities in designing artificial metalloenzymes described in recent review articles. This will provide an equitable insight for those new to and interested in the field.
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Affiliation(s)
- Paul Ebensperger
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, D-79104Freiburg i. Br., Germany
| | - Claudia Jessen-Trefzer
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, D-79104Freiburg i. Br., Germany
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63
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Unnatural biosynthesis by an engineered microorganism with heterologously expressed natural enzymes and an artificial metalloenzyme. Nat Chem 2021; 13:1186-1191. [PMID: 34650235 PMCID: PMC8879416 DOI: 10.1038/s41557-021-00801-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 08/26/2021] [Indexed: 11/21/2022]
Abstract
Synthetic biology enables microbial hosts to produce complex molecules that are otherwise produced by organisms that are rare or difficult to cultivate, but the structures of these molecules are limited to those formed by chemical reactions catalyzed by natural enzymes. The integration of artificial metalloenzymes (ArMs) that catalyze unnatural reactions into metabolic networks could broaden the cache of molecules produced biosynthetically by microorganisms. We report an engineered microbial cell expressing a heterologous biosynthetic pathway, which contains both natural enzymes and ArMs, that produces an unnatural product with high diastereoselectivity. To create this hybrid biosynthetic organism, we engineered Escherichia coli (E. coli) with a heterologous terpene biosynthetic pathway and an ArM containing an iridium-porphyrin complex that was transported into the cell with a heterologous transport system. We improved the diastereoselectivity and product titer of the unnatural product by evolving the ArM and selecting the appropriate gene induction and cultivation conditions. This work shows that synthetic biology and synthetic chemistry can produce, together with natural and artificial enzymes in whole cells, molecules that were previously inaccessible to nature.
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64
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Liu Q, Tian J, Liu J, Zhu M, Gao Z, Hu X, Midgley AC, Wu J, Wang X, Kong D, Zhuang J, Liu J, Yan X, Huang X. Modular Assembly of Tumor-Penetrating and Oligomeric Nanozyme Based on Intrinsically Self-Assembling Protein Nanocages. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2103128. [PMID: 34350648 DOI: 10.1002/adma.202103128] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/26/2021] [Indexed: 06/13/2023]
Abstract
Biomimetic design of nanomaterials with enzyme-like characteristics has emerged as a promising method for the generation of novel therapeutics. However, synthesis of nanomaterials while maintaining a high degree of control over both geometry and valency poses a prominent challenge. Herein, the authors introduce a nanomaterial-based synthetic biology strategy for accurate and quantitative tailoring of high-ordered nanostructures that uses a "bottom-up" hierarchical incorporation of protein building blocks. The assembled nano-oligomers possessed tunable protein motifs and multivalent binding domains, which facilitated prolonged blood circulation time, accumulation within tumor cells through direct targeting of cell receptors, and deep tumor tissue penetration via a transcytosis mechanism. Using these protein/protein nano-oligomers as scaffolds, the authors created a new series of artificial nano-scaled metalloenzymes (nanozymes) by the in situ incorporation of metal nanoclusters within the cavity of the protein nanocages. Nanozymes were capable of mimicking peroxidase-like activity and generated cytotoxic free radicals. Compared to nanozyme alone, the systemic delivery of oligomeric nanozymes demonstrated significantly enhanced therapeutic and anti-tumor benefits. This study shows a new insight into nanotechnology by taking advantage of synthetic biotechnology.
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Affiliation(s)
- Qiqi Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Jingwei Tian
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Jinjian Liu
- Key Laboratory of Radiopharmacokinetics for Innovative Drugs, Chinese Academy of Medical Sciences, and Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300192, China
| | - Mingsheng Zhu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Zhanxia Gao
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Xueyan Hu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Adam C Midgley
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Jin Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
- Joint Laboratory of Nanozymes, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xinyue Wang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Deling Kong
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Jie Zhuang
- School of Medicine, Nankai University, Tianjin, 300071, China
- Joint Laboratory of Nanozymes, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jianfeng Liu
- Key Laboratory of Radiopharmacokinetics for Innovative Drugs, Chinese Academy of Medical Sciences, and Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300192, China
| | - Xiyun Yan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
- Joint Laboratory of Nanozymes, College of Life Sciences, Nankai University, Tianjin, 300071, China
- CAS Engineering Laboratory for Nanozymes, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinglu Huang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
- Joint Laboratory of Nanozymes, College of Life Sciences, Nankai University, Tianjin, 300071, China
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65
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Ren X, Fasan R. Engineered and Artificial Metalloenzymes for Selective C-H Functionalization. CURRENT OPINION IN GREEN AND SUSTAINABLE CHEMISTRY 2021; 31:100494. [PMID: 34395950 PMCID: PMC8357270 DOI: 10.1016/j.cogsc.2021.100494] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The direct functionalization of C-H bonds constitutes a powerful strategy to construct and diversify organic molecules. However, controlling the chemo- and site-selectivity of this transformation in particularly complex molecular settings represents a significant challenge. Metalloenzymes are ideal platforms for achieving catalyst-controlled selective C-H bond functionalization as their reactivities can be tuned by protein engineering and/or redesign of their cofactor environment. In this review, we highlight recent progress in the development of engineered and artificial metalloenzymes for C-H functionalization, with a focus on biocatalytic strategies for selective C-H oxyfunctionalization and halogenation as well as C-H amination and C-H carbene insertion via abiological nitrene and carbene transfer chemistries. Engineered heme- and non-heme iron dependent enzymes have emerged as promising scaffolds for executing these transformations with high chemo-, regio- and stereocontrol as well as tunable selectivity. These emerging systems and methodologies have expanded the toolbox of sustainable strategies for organic synthesis and created new opportunities for the generation of chiral building blocks, the late-stage C-H functionalization of complex molecules, and the total synthesis of natural products.
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Affiliation(s)
- Xinkun Ren
- Department of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester NY 14627, USA
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester NY 14627, USA
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66
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Gutiérrez S, Tomás‐Gamasa M, Mascareñas JL. Exporting Metal‐Carbene Chemistry to Live Mammalian Cells: Copper‐Catalyzed Intracellular Synthesis of Quinoxalines Enabled by N−H Carbene Insertions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sara Gutiérrez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela 15705 Santiago de Compostela Spain
| | - María Tomás‐Gamasa
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela 15705 Santiago de Compostela Spain
| | - José L. Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela 15705 Santiago de Compostela Spain
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67
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Gutiérrez S, Tomás‐Gamasa M, Mascareñas JL. Exporting Metal-Carbene Chemistry to Live Mammalian Cells: Copper-Catalyzed Intracellular Synthesis of Quinoxalines Enabled by N-H Carbene Insertions. Angew Chem Int Ed Engl 2021; 60:22017-22025. [PMID: 34390304 PMCID: PMC8518842 DOI: 10.1002/anie.202108899] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Indexed: 12/17/2022]
Abstract
Implementing catalytic organometallic transformations in living settings can offer unprecedented opportunities in chemical biology and medicine. Unfortunately, the number of biocompatible reactions so far discovered is very limited, and essentially restricted to uncaging processes. Here, we demonstrate the viability of performing metal carbene transfer reactions in live mammalian cells. In particular, we show that copper (II) catalysts can promote the intracellular annulation of alpha-keto diazocarbenes with ortho-amino arylamines, in a process that is initiated by an N-H carbene insertion. The potential of this transformation is underscored by the in cellulo synthesis of a product that alters mitochondrial functions, and by demonstrating cell selective biological responses using targeted copper catalysts. Considering the wide reactivity spectrum of metal carbenes, this work opens the door to significantly expanding the repertoire of life-compatible abiotic reactions.
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Affiliation(s)
- Sara Gutiérrez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)Departamento de Química OrgánicaUniversidade de Santiago de Compostela15705Santiagode CompostelaSpain
| | - María Tomás‐Gamasa
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)Departamento de Química OrgánicaUniversidade de Santiago de Compostela15705Santiagode CompostelaSpain
| | - José L. Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)Departamento de Química OrgánicaUniversidade de Santiago de Compostela15705Santiagode CompostelaSpain
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68
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Baiyoumy A, Vallapurackal J, Schwizer F, Heinisch T, Kardashliev T, Held M, Panke S, Ward TR. Directed Evolution of a Surface-Displayed Artificial Allylic Deallylase Relying on a GFP Reporter Protein. ACS Catal 2021; 11:10705-10712. [PMID: 34504734 PMCID: PMC8419837 DOI: 10.1021/acscatal.1c02405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/26/2021] [Indexed: 12/14/2022]
Abstract
Artificial metalloenzymes (ArMs) combine characteristics of both homogeneous catalysts and enzymes. Merging abiotic and biotic features allows for the implementation of new-to-nature reactions in living organisms. Here, we present the directed evolution of an artificial metalloenzyme based on Escherichia coli surface-displayed streptavidin (SavSD hereafter). Through the binding of a ruthenium-pianostool cofactor to SavSD, an artificial allylic deallylase (ADAse hereafter) is assembled, which displays catalytic activity toward the deprotection of alloc-protected 3-hydroxyaniline. The uncaged aminophenol acts as a gene switch and triggers the overexpression of a fluorescent green fluorescent protein (GFP) reporter protein. This straightforward readout of ADAse activity allowed the simultaneous saturation mutagenesis of two amino acid residues in Sav near the ruthenium cofactor, expediting the screening of 2762 individual clones. A 1.7-fold increase of in vivo activity was observed for SavSD S112T-K121G compared to the wild-type SavSD (wt-SavSD). Finally, the best performing Sav isoforms were purified and tested in vitro (SavPP hereafter). For SavPP S112M-K121A, a total turnover number of 372 was achieved, corresponding to a 5.9-fold increase vs wt-SavPP. To analyze the marked difference in activity observed between the surface-displayed and purified ArMs, the oligomeric state of SavSD was determined. For this purpose, crosslinking experiments of E. coli cells overexpressing SavSD were carried out, followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot. The data suggest that SavSD is most likely displayed as a monomer on the surface of E. coli. We hypothesize that the difference between the in vivo and in vitro screening results may reflect the difference in the oligomeric state of SavSD vs soluble SavPP (monomeric vs tetrameric). Accordingly, care should be applied when evolving oligomeric proteins using E. coli surface display.
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Affiliation(s)
- Alain Baiyoumy
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
- Molecular
Systems Engineering, National Competence
Center in Research (NCCR), 4058 Basel, Switzerland
| | - Jaicy Vallapurackal
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
- Molecular
Systems Engineering, National Competence
Center in Research (NCCR), 4058 Basel, Switzerland
| | - Fabian Schwizer
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Tillmann Heinisch
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
| | | | - Martin Held
- ETH
Zürich, D-BSSE, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Sven Panke
- ETH
Zürich, D-BSSE, Mattenstrasse 26, 4058 Basel, Switzerland
- Molecular
Systems Engineering, National Competence
Center in Research (NCCR), 4058 Basel, Switzerland
| | - Thomas R. Ward
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
- Molecular
Systems Engineering, National Competence
Center in Research (NCCR), 4058 Basel, Switzerland
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69
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Yang J, Li K, Li C, Gu J. In Situ Coupling of Catalytic Centers into Artificial Substrate Mesochannels as Super-Active Metalloenzyme Mimics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2101455. [PMID: 34310077 DOI: 10.1002/smll.202101455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/21/2021] [Indexed: 06/13/2023]
Abstract
Highly evolved substrate channels in natural enzymes facilitate the rapid capture of substrates and direct transfer of intermediates between cascaded catalytic units, thus rationalizing their efficient catalysis. In this study, a nanoscale ordered mesoporous Ce-based metal-organic framework (OMUiO-66(Ce)) is designed as an artificial substrate channel, where MnO2 is coupled to Ce-O clusters as a super-active catalase (CAT). An in situ soft template reduction strategy is developed to deposit well-dispersed and exposed MnO2 in the mesochannels of OMUiO-66(Ce). Several synthesis parameters are optimized to minimize the particle size to ≈150 nm for efficient intracellular endocytosis. The mesochannels provide interaction guidance that not only rapidly drove H2 O2 substrates to CAT-like catalytic centers, but also seamlessly transfer H2 O2 intermediates between superoxide dismutase-like and CAT-like biocatalytic cascades. As a result, the biomimetic system exhibits high efficiency, low dosage, and long-lasting intracellular antioxidant function. Under disease-related oxidative stress, the artificial substrate channels promote the rate of the reactions catalyzed by MnO2 , which exceeds that of the reactions catalyzed by natural CAT. Based on this observation, a set of design rules for substrate channels are proposed to guide the rational design of super-active biomimetic systems.
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Affiliation(s)
- Jian Yang
- Shanghai Engineering Research Center of Hierarchical Nanomaterials, Shanghai, 200237, China
- Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Ke Li
- Shanghai Engineering Research Center of Hierarchical Nanomaterials, Shanghai, 200237, China
- Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Chunzhong Li
- Shanghai Engineering Research Center of Hierarchical Nanomaterials, Shanghai, 200237, China
- Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jinlou Gu
- Shanghai Engineering Research Center of Hierarchical Nanomaterials, Shanghai, 200237, China
- Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai, 200237, China
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70
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Abstract
The Pd-catalyzed carbon-carbon bond formation pioneered by Heck in 1969 has dominated medicinal chemistry development for the ensuing fifty years. As the demand for more complex three-dimensional active pharmaceuticals continues to increase, preparative enzyme-mediated assembly, by virtue of its exquisite selectivity and sustainable nature, is poised to provide a practical and affordable alternative for accessing such compounds. In this minireview, we summarize recent state-of-the-art developments in practical enzyme-mediated assembly of carbocycles. When appropriate, background information on the enzymatic transformation is provided and challenges and/or limitations are also highlighted.
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Affiliation(s)
- Weijin Wang
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Douglass F Taber
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Hans Renata
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
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71
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Deiana L, Rafi AA, Naidu VR, Tai CW, Bäckvall JE, Córdova A. Artificial plant cell walls as multi-catalyst systems for enzymatic cooperative asymmetric catalysis in non-aqueous media. Chem Commun (Camb) 2021; 57:8814-8817. [PMID: 34382975 DOI: 10.1039/d1cc02878b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The assembly of cellulose-based artificial plant cell wall (APCW) structures that contain different types of catalysts is a powerful strategy for the development of cascade reactions. Here we disclose an APCW catalytic system containing a lipase enzyme and nanopalladium particles that transform a racemic amine into the corresponding enantiomerically pure amide in high yield via a dynamic kinetic resolution.
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Affiliation(s)
- Luca Deiana
- Department of Natural Sciences, Mid Sweden University, Holmgatan 10, 85 179 Sundsvall, Sweden.
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72
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Wang Y, Xue P, Cao M, Yu T, Lane ST, Zhao H. Directed Evolution: Methodologies and Applications. Chem Rev 2021; 121:12384-12444. [PMID: 34297541 DOI: 10.1021/acs.chemrev.1c00260] [Citation(s) in RCA: 203] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Directed evolution aims to expedite the natural evolution process of biological molecules and systems in a test tube through iterative rounds of gene diversifications and library screening/selection. It has become one of the most powerful and widespread tools for engineering improved or novel functions in proteins, metabolic pathways, and even whole genomes. This review describes the commonly used gene diversification strategies, screening/selection methods, and recently developed continuous evolution strategies for directed evolution. Moreover, we highlight some representative applications of directed evolution in engineering nucleic acids, proteins, pathways, genetic circuits, viruses, and whole cells. Finally, we discuss the challenges and future perspectives in directed evolution.
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Affiliation(s)
- Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mingfeng Cao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tianhao Yu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stephan T Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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73
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Pons A, Delion L, Poisson T, Charette AB, Jubault P. Asymmetric Synthesis of Fluoro, Fluoromethyl, Difluoromethyl, and Trifluoromethylcyclopropanes. Acc Chem Res 2021; 54:2969-2990. [PMID: 34232626 DOI: 10.1021/acs.accounts.1c00261] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fluorine-containing cyclopropanes are a subclass of cyclopropane derivatives that have generated considerable interest in medicinal chemistry for several decades. The replacement of a cyclopropane C-H or C-CH3 bond with fluorine or a fluorinated group (such as CF3 or CF2H) can lead sometimes to synergistic effects in terms of biological activity and improved metabolic profile of a cyclopropane containing bioactive compound. In this context, the preparation of fluoro-, difluoromethyl-, or trifluoromethyl-cyclopropane is particularly attractive and important but quite challenging considering the unique electronic properties that result from the incorporation of a fluorine atom into a substrate or a reagent. In the past decade, we have sought to develop new routes for the stereoselective synthesis of these building blocks using the most reliable cyclopropanation methods and convenient and readily available starting materials. The challenge that had to be undertaken was how we could use the unique properties of the fluorine atom to improve upon the efficiency of a given process rather than shutting it down. This could be overcome by defining new substrate/reagent reactivity guidelines and carefully selecting whether the fluorinated group was introduced on the electrophilic or nucleophilic partner for a given reaction. In this Account, we describe our contributions in this area that take advantage of diazo-derived rhodium carbenes, zinc carbenoids, ring closure processes, and biocatalytic methods to access these important potential drug subunits. Our initial investigation relied on the development of a Michael-initiated ring closure reaction using the Reformatsky enolate derived from readily available ethyl dibromofluoroacetate and α,β-unsaturated electrophiles. The reaction proceeded extremely well but with modest to good diastereoselectivities with ester acrylates. Further extension to various fluorinated nucleophiles such as oxazolidinone based and DABCO ylides led to similar selectivities.In order to access enantioenriched fluorocyclopropanes, we then investigated the chiral dioxaborolane mediated zinc carbenoid based approaches using the fluoroiodomethylzinc carbenoid/allylic alcohol combination or the iodomethylzinc carbenoid/fluoroallylic alcohol combination. Quite surprisingly, both approaches were equally successful at providing the corresponding fluorocyclopropanes with excellent diastereo- and enantioselectivities.To broaden the scope of fluorinated cyclopropane building blocks that could be prepared with good enantiocontrol, we then investigated the rhodium-catalyzed cyclopropanation of fluoro-, difluoromethyl-, and trifluoromethyl-substituted alkenes with acceptor-acceptor and donor-acceptor diazo reagents. Depending on the substrate/reagent combination, Hashimoto's Rh2((S)-TCPTTL)4 or Davies' Rh2((S)-BTPCP)4 catalyst proved be the most efficient catalysts providing the cyclopropane derivatives with the highest enantioselectivities.More recently, a collaboration with Fasan's group led to the use of engineered myoglobins to catalyze the reaction of ethyl diazoacetate and difluoromethyl-substituted alkenes. This biocatalyzed process led to high turnover number and high enantioselectivities.Although our work has significantly increased the number of tools in the organic chemist's toolbox, continuous efforts in this area would be beneficial to the development of diastereo- and enantioselective approaches to allow the preparation of any elusive isomers of these valuable chiral building blocks.
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Affiliation(s)
- Amandine Pons
- Normandie University, INSA Rouen, UNIROUEN, CNRS, COBRA UMR 6014, 7600 Rouen, France
| | - Laetitia Delion
- Normandie University, INSA Rouen, UNIROUEN, CNRS, COBRA UMR 6014, 7600 Rouen, France
- Université de Montréal, Centre in Green Chemistry and Catalysis, Department of Chemistry, 1374, av. Thérèse Lavoie-Roux, Montréal, QC H2V 0B3, Canada
| | - Thomas Poisson
- Normandie University, INSA Rouen, UNIROUEN, CNRS, COBRA UMR 6014, 7600 Rouen, France
- Institut universitaire de France, Paris 75231, France
| | - André B. Charette
- Université de Montréal, Centre in Green Chemistry and Catalysis, Department of Chemistry, 1374, av. Thérèse Lavoie-Roux, Montréal, QC H2V 0B3, Canada
| | - Philippe Jubault
- Normandie University, INSA Rouen, UNIROUEN, CNRS, COBRA UMR 6014, 7600 Rouen, France
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74
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Upp DM, Huang R, Li Y, Bultman MJ, Roux B, Lewis JC. Engineering Dirhodium Artificial Metalloenzymes for Diazo Coupling Cascade Reactions*. Angew Chem Int Ed Engl 2021; 60:23672-23677. [PMID: 34288306 DOI: 10.1002/anie.202107982] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Indexed: 11/08/2022]
Abstract
Artificial metalloenzymes (ArMs) are commonly used to control the stereoselectivity of catalytic reactions, but controlling chemoselectivity remains challenging. In this study, we engineer a dirhodium ArM to catalyze diazo cross-coupling to form an alkene that, in a one-pot cascade reaction, is reduced to an alkane with high enantioselectivity (typically >99 % ee) by an alkene reductase. The numerous protein and small molecule components required for the cascade reaction had minimal effect on ArM catalysis. Directed evolution of the ArM led to improved yields and E/Z selectivities for a variety of substrates, which translated to cascade reaction yields. MD simulations of ArM variants were used to understand the structural role of the cofactor on ArM conformational dynamics. These results highlight the ability of ArMs to control both catalyst stereoselectivity and chemoselectivity to enable reactions in complex media that would otherwise lead to undesired side reactions.
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Affiliation(s)
- David M Upp
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Rui Huang
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Ying Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Max J Bultman
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Benoit Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.,Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
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75
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Fan G, Wasuwanich P, Furst AL. Biohybrid Systems for Improved Bioinspired, Energy-Relevant Catalysis. Chembiochem 2021; 22:2353-2367. [PMID: 33594779 DOI: 10.1002/cbic.202100037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/15/2021] [Indexed: 12/31/2022]
Abstract
Biomimetic catalysts, ranging from small-molecule metal complexes to supramolecular assembles, possess many exciting properties that could address salient challenges in industrial-scale manufacturing. Inspired by natural enzymes, these biohybrid catalytic systems demonstrate superior characteristics, including high activity, enantioselectivity, and enhanced aqueous solubility, over their fully synthetic counterparts. However, instability and limitations in the prediction of structure-function relationships are major drawbacks that often prevent the application of biomimetic catalysts outside of the laboratory. Despite these obstacles, recent advances in synthetic enzyme models have improved our understanding of complicated biological enzymatic processes and enabled the production of catalysts with increased efficiency. This review outlines important developments and future prospects for the design and application of bioinspired and biohybrid systems at multiple length scales for important, biologically relevant, clean energy transformations.
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Affiliation(s)
- Gang Fan
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Pris Wasuwanich
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Ariel L Furst
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
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76
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Pott M, Tinzl M, Hayashi T, Ota Y, Dunkelmann D, Mittl PRE, Hilvert D. Noncanonical Heme Ligands Steer Carbene Transfer Reactivity in an Artificial Metalloenzyme*. Angew Chem Int Ed Engl 2021; 60:15063-15068. [PMID: 33880851 DOI: 10.1002/anie.202103437] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Indexed: 11/06/2022]
Abstract
Changing the primary metal coordination sphere is a powerful strategy for tuning metalloprotein properties. Here we used amber stop codon suppression with engineered pyrrolysyl-tRNA synthetases, including two newly evolved enzymes, to replace the proximal histidine in myoglobin with Nδ -methylhistidine, 5-thiazoylalanine, 4-thiazoylalanine and 3-(3-thienyl)alanine. In addition to tuning the heme redox potential over a >200 mV range, these noncanonical ligands modulate the protein's carbene transfer activity with ethyl diazoacetate. Variants with increased reduction potential proved superior for cyclopropanation and N-H insertion, whereas variants with reduced Eo values gave higher S-H insertion activity. Given the functional importance of histidine in many enzymes, these genetically encoded analogues could be valuable tools for probing mechanism and enabling new chemistries.
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Affiliation(s)
- Moritz Pott
- Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Matthias Tinzl
- Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Takahiro Hayashi
- Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Yusuke Ota
- Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Daniel Dunkelmann
- Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Peer R E Mittl
- Department of Biochemistry, University of Zürich, 8057, Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
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77
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Pott M, Tinzl M, Hayashi T, Ota Y, Dunkelmann D, Mittl PRE, Hilvert D. Noncanonical Heme Ligands Steer Carbene Transfer Reactivity in an Artificial Metalloenzyme**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Moritz Pott
- Laboratory of Organic Chemistry ETH Zürich 8093 Zürich Switzerland
| | - Matthias Tinzl
- Laboratory of Organic Chemistry ETH Zürich 8093 Zürich Switzerland
| | - Takahiro Hayashi
- Laboratory of Organic Chemistry ETH Zürich 8093 Zürich Switzerland
| | - Yusuke Ota
- Laboratory of Organic Chemistry ETH Zürich 8093 Zürich Switzerland
| | | | - Peer R. E. Mittl
- Department of Biochemistry University of Zürich 8057 Zürich Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry ETH Zürich 8093 Zürich Switzerland
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78
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Man Ngo F, Tse ECM. Bioinorganic Platforms for Sensing, Biomimicry, and Energy Catalysis. CHEM LETT 2021. [DOI: 10.1246/cl.200875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Fung Man Ngo
- Department of Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, University of Hong Kong, Hong Kong SAR, P. R. China
- Advanced Functional Materials Laboratory, HKU Zhejiang Institute of Research and Innovation, Zhejiang 311305, P. R. China
| | - Edmund C. M. Tse
- Department of Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, University of Hong Kong, Hong Kong SAR, P. R. China
- Advanced Functional Materials Laboratory, HKU Zhejiang Institute of Research and Innovation, Zhejiang 311305, P. R. China
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79
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Biggs GS, Klein OJ, Maslen SL, Skehel JM, Rutherford TJ, Freund SMV, Hollfelder F, Boss SR, Barker PD. Controlled Ligand Exchange Between Ruthenium Organometallic Cofactor Precursors and a Naïve Protein Scaffold Generates Artificial Metalloenzymes Catalysing Transfer Hydrogenation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- George S. Biggs
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Oskar James Klein
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Department of Biochemistry University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
| | - Sarah L. Maslen
- MRC Laboratory of Molecular Biology Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH UK
| | - J. Mark Skehel
- MRC Laboratory of Molecular Biology Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH UK
| | - Trevor J. Rutherford
- MRC Laboratory of Molecular Biology Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH UK
| | - Stefan M. V. Freund
- MRC Laboratory of Molecular Biology Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH UK
| | - Florian Hollfelder
- Department of Biochemistry University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
| | - Sally R. Boss
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Paul D. Barker
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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80
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Biggs GS, Klein OJ, Maslen SL, Skehel JM, Rutherford TJ, Freund SMV, Hollfelder F, Boss SR, Barker PD. Controlled Ligand Exchange Between Ruthenium Organometallic Cofactor Precursors and a Naïve Protein Scaffold Generates Artificial Metalloenzymes Catalysing Transfer Hydrogenation. Angew Chem Int Ed Engl 2021; 60:10919-10927. [PMID: 33616271 PMCID: PMC8251807 DOI: 10.1002/anie.202015834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Indexed: 11/05/2022]
Abstract
Many natural metalloenzymes assemble from proteins and biosynthesised complexes, generating potent catalysts by changing metal coordination. Here we adopt the same strategy to generate artificial metalloenzymes (ArMs) using ligand exchange to unmask catalytic activity. By systematically testing RuII (η6 -arene)(bipyridine) complexes designed to facilitate the displacement of functionalised bipyridines, we develop a fast and robust procedure for generating new enzymes via ligand exchange in a protein that has not evolved to bind such a complex. The resulting metal cofactors form peptidic coordination bonds but also retain a non-biological ligand. Tandem mass spectrometry and 19 F NMR spectroscopy were used to characterise the organometallic cofactors and identify the protein-derived ligands. By introduction of ruthenium cofactors into a 4-helical bundle, transfer hydrogenation catalysts were generated that displayed a 35-fold rate increase when compared to the respective small molecule reaction in solution.
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Affiliation(s)
- George S. Biggs
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Oskar James Klein
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Department of BiochemistryUniversity of CambridgeTennis Court RoadCambridgeCB2 1GAUK
| | - Sarah L. Maslen
- MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB2 0QHUK
| | - J. Mark Skehel
- MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB2 0QHUK
| | - Trevor J. Rutherford
- MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB2 0QHUK
| | - Stefan M. V. Freund
- MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB2 0QHUK
| | - Florian Hollfelder
- Department of BiochemistryUniversity of CambridgeTennis Court RoadCambridgeCB2 1GAUK
| | - Sally R. Boss
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Paul D. Barker
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
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81
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Lin YW. Biodegradation of aromatic pollutants by metalloenzymes: A structural-functional-environmental perspective. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.213774] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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82
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Balhara R, Chatterjee R, Jindal G. A computational approach to understand the role of metals and axial ligands in artificial heme enzyme catalyzed C-H insertion. Phys Chem Chem Phys 2021; 23:9500-9511. [PMID: 33885085 DOI: 10.1039/d1cp00412c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Engineered heme enzymes such as myoglobin and cytochrome P450s metalloproteins are gaining widespread importance due to their efficiency in catalyzing non-natural reactions. In a recent strategy, the naturally occurring Fe metal in the heme unit was replaced with non-native metals such as Ir, Rh, Co, Cu, etc., and axial ligands to generate artificial metalloenzymes. Determining the best metal-ligand for a chemical transformation is not a trivial task. Here we demonstrate how computational approaches can be used in deciding the best metal-ligand combination which would be highly beneficial in designing new enzymes as well as small molecule catalysts. We have used Density Functional Theory (DFT) to shed light on the enhanced reactivity of an Ir system with varying axial ligands. We look at the insertion of a carbene group generated from diazo precursors via N2 extrusion into a C-H bond. For both Ir(Me) and Fe systems, the first step, i.e., N2 extrusion is the rate determining step. Strikingly, neither the better ligand overlap with 5d orbitals on Ir nor the electrophilicity on the carbene centre play a significant role. A comparison of Fe and Ir systems reveals that a lower distortion in the Ir(Me)-porphyrin on moving from the reactant to the transition state renders it catalytically more active. We notice that for both metal porphyrins, the free energy barriers are affected by axial ligand substitution. Further, for Fe porphyrin, the axial ligand also changes the preferred spin state. We show that for the carbene insertion into the C-H bond, Fe porphyrin systems undergo a stepwise HAT (hydrogen atom transfer) instead of a concerted hydride transfer process. Importantly, we find that the substitution of the axial Me ligand on Ir to imidazole or chloride, or without an axial substitution changes the rate determining step of the reaction. Therefore, an optimum ligand that can balance the barriers for both steps of the catalytic cycle is essential. We subsequently used the QM cluster approach to delineate the protein environment's role and mutations in improving the catalytic activity of the Ir(Me) system.
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Affiliation(s)
- Reena Balhara
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India.
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83
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De novo biosynthesis of a nonnatural cobalt porphyrin cofactor in E. coli and incorporation into hemoproteins. Proc Natl Acad Sci U S A 2021; 118:2017625118. [PMID: 33850014 DOI: 10.1073/pnas.2017625118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Enzymes that bear a nonnative or artificially introduced metal center can engender novel reactivity and enable new spectroscopic and structural studies. In the case of metal-organic cofactors, such as metalloporphyrins, no general methods exist to build and incorporate new-to-nature cofactor analogs in vivo. We report here that a common laboratory strain, Escherichia coli BL21(DE3), biosynthesizes cobalt protoporphyrin IX (CoPPIX) under iron-limited, cobalt-rich growth conditions. In supplemented minimal media containing CoCl2, the metabolically produced CoPPIX is directly incorporated into multiple hemoproteins in place of native heme b (FePPIX). Five cobalt-substituted proteins were successfully expressed with this new-to-nature cobalt porphyrin cofactor: myoglobin H64V V68A, dye decolorizing peroxidase, aldoxime dehydratase, cytochrome P450 119, and catalase. We show conclusively that these proteins incorporate CoPPIX, with the CoPPIX making up at least 95% of the total porphyrin content. In cases in which the native metal ligand is a sulfur or nitrogen, spectroscopic parameters are consistent with retention of native metal ligands. This method is an improvement on previous approaches with respect to both yield and ease-of-implementation. Significantly, this method overcomes a long-standing challenge to incorporate nonnatural cofactors through de novo biosynthesis. By utilizing a ubiquitous laboratory strain, this process will facilitate spectroscopic studies and the development of enzymes for CoPPIX-mediated biocatalysis.
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84
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Carminati DM, Decaens J, Couve-Bonnaire S, Jubault P, Fasan R. Biocatalytic Strategy for the Highly Stereoselective Synthesis of CHF 2 -Containing Trisubstituted Cyclopropanes. Angew Chem Int Ed Engl 2021; 60:7072-7076. [PMID: 33337576 PMCID: PMC7969403 DOI: 10.1002/anie.202015895] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Indexed: 01/01/2023]
Abstract
The difluoromethyl (CHF2 ) group has attracted significant attention in drug discovery and development efforts, owing to its ability to serve as fluorinated bioisostere of methyl, hydroxyl, and thiol groups. Herein, we report an efficient biocatalytic method for the highly diastereo- and enantioselective synthesis of CHF2 -containing trisubstituted cyclopropanes. Using engineered myoglobin catalysts, a broad range of α-difluoromethyl alkenes are cyclopropanated in the presence of ethyl diazoacetate to give CHF2 -containing cyclopropanes in high yield (up to >99 %, up to 3000 TON) and with excellent stereoselectivity (up to >99 % de and ee). Enantiodivergent selectivity and extension of the method to the stereoselective cyclopropanation of mono- and trifluoromethylated olefins was also achieved. This methodology represents a powerful strategy for the stereoselective synthesis of high-value fluorinated building blocks for medicinal chemistry, as exemplified by the formal total synthesis of a CHF2 isostere of a TRPV1 inhibitor.
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Affiliation(s)
- Daniela M Carminati
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, NY, 14627, USA
| | - Jonathan Decaens
- Normandie Univ, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000, Rouen, France
| | | | - Philippe Jubault
- Normandie Univ, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000, Rouen, France
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, NY, 14627, USA
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85
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Carminati DM, Decaens J, Couve‐Bonnaire S, Jubault P, Fasan R. Biocatalytic Strategy for the Highly Stereoselective Synthesis of CHF
2
‐Containing Trisubstituted Cyclopropanes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Daniela M. Carminati
- Department of Chemistry University of Rochester 120 Trustee Road Rochester NY 14627 USA
| | - Jonathan Decaens
- Normandie Univ INSA Rouen UNIROUEN CNRS, COBRA (UMR 6014) 76000 Rouen France
| | | | - Philippe Jubault
- Normandie Univ INSA Rouen UNIROUEN CNRS, COBRA (UMR 6014) 76000 Rouen France
| | - Rudi Fasan
- Department of Chemistry University of Rochester 120 Trustee Road Rochester NY 14627 USA
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86
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Cailler LP, Kroitor AP, Martynov AG, Gorbunova YG, Sorokin AB. Selective carbene transfer to amines and olefins catalyzed by ruthenium phthalocyanine complexes with donor substituents. Dalton Trans 2021; 50:2023-2031. [PMID: 33443525 DOI: 10.1039/d0dt04090h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron-rich ruthenium phthalocyanine complexes were evaluated in carbene transfer reactions from ethyl diazoacetate (EDA) to aromatic and aliphatic olefins as well as to a wide range of aromatic, heterocyclic and aliphatic amines for the first time. It was revealed that the ruthenium octabutoxyphthalocyanine carbonyl complex [(BuO)8Pc]Ru(CO) is the most efficient catalyst converting electron-rich and electron-poor aromatic olefins to cyclopropane derivatives with high yields (typically 80-100%) and high TON (up to 1000) under low catalyst loading and nearly equimolar substrate/EDA ratio. This catalyst shows a rare efficiency in the carbene insertion into amine N-H bonds. Using a 0.05 mol% catalyst loading, a high amine concentration (1 M) and 1.1 eq. of EDA, a number of structurally divergent amines were selectively converted to mono-substituted glycine derivatives with up to quantitative yields and turnover numbers reaching 2000. High selectivity, large substrate scope, low catalyst loading and practical reaction conditions place [(BuO)8Pc]Ru(CO) among the most efficient catalysts for the carbene insertion into amines.
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Affiliation(s)
- Lucie P Cailler
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, IRCELYON, 2 av. A. Einstein, 69626 Villeurbanne, France.
| | - Andrey P Kroitor
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leniskii pr., 31, bldg. 4, 119071 Moscow, Russia.
| | - Alexander G Martynov
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leniskii pr., 31, bldg. 4, 119071 Moscow, Russia.
| | - Yulia G Gorbunova
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leniskii pr., 31, bldg. 4, 119071 Moscow, Russia. and N. S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leniskii pr., 31, 11991 Moscow, Russia.
| | - Alexander B Sorokin
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, IRCELYON, 2 av. A. Einstein, 69626 Villeurbanne, France.
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87
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Vong K, Nasibullin I, Tanaka K. Exploring and Adapting the Molecular Selectivity of Artificial Metalloenzymes. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200316] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kenward Vong
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- GlycoTargeting Research Laboratory, RIKEN Baton Zone Program, Wako, Saitama 351-0198, Japan
| | - Igor Nasibullin
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, Kazan 420008, Russia
| | - Katsunori Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8552, Japan
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, Kazan 420008, Russia
- GlycoTargeting Research Laboratory, RIKEN Baton Zone Program, Wako, Saitama 351-0198, Japan
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88
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Oohora K, Hayashi T. Myoglobins engineered with artificial cofactors serve as artificial metalloenzymes and models of natural enzymes. Dalton Trans 2021; 50:1940-1949. [PMID: 33433532 DOI: 10.1039/d0dt03597a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Metalloenzymes naturally achieve various reactivities by assembling limited types of cofactors with endogenous amino acid residues. Enzymes containing metal porphyrinoid cofactors such as heme, cobalamin and F430 exert precise control over the reactivities of the cofactors with protein matrices. This perspective article focuses on our recent efforts to assemble metal complexes of non-natural porphyrinoids within the protein matrix of myoglobin, an oxygen storage hemoprotein. Engineered myoglobins with suitable metal complexes as artificial cofactors demonstrate unique reactivities toward C-H bond hydroxylation, olefin cyclopropanation, methyl group transfer and methane generation. In these cases, the protein matrix enhances the catalytic activities of the cofactors and allows us to monitor the active intermediates. The present findings indicate that placing artificial cofactors in protein matrices provides a useful strategy for creating artificial metalloenzymes that catalyse otherwise unfavourable reactions and providing enzyme models for elucidating the complicated reaction mechanisms of natural enzymes.
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Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan.
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89
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Cao Y, Li X, Ge J. Enzyme Catalyst Engineering toward the Integration of Biocatalysis and Chemocatalysis. Trends Biotechnol 2021; 39:1173-1183. [PMID: 33551176 DOI: 10.1016/j.tibtech.2021.01.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 01/30/2023]
Abstract
Enzymatic catalysis, which has been driving biological processes in a green, mild, and efficient manner for billions of years, is increasingly being used in industrial processes to manufacture chemicals, pharmaceuticals, and materials for human society. Since enzymes were discovered, strategies to adapt enzymes for use as catalysts for industrial processes, such as chemical modification, immobilization, site-directed mutagenesis, directed evolution of enzymes, artificial metalloenzymes, and computational design, have been continuously pursued. In contrast to these strategies, editing enzymes to easily integrate biocatalysis with chemocatalysis is a potential way to apply enzymes in industry. Enzyme catalyst editing focuses on fine-tuning the microenvironment surrounding the enzyme or achieving a new catalytic function to construct better biocatalysis under non-natural conditions for the enzyme.
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Affiliation(s)
- Yufei Cao
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Xiaoyang Li
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Jun Ge
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China.
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90
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Nam D, Steck V, Potenzino RJ, Fasan R. A Diverse Library of Chiral Cyclopropane Scaffolds via Chemoenzymatic Assembly and Diversification of Cyclopropyl Ketones. J Am Chem Soc 2021; 143:2221-2231. [DOI: 10.1021/jacs.0c09504] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Donggeon Nam
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Viktoria Steck
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Robert J. Potenzino
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
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91
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Liu H, Li Y, Sun S, Xin Q, Liu S, Mu X, Yuan X, Chen K, Wang H, Varga K, Mi W, Yang J, Zhang XD. Catalytically potent and selective clusterzymes for modulation of neuroinflammation through single-atom substitutions. Nat Commun 2021; 12:114. [PMID: 33414464 PMCID: PMC7791071 DOI: 10.1038/s41467-020-20275-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 11/17/2020] [Indexed: 01/29/2023] Open
Abstract
Emerging artificial enzymes with reprogrammed and augmented catalytic activity and substrate selectivity have long been pursued with sustained efforts. The majority of current candidates have rather poor catalytic activity compared with natural molecules. To tackle this limitation, we design artificial enzymes based on a structurally well-defined Au25 cluster, namely clusterzymes, which are endowed with intrinsic high catalytic activity and selectivity driven by single-atom substitutions with modulated bond lengths. Au24Cu1 and Au24Cd1 clusterzymes exhibit 137 and 160 times higher antioxidant capacities than natural trolox, respectively. Meanwhile, the clusterzymes demonstrate preferential enzyme-mimicking catalytic activities, with Au25, Au24Cu1 and Au24Cd1 displaying compelling selectivity in glutathione peroxidase-like (GPx-like), catalase-like (CAT-like) and superoxide dismutase-like (SOD-like) activities, respectively. Au24Cu1 decreases peroxide in injured brain via catalytic reactions, while Au24Cd1 preferentially uses superoxide and nitrogenous signal molecules as substrates, and significantly decreases inflammation factors, indicative of an important role in mitigating neuroinflammation.
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Affiliation(s)
- Haile Liu
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, 300350, Tianjin, China
| | - Yonghui Li
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, 300350, Tianjin, China
| | - Si Sun
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, 300350, Tianjin, China
| | - Qi Xin
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, 300350, Tianjin, China
| | - Shuhu Liu
- Beijing Synchrotron Radiation Facility (BSRF), Institute of High Energy Physics (IHEP), Chinese Academy of Sciences (CAS), 100049, Beijing, China
| | - Xiaoyu Mu
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, 300350, Tianjin, China
| | - Xun Yuan
- School of Materials Science and Engineering, Qingdao University of Science and Technology, 266042, Qingdao, Shandong, China
| | - Ke Chen
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, 300350, Tianjin, China
| | - Hao Wang
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, 300350, Tianjin, China
| | - Kalman Varga
- Department of Physics and Astronomy, Vanderbilt University, Nashville, TN, 37235, USA
| | - Wenbo Mi
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, 300350, Tianjin, China
| | - Jiang Yang
- School of Medicine, Sun Yat-sen University, 510060, Guangzhou, China
| | - Xiao-Dong Zhang
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, 300350, Tianjin, China.
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, 300072, Tianjin, China.
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92
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Nan J, Ma Q, Yin J, Liang C, Tian L, Ma Y. RhIII-Catalyzed formal [5 + 1] cyclization of 2-pyrrolyl/indolylanilines using vinylene carbonate as a C1 synthon. Org Chem Front 2021. [DOI: 10.1039/d1qo00040c] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A rhodium(iii)-catalyzed formal C–H [5 + 1] cyclization of 2-pyrrolyl/indolylanilines with vinylene carbonate has been explored towards the potent assembly of diverse 4-methylpyrrolo[1,2-a]quinoxalines.
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Affiliation(s)
- Jiang Nan
- Shaanxi Key Laboratory of Chemical Additives for Industry
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi'an 710021
- China
| | - Qiong Ma
- Shaanxi Key Laboratory of Chemical Additives for Industry
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi'an 710021
- China
| | - Jiacheng Yin
- Shaanxi Key Laboratory of Chemical Additives for Industry
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi'an 710021
- China
| | - Chengyuan Liang
- School of Food and Biological Engineering
- Shaanxi University of Science and Technology
- Xi'an 710021
- China
| | - Lei Tian
- School of Food and Biological Engineering
- Shaanxi University of Science and Technology
- Xi'an 710021
- China
| | - Yangmin Ma
- Shaanxi Key Laboratory of Chemical Additives for Industry
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi'an 710021
- China
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93
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Vornholt T, Christoffel F, Pellizzoni MM, Panke S, Ward TR, Jeschek M. Systematic engineering of artificial metalloenzymes for new-to-nature reactions. SCIENCE ADVANCES 2021; 7:eabe4208. [PMID: 33523952 DOI: 10.1126/sciadv.abe4208] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Artificial metalloenzymes (ArMs) catalyzing new-to-nature reactions could play an important role in transitioning toward a sustainable economy. While ArMs have been created for various transformations, attempts at their genetic optimization have been case specific and resulted mostly in modest improvements. To realize their full potential, methods to rapidly discover active ArM variants for ideally any reaction of interest are required. Here, we introduce a reaction-independent, automation-compatible platform, which relies on periplasmic compartmentalization in Escherichia coli to rapidly and reliably engineer ArMs based on the biotin-streptavidin technology. We systematically assess 400 ArM mutants for five bioorthogonal transformations involving different metals, reaction mechanisms, and reactants, which include novel ArMs for gold-catalyzed hydroamination and hydroarylation. Activity enhancements up to 15-fold highlight the potential of the systematic approach. Furthermore, we suggest smart screening strategies and build machine learning models that accurately predict ArM activity from sequence, which has crucial implications for future ArM development.
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Affiliation(s)
- Tobias Vornholt
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
| | - Fadri Christoffel
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - Michela M Pellizzoni
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
| | - Thomas R Ward
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - Markus Jeschek
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland.
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
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94
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Yang ZJ, Gong QT, Yu Y, Lu WF, Wu ZN, Wang N, Yu XQ. Fast and high-efficiency synthesis of 2-substituted benzothiazoles via combining enzyme catalysis and photoredox catalysis in one-pot. Bioorg Chem 2020; 107:104607. [PMID: 33450543 DOI: 10.1016/j.bioorg.2020.104607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 01/28/2023]
Abstract
An efficient and green method, combining enzymatic and visible-light catalysis for synthesis of the widely applicable 2-substituted benzothiazoles, has been developed. This method features a relay catalysis protocol consisting of biocatalytic promiscuity and visible-light-induced subsequent oxidization of 2-phenyl benzothiazolines. The whole reaction process is very high-efficiency, achieving 99% yield in just 10 min, under an air atmosphere, nearly 100% atomic utilization, and the 2-substituted benzothiazole products were obtained in good to excellent yields with a wide range of substrates. This reaction is the other example of combining the non-natural catalytic activity of hydrolases with visible-light catalysis for organic synthesis and the catalytic system does not require additional oxidants or metals, which is good for the environment.
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Affiliation(s)
- Zeng-Jie Yang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, PR China
| | - Qing-Tian Gong
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, PR China
| | - Yuan Yu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, PR China
| | - Wei-Fan Lu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, PR China
| | - Zhe-Ning Wu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, PR China
| | - Na Wang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, PR China.
| | - Xiao-Qi Yu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, PR China.
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95
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Costa PFA, de Abreu R, Fontana AB, Fiedler HD, Kirby AJ, Quina FH, Nome F, Gerola AP. The role of hydrophobicity in supramolecular polymer/surfactant catalysts: An understandable model for enzymatic catalysis. J Colloid Interface Sci 2020; 588:456-468. [PMID: 33429342 DOI: 10.1016/j.jcis.2020.12.081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 12/24/2022]
Abstract
Enzymes are highly significant catalysts, essential to biological systems, and a source of inspiration for the design of artificial enzymes. Although many models have been developed describing enzymatic catalysis, a deeper understanding of these biocatalysts remains a major challenge. Herein we detail the formation, characterization, performance, and catalytic mechanisms of a series of bio-inspired supramolecular polymer/surfactant complexes acting as artificial enzymes. The supramolecular complexes were characterized and exhibited exceptional catalytic efficiency for the dephosphorylation of an activated phosphate diester, the reaction rate being highly responsive to: (a) pH, (b) surfactant concentration, and (c) the length of the hydrophobic chain of the surfactant. Under optimal conditions (at pH > 8 for the more hydrophobic systems and at pre-micellar concentrations), enzyme-like rate enhancements of up to 6.0 × 109-fold over the rate of the spontaneous hydrolysis reaction in water were verified. The catalytic performance is a consequence of synergy between the hydrophobicity of the aggregates and the catalytic functionalities of the polymer and the catalytic mechanism is modulated by the nature of the hydrophobic pockets of these catalysts, changing from a general base mechanism to a nucleophilic mechanism as the hydrophobicity increases. Taken as a whole, the present results provide fundamental insights, through an understandable model, which are highly relevant to the design of novel bioinspired enzyme surrogates with multifunctional potentialities for future practical applications.
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Affiliation(s)
- Paulo F A Costa
- Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Rafael de Abreu
- Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Andressa B Fontana
- Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Haidi D Fiedler
- Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Anthony J Kirby
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Frank H Quina
- Institute of Chemistry, University of São Paulo, CEP 05508-000 São Paulo, Brazil
| | - Faruk Nome
- Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Adriana P Gerola
- Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis 88040-900, SC, Brazil.
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96
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Koo J, Yang J, Park H. Cell-free Systems: Recent Advances and Future Outlook. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0013-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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97
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Ren X, Liu N, Chandgude AL, Fasan R. An Enzymatic Platform for the Highly Enantioselective and Stereodivergent Construction of Cyclopropyl‐δ‐lactones. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007953] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xinkun Ren
- Department of Chemistry University of Rochester 120 Trustee Road Rochester NY 16427 USA
| | - Ningyu Liu
- Department of Chemistry University of Rochester 120 Trustee Road Rochester NY 16427 USA
| | - Ajay L. Chandgude
- Department of Chemistry University of Rochester 120 Trustee Road Rochester NY 16427 USA
| | - Rudi Fasan
- Department of Chemistry University of Rochester 120 Trustee Road Rochester NY 16427 USA
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98
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Newmister SA, Srivastava KR, Espinoza RV, Caddell Haatveit K, Khatri Y, Martini RM, Garcia-Borràs M, Podust LM, Houk KN, Sherman DH. Molecular Basis of Iterative C─H Oxidation by TamI, a Multifunctional P450 monooxygenase from the Tirandamycin Biosynthetic Pathway. ACS Catal 2020; 10:13445-13454. [PMID: 33569241 DOI: 10.1021/acscatal.0c03248] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Biocatalysis offers an expanding and powerful strategy to construct and diversify complex molecules by C─H bond functionalization. Due to their high selectivity, enzymes have become an essential tool for C─H bond functionalization and offer complementary reactivity to small-molecule catalysts. Hemoproteins, particularly cytochromes P450, have proven effective for selective oxidation of unactivated C─H bonds. Previously, we reported the in vitro characterization of an oxidative tailoring cascade in which TamI, a multifunctional P450 functions co-dependently with the TamL flavoprotein to catalyze regio- and stereoselective hydroxylations and epoxidation to yield tirandamycin A and tirandamycin B. TamI follows a defined order including 1) C10 hydroxylation, 2) C11/C12 epoxidation, and 3) C18 hydroxylation. Here we present a structural, biochemical, and computational investigation of TamI to understand the molecular basis of its substrate binding, diverse reactivity, and specific reaction sequence. The crystal structure of TamI in complex with tirandamycin C together with molecular dynamics simulations and targeted mutagenesis suggest that hydrophobic interactions with the polyene chain of its natural substrate are critical for molecular recognition. QM calculations and molecular dynamics simulations of TamI with variant substrates provided detailed information on the molecular basis of sequential reactivity, and pattern of regio- and stereo-selectivity in catalyzing the three-step oxidative cascade.
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Affiliation(s)
- Sean A. Newmister
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kinshuk Raj Srivastava
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Laboratory of Biocatalysis & Enzyme Engineering, Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Rosa V. Espinoza
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kersti Caddell Haatveit
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Yogan Khatri
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Rachel M. Martini
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Larissa M. Podust
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - David. H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Micobiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
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99
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Kato S, Onoda A, Taniguchi N, Schwaneberg U, Hayashi T. Directed Evolution of a Cp*Rh III -Linked Biohybrid Catalyst Based on a Screening Platform with Affinity Purification. Chembiochem 2020; 22:679-685. [PMID: 33026156 PMCID: PMC7894531 DOI: 10.1002/cbic.202000681] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Indexed: 12/12/2022]
Abstract
Directed evolution of Cp*RhIII‐linked nitrobindin (NB), a biohybrid catalyst, was performed based on an in vitro screening approach. A key aspect of this effort was the establishment of a high‐throughput screening (HTS) platform that involves an affinity purification step employing a starch‐agarose resin for a maltose binding protein (MBP) tag. The HTS platform enables efficient preparation of the purified MBP‐tagged biohybrid catalysts in a 96‐well format and eliminates background influence of the host E. coli cells. Three rounds of directed evolution and screening of more than 4000 clones yielded a Cp*RhIII‐linked NB(T98H/L100K/K127E) variant with a 4.9‐fold enhanced activity for the cycloaddition of acetophenone oximes with alkynes. It is confirmed that this HTS platform for directed evolution provides an efficient strategy for generating highly active biohybrid catalysts incorporating a synthetic metal cofactor.
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Affiliation(s)
- Shunsuke Kato
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Akira Onoda
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Faculty of Environmental Earth Science, Hokkaido University, North 10 West 5, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan
| | - Naomasa Taniguchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen, 52074, Germany
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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100
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Huang Y, Chen J, Zhu L, Ma K, Kang K, Yang M, Lu S, Yan M, Wan Y, Deng S. Electrochemiluminescence-Repurposed Abiological Catalysts in Full Protein Tag for Ultrasensitive Immunoassay. Anal Chem 2020; 92:14076-14084. [PMID: 32938180 DOI: 10.1021/acs.analchem.0c03114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Being announced as one of the "2019 Top Ten Emerging Technologies in Chemistry" by IUPAC, the directed evolution of artificial metalloenzymes has led to a broad scope of abiotic processes. Here, inspired by those key proteins in bioluminescence, a rudimentary expression of bio-electrochemiluminescent (ECL) macromolecules was achieved via the complexation of zinc proto-porphyrin IX (ZnPPIX) within apo-hemoglobin (apo-Hb). A high-yield monochromic irradiation at 644 nm could be provoked potentiostatically from the reconstituted holo-HbZnPPIX in solutions. Its secondary structure integrity was elucidated by UV and circular dichroism spectrometry, while voltammetry-hyphenated surface plasmon resonance authenticated its ligation conservativeness in electrical fields. Further conjugation with streptavidin rendered a homogeneous Janus fusion of both receptor and reporter domains, enabling a new abiological catalyst-linked ECL bioassay. On the other hand, singular ZnPPIX inside each tetrameric subunit of Hb accomplished an overall signal amplification without the bother of luminogenic heterojunctions. This pH-tolerant and non-photobleaching optics was essentialized to be the unique configuration interaction between Zn and O2, by which the direct electrochemistry of proteins catalyzed the transient progression of O2 → O2·- → O2* + hυ selectively. Such principle was implemented as a signal-on strategy for the determination of a characteristic cancer biomarker, the vascular endothelial growth factor, resulting in competent performance at a low detection limit of 0.6 pg·mL-1 and a wide calibration range along with good stability and reliability in real practices. This simple mutation repurposed the O2-transport Hb in the erythrocytes of almost all vertebrates into a cluster of oxidoreductases with intrinsic ECL activity, which would enrich the chromophore library. More importantly, its genetically engineered variants may come in handy in biomedical diagnosis and visual electrophysiology.
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Affiliation(s)
- Yaqi Huang
- School of Mechanical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.,School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Jialiang Chen
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Longyi Zhu
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Kefeng Ma
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Kai Kang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Meng Yang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Shaohui Lu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Minchuan Yan
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Ying Wan
- School of Mechanical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Shengyuan Deng
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
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