1
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Ahmed H, Ghosh B, Breitenlechner S, Feßner M, Merten C, Bach T. Intermolecular Enantioselective Amination Reactions Mediated by Visible Light and a Chiral Iron Porphyrin Complex. Angew Chem Int Ed Engl 2024:e202407003. [PMID: 38695376 DOI: 10.1002/anie.202407003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Indexed: 06/15/2024]
Abstract
In the presence of 1 mol % of a chiral iron porphyrin catalyst, various 3-arylmethyl-substituted 2-quinolones and 2-pyridones underwent an enantioselective amination reaction (20 examples; 93-99 % ee). The substrates were used as the limiting reagents, and fluorinated aryl azides (1.5 equivalents) served as nitrene precursors. The reaction is triggered by visible light which allows a facile dediazotation at ambient temperature. The selectivity of the reaction is governed by a two-point hydrogen bond interaction between the ligand of the iron catalyst and the substrate. Hydrogen bonding directs the amination to a specific hydrogen atom within the substrate that is displaced by the nitrogen substituent either in a concerted fashion or by a rebound mechanism.
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Affiliation(s)
- Hussayn Ahmed
- Technische Universität München, School of Natural Sciences, Department of Chemistry and Catalysis Research Center, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Biki Ghosh
- Technische Universität München, School of Natural Sciences, Department of Chemistry and Catalysis Research Center, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Stefan Breitenlechner
- Technische Universität München, School of Natural Sciences, Department of Chemistry and Catalysis Research Center, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Malte Feßner
- Ruhr-Universität Bochum, Faculty for Chemistry and Biochemistry, Universitätsstraße 150, D-44801, Bochum
| | - Christian Merten
- Ruhr-Universität Bochum, Faculty for Chemistry and Biochemistry, Universitätsstraße 150, D-44801, Bochum
| | - Thorsten Bach
- Technische Universität München, School of Natural Sciences, Department of Chemistry and Catalysis Research Center, Lichtenbergstraße 4, 85747, Garching, Germany
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2
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Fansher D, Besna JN, Fendri A, Pelletier JN. Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants. ACS Catal 2024; 14:5560-5592. [PMID: 38660610 PMCID: PMC11036407 DOI: 10.1021/acscatal.4c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many researchers have evolved this enzyme to generate a variety of products. However, the abundance of information on increasingly diversified variants of P450 BM3 that catalyze a broad array of chemistry is not in a format that enables easy extraction and interpretation. We present a database that categorizes variants by their catalyzed reactions and includes details about substrates to provide reaction context. This database of >1500 P450 BM3 variants is downloadable and machine-readable and includes instructions to maximize ease of gathering information. The database allows rapid identification of commonly reported substitutions, aiding researchers who are unfamiliar with the enzyme in identifying starting points for enzyme engineering. For those actively engaged in engineering P450 BM3, the database, along with this review, provides a powerful and user-friendly platform to understand, predict, and identify the attributes of P450 BM3 variants, encouraging the further engineering of this enzyme.
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Affiliation(s)
- Douglas
J. Fansher
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Jonathan N. Besna
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
| | - Ali Fendri
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Joelle N. Pelletier
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
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3
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Krishnan A, Waheed SO, Varghese A, Cherilakkudy FH, Schofield CJ, Karabencheva-Christova TG. Unusual catalytic strategy by non-heme Fe(ii)/2-oxoglutarate-dependent aspartyl hydroxylase AspH. Chem Sci 2024; 15:3466-3484. [PMID: 38455014 PMCID: PMC10915816 DOI: 10.1039/d3sc05974j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
Biocatalytic C-H oxidation reactions are of important synthetic utility, provide a sustainable route for selective synthesis of important organic molecules, and are an integral part of fundamental cell processes. The multidomain non-heme Fe(ii)/2-oxoglutarate (2OG) dependent oxygenase AspH catalyzes stereoselective (3R)-hydroxylation of aspartyl- and asparaginyl-residues. Unusually, compared to other 2OG hydroxylases, crystallography has shown that AspH lacks the carboxylate residue of the characteristic two-His-one-Asp/Glu Fe-binding triad. Instead, AspH has a water molecule that coordinates Fe(ii) in the coordination position usually occupied by the Asp/Glu carboxylate. Molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) studies reveal that the iron coordinating water is stabilized by hydrogen bonding with a second coordination sphere (SCS) carboxylate residue Asp721, an arrangement that helps maintain the six coordinated Fe(ii) distorted octahedral coordination geometry and enable catalysis. AspH catalysis follows a dioxygen activation-hydrogen atom transfer (HAT)-rebound hydroxylation mechanism, unusually exhibiting higher activation energy for rebound hydroxylation than for HAT, indicating that the rebound step may be rate-limiting. The HAT step, along with substrate positioning modulated by the non-covalent interactions with SCS residues (Arg688, Arg686, Lys666, Asp721, and Gln664), are essential in determining stereoselectivity, which likely proceeds with retention of configuration. The tetratricopeptide repeat (TPR) domain of AspH influences substrate binding and manifests dynamic motions during catalysis, an observation of interest with respect to other 2OG oxygenases with TPR domains. The results provide unique insights into how non-heme Fe(ii) oxygenases can effectively catalyze stereoselective hydroxylation using only two enzyme-derived Fe-ligating residues, potentially guiding enzyme engineering for stereoselective biocatalysis, thus advancing the development of non-heme Fe(ii) based biomimetic C-H oxidation catalysts, and supporting the proposal that the 2OG oxygenase superfamily may be larger than once perceived.
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Affiliation(s)
- Anandhu Krishnan
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Ann Varghese
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | | | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford OX1 3TA Oxford UK
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4
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Kagawa Y, Oohora K, Hayashi T. Intramolecular C-H bond amination catalyzed by myoglobin reconstituted with iron porphycene. J Inorg Biochem 2024; 252:112459. [PMID: 38181613 DOI: 10.1016/j.jinorgbio.2023.112459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/10/2023] [Accepted: 12/16/2023] [Indexed: 01/07/2024]
Abstract
C-H bond amination is an effective way to obtain nitrogen-containing products. In this work, we demonstrate that myoglobin reconstituted with iron porphycene (rMb(FePc)) catalyzes intramolecular C(sp3)-H bond amination of arylsulfonyl azides to yield corresponding sultam analogs. The total turnover number of rMb(FePc) is up to 5.7 × 104 for the C-H bond amination of 2,4,6-triisopropylbenzenesulfonyl azide. Moreover, rMb(FePc) exhibits higher selectivity for the desired C-H bond amination than the competing azide reduction compared to native myoglobin. Kinetic studies reveal that the kcat value of rMb(FePc) is 4-fold higher than that of native myoglobin. Furthermore, H64A, H64V and H64I mutants of rMb(FePc) enhance the turnover number (TON) and enantioselectivity for the C-H bond amination of 2,4,6-triethylbenzenesulfonyl azide. The present findings indicate that iron porphycene is an attractive artificial cofactor for myoglobin toward the C-H bond amination reaction.
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Affiliation(s)
- Yoshiyuki Kagawa
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan; Innovative Catalysis Science Division, Institute for Open and Transdisciplinary Research Initiatives (ICS-OTRI), Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.
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5
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Tinzl M, Diedrich JV, Mittl PRE, Clémancey M, Reiher M, Proppe J, Latour JM, Hilvert D. Myoglobin-Catalyzed Azide Reduction Proceeds via an Anionic Metal Amide Intermediate. J Am Chem Soc 2024; 146:1957-1966. [PMID: 38264790 PMCID: PMC10811658 DOI: 10.1021/jacs.3c09279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 01/25/2024]
Abstract
Nitrene transfer reactions catalyzed by heme proteins have broad potential for the stereoselective formation of carbon-nitrogen bonds. However, competition between productive nitrene transfer and the undesirable reduction of nitrene precursors limits the broad implementation of such biocatalytic methods. Here, we investigated the reduction of azides by the model heme protein myoglobin to gain mechanistic insights into the factors that control the fate of key reaction intermediates. In this system, the reaction proceeds via a proposed nitrene intermediate that is rapidly reduced and protonated to give a reactive ferrous amide species, which we characterized by UV/vis and Mössbauer spectroscopies, quantum mechanical calculations, and X-ray crystallography. Rate-limiting protonation of the ferrous amide to produce the corresponding amine is the final step in the catalytic cycle. These findings contribute to our understanding of the heme protein-catalyzed reduction of azides and provide a guide for future enzyme engineering campaigns to create more efficient nitrene transferases. Moreover, harnessing the reduction reaction in a chemoenzymatic cascade provided a potentially practical route to substituted pyrroles.
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Affiliation(s)
- Matthias Tinzl
- Laboratory
of Organic Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Johannes V. Diedrich
- Institute
of Physical and Theoretical Chemistry, TU
Braunschweig, 38106 Braunschweig, Germany
| | - Peer R. E. Mittl
- Department
of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Martin Clémancey
- Université
Grenoble AlpesCNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des
Métaux, 17 Rue des Martyrs, Grenoble F-38054 Cedex, France
| | - Markus Reiher
- Institute
for Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
| | - Jonny Proppe
- Institute
of Physical and Theoretical Chemistry, TU
Braunschweig, 38106 Braunschweig, Germany
| | - Jean-Marc Latour
- Université
Grenoble AlpesCNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des
Métaux, 17 Rue des Martyrs, Grenoble F-38054 Cedex, France
| | - Donald Hilvert
- Laboratory
of Organic Chemistry, ETH Zürich, 8093 Zürich, Switzerland
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6
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Roy S, Vargas DA, Ma P, Sengupta A, Zhu L, Houk KN, Fasan R. Stereoselective Construction of β-, γ-, and δ-Lactam Rings via Enzymatic C-H Amidation. Nat Catal 2024; 7:65-76. [PMID: 38584987 PMCID: PMC10997382 DOI: 10.1038/s41929-023-01068-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 10/23/2023] [Indexed: 04/09/2024]
Abstract
Lactam rings are found in many biologically active natural products and pharmaceuticals, including important classes of antibiotics. Methods for the asymmetric synthesis of these molecules are therefore highly desirable, particularly through the selective functionalization of unreactive aliphatic C-H bonds. Here we show the development of a strategy for the asymmetric synthesis of β-, γ-, and δ-lactams via hemoprotein-catalysed intramolecular C-H amidation reaction with readily available dioxazolone reagents. Engineered myoglobin variants serve as excellent biocatalysts for this transformation yielding the desired lactam products in high yields, high enantioselectivity, and on preparative scale. Mechanistic and computational studies elucidate the nature of the C-H amination and enantiodetermining steps and provide insights into protein-mediated control of regioselectivity and stereoselectivity. Additionally, an alkaloid natural product and a drug molecule were synthesized chemoenzymatically in much fewer steps (7-8 vs. 11-12) than previously reported, further demonstrating the power of biosynthetic strategy for the preparation of complex bioactive molecules.
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Affiliation(s)
- Satyajit Roy
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York, 14627, United States
- Current affiliation: Department of Chemistry and Biochemistry, University of Texas at Dallas, 800 W. Campbell Road, Richardson, TX 75080, United States
| | - David A. Vargas
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York, 14627, United States
- Current affiliation: Process Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Pengchen Ma
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095, United States
- School of Chemistry, Xi’an Key Laboratory of Sustainable Energy Materials Chemistry, MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Xi’an Jiaotong University, Xi’an, China
| | - Arkajyoti Sengupta
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095, United States
| | - Ledong Zhu
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York, 14627, United States
- Current affiliation: Department of Chemistry and Biochemistry, University of Texas at Dallas, 800 W. Campbell Road, Richardson, TX 75080, United States
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7
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Qin ZY, Gao S, Zou Y, Liu Z, Wang JB, Houk KN, Arnold FH. Biocatalytic Construction of Chiral Pyrrolidines and Indolines via Intramolecular C(sp 3)-H Amination. ACS CENTRAL SCIENCE 2023; 9:2333-2338. [PMID: 38161360 PMCID: PMC10755850 DOI: 10.1021/acscentsci.3c00516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2024]
Abstract
Nature harnesses exquisite enzymatic cascades to construct N-heterocycles and further uses these building blocks to assemble the molecules of life. Here we report an enzymatic platform to construct important chiral N-heterocyclic products, pyrrolidines and indolines, via abiological intramolecular C(sp3)-H amination of organic azides. Directed evolution of cytochrome P411 (a P450 enzyme with serine as the heme-ligating residue) yielded variant P411-PYS-5149, capable of catalyzing the insertion of alkyl nitrene into C(sp3)-H bonds to build pyrrolidine derivatives with good enantioselectivity and catalytic efficiency. Further evolution of activity on aryl azide substrates yielded variant P411-INS-5151 that catalyzes intramolecular C(sp3)-H amination to afford chiral indolines. In addition, we show that these enzymatic aminations can be coupled with a P411-based carbene transferase or a tryptophan synthase to generate an α-amino lactone or a noncanonical amino acid, respectively, underscoring the power of new-to-nature biocatalysis in complexity-building chemical synthesis.
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Affiliation(s)
- Zi-Yang Qin
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Shilong Gao
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Yike Zou
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095, United States
| | - Zhen Liu
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - James B. Wang
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Kendall N. Houk
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095, United States
| | - Frances H. Arnold
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
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8
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Mahajan M, Mondal B. How Axial Coordination Regulates the Electronic Structure and C-H Amination Reactivity of Fe-Porphyrin-Nitrene? JACS AU 2023; 3:3494-3505. [PMID: 38155653 PMCID: PMC10751768 DOI: 10.1021/jacsau.3c00670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023]
Abstract
Detailed electronic structure and its correlation with the intramolecular C-H amination reactivity of Fe-porphyrin-nitrene intermediates bearing different "axial" coordination have been investigated using multiconfigurational complete active space self-consistent field (CASSCF), N-electron valence perturbation theory (NEVPT2), and hybrid density functional theory (DFT-B3LYP) calculations. Three types of "axial" coordination, -OMe/-O(H)Me (1-Sul/2-Sul), -SMe/-S(H)Me (3-Sul/4-Sul), and -NMeIm (MeIm = 3-methyl-imidazole) (5-Sul) mimicking serine, cysteine, and histidine, respectively, along with no axial coordination (6-Sul) have been considered to decipher how the "axial" coordination of different strengths regulates the electronic integrity of the Fe-N core and nitrene-transfer reactivity of Fe-porphyrin-nitrene intermediates. CASSCF-based natural orbitals reveal two distinct classes of electronic structures: Fe-nitrenes (1-Sul and 3-Sul) with relatively stronger axial coordination (-OMe and -SMe) display "imidyl" nature and those (2-Sul, 4-Sul, and 6-Sul) with weaker axial coordination (-O(H)Me, -S(H)Me and no axial coordination) exhibit "imido-like" character. A borderline between the two classes is also observed with NMeIm axial coordination (5-Sul). Axial coordination of different strengths not only regulates the electronic structure but also modulates the Fe-3d orbital energies, as revealed through the d-d transition energies obtained by CASSCF/NEVPT2 calculations. The relatively lower energy of Fe-3dz2 orbital allows easy access to low-lying high-spin quintet states in the cases of weaker "axial" coordination (2-Sul, 4-Sul, and 6-Sul), and the associated hydrogen atom transfer (HAT) reactivity appears to involve two-state triplet-quintet reactivity through minimum energy crossing point (3,5MECP) between the spin states. In stark contrast, Fe-nitrenes with relatively stronger "axial" coordination (1-Sul and 3-Sul) undergo triplet-only HAT reactivity. Overall, this in-depth electronic structure investigation and HAT reactivity evaluation reveal that the weaker axial coordination in Fe-porphyrin-nitrene complexes (2-Sul, 4-Sul, and 6-Sul) can promote more efficient C-H oxidation through the quintet spin state.
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Affiliation(s)
- Mayank Mahajan
- School of Chemical Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh 175075, India
| | - Bhaskar Mondal
- School of Chemical Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh 175075, India
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9
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Nam D, Bacik JP, Khade RL, Aguilera MC, Wei Y, Villada JD, Neidig ML, Zhang Y, Ando N, Fasan R. Mechanistic manifold in a hemoprotein-catalyzed cyclopropanation reaction with diazoketone. Nat Commun 2023; 14:7985. [PMID: 38042860 PMCID: PMC10693563 DOI: 10.1038/s41467-023-43559-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 11/14/2023] [Indexed: 12/04/2023] Open
Abstract
Hemoproteins have recently emerged as promising biocatalysts for new-to-nature carbene transfer reactions. However, mechanistic understanding of the interplay between productive and unproductive pathways in these processes is limited. Using spectroscopic, structural, and computational methods, we investigate the mechanism of a myoglobin-catalyzed cyclopropanation reaction with diazoketones. These studies shed light on the nature and kinetics of key catalytic steps in this reaction, including the formation of an early heme-bound diazo complex intermediate, the rate-determining nature of carbene formation, and the cyclopropanation mechanism. Our analyses further reveal the existence of a complex mechanistic manifold for this reaction that includes a competing pathway resulting in the formation of an N-bound carbene adduct of the heme cofactor, which was isolated and characterized by X-ray crystallography, UV-Vis, and Mössbauer spectroscopy. This species can regenerate the active biocatalyst, constituting a non-productive, yet non-destructive detour from the main catalytic cycle. These findings offer a valuable framework for both mechanistic analysis and design of hemoprotein-catalyzed carbene transfer reactions.
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Affiliation(s)
- Donggeon Nam
- Department of Chemistry, University of Rochester, Rochester, NY, 14627, USA
| | - John-Paul Bacik
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Rahul L Khade
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ, 07030, USA
| | | | - Yang Wei
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ, 07030, USA
| | - Juan D Villada
- Department of Chemistry, University of Rochester, Rochester, NY, 14627, USA
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Michael L Neidig
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK.
| | - Yong Zhang
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ, 07030, USA.
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, NY, 14627, USA.
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, 75080, USA.
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10
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Cárdenas-Moreno Y, González-Bacerio J, García Arellano H, Del Monte-Martínez A. Oxidoreductase enzymes: Characteristics, applications, and challenges as a biocatalyst. Biotechnol Appl Biochem 2023; 70:2108-2135. [PMID: 37753743 DOI: 10.1002/bab.2513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 09/03/2023] [Indexed: 09/28/2023]
Abstract
Oxidoreductases are enzymes with distinctive characteristics that favor their use in different areas, such as agriculture, environmental management, medicine, and analytical chemistry. Among these enzymes, oxidases, dehydrogenases, peroxidases, and oxygenases are very interesting. Because their substrate diversity, they can be used in different biocatalytic processes by homogeneous and heterogeneous catalysis. Immobilization of these enzymes has favored their use in the solution of different biotechnological problems, with a notable increase in the study and optimization of this technology in the last years. In this review, the main structural and catalytical features of oxidoreductases, their substrate specificity, immobilization, and usage in biocatalytic processes, such as bioconversion, bioremediation, and biosensors obtainment, are presented.
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Affiliation(s)
- Yosberto Cárdenas-Moreno
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
| | - Jorge González-Bacerio
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
- Department of Biochemistry, Faculty of Biology, University of Havana, Havana, Cuba
| | - Humberto García Arellano
- Department of Environmental Sciences, Division of Health and Biological Sciences, Metropolitan Autonomous University, Lerma, Mexico, Mexico
| | - Alberto Del Monte-Martínez
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
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11
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Zhang Y, Chu JM. Computational Mechanistic Investigations of Biocatalytic Nitrenoid C-H Functionalizations via Engineered Heme Proteins. Chembiochem 2023; 24:e202300260. [PMID: 37134298 DOI: 10.1002/cbic.202300260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/05/2023]
Abstract
Engineered heme proteins were developed to possess numerous excellent biocatalytic nitrenoid C-H functionalizations. Computational approaches such as density functional theory (DFT), hybrid quantum mechanics/molecular mechanics (QM/MM), and molecular dynamics (MD) calculations were employed to help understand some important mechanistic aspects of these heme nitrene transfer reactions. This review summarizes advances of computational reaction pathway results of these biocatalytic intramolecular and intermolecular C-H aminations/amidations, focusing on mechanistic origins of reactivity, regioselectivity, enantioselectivity, diastereoselectivity as well as effects of substrate substituent, axial ligand, metal center, and protein environment. Some important common and distinctive mechanistic features of these reactions were also described with brief outlook of future development.
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Affiliation(s)
- Yong Zhang
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, 1 Castle Point Terrace, Hoboken, NJ 07030, USA
| | - Jia-Min Chu
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, 1 Castle Point Terrace, Hoboken, NJ 07030, USA
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12
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Yu K, Zou Z, Igareta NV, Tachibana R, Bechter J, Köhler V, Chen D, Ward TR. Artificial Metalloenzyme-Catalyzed Enantioselective Amidation via Nitrene Insertion in Unactivated C( sp3)-H Bonds. J Am Chem Soc 2023. [PMID: 37471698 PMCID: PMC10401721 DOI: 10.1021/jacs.3c03969] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Enantioselective C-H amidation offers attractive means to assemble C-N bonds to synthesize high-added value, nitrogen-containing molecules. In recent decades, complementary enzymatic and homogeneous-catalytic strategies for C-H amidation have been reported. Herein, we report on an artificial metalloenzyme (ArM) resulting from anchoring a biotinylated Ir-complex within streptavidin (Sav). The resulting ArM catalyzes the enantioselective amidation of unactivated C(sp3)-H bonds. Chemogenetic optimization of the Ir cofactor and Sav led to significant improvement in both the activity and enantioselectivity. Up to >700 TON and 92% ee for the amidation of unactivated C(sp3)-H bonds was achieved. The single crystal X-ray analysis of the artificial nitrene insertase (ANIase) combined with quantum mechanics-molecular mechanics (QM-MM) calculations sheds light on critical second coordination sphere contacts leading to improved catalytic performance.
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Affiliation(s)
- Kun Yu
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel CH-4058, Switzerland
| | - Zhi Zou
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel CH-4058, Switzerland
| | - Nico V Igareta
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel CH-4058, Switzerland
| | - Ryo Tachibana
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel CH-4058, Switzerland
| | - Julia Bechter
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel CH-4058, Switzerland
| | - Valentin Köhler
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel CH-4058, Switzerland
| | - Dongping Chen
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel CH-4058, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel CH-4058, Switzerland
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13
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Wang Y, Yu L, Shao J, Zhu Z, Zhang L. Structure-driven protein engineering for production of valuable natural products. TRENDS IN PLANT SCIENCE 2023; 28:460-470. [PMID: 36473772 DOI: 10.1016/j.tplants.2022.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/25/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
Proteins are the most frequently used biocatalysts, and their structures determine their functions. Modifying the functions of proteins on the basis of their structures lies at the heart of protein engineering, opening a new horizon for metabolic engineering by efficiently generating stable enzymes. Many attempts at classical metabolic engineering have focused on improving specific metabolic fluxes and producing more valuable natural products by increasing gene expression levels and enzyme concentrations. However, most naturally occurring enzymes show limitations, and such limitations have hindered practical applications. Here we review recent advances in protein engineering in synthetic biology, chemoenzymatic synthesis, and plant metabolic engineering and describe opportunities for designing and constructing novel enzymes or proteins with desirable properties to obtain more active natural products.
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Affiliation(s)
- Yun Wang
- Institute of Interdisciplinary Integrative Medicine Research, Medical School of Nantong University, Nantong 226001, China; Biomedical Innovation R&D Centre, School of Medicine, Shanghai University, Shanghai 200444, China
| | - Luyao Yu
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Jie Shao
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Zhanpin Zhu
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Lei Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Medical School of Nantong University, Nantong 226001, China; Biomedical Innovation R&D Centre, School of Medicine, Shanghai University, Shanghai 200444, China; Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China; Innovative Drug R&D Center, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
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14
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Roy S, Vargas DA, Ma P, Sengupta A, Zhu L, Houk KN, Fasan R. Stereoselective Construction of β-, γ-, and δ-Lactam Rings via Enzymatic C-H Amidation. RESEARCH SQUARE 2023:rs.3.rs-2429100. [PMID: 36711830 PMCID: PMC9882675 DOI: 10.21203/rs.3.rs-2429100/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Lactam rings are found in many biologically active natural products and pharmaceuticals, including important classes of antibiotics. Given their widespread presence in bioactive molecules, methods for the asymmetric synthesis of these molecules, in particular through the selective functionalization of ubiquitous yet unreactive aliphatic C-H bonds, are highly desirable. In this study, we report the development of a novel strategy for the asymmetric synthesis of 4-, 5-, and 6-membered lactams via an unprecedented hemoprotein-catalyzed intramolecular C-H amidation reaction with readily available dioxazolone reagents. Engineered myoglobin variants serve as excellent biocatalysts for this transformation producing an array of β-, γ-, and δ-lactam molecules in high yields, with high enantioselectivity, and on preparative scale. Mechanistic and computational studies elucidate the nature of the C-H amination and enantiodetermining steps in these reactions and provide insights into protein-mediated control of regioselectivity and stereoselectivity. Using this system, it was possible to accomplish the chemoenzymatic total synthesis of an alkaloid natural product and a drug molecule in much fewer steps (7-8 vs. 11-12) than previously possible, which showcases the power of this biosynthetic strategy toward enabling the preparation of complex bioactive molecules.
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Affiliation(s)
- Satyajit Roy
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York, 14627, United States
| | - David A. Vargas
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York, 14627, United States
- Current affiliation: Process Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Pengchen Ma
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095, United States
- School of Chemistry, Xi’an Key Laboratory of Sustainable Energy Materials Chemistry, MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Xi’an Jiaotong University, Xi’an, China
| | - Arkajyoti Sengupta
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095, United States
| | - Ledong Zhu
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York, 14627, United States
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15
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Ren X, Couture BM, Liu N, Lall MS, Kohrt JT, Fasan R. Enantioselective Single and Dual α-C-H Bond Functionalization of Cyclic Amines via Enzymatic Carbene Transfer. J Am Chem Soc 2022; 145:537-550. [PMID: 36542059 PMCID: PMC9837850 DOI: 10.1021/jacs.2c10775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cyclic amines are ubiquitous structural motifs found in pharmaceuticals and biologically active natural products, making methods for their elaboration via direct C-H functionalization of considerable synthetic value. Herein, we report the development of an iron-based biocatalytic strategy for enantioselective α-C-H functionalization of pyrrolidines and other saturated N-heterocycles via a carbene transfer reaction with diazoacetone. Currently unreported for organometallic catalysts, this transformation can be accomplished in high yields, high catalytic activity, and high stereoselectivity (up to 99:1 e.r. and 20,350 TON) using engineered variants of cytochrome P450 CYP119 from Sulfolobus solfataricus. This methodology was further extended to enable enantioselective α-C-H functionalization in the presence of ethyl diazoacetate as carbene donor (up to 96:4 e.r. and 18,270 TON), and the two strategies were combined to achieve a one-pot as well as a tandem dual C-H functionalization of a cyclic amine substrate with enzyme-controlled diastereo- and enantiodivergent selectivity. This biocatalytic approach is amenable to gram-scale synthesis and can be applied to drug scaffolds for late-stage C-H functionalization. This work provides an efficient and tunable method for direct asymmetric α-C-H functionalization of saturated N-heterocycles, which should offer new opportunities for the synthesis, discovery, and optimization of bioactive molecules.
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Affiliation(s)
- Xinkun Ren
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Bo M. Couture
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Ningyu Liu
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Manjinder S. Lall
- Pfizer
Inc., Medicine and Design, Groton, Connecticut 06340, United States
| | - Jeffrey T. Kohrt
- Pfizer
Inc., Medicine and Design, Groton, Connecticut 06340, United States
| | - Rudi Fasan
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States,
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16
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Wei Y, Conklin M, Zhang Y. Biocatalytic Intramolecular C-H aminations via Engineered Heme Proteins: Full Reaction Pathways and Axial Ligand Effects. Chemistry 2022; 28:e202202006. [PMID: 35840505 PMCID: PMC9804930 DOI: 10.1002/chem.202202006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Indexed: 01/09/2023]
Abstract
Engineered heme protein biocatalysts provide an efficient and sustainable approach to develop amine-containing compounds through C-H amination. A quantum chemical study to reveal the complete heme catalyzed intramolecular C-H amination pathway and protein axial ligand effect was reported, using reactions of an experimentally used arylsulfonylazide with hemes containing L=none, SH- , MeO- , and MeOH to simulate no axial ligand, negatively charged Cys and Ser ligands, and a neutral ligand for comparison. Nitrene formation was found as the overall rate-determining step (RDS) and the catalyst with Ser ligand has the best reactivity, consistent with experimental reports. Both RDS and non-RDS (nitrene transfer) transition states follow the barrier trend of MeO- <SH- <MeOH<None due to the charge donation capability of the axial ligand to influence the key charge transfer process as the electronic driving forces. Results also provide new ideas for future biocatalyst design with enhanced reactivities.
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Affiliation(s)
- Yang Wei
- Department of Chemistry and Chemical BiologyStevens Institute of Technology1 Castle Point on HudsonHobokenNJ 07030USA,Department of Chemistry and BiochemistryLoyola University Chicago1032 W Sheridan RdChicagoIL 60660USA
| | - Melissa Conklin
- Department of Chemistry and Chemical BiologyStevens Institute of Technology1 Castle Point on HudsonHobokenNJ 07030USA
| | - Yong Zhang
- Department of Chemistry and Chemical BiologyStevens Institute of Technology1 Castle Point on HudsonHobokenNJ 07030USA
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17
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Thomson RES, D'Cunha SA, Hayes MA, Gillam EMJ. Use of engineered cytochromes P450 for accelerating drug discovery and development. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 95:195-252. [PMID: 35953156 DOI: 10.1016/bs.apha.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Numerous steps in drug development, including the generation of authentic metabolites and late-stage functionalization of candidates, necessitate the modification of often complex molecules, such as natural products. While it can be challenging to make the required regio- and stereoselective alterations to a molecule using purely chemical catalysis, enzymes can introduce changes to complex molecules with a high degree of stereo- and regioselectivity. Cytochrome P450 enzymes are biocatalysts of unequalled versatility, capable of regio- and stereoselective functionalization of unactivated CH bonds by monooxygenation. Collectively they catalyze over 60 different biotransformations on structurally and functionally diverse organic molecules, including natural products, drugs, steroids, organic acids and other lipophilic molecules. This catalytic versatility and substrate range makes them likely candidates for application as potential biocatalysts for industrial chemistry. However, several aspects of the P450 catalytic cycle and other characteristics have limited their implementation to date in industry, including: their lability at elevated temperature, in the presence of solvents, and over lengthy incubation times; the typically low efficiency with which they metabolize non-natural substrates; and their lack of specificity for a single metabolic pathway. Protein engineering by rational design or directed evolution provides a way to engineer P450s for industrial use. Here we review the progress made to date toward engineering the properties of P450s, especially eukaryotic forms, for industrial application, and including the recent expansion of their catalytic repertoire to include non-natural reactions.
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Affiliation(s)
- Raine E S Thomson
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Stephlina A D'Cunha
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Martin A Hayes
- Compound Synthesis and Management, Discovery Sciences, BioPharmaceuticals R&D AstraZeneca, Mölndal, Sweden
| | - Elizabeth M J Gillam
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
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18
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Co-Crystal Structure-Guided Optimization of Dual-Functional Small Molecules for Improving the Peroxygenase Activity of Cytochrome P450BM3. Int J Mol Sci 2022; 23:ijms23147901. [PMID: 35887253 PMCID: PMC9317928 DOI: 10.3390/ijms23147901] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 12/24/2022] Open
Abstract
We recently developed an artificial P450–H2O2 system assisted by dual-functional small molecules (DFSMs) to modify the P450BM3 monooxygenase into its peroxygenase mode, which could be widely used for the oxidation of non-native substrates. Aiming to further improve the DFSM-facilitated P450–H2O2 system, a series of novel DFSMs having various unnatural amino acid groups was designed and synthesized, based on the co-crystal structure of P450BM3 and a typical DFSM, N-(ω-imidazolyl)-hexanoyl-L-phenylalanine, in this study. The size and hydrophobicity of the amino acid residue in the DFSM drastically affected the catalytic activity (up to 5-fold), stereoselectivity, and regioselectivity of the epoxidation and hydroxylation reactions. Docking simulations illustrated that the differential catalytic ability among the DFSMs is closely related to the binding affinity and the distance between the catalytic group and heme iron. This study not only enriches the DFSM toolbox to provide more options for utilizing the peroxide-shunt pathway of cytochrome P450BM3, but also sheds light on the great potential of the DFSM-driven P450 peroxygenase system in catalytic applications based on DFSM tunability.
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19
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Recent developments in promiscuous enzymatic reactions for carbon-nitrogen bond formation. Bioorg Chem 2022; 127:106014. [PMID: 35841668 DOI: 10.1016/j.bioorg.2022.106014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/07/2022] [Accepted: 07/06/2022] [Indexed: 11/21/2022]
Abstract
Biocatalytic promiscuity is a new field of enzyme application in biochemistry, which has received much attention and has developed rapidly in recent years. The promiscuous biocatalysis has been promoted as a useful supplement to traditional strategy for the formation of C-heteroatom bonds. The generation of carbon-nitrogen (CN) bonds is an important issue in synthetic chemistry and is indispensable for the manufacturing of various pharmaceuticals and agrochemicals. Therefore, numerous efficient and reliable synthetic methods for the formation of CN bonds have been developed in recent years. Enzymatic CN bond forming reactions catalyzed by lipases, cytochrome P450 monooxygenases, glycosyltransferases, amine dehydrogenases, proteases, acylases, amylases and halohydrin dehalogenases are well established for synthetic purposes. This review introduces the recent progress in the construction of CN bonds using promiscuous enzymes.
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20
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Mai BK, Neris NM, Yang Y, Liu P. C-N Bond Forming Radical Rebound Is the Enantioselectivity-Determining Step in P411-Catalyzed Enantioselective C(sp 3)-H Amination: A Combined Computational and Experimental Investigation. J Am Chem Soc 2022; 144:11215-11225. [PMID: 35583461 DOI: 10.1021/jacs.2c02283] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Engineered metalloenzymes represent promising catalysts for stereoselective C-H functionalization reactions. Recently, P450 enzymes have been evolved to allow for new-to-nature intramolecular C(sp3)-H amination reactions via a nitrene transfer mechanism, giving rise to diamine derivatives with excellent enantiocontrol. To shed light on the origin of enantioselectivity, a combined computational and experimental study was carried out. Hybrid quantum mechanics/molecular mechanics calculations were performed to investigate the activation energies and enantioselectivities of both the hydrogen atom transfer (HAT) and the subsequent C-N bond forming radical rebound steps. Contrary to previously hypothesized enantioinduction mechanisms, our calculations show that the radical rebound step is enantioselectivity-determining, whereas the preceding HAT step is only moderately stereoselective. Furthermore, the selectivity in the initial HAT is ablated by rapid conformational change of the radical intermediate prior to C-N bond formation. This finding is corroborated by our experimental study using a set of enantiomerically pure, monodeuterated substrates. Furthermore, classical and ab initio molecular dynamics simulations were carried out to investigate the conformational flexibility of the carbon-centered radical intermediate. This key radical species undergoes a facile conformational change in the enzyme active site from the pro-(R) to the pro-(S) configuration, whereas the radical rebound is slower due to the spin-state change and ring strain of the cyclization process, thereby allowing stereoablative C-N bond formation. Together, these studies revealed an underappreciated enantioinduction mechanism in biocatalytic C(sp3)-H functionalizations involving radical intermediates, opening up new avenues for the development of other challenging asymmetric C(sp3)-H functionalizations.
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Affiliation(s)
- Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Natalia M Neris
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Biomolecular Science and Engineering (BMSE) Program, University of California, Santa Barbara, California 93106, United States
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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21
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Liu Y, Lai KL, Vong K. Transition Metal Scaffolds Used To Bring New‐to‐Nature Reactions into Biological Systems. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202200215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yifei Liu
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
| | - Ka Lun Lai
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
| | - Kenward Vong
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
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22
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Ren X, Chandgude AL, Carminati DM, Shen Z, Khare SD, Fasan R. Highly stereoselective and enantiodivergent synthesis of cyclopropylphosphonates with engineered carbene transferases. Chem Sci 2022; 13:8550-8556. [PMID: 35974764 PMCID: PMC9337741 DOI: 10.1039/d2sc01965e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/06/2022] [Indexed: 12/18/2022] Open
Abstract
Organophosphonate compounds have represented a rich source of biologically active compounds, including enzyme inhibitors, antibiotics, and antimalarial agents. Here, we report the development of a highly stereoselective strategy for olefin cyclopropanation in the presence of a phosphonyl diazo reagent as carbene precursor. In combination with a ‘substrate walking’ protein engineering strategy, two sets of efficient and enantiodivergent myoglobin-based biocatalysts were developed for the synthesis of both (1R,2S) and (1S,2R) enantiomeric forms of the desired cyclopropylphosphonate ester products. This methodology enables the efficient transformation of a broad range of vinylarene substrates at a preparative scale (i.e. gram scale) with up to 99% de and ee. Mechanistic studies provide insights into factors that contribute to make this reaction inherently more challenging than hemoprotein-catalyzed olefin cyclopropanation with ethyl diazoacetate investigated previously. This work expands the range of synthetically useful, enzyme-catalyzed transformations and paves the way to the development of metalloprotein catalysts for abiological carbene transfer reactions involving non-canonical carbene donor reagents. Two enantiocomplementary myoglobin-based carbene transfer biocatalysts were developed for the synthesis of cyclopropylphosphonate esters with high diastereo- and enantioselectivity and in high yields.![]()
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Affiliation(s)
- Xinkun Ren
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
| | - Ajay L. Chandgude
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
| | - Daniela M. Carminati
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
| | - Zhuofan Shen
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, USA
| | - Sagar D. Khare
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, USA
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
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23
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Miller DC, Athavale SV, Arnold FH. Combining chemistry and protein engineering for new-to-nature biocatalysis. NATURE SYNTHESIS 2022; 1:18-23. [PMID: 35415721 DOI: 10.1038/s44160-021-00008-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biocatalysis, the application of enzymes to solve synthetic problems of human import, has blossomed into a powerful technology for chemical innovation. In the past decade, a threefold partnership, where nature provides blueprints for enzymatic catalysis, chemists introduce innovative activity modes with abiological substrates, and protein engineers develop new tools and algorithms to tune and improve enzymatic function, has unveiled the frontier of new-to-nature enzyme catalysis. In this perspective, we highlight examples of interdisciplinary studies which have helped to expand the scope of biocatalysis, including concepts of enzymatic versatility explored through the lens of biomimicry, to achieve both activities and selectivities that are not currently possible with chemocatalysis. We indicate how modern tools, such as directed evolution, computational protein design and machine learning-based protein engineering methods, have already impacted and will continue to influence enzyme engineering for new abiological transformations. A sustained collaborative effort across disciplines is anticipated to spur further advances in biocatalysis in the coming years.
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Affiliation(s)
- David C Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology Pasadena, California, 91125
| | - Soumitra V Athavale
- Division of Chemistry and Chemical Engineering, California Institute of Technology Pasadena, California, 91125
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology Pasadena, California, 91125
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24
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Coin G, Latour JM. Nitrene transfers mediated by natural and artificial iron enzymes. J Inorg Biochem 2021; 225:111613. [PMID: 34634542 DOI: 10.1016/j.jinorgbio.2021.111613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/30/2021] [Accepted: 09/13/2021] [Indexed: 12/19/2022]
Abstract
Amines are ubiquitous in biology and pharmacy. As a consequence, introducing N functionalities in organic molecules is attracting strong continuous interest. The past decade has witnessed the emergence of very efficient and selective catalytic systems achieving this goal thanks to engineered hemoproteins. In this review, we examine how these enzymes have been engineered focusing rather on the rationale behind it than the methodology employed. These studies are put in perspective with respect to in vitro and in vivo nitrene transfer processes performed by cytochromes P450. An emphasis is put on mechanistic aspects which are confronted to current molecular knowledge of these reactions. Forthcoming developments are delineated.
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Affiliation(s)
- Guillaume Coin
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, DIESE, LCBM, pmb, F-38000 Grenoble, France; Univ. Grenoble Alpes, CNRS UMR 5250, DCM, CIRE, F-38000 Grenoble, France
| | - Jean-Marc Latour
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, DIESE, LCBM, pmb, F-38000 Grenoble, France.
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25
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Ren X, Fasan R. Engineered and Artificial Metalloenzymes for Selective C-H Functionalization. CURRENT OPINION IN GREEN AND SUSTAINABLE CHEMISTRY 2021; 31:100494. [PMID: 34395950 PMCID: PMC8357270 DOI: 10.1016/j.cogsc.2021.100494] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The direct functionalization of C-H bonds constitutes a powerful strategy to construct and diversify organic molecules. However, controlling the chemo- and site-selectivity of this transformation in particularly complex molecular settings represents a significant challenge. Metalloenzymes are ideal platforms for achieving catalyst-controlled selective C-H bond functionalization as their reactivities can be tuned by protein engineering and/or redesign of their cofactor environment. In this review, we highlight recent progress in the development of engineered and artificial metalloenzymes for C-H functionalization, with a focus on biocatalytic strategies for selective C-H oxyfunctionalization and halogenation as well as C-H amination and C-H carbene insertion via abiological nitrene and carbene transfer chemistries. Engineered heme- and non-heme iron dependent enzymes have emerged as promising scaffolds for executing these transformations with high chemo-, regio- and stereocontrol as well as tunable selectivity. These emerging systems and methodologies have expanded the toolbox of sustainable strategies for organic synthesis and created new opportunities for the generation of chiral building blocks, the late-stage C-H functionalization of complex molecules, and the total synthesis of natural products.
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Affiliation(s)
- Xinkun Ren
- Department of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester NY 14627, USA
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester NY 14627, USA
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26
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Chen H, Huang M, Yan W, Bai WJ, Wang X. Enzymatic Regio- and Enantioselective C–H Oxyfunctionalization of Fatty Acids. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03292] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hao Chen
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Mengfei Huang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Wenliang Yan
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Wen-Ju Bai
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Xiqing Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, China
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27
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Li Y, Yuan B, Sun Z, Zhang W. C–H bond functionalization reactions enabled by photobiocatalytic cascades. GREEN SYNTHESIS AND CATALYSIS 2021. [DOI: 10.1016/j.gresc.2021.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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28
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Martin CP, Chen M, Martinez MF, Ding Y, Caranto JD. The Ferric-Superoxo Intermediate of the TxtE Nitration Pathway Resists Reduction, Facilitating Its Reaction with Nitric Oxide. Biochemistry 2021; 60:2436-2446. [PMID: 34319079 DOI: 10.1021/acs.biochem.1c00416] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
TxtE is a cytochrome P450 (CYP) homologue that mediates the nitric oxide (NO)-dependent direct nitration of l-tryptophan (Trp) to form 4-nitro-l-tryptophan (4-NO2-Trp). A recent report showed evidence that TxtE activity requires NO to react with a ferric-superoxo intermediate. Given this minimal mechanism, it is not clear how TxtE avoids Trp hydroxylation, a mechanism that also traverses the ferric-superoxo intermediate. To provide insight into canonical CYP intermediates that TxtE can access, electron coupling efficiencies to form 4-NO2-Trp under single- or limited-turnover conditions were measured and compared to steady-state efficiencies. As previously reported, Trp nitration by TxtE is supported by the engineered self-sufficient variant, TB14, as well as by reduced putidaredoxin. Ferrous (FeII) TxtE exhibits excellent electron coupling (70%), which is 50-fold higher than that observed under turnover conditions. In addition, two- or four-electron reduced TB14 exhibits electron coupling (∼6%) that is 2-fold higher than that of one-electron reduced TB14 (3%). The combined results suggest (1) autoxidation is the sole TxtE uncoupling pathway and (2) the TxtE ferric-superoxo intermediate cannot be reduced by these electron transfer partners. The latter conclusion is further supported by ultraviolet-visible absorption spectral time courses showing neither spectral nor kinetic evidence for reduction of the ferric-superoxo intermediate. We conclude that resistance of the ferric-superoxo intermediate to reduction is a key feature of TxtE that increases the lifetime of the intermediate and enables its reaction with NO and efficient nitration activity.
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Affiliation(s)
- Christopher P Martin
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Room 255, Orlando, Florida 32816, United States
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, 1345 Center Drive, Room P6-27, Gainesville, Florida 32610, United States
| | - Maria F Martinez
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Room 255, Orlando, Florida 32816, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, 1345 Center Drive, Room P6-27, Gainesville, Florida 32610, United States
| | - Jonathan D Caranto
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Room 255, Orlando, Florida 32816, United States
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29
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Vong K, Nasibullin I, Tanaka K. Exploring and Adapting the Molecular Selectivity of Artificial Metalloenzymes. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200316] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kenward Vong
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- GlycoTargeting Research Laboratory, RIKEN Baton Zone Program, Wako, Saitama 351-0198, Japan
| | - Igor Nasibullin
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, Kazan 420008, Russia
| | - Katsunori Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8552, Japan
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, Kazan 420008, Russia
- GlycoTargeting Research Laboratory, RIKEN Baton Zone Program, Wako, Saitama 351-0198, Japan
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30
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Marshall JR, Mangas-Sanchez J, Turner NJ. Expanding the synthetic scope of biocatalysis by enzyme discovery and protein engineering. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.131926] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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31
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Wang Z, Shaik S, Wang B. Conformational Motion of Ferredoxin Enables Efficient Electron Transfer to Heme in the Full-Length P450 TT. J Am Chem Soc 2021; 143:1005-1016. [PMID: 33426875 DOI: 10.1021/jacs.0c11279] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450 monooxygenases (P450s) are versatile biocatalysts used in natural products biosynthesis, xenobiotic metabolisms, and biotechnologies. In P450s, the electrons required for O2 activation are supplied by NAD(P)H through stepwise electron transfers (ETs) mediated by redox partners. While much is known about the machinery of the catalytic cycle of P450s, the mechanisms of long-range ET are largely unknown. Very recently, the first crystal structure of full-length P450TT was solved. This enables us to decipher the interdomain ET mechanism between the [2Fe-2S]-containing ferredoxin and the heme, by use of molecular dynamics simulations. In contrast to the "distal" conformation characterized in the crystal structure where the [2Fe-2S] cluster is ∼28 Å away from heme-Fe, our simulations demonstrated a "proximal" conformation of [2Fe-2S] that is ∼17 Å [and 13.7 Å edge-to-edge] away from heme-Fe, which may enable the interdomain ET. Key residues involved in ET pathways and interdomain complexation were identified, some of which have already been verified by recent mutation studies. The conformational transit of ferredoxin between "distal" and "proximal" was found to be controlled mostly by the long-range electrostatic interactions between the ferredoxin domain and the other two domains. Furthermore, our simulations show that the full-length P450TT utilizes a flexible ET pathway that resembles either P450Scc or P450cam. Thus, this study provides a uniform picture of the ET process between reductase domains and heme domain.
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Affiliation(s)
- Zhanfeng Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
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32
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Bokel A, Hutter MC, Urlacher VB. Molecular evolution of a cytochrome P450 for the synthesis of potential antidepressant (2R,6R)-hydroxynorketamine. Chem Commun (Camb) 2021; 57:520-523. [PMID: 33331834 DOI: 10.1039/d0cc06729f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Saturation mutagenesis at seven first-sphere residues of the cytochrome P450 monooxygenase 154E1 (CYP154E1) from Thermobifida fusca YX was applied to construct a variant with only three substitutions that enabled the effective two-step synthesis of the potential antidepressant (2R,6R)-hydroxynorketamine. A recombinant E. coli whole-cell system was essential for GC/MS based medium-throughput screening and at the same time facilitated the oxidation of the substrate (R)-ketamine at a higher scale for product isolation and subsequent NMR analysis.
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Affiliation(s)
- Ansgar Bokel
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, Düsseldorf 40225, Germany.
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33
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Markel U, Lanvers P, Sauer DF, Wittwer M, Dhoke GV, Davari MD, Schiffels J, Schwaneberg U. A Photoclick-Based High-Throughput Screening for the Directed Evolution of Decarboxylase OleT. Chemistry 2021; 27:954-958. [PMID: 32955127 PMCID: PMC7839715 DOI: 10.1002/chem.202003637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/15/2020] [Indexed: 11/30/2022]
Abstract
Enzymatic oxidative decarboxylation is an up-and-coming reaction yet lacking efficient screening methods for the directed evolution of decarboxylases. Here, we describe a simple photoclick assay for the detection of decarboxylation products and its application in a proof-of-principle directed evolution study on the decarboxylase OleT. The assay was compatible with two frequently used OleT operation modes (directly using hydrogen peroxide as the enzyme's co-substrate or using a reductase partner) and the screening of saturation mutagenesis libraries identified two enzyme variants shifting the enzyme's substrate preference from long chain fatty acids toward styrene derivatives. Overall, this photoclick assay holds promise to speed-up the directed evolution of OleT and other decarboxylases.
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Affiliation(s)
- Ulrich Markel
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Pia Lanvers
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Daniel F. Sauer
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Malte Wittwer
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Gaurao V. Dhoke
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Mehdi D. Davari
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Johannes Schiffels
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Ulrich Schwaneberg
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
- DWI—Leibniz Institute for Interactive MaterialsForckenbeckstraße 5052074AachenGermany
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34
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Wang YC, Lai XJ, Huang K, Yadav S, Qiu G, Zhang L, Zhou H. Unravelling nitrene chemistry from acyclic precursors: recent advances and challenges. Org Chem Front 2021. [DOI: 10.1039/d0qo01360a] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Recent advances in nitrene chemistry from acyclic precursors are reviewed in this paper.
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Affiliation(s)
- Yu-Chao Wang
- College of Biological
- Chemical Sciences and Engineering
- Jiaxing University
- Jiaxing 314001
- China
| | - Xiao-Jing Lai
- College of Biological
- Chemical Sciences and Engineering
- Jiaxing University
- Jiaxing 314001
- China
| | - Keke Huang
- College of Biological
- Chemical Sciences and Engineering
- Jiaxing University
- Jiaxing 314001
- China
| | - Sarita Yadav
- College of Biological
- Chemical Sciences and Engineering
- Jiaxing University
- Jiaxing 314001
- China
| | - Guanyinsheng Qiu
- College of Biological
- Chemical Sciences and Engineering
- Jiaxing University
- Jiaxing 314001
- China
| | - Lianpeng Zhang
- School of Materials Science and Engineering
- Southwest Forestry University
- Kunming 650224
- China
| | - Hongwei Zhou
- College of Biological
- Chemical Sciences and Engineering
- Jiaxing University
- Jiaxing 314001
- China
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35
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Wang C, Wu P, Wang Z, Wang B. The molecular mechanism of P450-catalyzed amination of the pyrrolidine derivative of lidocaine: insights from multiscale simulations. RSC Adv 2021; 11:27674-27680. [PMID: 35480638 PMCID: PMC9037892 DOI: 10.1039/d1ra04564d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/09/2021] [Indexed: 11/23/2022] Open
Abstract
Nitrogen heterocycles are key and prevalent motifs in drugs. Evolved variants of cytochrome P450BM3 (CYP102A1) from Bacillus megaterium employ high-valent oxo-iron(iv) species to catalyze the synthesis of imidazolidine-4-ones via an intramolecular C–H amination. Herein, we use multi-scale simulations, including classical molecular dynamics (MD) simulations, quantum mechanical/molecular mechanical (QM/MM) calculations and QM calculations, to reveal the molecular mechanism of the intramolecular C–H amination of the pyrrolidine derivative of lidocaine bearing cyclic amino moieties catalyzed by the variant RP/FV/EV of P450BM3, which bears five mutations compared to wild type. Our calculations show that overall catalysis includes both the enzymatic transformation in P450 and non-enzymatic transformation in water solution. The enzymatic transformation involves the exclusive hydroxylation of the C–H bond of the pyrrolidine derivative of lidocaine, leading to the hydroxylated intermediate, during which the substrate radical would be bypassed. The following dehydration and C–N coupling reactions are found to be much favored in aqueous situation compared to that in the non-polar protein environment. The present findings expand our understanding of the P450-catalyzed C(sp3)–H amination reaction. Nitrogen heterocycles are key and prevalent motifs in drugs.![]()
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Affiliation(s)
- Conger Wang
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Peng Wu
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zhanfeng Wang
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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36
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Li F, Su J, Xu Y, Liu J, Yu Y, Wang C, Li Z, Li C, Wang L. A glucose oxidase-hemoglobin system for efficient oxysulfonylation of alkenes/alkynes in water. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2020.111336] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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37
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Zhang H, Sun MC, Yin LM, Wei D, Song MP, Yang D, Niu JL. Direct intramolecular C(sp 3)–H bond sulfonamidation to synthesize benzosultam derivatives under metal-free conditions. Org Chem Front 2021. [DOI: 10.1039/d1qo01235e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An efficient intramolecular C(sp3)–H bond amination under metal-free conditions has been developed to provide a straightforward method for the synthesis of 5-membered cyclic sulfonamides (benzosultams).
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Affiliation(s)
- He Zhang
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Meng-Chan Sun
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Li-Ming Yin
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Donghui Wei
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Mao-Ping Song
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Dandan Yang
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Jun-Long Niu
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
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38
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Efficient synthesis of cyano-containing multi-substituted indoles catalyzed by lipase. Bioorg Chem 2020; 107:104583. [PMID: 33421956 DOI: 10.1016/j.bioorg.2020.104583] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND Indoles are important bioactive compounds that have been extensively studied in organic chemistry. In this work, a green and efficient process for the synthesis of Indoles from 1,3-diketones with fumaronitrile was developed. RESULTS Under optimal conditions (1,3-diketones (0.5 mmol), fumaronitrile (1 mmol), water (2 ml), lipase (15 mg), 30 °C, 24 h), high yields and satisfactory regioselectivity of cyano-containing multi-substituted indoles could be obtained when CRL (C. rugosa lipase) was used as the catalyst. CONCLUSION This enzymatic method demonstrates the great potential for the synthesis of indoles and extends the application of enzyme in organic synthesis.
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39
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Wang S, Jiang S, Chen H, Bai WJ, Wang X. Directed Evolution of a Hydroxylase into a Decarboxylase for Synthesis of 1-Alkenes from Fatty Acids. ACS Catal 2020. [DOI: 10.1021/acscatal.0c04345] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shuaibo Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Shengsheng Jiang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Hao Chen
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Wen-Ju Bai
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Xiqing Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, China
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40
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Roda S, Santiago G, Guallar V. Mapping enzyme-substrate interactions: its potential to study the mechanism of enzymes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:1-31. [PMID: 32951809 DOI: 10.1016/bs.apcsb.2020.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
With the increase of the need to use more sustainable processes for the industry in our society, the modeling of enzymes has become crucial to fully comprehend their mechanism of action and use this knowledge to enhance and design their properties. A lot of methods to study enzymes computationally exist and they have been classified on sequence-based, structure-based, and the more new artificial intelligence-based ones. Albeit the abundance of methods to help predict the function of an enzyme, molecular modeling is crucial when trying to understand the enzyme mechanism, as they aim to correlate atomistic information with experimental data. Among them, methods that simulate the system dynamics at a molecular mechanics level of theory (classical force fields) have shown to offer a comprehensive study. In this book chapter, we will analyze these techniques, emphasizing the importance of precise modeling of enzyme-substrate interactions. In the end, a brief explanation of the transference of the information from research studies to the industry is given accompanied with two examples of family enzymes where their modeling has helped their exploitation.
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Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | | | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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