1
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Jiang Y, Kim A, Olive C, Lewis JC. Selective C-H Halogenation of Alkenes and Alkynes Using Flavin-Dependent Halogenases. Angew Chem Int Ed Engl 2024; 63:e202317860. [PMID: 38280216 PMCID: PMC10947852 DOI: 10.1002/anie.202317860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 01/29/2024]
Abstract
Single component flavin-dependent halogenases (FDHs) possess both flavin reductase and FDH activity in a single enzyme. We recently reported that the single component FDH AetF catalyzes site-selective bromination and iodination of a variety of aromatic substrates and enantioselective bromolactonization and iodoetherification of styrenes bearing pendant carboxylic acid or alcohol substituents. Given this inherent reactivity and selectivity, we explored the utility of AetF as catalyst for alkene and alkyne C-H halogenation. We find that AetF catalyzes halogenation of a range of 1,1-disubstituted styrenes, often with high stereoselectivity. Despite the utility of haloalkenes for cross-coupling and other applications, accessing these compounds in a stereoselective manner typically requires functional group interconversion processes, and selective halogenation of 1,1'-disubstituted olefins remains rare. We also establish that AetF and homologues of this enzyme can halogenate terminal alkynes. Mutagenesis studies and deuterium kinetic isotope effects are used to support a mechanistic proposal involving covalent catalysis for halogenation of unactivated alkynes by AetF homologues. These findings expand the scope of FDH catalysis and continue to show the unique utility of single component FDHs for biocatalysis.
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Affiliation(s)
- Yuhua Jiang
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Ahram Kim
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Cahmlo Olive
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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2
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Li J, Kumar A, Lewis JC. Non-native Intramolecular Radical Cyclization Catalyzed by a B 12 -Dependent Enzyme. Angew Chem Int Ed Engl 2023; 62:e202312893. [PMID: 37874184 DOI: 10.1002/anie.202312893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/12/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023]
Abstract
Despite the unique reactivity of vitamin B12 and its derivatives, B12 -dependent enzymes remain underutilized in biocatalysis. In this study, we repurposed the B12 -dependent transcription factor CarH to enable non-native radical cyclization reactions. An engineered variant of this enzyme, CarH*, catalyzes the formation γ- and δ-lactams through either redox-neutral or reductive ring closure with marked enhancement of reactivity and selectivity relative to the free B12 cofactor. CarH* also catalyzes an unusual spirocyclization by dearomatization of pendant arenes to produce bicyclic 1,3-diene products instead of 1,4-dienes provided by existing methods. These results and associated mechanistic studies highlight the importance of protein scaffolds for controlling the reactivity of B12 and expanding the synthetic utility of B12 -dependent enzymes.
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Affiliation(s)
- Jianbin Li
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Amardeep Kumar
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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3
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Abstract
The ability to site-selectively modify equivalent functional groups in a molecule has the potential to streamline syntheses and increase product yields by lowering step counts. Enzymes catalyze site-selective transformations throughout primary and secondary metabolism, but leveraging this capability for non-native substrates and reactions requires a detailed understanding of the potential and limitations of enzyme catalysis and how these bounds can be extended by protein engineering. In this review, we discuss representative examples of site-selective enzyme catalysis involving functional group manipulation and C-H bond functionalization. We include illustrative examples of native catalysis, but our focus is on cases involving non-native substrates and reactions often using engineered enzymes. We then discuss the use of these enzymes for chemoenzymatic transformations and target-oriented synthesis and conclude with a survey of tools and techniques that could expand the scope of non-native site-selective enzyme catalysis.
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Affiliation(s)
- Dibyendu Mondal
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Harrison M Snodgrass
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christian A Gomez
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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4
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Kumar A, Yang X, Li J, Lewis JC. First and second sphere interactions accelerate non-native N-alkylation catalysis by the thermostable, methanol-tolerant B 12-dependent enzyme MtaC. Chem Commun (Camb) 2023; 59:4798-4801. [PMID: 37000588 PMCID: PMC10134074 DOI: 10.1039/d3cc01071f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
The corrinoid protein MtaC, which is natively involved in methyl transferase catalysis, catalyzes N-alkylation of aniline using ethyl diazoacetate. Our results show how the native preference of B12 scaffolds for radical versus polar chemistry translates to non-native catalysis, which could guide selection of B12-dependent proteins for biocatalysis. MtaC also has high thermal stability and organic solvent tolerance, remaining folded even in pure methanol.
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Affiliation(s)
- Amardeep Kumar
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
| | - Xinhang Yang
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
| | - Jianbin Li
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
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5
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Gomez CA, Mondal D, Du Q, Chan N, Lewis JC. Directed Evolution of an Iron(II)- and α-Ketoglutarate-Dependent Dioxygenase for Site-Selective Azidation of Unactivated Aliphatic C-H Bonds. Angew Chem Int Ed Engl 2023; 62:e202301370. [PMID: 36757808 PMCID: PMC10050089 DOI: 10.1002/anie.202301370] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/10/2023]
Abstract
FeII - and α-ketoglutarate-dependent halogenases and oxygenases can catalyze site-selective functionalization of C-H bonds via a variety of C-X bond forming reactions, but achieving high chemoselectivity for functionalization using non-native functional groups remains rare. The current study shows that directed evolution can be used to engineer variants of the dioxygenase SadX that address this challenge. Site-selective azidation of succinylated amino acids and a succinylated amine was achieved as a result of mutations throughout the SadX structure. The installed azide group was reduced to a primary amine, and the succinyl group required for azidation was enzymatically cleaved to provide the corresponding amine. These results provide a promising starting point for evolving additional SadX variants with activity on structurally distinct substrates and for enabling enzymatic C-H functionalization with other non-native functional groups.
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Affiliation(s)
- Christian A Gomez
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Dibyendu Mondal
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
- Kalsec Inc., 3713W. Main St., Kalamazoo, MI 49006, USA
| | - Qian Du
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Natalie Chan
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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6
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Jiang Y, Lewis JC. Asymmetric catalysis by flavin-dependent halogenases. Chirality 2023. [PMID: 36916449 DOI: 10.1002/chir.23550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 03/16/2023]
Abstract
In nature, flavin-dependent halogenases (FDHs) catalyze site-selective chlorination and bromination of aromatic natural products. This ability has led to extensive efforts to engineer FDHs for selective chlorination, bromination, and iodination of electron rich aromatic compounds. On the other hand, FDHs are unique among halogenases and haloperoxidases that exhibit catalyst-controlled site selectivity in that no examples of enantioselective FDH catalysis in natural product biosynthesis have been characterized. Over the past several years, our group has established that FDHs can catalyze enantioselective reactions involving desymmetrization, atroposelective halogenation, and halocyclization. Achieving high activity and selectivity for these reactions has required extensive mutagenesis and mitigation of problems resulting from hypohalous acid generated during FDH catalysis. The single-component flavin reductase/FDH AetF is unique among the wild type enzyme we have studied in that it provides high activity and selectivity toward several asymmetric transformations. These results highlight the ability of FDH active sites to tolerate different substrate topologies and suggest that they could be useful for a broad range of oxidative halogenations.
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Affiliation(s)
- Yuhua Jiang
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
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7
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Gomez CA, Mondal D, Du Q, Chan N, Lewis JC. Directed Evolution of an Iron(II)‐ and α‐Ketoglutarate‐Dependent Dioxygenase for Site‐Selective Azidation of Unactivated Aliphatic C‐H Bonds. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202301370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
| | | | - Qian Du
- Indiana University Bloomington Chemistry UNITED STATES
| | - Natalie Chan
- Indiana University Bloomington Chemistry UNITED STATES
| | - Jared C Lewis
- Indiana University Department of Chemistry 212 S. Hawthorne Drive 47405 Bloomington UNITED STATES
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8
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Liu B, Zubi YS, Lewis JC. Iridium(III) Polypyridine Artificial Metalloenzymes with Tunable Photophysical Properties: a New Platform for Visible Light Photocatalysis in Aqueous Solution. Dalton Trans 2023; 52:5034-5038. [PMID: 37060130 PMCID: PMC10187040 DOI: 10.1039/d3dt00932g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Artificial metalloenzymes (ArMs) can combine the unique features of both metal complexes and enzymes by incorporating a cofactor within a protein scaffold. Herein, we describe a panel of ArMs constructed...
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Affiliation(s)
- Bingqing Liu
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
| | - Yasmine S Zubi
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
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9
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Jiang Y, Snodgrass HM, Zubi YS, Roof CV, Guan Y, Mondal D, Honeycutt NH, Lee JW, Lewis RD, Martinez CA, Lewis JC. The Single-Component Flavin Reductase/Flavin-Dependent Halogenase AetF is a Versatile Catalyst for Selective Bromination and Iodination of Arenes and Olefins. Angew Chem Int Ed Engl 2022; 61:e202214610. [PMID: 36282507 PMCID: PMC9772203 DOI: 10.1002/anie.202214610] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Indexed: 11/05/2022]
Abstract
Flavin-dependent halogenases (FDHs) natively catalyze selective halogenation of electron rich aromatic and enolate groups. Nearly all FDHs reported to date require a separate flavin reductase to supply them with FADH2 , which complicates biocatalysis applications. In this study, we establish that the single component flavin reductase/flavin dependent halogenase AetF catalyzes halogenation of a diverse set of substrates using a commercially available glucose dehydrogenase to drive its halogenase activity. High site selectivity, activity on relatively unactivated substrates, and high enantioselectivity for atroposelective bromination and bromolactonization was demonstrated. Site-selective iodination and enantioselective cycloiodoetherification was also possible using AetF. The substrate and reaction scope of AetF suggest that it has the potential to greatly improve the utility of biocatalytic halogenation.
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Affiliation(s)
- Yuhua Jiang
- Department of ChemistryIndiana UniversityBloomingtonIN 47405USA
| | | | - Yasmine S. Zubi
- Department of ChemistryIndiana UniversityBloomingtonIN 47405USA
| | - Caitlin V. Roof
- Department of ChemistryIndiana UniversityBloomingtonIN 47405USA
| | - Yanfei Guan
- Chemical Research & DevelopmentPfizer Worldwide Research & DevelopmentGrotonConnecticut 06340USA
| | - Dibyendu Mondal
- Department of ChemistryIndiana UniversityBloomingtonIN 47405USA
- Kalsec Inc.3713W. Main St.KalamazooMichigan 49006USA
| | | | - Johnny W. Lee
- Chemical Research & DevelopmentPfizer Worldwide Research & DevelopmentGrotonConnecticut 06340USA
| | - Russell D. Lewis
- Chemical Research & DevelopmentPfizer Worldwide Research & DevelopmentGrotonConnecticut 06340USA
| | - Carlos A. Martinez
- Chemical Research & DevelopmentPfizer Worldwide Research & DevelopmentGrotonConnecticut 06340USA
| | - Jared C. Lewis
- Department of ChemistryIndiana UniversityBloomingtonIN 47405USA
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10
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Jiang Y, Snodgrass HM, Zubi YS, Roof CV, Guan Y, Mondal D, Moneycutt NH, Lee JW, Lewis RD, Martinez CA, Lewis JC. The Single‐Component Flavin Reductase/Flavin‐Dependent Halogenase AetF is a Versatile Catalyst for Selective Bromination and Iodination of Arenes and Olefins. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202214610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yuhua Jiang
- Indiana University Bloomington Chemistry UNITED STATES
| | | | | | | | - Yanfei Guan
- Pfizer Global Research and Development Process Chemistry UNITED STATES
| | | | | | - Johnny W. Lee
- Pfizer Global Research and Development Process Chemistry UNITED STATES
| | - Russell D. Lewis
- Pfizer Global Research and Development Process Chemistry UNITED STATES
| | | | - Jared C Lewis
- Indiana University Department of Chemistry 212 S. Hawthorne Drive 47405 Bloomington UNITED STATES
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11
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Jiang Y, Mondal D, Lewis JC. Expanding the Reactivity of Flavin-Dependent Halogenases toward Olefins via Enantioselective Intramolecular Haloetherification and Chemoenzymatic Oxidative Rearrangements. ACS Catal 2022. [DOI: 10.1021/acscatal.2c03383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuhua Jiang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Dibyendu Mondal
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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12
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Andorfer MC, Evans D, Yang S, He CQ, Girlich AM, Vergara-Coll J, Sukumar N, Houk KN, Lewis JC. Analysis of Laboratory-Evolved Flavin-Dependent Halogenases Affords a Computational Model for Predicting Halogenase Site Selectivity. Chem Catal 2022; 2:2658-2674. [PMID: 36569427 PMCID: PMC9784200 DOI: 10.1016/j.checat.2022.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Flavin-dependent halogenases (FDHs) catalyze selective halogenation of electron-rich aromatic compounds without the need for harsh oxidants required by conventional oxidative halogenation reactions. Predictive models for halogenase site selectivity could greatly improve their utility for chemical synthesis. Toward this end, we analyzed the structures and selectivity of three halogenase variants evolved to halogenate tryptamine with orthogonal selectivity. Crystal structures and reversion mutations revealed key residues involved in altering halogenase selectivity. Density functional theory calculations and molecular dynamics simulations are both consistent with hypohalous acid as the active halogenating species in FDH catalysis. This model was used to accurately predict the site selectivity of halogenase variants toward different synthetic substrates, providing a valuable tool for implementing halogenases in biocatalysis efforts.
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Affiliation(s)
- Mary C. Andorfer
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
- Present address: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- These authors contributed equally
| | - Declan Evans
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- These authors contributed equally
| | - Song Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Present address: Merck Research Laboratories, South San Francisco, CA, USA
| | - Cyndi Qixin He
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Present address: Merck Research Laboratories, Kenilworth, NJ, USA
| | - Anna M. Girlich
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | | | - Narayanasami Sukumar
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Building 436E, Argonne, IL 60439, USA
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
- Lead contact
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13
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Chan NH, Gomez CA, Vennelakanti V, Du Q, Kulik HJ, Lewis JC. Non-Native Anionic Ligand Binding and Reactivity in Engineered Variants of the Fe(II)- and α-Ketoglutarate-Dependent Oxygenase, SadA. Inorg Chem 2022; 61:14477-14485. [PMID: 36044713 PMCID: PMC9789792 DOI: 10.1021/acs.inorgchem.2c02872] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mononuclear non-heme Fe(II)- and α-ketoglutarate-dependent oxygenases (FeDOs) catalyze a site-selective C-H hydroxylation. Variants of these enzymes in which a conserved Asp/Glu residue in the Fe(II)-binding facial triad is replaced by Ala/Gly can, in some cases, bind various anionic ligands and catalyze non-native chlorination and bromination reactions. In this study, we explore the binding of different anions to an FeDO facial triad variant, SadX, and the effects of that binding on HO• vs X• rebound. We establish not only that chloride and bromide enable non-native halogenation reactions but also that all anions investigated, including azide, cyanate, formate, and fluoride, significantly accelerate and influence the site selectivity of SadX hydroxylation catalysis. Azide and cyanate also lead to the formation of products resulting from N3•, NCO•, and OCN• rebound. While fluoride rebound is not observed, the rate acceleration provided by this ligand leads us to calculate barriers for HO• and F• rebound from a putative Fe(III)(OH)(F) intermediate. These calculations suggest that the lack of fluorination is due to the relative barriers of the HO• and F• rebound transition states rather than an inaccessible barrier for F• rebound. Together, these results improve our understanding of the FeDO facial triad variant tolerance of different anionic ligands, their ability to promote rebound involving these ligands, and inherent rebound preferences relative to HO• that will aid efforts to develop non-native catalysis using these enzymes.
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Affiliation(s)
- Natalie H. Chan
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Christian A. Gomez
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Qian Du
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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14
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Snodgrass HM, Mondal D, Lewis JC. Directed Evolution of Flavin-Dependent Halogenases for Site- and Atroposelective Halogenation of 3-Aryl-4(3 H)-Quinazolinones via Kinetic or Dynamic Kinetic Resolution. J Am Chem Soc 2022; 144:16676-16682. [PMID: 36044712 DOI: 10.1021/jacs.2c07422] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In this study, we engineer a variant of the flavin-dependent halogenase RebH that catalyzes site- and atroposelective halogenation of 3-aryl-4(3H)-quinazolinones via kinetic or dynamic kinetic resolution. The required directed evolution uses a combination of random and site-saturation mutagenesis, substrate walking using two probe substrates, and a two-tiered screening approach involving the analysis of variant conversion and then enantioselectivity of improved variants. The resulting variant, 3-T, provides >99:1 e.r. for the (M)-atropisomer of the major brominated product, 25-fold improved conversion, and 91-fold improved site selectivity relative to the parent enzyme on the probe substrate used in the final rounds of evolution. This high activity and selectivity translate well to several additional substrates with varied steric and electronic properties. Computational modeling and docking simulations are used to rationalize the effects of key mutations on substrate binding. Given the range of substrates that have been used for atroposelective synthesis via electrophilic halogenation in the literature, these results suggest that flavin-dependent halogenases (FDHs) could find many additional applications for atroposelective catalysis. More broadly, this study highlights how RebH can be engineered to accept structurally diverse substrates that enable its use for enantioselective catalysis.
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Affiliation(s)
- Harrison M Snodgrass
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Dibyendu Mondal
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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15
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Gerroll BHR, Lewis JC, Baker LA. Cobalamin-Mediated Electrocatalytic Reduction of Ethyl Chloroacetate in Dimethylformamide. J Electrochem Soc 2022; 169:055501. [PMID: 35812015 PMCID: PMC9265244 DOI: 10.1149/1945-7111/ac6a13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The catalytic reduction of ethyl chloroacetate (ECA) by hydroxocobalamin (HOCbl) in dimethylformamide was studied electrochemically and spectroelectrochemically to identify initial steps in the reaction between the electrogenerated Co(I) center of cobalamin (cob(I)alamin) and ECA. Cyclic voltammograms of HOCbl in the presence of ECA show a small increase in current related to reduction of Co(II) to Co(I), and a new peak at more negative potentials related to reduction of an ethyl carboxymethyl-Cbl intermediate. The oxidation state of HOCbl during catalysis was monitored by means of spectroelectrochemical controlled-potential bulk electrolysis. Addition of ECA to electrogenerated cob(I)alamin initially generates the Co(II) form (cob(II)alamin) followed by a gradual formation of an ethyl carboxymethyl-Cbl intermediate. Controlled-potential bulk electrolysis was performed to identify products formed from catalytic reduction of ECA by electrogenerated cob(I)alamin and quantify the number of electrons transferred per molecule of ECA. Product distributions and coulometric results, together with the results of voltammograms and spectroelectrochemical controlled-potential bulk electrolysis, were interpreted to propose a reaction mechanism.
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Affiliation(s)
| | - Jared C. Lewis
- Department of Chemistry, Indiana University Bloomington, Indiana 47405, United States
| | - Lane A. Baker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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16
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Zubi YS, Seki K, Li Y, Hunt AC, Liu B, Roux B, Jewett MC, Lewis JC. Metal-responsive regulation of enzyme catalysis using genetically encoded chemical switches. Nat Commun 2022; 13:1864. [PMID: 35387988 PMCID: PMC8987029 DOI: 10.1038/s41467-022-29239-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/03/2022] [Indexed: 11/09/2022] Open
Abstract
Dynamic control over protein function is a central challenge in synthetic biology. To address this challenge, we describe the development of an integrated computational and experimental workflow to incorporate a metal-responsive chemical switch into proteins. Pairs of bipyridinylalanine (BpyAla) residues are genetically encoded into two structurally distinct enzymes, a serine protease and firefly luciferase, so that metal coordination biases the conformations of these enzymes, leading to reversible control of activity. Computational analysis and molecular dynamics simulations are used to rationally guide BpyAla placement, significantly reducing experimental workload, and cell-free protein synthesis coupled with high-throughput experimentation enable rapid prototyping of variants. Ultimately, this strategy yields enzymes with a robust 20-fold dynamic range in response to divalent metal salts over 24 on/off switches, demonstrating the potential of this approach. We envision that this strategy of genetically encoding chemical switches into enzymes will complement other protein engineering and synthetic biology efforts, enabling new opportunities for applications where precise regulation of protein function is critical.
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Affiliation(s)
- Yasmine S Zubi
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Kosuke Seki
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Ying Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Andrew C Hunt
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Bingqing Liu
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
| | - Michael C Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA.
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17
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Zubi YS, Liu B, Gu Y, Sahoo D, Lewis JC. Controlling the optical and catalytic properties of artificial metalloenzyme photocatalysts using chemogenetic engineering. Chem Sci 2022; 13:1459-1468. [PMID: 35222930 PMCID: PMC8809394 DOI: 10.1039/d1sc05792h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/08/2022] [Indexed: 11/21/2022] Open
Abstract
Visible light photocatalysis enables a broad range of organic transformations that proceed via single electron or energy transfer. Metal polypyridyl complexes are among the most commonly employed visible light photocatalysts. The photophysical properties of these complexes have been extensively studied and can be tuned by modifying the substituents on the pyridine ligands. On the other hand, ligand modifications that enable substrate binding to control reaction selectivity remain rare. Given the exquisite control that enzymes exert over electron and energy transfer processes in nature, we envisioned that artificial metalloenzymes (ArMs) created by incorporating Ru(ii) polypyridyl complexes into a suitable protein scaffold could provide a means to control photocatalyst properties. This study describes approaches to create covalent and non-covalent ArMs from a variety of Ru(ii) polypyridyl cofactors and a prolyl oligopeptidase scaffold. A panel of ArMs with enhanced photophysical properties were engineered, and the nature of the scaffold/cofactor interactions in these systems was investigated. These ArMs provided higher yields and rates than Ru(Bpy)3 2+ for the reductive cyclization of dienones and the [2 + 2] photocycloaddition between C-cinnamoyl imidazole and 4-methoxystyrene, suggesting that protein scaffolds could provide a means to improve the efficiency of visible light photocatalysts.
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Affiliation(s)
- Yasmine S Zubi
- Department of Chemistry, Indiana University Bloomington Indiana 47405 USA
| | - Bingqing Liu
- Department of Chemistry, Indiana University Bloomington Indiana 47405 USA
| | - Yifan Gu
- Department of Chemistry, University of Chicago Chicago IL 60637 USA
| | - Dipankar Sahoo
- Department of Chemistry, Indiana University Bloomington Indiana 47405 USA
| | - Jared C Lewis
- Department of Chemistry, Indiana University Bloomington Indiana 47405 USA
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18
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Yang X, Gerroll BHR, Jiang Y, Kumar A, Zubi YS, Baker LA, Lewis JC. Controlling Non-Native Cobalamin Reactivity and Catalysis in the Transcription Factor CarH. ACS Catal 2022; 12:935-942. [PMID: 35340760 DOI: 10.1021/acscatal.1c04748] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Vitamin B12 derivatives catalyze a wide range of organic transformations, but B12-dependent enzymes are underutilized in biocatalysis relative to other metalloenzymes. In this study, we engineered a variant of the transcription factor CarH, called CarH*, that catalyzes styrene C-H alkylation with improved yields (2-6.5-fold) and selectivity relative to cobalamin. While the native function of CarH involves transcription regulation via adenosylcobalamin (AdoCbl) Co(III)-carbon bond cleavage and β-hydride elimination to generate 4',5'-didehydroadenosine, CarH*-catalyzed styrene alkylation proceeds via non-native oxidative addition and olefin addition coupled with a native-like β-hydride elimination. Mechanistic studies on this reaction echo findings from earlier studies on AdoCbl homolysis to suggest that CarH* selectivity results from its ability to impart a cage effect on radical intermediates. These findings lay the groundwork for the development of B12-dependent enzymes as catalysts for non-native transformations.
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Affiliation(s)
- Xinhang Yang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | | | - Yuhua Jiang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Amardeep Kumar
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Yasmine S. Zubi
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Lane A. Baker
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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19
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Upp DM, Huang R, Li Y, Bultman MJ, Roux B, Lewis JC. Frontispiz: Engineering Dirhodium Artificial Metalloenzymes for Diazo Coupling Cascade Reactions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202184462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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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20
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Upp DM, Huang R, Li Y, Bultman MJ, Roux B, Lewis JC. Frontispiece: Engineering Dirhodium Artificial Metalloenzymes for Diazo Coupling Cascade Reactions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/anie.202184462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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Lewis JC, Lim M, Lai L, Mendoza E, Albertson TE, Chenoweth JA. Evaluation of N-acetylcysteine dose for the treatment of massive acetaminophen ingestion. Clin Toxicol (Phila) 2021; 60:507-513. [PMID: 34581655 DOI: 10.1080/15563650.2021.1984503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
METHODS The use of N-acetylcysteine (NAC) remains the standard of care for treatment of acetaminophen (APAP) toxicity and overdose. Currently, there is growing evidence to suggest that massive acetaminophen overdose is associated with increased hepatotoxicity despite timely administration of NAC. This raises the question as to whether an increased dose of intravenous (IV) NAC should be used in the setting of massive APAP ingestion. This study aimed to evaluate the rate of hepatotoxicity after massive APAP overdose treated with 3 different NAC treatment regimens. METHODS This was a retrospective cohort study conducted by electronic medical record review of cases reported to a statewide poison control system between 2007 and 2020. Inclusion criteria were single APAP or APAP combination-medication ingestion; acute massive acetaminophen (APAP) ingestion (defined as APAP concentration ≥ 2 times above the Rumack-Matthew 150 nomogram); received one of the three NAC regimens: standard dose IV NAC, oral (PO) NAC, or high dose IV NAC. The risk of hepatotoxicity was evaluated using a multivariate logistic regression model with standard dose IV NAC as the base variable for comparison. RESULTS A total of 373 patients met inclusion for the study. Of those, 135 cases were treated with standard dose IV NAC, 121 cases treated with PO NAC, and 117 cases treated with high dose IV NAC. The risk of developing hepatotoxicity was not statistically significant between the high dose IV NAC (OR 1.05, 95% CI 0.52 - 2.09) or oral NAC (OR 0.69, 95% CI 0.33 - 1.46) when compared to standard dose IV NAC. When adjusted for APAP combination medications, initial APAP ratio, initial elevated AST/ALT, and treatment within 8 h, there remained no difference between treatment regimens. CONCLUSION This study was unable to detect a large absolute reduction in the rate of hepatotoxicity after massive APAP ingestion in patients treated with high dose IV NAC or PO NAC when compared to standard dose IV NAC; even when treatment was initiated within 8 h of ingestion.
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Affiliation(s)
- J C Lewis
- Sacramento Division, California Poison Control System, Sacramento, CA, USA.,University of California San Francisco School of Pharmacy, San Francisco, CA, USA.,Department of Internal Medicine, University of California Davis Health, Sacramento, CA, USA
| | - M Lim
- Department of Pharmacy Services, University of California Davis Health, Sacramento, CA, USA
| | - L Lai
- Sacramento Division, California Poison Control System, Sacramento, CA, USA
| | - E Mendoza
- University of California San Francisco School of Pharmacy, San Francisco, CA, USA
| | - T E Albertson
- Sacramento Division, California Poison Control System, Sacramento, CA, USA.,University of California San Francisco School of Pharmacy, San Francisco, CA, USA.,Department of Internal Medicine, University of California Davis Health, Sacramento, CA, USA
| | - J A Chenoweth
- Sacramento Division, California Poison Control System, Sacramento, CA, USA.,Department of Emergency Medicine, University of California Davis Health, Sacramento, CA, USA
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23
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Jones K, Snodgrass HM, Belsare K, Dickinson BC, Lewis JC. Phage-Assisted Continuous Evolution and Selection of Enzymes for Chemical Synthesis. ACS Cent Sci 2021; 7:1581-1590. [PMID: 34584960 PMCID: PMC8461764 DOI: 10.1021/acscentsci.1c00811] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Indexed: 05/04/2023]
Abstract
Ligand-dependent biosensors are valuable tools for coupling the intracellular concentrations of small molecules to easily detectable readouts such as absorbance, fluorescence, or cell growth. While ligand-dependent biosensors are widely used for monitoring the production of small molecules in engineered cells and for controlling or optimizing biosynthetic pathways, their application to directed evolution for biocatalysts remains underexplored. As a consequence, emerging continuous evolution technologies are rarely applied to biocatalyst evolution. Here, we develop a panel of ligand-dependent biosensors that can detect a range of small molecules. We demonstrate that these biosensors can link enzymatic activity to the production of an essential phage protein to enable biocatalyst-dependent phage-assisted continuous evolution (PACE) and phage-assisted continuous selection (PACS). By combining these phage-based evolution and library selection technologies, we demonstrate that we can evolve enzyme variants with improved and expanded catalytic properties. Finally, we show that the genetic diversity resulting from a highly mutated PACS library is enriched for active enzyme variants with altered substrate scope. These results lay the foundation for using phage-based continuous evolution and selection technologies to engineer biocatalysts with novel substrate scope and reactivity.
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Affiliation(s)
- Krysten
A. Jones
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Harrison M. Snodgrass
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Ketaki Belsare
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Bryan C. Dickinson
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- E-mail:
| | - Jared C. Lewis
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
- E-mail:
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24
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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25
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Huang R, Chen H, Upp DM, Lewis JC, Zhang YHPJ. Correction to “A High-Throughput Method for Directed Evolution of NAD(P) +-Dependent Dehydrogenases for the Reduction of Biomimetic Nicotinamide Analogues”. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Chan NH, Gair JJ, Roy M, Qiu Y, Wang DS, Durak LJ, Chen L, Filatov AS, Lewis JC. Insight into the Scope and Mechanism for Transmetalation of Hydrocarbyl Ligands on Complexes Relevant to C–H Activation. Organometallics 2020. [DOI: 10.1021/acs.organomet.0c00628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Natalie H. Chan
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Joseph J. Gair
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Michael Roy
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Yehao Qiu
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Duo-Sheng Wang
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Landon J. Durak
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Liwei Chen
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Alexander S. Filatov
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
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27
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Salazar CA, Gair JJ, Flesch KN, Guzei IA, Lewis JC, Stahl SS. Catalytic Behavior of Mono-N-Protected Amino-Acid Ligands in Ligand-Accelerated C-H Activation by Palladium(II). Angew Chem Int Ed Engl 2020; 59:10873-10877. [PMID: 32196853 PMCID: PMC7311301 DOI: 10.1002/anie.202002484] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Indexed: 11/10/2022]
Abstract
Mono-N-protected amino acids (MPAAs) are increasingly common ligands in Pd-catalyzed C-H functionalization reactions. Previous studies have shown how these ligands accelerate catalytic turnover by facilitating the C-H activation step. Here, it is shown that MPAA ligands exhibit a second property commonly associated with ligand-accelerated catalysis: the ability to support catalytic turnover at substoichiometric ligand-to-metal ratios. This catalytic role of the MPAA ligand is characterized in stoichiometric C-H activation and catalytic C-H functionalization reactions. Palladacycle formation with substrates bearing carboxylate and pyridine directing groups exhibit a 50-100-fold increase in rate when only 0.05 equivalents of MPAA are present relative to PdII . These and other mechanistic data indicate that facile exchange between MPAAs and anionic ligands coordinated to PdII enables a single MPAA to support C-H activation at multiple PdII centers.
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Affiliation(s)
- Chase A Salazar
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Joseph J Gair
- Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA
| | - Kaylin N Flesch
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ilia A Guzei
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Shannon S Stahl
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
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28
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Salazar CA, Gair JJ, Flesch KN, Guzei IA, Lewis JC, Stahl SS. Catalytic Behavior of Mono‐
N
‐Protected Amino‐Acid Ligands in Ligand‐Accelerated C−H Activation by Palladium(II). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chase A. Salazar
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Joseph J. Gair
- Department of Chemistry University of Chicago Chicago IL 60637 USA
| | - Kaylin N. Flesch
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Ilia A. Guzei
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Jared C. Lewis
- Department of Chemistry Indiana University Bloomington IN 47405 USA
| | - Shannon S. Stahl
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
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29
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Huang R, Chen H, Upp DM, Lewis JC, Zhang YHPJ. A High-Throughput Method for Directed Evolution of NAD(P) +-Dependent Dehydrogenases for the Reduction of Biomimetic Nicotinamide Analogues. ACS Catal 2019; 9:11709-11719. [PMID: 34765284 DOI: 10.1021/acscatal.9b03840] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Engineering flavin-free NAD(P)+-dependent dehydrogenases to reduce biomimetic nicotinamide analogues (mNAD+s) is of importance for eliminating the need for costly NAD(P)+ in coenzyme regeneration systems. Current redox dye-based screening methods for engineering the mNAD+ specificity of dehydrogenases are frequently encumbered by a background signal from endogenous NAD(P) and intracellular reducing compounds, making the detection of low mNAD+-based activities a limiting factor for directed evolution. Here, we develop a high-throughput screening method, NAD(P)-eliminated solid-phase assay (NESPA), which can reliably identify mNAD+-active mutants of dehydrogenases with a minimal background signal. This method involves (1) heat lysis of colonies to permeabilize the cell membrane, (2) colony transfer onto filter paper, (3) washing to remove endogenous NAD(P) and reducing compounds, (4) enzyme-coupled assay for mNADH-dependent color production, and (5) digital imaging of colonies to identify mNAD+-active mutants. This method was used to improve the activity of 6-phosphogluconate dehydrogenase on nicotinamide mononucleotide (NMN+). The best mutant obtained after six rounds of directed evolution exhibits a 50-fold enhancement in catalytic efficiency (k cat/K M) and a specific activity of 17.7 U/mg on NMN+, which is comparable to the wild-type enzyme on its natural coenzyme, NADP+. The engineered dehydrogenase was then used to construct an NMNH regeneration system to drive an ene-reductase catalysis. A comparable level of turnover frequency and product yield was observed using the engineered system relative to NADPH regeneration by using the wild-type dehydrogenase. NESPA provides a simple and accurate readout of mNAD+-based activities and the screening at high-throughput levels (approximately tens of thousands per round), thus opening up an avenue for the evolution of dehydrogenases with specific activities on mNAD+s similar to the levels of natural enzyme/coenzyme pairs.
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Affiliation(s)
- Rui Huang
- Biological Systems Engineering Department, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Hui Chen
- Biological Systems Engineering Department, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - David M. Upp
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Yi-Heng P. Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
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30
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Fisher B, Snodgrass HM, Jones KA, Andorfer MC, Lewis JC. Site-Selective C-H Halogenation Using Flavin-Dependent Halogenases Identified via Family-Wide Activity Profiling. ACS Cent Sci 2019; 5:1844-1856. [PMID: 31807686 PMCID: PMC6891866 DOI: 10.1021/acscentsci.9b00835] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Indexed: 05/19/2023]
Abstract
Enzymes are powerful catalysts for site-selective C-H bond functionalization. Identifying suitable enzymes for this task and for biocatalysis in general remains challenging, however, due to the fundamental difficulty of predicting catalytic activity from sequence information. In this study, family-wide activity profiling was used to obtain sequence-function information on flavin-dependent halogenases (FDHs). This broad survey provided a number of insights into FDH activity, including halide specificity and substrate preference, that were not apparent from the more focused studies reported to date. Regions of FDH sequence space that are most likely to contain enzymes suitable for halogenating small-molecule substrates were also identified. FDHs with novel substrate scope and complementary regioselectivity on large, three-dimensionally complex compounds were characterized and used for preparative-scale late-stage C-H functionalization. In many cases, these enzymes provide activities that required several rounds of directed evolution to accomplish in previous efforts, highlighting that this approach can achieve significant time savings for biocatalyst identification and provide advanced starting points for further evolution.
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Affiliation(s)
- Brian
F. Fisher
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Harrison M. Snodgrass
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krysten A. Jones
- Department
of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Mary C. Andorfer
- Department
of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jared C. Lewis
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
- E-mail:
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31
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Jones K, Kentala K, Beck MW, An W, Lippert AR, Lewis JC, Dickinson BC. Development of a Split Esterase for Protein-Protein Interaction-Dependent Small-Molecule Activation. ACS Cent Sci 2019; 5:1768-1776. [PMID: 31807678 PMCID: PMC6891849 DOI: 10.1021/acscentsci.9b00567] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Indexed: 05/21/2023]
Abstract
Split reporters based on fluorescent proteins and luciferases have emerged as valuable tools for measuring interactions in biological systems. Relatedly, biosensors that transduce measured input signals into outputs that influence the host system are key components of engineered gene circuits for synthetic biology applications. While small-molecule-based imaging agents are widely used in biological studies, and small-molecule-based drugs and chemical probes can target a range of biological processes, a general method for generating a target small molecule in a biological system based on a measured input signal is lacking. Here, we develop a proximity-dependent split esterase that selectively unmasks ester-protected small molecules in an interaction-dependent manner. Exploiting the versatility of an ester-protected small-molecule output, we demonstrate fluorescent, chemiluminescent, and pharmacological probe generation, each created by masking key alcohol functional groups on a target small molecule. We show that the split esterase system can be used in combination with ester-masked fluorescent or luminescent probes to measure protein-protein interactions and protein-protein interaction inhibitor engagement. We demonstrate that the esterase-based reporter system is compatible with other commonly used split reporter imaging systems for the simultaneous detection of multiple protein-protein interactions. Finally, we develop a system for selective small-molecule-dependent cell killing by unmasking a cytotoxic molecule using an inducible split esterase. Presaging utility in future synthetic biology-based therapeutic applications, we also show that the system can be used for intercellular cell killing via a bystander effect, where one activated cell unmasks a cytotoxic molecule and kills cells physically adjacent to the activated cells. Collectively, this work illustrates that the split esterase system is a valuable new addition to the split protein toolbox, with particularly exciting potential in synthetic biology applications.
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Affiliation(s)
- Krysten
A. Jones
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Kaitlin Kentala
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Michael W. Beck
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Weiwei An
- Department
of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4),
Center for Global Health Impact (CGHI), Southern Methodist University, Dallas, Texas 75275-0314, United States
| | - Alexander R. Lippert
- Department
of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4),
Center for Global Health Impact (CGHI), Southern Methodist University, Dallas, Texas 75275-0314, United States
| | - Jared C. Lewis
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Bryan C. Dickinson
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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32
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Gair JJ, Haines BE, Filatov AS, Musaev DG, Lewis JC. Di-Palladium Complexes are Active Catalysts for Mono-N-Protected Amino Acid-Accelerated Enantioselective C–H Functionalization. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03887] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Joseph J. Gair
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Brandon E. Haines
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Alexander S. Filatov
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Djamaladdin G. Musaev
- Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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33
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Ellis-Guardiola K, Rui H, Beckner RL, Srivastava P, Sukumar N, Roux B, Lewis JC. Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase. Biochemistry 2019; 58:1616-1626. [PMID: 30786206 PMCID: PMC6714975 DOI: 10.1021/acs.biochem.9b00031] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes in the prolyl oligopeptidase family possess unique structures and substrate specificities that are important for their biological activity and for potential biocatalytic applications. The crystal structures of Pyrococcus furiosus ( Pfu) prolyl oligopeptidase (POP) and the corresponding S477C mutant were determined to 1.9 and 2.2 Å resolution, respectively. The wild type enzyme crystallized in an open conformation, indicating that this state is readily accessible, and it contained bound chloride ions and a prolylproline ligand. These structures were used as starting points for molecular dynamics simulations of Pfu POP conformational dynamics. The simulations showed that large-scale domain opening and closing occurred spontaneously, providing facile substrate access to the active site. Movement of the loop containing the catalytically essential histidine into a conformation similar to those found in structures with fully formed catalytic triads also occurred. This movement was modulated by chloride binding, providing a rationale for experimentally observed activation of POP peptidase catalysis by chloride. Thus, the structures and simulations reported in this study, combined with existing biochemical data, provide a number of insights into POP catalysis.
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Affiliation(s)
| | - Huan Rui
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Ryan L. Beckner
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Poonam Srivastava
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Narayanasami Sukumar
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Benoît 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
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34
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Gair JJ, Qiu Y, Khade RL, Chan NH, Filatov AS, Zhang Y, Lewis JC. Synthesis, Characterization, and Theoretical Investigation of a Transition State Analogue for Proton Transfer during C–H Activation by a Rhodium-Pincer Complex. Organometallics 2019. [DOI: 10.1021/acs.organomet.8b00887] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Joseph J. Gair
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Yehao Qiu
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Rahul L. Khade
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
| | - Natalie H. Chan
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Alexander S. Filatov
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Yong Zhang
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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35
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Lewis JC. Beyond the Second Coordination Sphere: Engineering Dirhodium Artificial Metalloenzymes To Enable Protein Control of Transition Metal Catalysis. Acc Chem Res 2019; 52:576-584. [PMID: 30830755 DOI: 10.1021/acs.accounts.8b00625] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Transition metal catalysis is a powerful tool for chemical synthesis, a standard by which understanding of elementary chemical processes can be measured, and a source of awe for those who simply appreciate the difficulty of cleaving and forming chemical bonds. Each of these statements is amplified in cases where the transition metal catalyst controls the selectivity of a chemical reaction. Enantioselective catalysis is a challenging but well-established phenomenon, and regio- or site-selective catalysis is increasingly common. On the other hand, transition-metal-catalyzed reactions are typically conducted under highly optimized conditions. Rigorous exclusion of air and water is common, and it is taken for granted that only a single substrate (of a particular class) will be present in a reaction, a desired site selectivity can be achieved by installing a directing group, and undesired reactivity can be blocked with protecting groups. These are all reasonable synthetic strategies, but they also highlight limits to catalyst control. The utility of transition metal catalysis could be greatly expanded if catalysts possessed the ability to regulate which molecules they encounter and the relative orientation of those molecules. The rapid and widespread adoption of stoichiometric bioorthogonal reactions illustrates the utility of robust reactions that proceed with high selectivity and specificity under mild reaction conditions. Expanding this capability beyond preprogrammed substrate pairs via catalyst control could therefore have an enormous impact on molecular science. Many metalloenzymes exhibit this level of catalyst control, and directed evolution can be used to rapidly improve the catalytic properties of these systems. On the other hand, the range of reactions catalyzed by enzymes is limited relative to that developed by chemists. The possibility of imparting enzyme-like activity, selectivity, and evolvability to reactions catalyzed by synthetic transition metal complexes has inspired the creation of artificial metalloenzymes (ArMs). The increasing levels of catalyst control exhibited by ArMs developed to date suggest that these systems could constitute a powerful platform for bioorthogonal transition metal catalysis and for selective catalysis in general. This Account outlines the development of a new class of ArMs based on a prolyl oligopeptidase (POP) scaffold. Studies conducted on POP ArMs containing a covalently linked dirhodium cofactor have shown that POP can impart enantioselectivity to a range of dirhodium-catalyzed reactions, increase reaction rates, and improve the specificity for reaction of dirhodium carbene intermediates with targeted organic substrates over components of cell lysate, including bulk water. Several design features of these ArMs enabled their evolution via random mutagenesis, which revealed that mutations throughout the POP scaffold, beyond the second sphere of the dirhodium cofactor, were important for ArM activity and selectivity. While it was anticipated that the POP scaffold would be capable of encapsulating and thus controlling the selectivity of bulky cofactors, molecular dynamics studies also suggest that POP conformational dynamics plays a role in its unique efficacy. These advances in scaffold selection, bioconjugation, and evolution form the basis of our ongoing efforts to control transition metal reactivity using protein scaffolds with the goal of enabling unique synthetic capabilities, including bioorthogonal catalysis.
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Affiliation(s)
- Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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36
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Affiliation(s)
- Greg Hughes
- Department of Process Research and Development Merck Sharp & Dohme Corporation , Rahway, New Jersey 07065, United States
| | - Jared C Lewis
- Searle Chemistry Lab, Department of Chemistry, The University of Chicago , 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
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37
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Abstract
Flavin-dependent halogenases (FDHs) catalyze the halogenation of organic substrates by coordinating reactions of reduced flavin, molecular oxygen, and chloride. Targeted and random mutagenesis of these enzymes have been used to both understand and alter their reactivity. These studies have led to insights into residues essential for catalysis and FDH variants with improved stability, expanded substrate scope, and altered site selectivity. Mutations throughout FDH structures have contributed to all of these advances. More recent studies have sought to rationalize the impact of these mutations on FDH function and to identify new FDHs to deepen our understanding of this enzyme class and to expand their utility for biocatalytic applications.
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Affiliation(s)
- Mary C Andorfer
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Jared C Lewis
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA;
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38
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Yang H, Swartz AM, Park HJ, Srivastava P, Ellis-Guardiola K, Upp DM, Lee G, Belsare K, Gu Y, Zhang C, Moellering RE, Lewis JC. Evolving artificial metalloenzymes via random mutagenesis. Nat Chem 2018; 10:318-324. [PMID: 29461523 PMCID: PMC5891097 DOI: 10.1038/nchem.2927] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 11/30/2017] [Indexed: 01/18/2023]
Abstract
Random mutagenesis has the potential to optimize the efficiency and selectivity of protein catalysts without requiring detailed knowledge of protein structure; however, introducing synthetic metal cofactors complicates the expression and screening of enzyme libraries, and activity arising from free cofactor must be eliminated. Here we report an efficient platform to create and screen libraries of artificial metalloenzymes (ArMs) via random mutagenesis, which we use to evolve highly selective dirhodium cyclopropanases. Error-prone PCR and combinatorial codon mutagenesis enabled multiplexed analysis of random mutations, including at sites distal to the putative ArM active site that are difficult to identify using targeted mutagenesis approaches. Variants that exhibited significantly improved selectivity for each of the cyclopropane product enantiomers were identified, and higher activity than previously reported ArM cyclopropanases obtained via targeted mutagenesis was also observed. This improved selectivity carried over to other dirhodium-catalysed transformations, including N-H, S-H and Si-H insertion, demonstrating that ArMs evolved for one reaction can serve as starting points to evolve catalysts for others.
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Affiliation(s)
- Hao Yang
- Merck Research Laboratories, 126 E. Lincoln Avenue, Rahway, New Jersey 07065, USA
| | - Alan M Swartz
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA
| | - Hyun June Park
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA
| | | | - Ken Ellis-Guardiola
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA
| | - David M Upp
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA
| | - Gihoon Lee
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Ketaki Belsare
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA
| | - Yifan Gu
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA
| | - Chen Zhang
- Provivi, Inc., 1701 Colorado Avenue, Santa Monica, California 90404, USA
| | - Raymond E Moellering
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Jared C Lewis
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA
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39
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Payne JT, Butkovich PH, Gu Y, Kunze KN, Park HJ, Wang DS, Lewis JC. Enantioselective Desymmetrization of Methylenedianilines via Enzyme-Catalyzed Remote Halogenation. J Am Chem Soc 2018; 140:546-549. [PMID: 29294291 PMCID: PMC5898188 DOI: 10.1021/jacs.7b09573] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Extensive effort has been devoted to engineering flavin-dependent halogenases (FDHs) with improved stability, expanded substrate scope, and altered regioselectivity. Here, we show that variants of rebeccamycin halogenase (RebH) catalyze enantioselective desymmetrization of methylenedianilines via halogenation of these substrates distal to their pro-stereogenic center. Structure-guided engineering was used to increase the conversion and selectivity of these reactions, and the synthetic utility of the halogenated products was shown via conversion of to a chiral α-substituted indole. These results constitute the first reported examples of asymmetric catalysis by FDHs.
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Affiliation(s)
| | - Paul H. Butkovich
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637
| | - Yifan Gu
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637
| | | | - Hyun June Park
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637
| | | | - Jared C. Lewis
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637
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40
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Gair JJ, Qiu Y, Chan NH, Filatov AS, Lewis JC. Rhodium Complexes of 2,6-Bis(dialkylphosphinomethyl)pyridines: Improved C–H Activation, Expanded Reaction Scope, and Catalytic Direct Arylation. Organometallics 2017. [DOI: 10.1021/acs.organomet.7b00532] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph J. Gair
- Department of Chemistry, University of Chicago, Chicago Illinois 60637, United States
| | - Yehao Qiu
- Department of Chemistry, University of Chicago, Chicago Illinois 60637, United States
| | - Natalie H. Chan
- Department of Chemistry, University of Chicago, Chicago Illinois 60637, United States
| | - Alexander S. Filatov
- Department of Chemistry, University of Chicago, Chicago Illinois 60637, United States
| | - Jared C. Lewis
- Department of Chemistry, University of Chicago, Chicago Illinois 60637, United States
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41
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Andorfer MC, Belsare KD, Girlich AM, Lewis JC. Aromatic Halogenation by Using Bifunctional Flavin Reductase-Halogenase Fusion Enzymes. Chembiochem 2017; 18:2099-2103. [PMID: 28879681 PMCID: PMC5898195 DOI: 10.1002/cbic.201700391] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Indexed: 11/11/2022]
Abstract
The remarkable site selectivity and broad substrate scope of flavin-dependent halogenases (FDHs) has led to much interest in their potential as biocatalysts. Multiple engineering efforts have demonstrated that FDHs can be tuned for non-native substrate scope and site selectivity. FDHs have also proven useful as in vivo biocatalysts and have been successfully incorporated into biosynthetic pathways to build new chlorinated aromatic compounds in several heterologous organisms. In both cases, reduced flavin cofactor, usually supplied by a separate flavin reductase (FR), is required. Herein, we report functional synthetic, fused FDH-FR proteins containing various FDHs and FRs joined by different linkers. We show that FDH-FR fusion proteins can increase product titers compared to the individual components for in vivo biocatalysis in Escherichia coli.
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Affiliation(s)
- Mary C Andorfer
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, SCL 302, Chicago, IL, 60637, USA
| | - Ketaki D Belsare
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, SCL 302, Chicago, IL, 60637, USA
| | - Anna M Girlich
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, SCL 302, Chicago, IL, 60637, USA
| | - Jared C Lewis
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, SCL 302, Chicago, IL, 60637, USA
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42
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Schwizer F, Okamoto Y, Heinisch T, Gu Y, Pellizzoni MM, Lebrun V, Reuter R, Köhler V, Lewis JC, Ward TR. Artificial Metalloenzymes: Reaction Scope and Optimization Strategies. Chem Rev 2017; 118:142-231. [PMID: 28714313 DOI: 10.1021/acs.chemrev.7b00014] [Citation(s) in RCA: 465] [Impact Index Per Article: 66.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The incorporation of a synthetic, catalytically competent metallocofactor into a protein scaffold to generate an artificial metalloenzyme (ArM) has been explored since the late 1970's. Progress in the ensuing years was limited by the tools available for both organometallic synthesis and protein engineering. Advances in both of these areas, combined with increased appreciation of the potential benefits of combining attractive features of both homogeneous catalysis and enzymatic catalysis, led to a resurgence of interest in ArMs starting in the early 2000's. Perhaps the most intriguing of potential ArM properties is their ability to endow homogeneous catalysts with a genetic memory. Indeed, incorporating a homogeneous catalyst into a genetically encoded scaffold offers the opportunity to improve ArM performance by directed evolution. This capability could, in turn, lead to improvements in ArM efficiency similar to those obtained for natural enzymes, providing systems suitable for practical applications and greater insight into the role of second coordination sphere interactions in organometallic catalysis. Since its renaissance in the early 2000's, different aspects of artificial metalloenzymes have been extensively reviewed and highlighted. Our intent is to provide a comprehensive overview of all work in the field up to December 2016, organized according to reaction class. Because of the wide range of non-natural reactions catalyzed by ArMs, this was done using a functional-group transformation classification. The review begins with a summary of the proteins and the anchoring strategies used to date for the creation of ArMs, followed by a historical perspective. Then follows a summary of the reactions catalyzed by ArMs and a concluding critical outlook. This analysis allows for comparison of similar reactions catalyzed by ArMs constructed using different metallocofactor anchoring strategies, cofactors, protein scaffolds, and mutagenesis strategies. These data will be used to construct a searchable Web site on ArMs that will be updated regularly by the authors.
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Affiliation(s)
- Fabian Schwizer
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yasunori Okamoto
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Tillmann Heinisch
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yifan Gu
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Michela M Pellizzoni
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Vincent Lebrun
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Raphael Reuter
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Valentin Köhler
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Jared C Lewis
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Thomas R Ward
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
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43
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Gair JJ, Haines BE, Filatov AS, Musaev DG, Lewis JC. Mono- N-protected amino acid ligands stabilize dimeric palladium(ii) complexes of importance to C-H functionalization. Chem Sci 2017; 8:5746-5756. [PMID: 29619194 PMCID: PMC5859881 DOI: 10.1039/c7sc01674c] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/15/2017] [Indexed: 11/21/2022] Open
Abstract
C–H activation, C–H functionalization, cyclopalladation, mono-protected amino acid, dimeric Pd amino acid complexes, MPAA coordination, relay of stereochemistry.
Mono-protected amino acid (MPAA) ligands are used in a number of Pd-catalyzed C–H functionalization reactions. MPAAs have been proposed to bind to Pd(ii) via κ2-(N,O) coordination, but such binding has not yet been experimentally validated. Herein, we report the synthesis and detailed characterization of a series of MPAA complexes prepared via cyclopalladation of dimethylbenzylamine in the presence of MPAAs. The isolated complexes exist as μ-carboxylato (MPAA) bridged dimers and feature potential M–M cooperativity and secondary sphere hydrogen bonding. Selective MPAA coordination and relay of stereochemistry, previously suggested to uniquely result from κ2-(N,O) MPAA coordination, are both observed. The isolated MPAA complexes undergo C–C and C–X (X = Cl, Br, I) bond formation when treated with electrophiles used for catalytic C–H functionalization. Stoichiometric iodination of MPAA palladacycles was found to proceed via a dinuclear palladium species with one equivalent of iodine in the rate limiting transition structure, and the isolated complexes also served as viable precatalysts for catalytic C–H functionalization. Together, these results provide a number of insights into the reactivity of Pd-MPAA complexes relevant to C–H bond functionalization.
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Affiliation(s)
- Joseph J Gair
- Department of Chemistry , The University of Chicago , Chicago , Illinois 60637 , USA .
| | - Brandon E Haines
- Cherry L. Emerson Center for Scientific Computation , Emory University , 1515 Dickey Drive , Atlanta , Georgia 30322 , USA .
| | - Alexander S Filatov
- Department of Chemistry , The University of Chicago , Chicago , Illinois 60637 , USA .
| | - Djamaladdin G Musaev
- Cherry L. Emerson Center for Scientific Computation , Emory University , 1515 Dickey Drive , Atlanta , Georgia 30322 , USA .
| | - Jared C Lewis
- Department of Chemistry , The University of Chicago , Chicago , Illinois 60637 , USA .
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44
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Belsare KD, Andorfer MC, Cardenas FS, Chael JR, Park HJ, Lewis JC. A Simple Combinatorial Codon Mutagenesis Method for Targeted Protein Engineering. ACS Synth Biol 2017; 6:416-420. [PMID: 28033708 DOI: 10.1021/acssynbio.6b00297] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Directed evolution is a powerful tool for optimizing enzymes, and mutagenesis methods that improve enzyme library quality can significantly expedite the evolution process. Here, we report a simple method for targeted combinatorial codon mutagenesis (CCM). To demonstrate the utility of this method for protein engineering, CCM libraries were constructed for cytochrome P450BM3, pfu prolyl oligopeptidase, and the flavin-dependent halogenase RebH; 10-26 sites were targeted for codon mutagenesis in each of these enzymes, and libraries with a tunable average of 1-7 codon mutations per gene were generated. Each of these libraries provided improved enzymes for their respective transformations, which highlights the generality, simplicity, and tunability of CCM for targeted protein engineering.
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Affiliation(s)
- Ketaki D. Belsare
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Mary C. Andorfer
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Frida S. Cardenas
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Julia R. Chael
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Hyun June Park
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Jared C. Lewis
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
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45
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Andorfer MC, Grob JE, Hajdin CE, Chael JR, Siuti P, Lilly J, Tan KL, Lewis JC. Understanding Flavin-Dependent Halogenase Reactivity via Substrate Activity Profiling. ACS Catal 2017; 7:1897-1904. [PMID: 28989809 PMCID: PMC5627516 DOI: 10.1021/acscatal.6b02707] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The activity of four native FDHs and four engineered FDH variants on 93 low molecular weight arenes was used to generate FDH substrate activity profiles. These profiles provided insights into how substrate class, functional group substitution, electronic activation, and binding impact FDH activity and selectivity. The enzymes studied could halogenate a far greater range of substrates than previously recognized, but significant differences in their substrate specificity and selectivity were observed. Trends between the electronic activation of each site on a substrate and halogenation conversion at that site were established, and these data, combined with docking simulations, suggest that substrate binding can override electronic activation even on compounds differing appreciably from native substrates. These findings provide a useful framework for understanding and exploiting FDH reactivity for organic synthesis.
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Affiliation(s)
- Mary C. Andorfer
- Department of Chemistry, University of Chicago, Chicago, IL 60637
| | - Jonathan E. Grob
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 250 Massachusetts Ave, Cambridge, MA 02139
| | - Christine E. Hajdin
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 250 Massachusetts Ave, Cambridge, MA 02139
| | - Julia R. Chael
- Department of Chemistry, University of Chicago, Chicago, IL 60637
| | - Piro Siuti
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 250 Massachusetts Ave, Cambridge, MA 02139
| | - Jeremiah Lilly
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 250 Massachusetts Ave, Cambridge, MA 02139
| | - Kian L. Tan
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 250 Massachusetts Ave, Cambridge, MA 02139
| | - Jared C. Lewis
- Department of Chemistry, University of Chicago, Chicago, IL 60637
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46
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Upp DM, Lewis JC. Selective C-H bond functionalization using repurposed or artificial metalloenzymes. Curr Opin Chem Biol 2017; 37:48-55. [PMID: 28135654 DOI: 10.1016/j.cbpa.2016.12.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 12/23/2016] [Indexed: 11/26/2022]
Abstract
Catalytic CH bond functionalization has become an important tool for organic synthesis. Metalloenzymes offer a solution to one of the foremost challenges in this field, site-selective CH functionalization, but they are only capable of catalyzing a subset of the CH functionalization reactions known to small molecule catalysts. To overcome this limitation, metalloenzymes have been repurposed by exploiting the reactivity of their native cofactors toward substrates not found in nature. Additionally, new reactivity has been accessed by incorporating synthetic metal cofactors into protein scaffolds to form artificial metalloenzymes. The selectivity and activity of these catalysts has been tuned using directed evolution. This review covers the recent progress in developing and optimizing both repurposed and artificial metalloenzymes as catalysts for selective CH bond functionalization.
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Affiliation(s)
- David M Upp
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Jared C Lewis
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA.
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47
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Abstract
Engineered variants of rebeccamycin halogenase were used to selectively halogenate a number of biologically active aromatic compounds. Subsequent Pd-catalyzed cross-coupling reactions on the crude extracts of these reactions were used to install aryl, amine, and ether substituents at the halogenation site. This simple, chemoenzymatic method enables non-directed functionalization of C-H bonds on a range of substrates to provide access to derivatives that would be challenging or inefficient to prepare by other means.
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Affiliation(s)
- Landon J. Durak
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - James T. Payne
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Jared C. Lewis
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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Abstract
RebH variants capable of chlorinating substituted indoles ortho-, meta-, and para- to the indole nitrogen were evolved by directly screening for altered selectivity on deuterium-substituted probe substrates using mass spectrometry. This systematic approach allowed for rapid accumulation of beneficial mutations using simple adaptive walks and should prove generally useful for altering and optimizing the selectivity of C-H functionalization catalysts. Analysis of the beneficial mutations showed that structure-guided selection of active site residues for targeted mutagenesis can be complicated either by activity/selectivity tradeoffs that reduce the possibility of detecting such mutations or by epistatic effects that actually eliminate the benefits of a mutation in certain contexts. As a corollary to this finding, the precise manner in which the beneficial mutations identified led to the observed changes in RebH selectivity is not clear. Docking simulations suggest that tryptamine binds to these variants as tryptophan does to native halogenases, but structural studies will be required to confirm these models and shed light on how particular mutations impact tryptamine binding. Similar directed evolution efforts on other enzymes or artificial metalloenzymes could enable a wide range of C-H functionalization reactions.
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Affiliation(s)
- Mary C Andorfer
- Department of Chemistry, University of Chicago, Chicago, IL 60637
| | - Hyun June Park
- Department of Chemistry, University of Chicago, Chicago, IL 60637
| | | | - Jared C Lewis
- Department of Chemistry, University of Chicago, Chicago, IL 60637
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Gu Y, Ellis-Guardiola K, Srivastava P, Lewis JC. Preparation, Characterization, and Oxygenase Activity of a Photocatalytic Artificial Enzyme. Chembiochem 2015; 16:1880-1883. [PMID: 26097041 DOI: 10.1002/cbic.201500165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Indexed: 11/12/2022]
Abstract
A bicyclo[6,1,0]nonyne-substituted 9-mesityl-10-methyl-acridinium cofactor was prepared and covalently linked to a prolyl oligopeptidase scaffold containing a genetically encoded 4-azido-L-phenylalanine residue in its active site. The resulting artificial enzyme catalyzed sulfoxidation when irradiated with visible light in the presence of air. This reaction proceeds by initial electron abstraction from the sulfide within the enzyme active site, and the protein scaffold extended the fluorescence lifetime of the acridium cofactor. The mode of sulfide activation and placement of the acridinium cofactor (5) in POP-ZA4 -5 make this artificial enzyme a promising platform for developing selective photocatalytic transformations.
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Affiliation(s)
- Yifan Gu
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637 (USA)
| | - Ken Ellis-Guardiola
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637 (USA)
| | - Poonam Srivastava
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637 (USA)
| | - Jared C Lewis
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637 (USA)
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50
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Lewis JC. Metallopeptide catalysts and artificial metalloenzymes containing unnatural amino acids. Curr Opin Chem Biol 2015; 25:27-35. [PMID: 25545848 PMCID: PMC4380757 DOI: 10.1016/j.cbpa.2014.12.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/03/2014] [Accepted: 12/11/2014] [Indexed: 01/24/2023]
Abstract
Metallopeptide catalysts and artificial metalloenzymes built from peptide scaffolds and catalytically active metal centers possess a number of exciting properties that could be exploited for selective catalysis. Control over metal catalyst secondary coordination spheres, compatibility with library based methods for optimization and evolution, and biocompatibility stand out in this regard. A wide range of unnatural amino acids (UAAs) have been incorporated into peptide and protein scaffolds using several distinct methods, and the resulting UAAs containing scaffolds can be used to create novel hybrid metal-peptide catalysts. Promising levels of selectivity have been demonstrated for several hybrid catalysts, and these provide a strong impetus and important lessons for the design of and optimization of hybrid catalysts.
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Affiliation(s)
- Jared C Lewis
- University of Chicago, Department of Chemistry, 5735 South Ellis Avenue, Chicago, IL 60637, United States.
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