1
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Zhang JG, Huls AJ, Palacios PM, Guo Y, Huang X. Biocatalytic Generation of Trifluoromethyl Radicals by Nonheme Iron Enzymes for Enantioselective Alkene Difunctionalization. J Am Chem Soc 2024; 146:34878-34886. [PMID: 39636656 DOI: 10.1021/jacs.4c14310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2024]
Abstract
The trifluoromethyl (-CF3) group represents a highly prevalent functionality in pharmaceuticals. Over the past few decades, significant advances have been made in the development of synthetic methods for trifluoromethylation. In contrast, there are currently no metalloenzymes known to catalyze the formation of C(sp3)-CF3 bonds. In this work, we demonstrate that a nonheme iron enzyme, hydroxymandelate synthase from Amycolatopsis orientalis (AoHMS), is capable of generating CF3 radicals from hypervalent iodine(III) reagents and directing them for enantioselective alkene trifluoromethyl azidation. A high-throughput screening (HTS) platform based on Staudinger ligation was established, enabling the rapid evaluation of AoHMS variants for this abiological transformation. The final optimized variant accepts a range of alkene substrates, producing the trifluoromethyl azidation products in up to 73% yield and 96:4 enantiomeric ratio (e.r.). The biocatalytic platform can be further extended to alkene pentafluoroethyl azidation and diazidation by altering the iodine(III) reagent. In addition, anion competition experiments provide insights into the radical rebound process for this abiological transformation. This study not only expands the catalytic repertoire of metalloenzymes for radical transformations but also creates a new enzymatic space for organofluorine synthesis.
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Affiliation(s)
- James G Zhang
- Department of Chemistry, Johns Hopkins University; Baltimore, Maryland 21218, United States
| | - Anthony J Huls
- Department of Chemistry, Johns Hopkins University; Baltimore, Maryland 21218, United States
| | - Philip M Palacios
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Xiongyi Huang
- Department of Chemistry, Johns Hopkins University; Baltimore, Maryland 21218, United States
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2
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Yang D, Chiang CH, Wititsuwannakul T, Brooks CL, Zimmerman PM, Narayan ARH. Engineering the Reaction Pathway of a Non-heme Iron Oxygenase Using Ancestral Sequence Reconstruction. J Am Chem Soc 2024; 146:34352-34363. [PMID: 39642058 DOI: 10.1021/jacs.4c08420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2024]
Abstract
Non-heme iron (FeII), α-ketoglutarate (α-KG)-dependent oxygenases are a family of enzymes that catalyze an array of transformations that cascade forward after the formation of radical intermediates. Achieving control over the reaction pathway is highly valuable and a necessary step toward broadening the applications of these biocatalysts. Numerous approaches have been used to engineer the reaction pathway of FeII/α-KG-dependent enzymes, including site-directed mutagenesis, DNA shuffling, and site-saturation mutagenesis, among others. Herein, we showcase a novel ancestral sequence reconstruction (ASR)-guided strategy in which evolutionary information is used to pinpoint the residues critical for controlling different reaction pathways. Following this, a combinatorial site-directed mutagenesis approach was used to quickly evaluate the importance of each residue. These results were validated using a DNA shuffling strategy and through quantum mechanical/molecular mechanical (QM/MM) simulations. Using this approach, we identified a set of active site residues together with a key hydrogen bond between the substrate and an active site residue, which are crucial for dictating the dominant reaction pathway. Ultimately, we successfully converted both extant and ancestral enzymes that perform benzylic hydroxylation into variants that can catalyze an oxidative ring-expansion reaction, showcasing the potential of utilizing ASR to accelerate the reaction pathway engineering within enzyme families that share common structural and mechanistic features.
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Affiliation(s)
- Di Yang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life Science Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Chang-Hwa Chiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life Science Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Charles L Brooks
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life Science Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Enhanced Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alison R H Narayan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life Science Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
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3
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Del Rio Flores A, Zhai R, Kastner DW, Seshadri K, Yang S, De Matias K, Shen Y, Cai W, Narayanamoorthy M, Do NB, Xue Z, Marzooqi DA, Kulik HJ, Zhang W. Enzymatic synthesis of azide by a promiscuous N-nitrosylase. Nat Chem 2024; 16:2066-2075. [PMID: 39333393 PMCID: PMC11611683 DOI: 10.1038/s41557-024-01646-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/29/2024] [Indexed: 09/29/2024]
Abstract
Azides are energy-rich compounds with diverse representation in a broad range of scientific disciplines, including material science, synthetic chemistry, pharmaceutical science and chemical biology. Despite ubiquitous usage of the azido group, the underlying biosynthetic pathways for its formation remain largely unknown. Here we report the characterization of an enzymatic route for de novo azide construction. We demonstrate that Tri17, a promiscuous ATP- and nitrite-dependent enzyme, catalyses organic azide synthesis through sequential N-nitrosation and dehydration of aryl hydrazines. Through biochemical, structural and computational analyses, we further propose a plausible molecular mechanism for azide synthesis that sets the stage for future biocatalytic applications and biosynthetic pathway engineering.
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Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - David W Kastner
- Department of Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kaushik Seshadri
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Siyue Yang
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Kyle De Matias
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Yuanbo Shen
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | | | - Nicholas B Do
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Zhaoqiang Xue
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Dunya Al Marzooqi
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA.
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4
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Zhang Q, Huang C, Tao Y, Zhang Y, Cui J, Wang D, Wang P, Zhang YY. Flexible Triboelectric Nanogenerators Based on Cadmium Metal-Organic Framework/Eethyl Cellulose Composites as Energy Harvesters for Selective Photoinduced Bromination Reaction. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2406623. [PMID: 39588860 DOI: 10.1002/smll.202406623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 11/19/2024] [Indexed: 11/27/2024]
Abstract
The fabrication of self-driven systems with flexibility and tunable output for organic photoinduction is highly desirable but challenging. In this study, a 3D cadmium metal-organic framework (Cd-MOF) is synthesized and used as a filler for ethyl cellulose (EC) to create mechanically durable and flexible Cd-MOF@EC composite films. Due to its well-established platform with periodically precise structure nature, the outputs of Cd-MOF-based TENG are much higher than those of ligand-based TENGs. Furthermore, composite films with different doping ratios of Cd-MOF are employed to assemble Cd-MOF@EC-based triboelectric nanogenerators (TENGs). The results reveal that a doping ratio of 10 wt.% Cd-MOF in Cd-MOF@EC provides the highest TENG output. Subsequently, a flexible 10 wt.% Cd-MOF@EC-based TENG (FCEC-TENG), working in the contact-separation model, is constructed to harvest mechanical energy from the human body, demonstrating excellent output performance and stability. The energy harvested from FCEC-TENG can directly illuminate 14 commercial white light-emitting diodes (LEDs), providing visible light for the photoinduction of the bromination reaction, and generating bromide with good yield and tolerance. This study presents an effective method for constructing flexible MOF-based TENG for self-powered photoinduced organic transformation systems.
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Affiliation(s)
- Qiang Zhang
- Center for Advanced Materials Research, Henan Key Laboratory of Functional Salt Materials, and School of Materials Electronics and Energy Storage, Zhongyuan University of Technology, Zhengzhou, 450007, P. R. China
| | - Chao Huang
- Center for Advanced Materials Research, Henan Key Laboratory of Functional Salt Materials, and School of Materials Electronics and Energy Storage, Zhongyuan University of Technology, Zhengzhou, 450007, P. R. China
| | - Yuanmeng Tao
- Center for Advanced Materials Research, Henan Key Laboratory of Functional Salt Materials, and School of Materials Electronics and Energy Storage, Zhongyuan University of Technology, Zhengzhou, 450007, P. R. China
| | - Yue Zhang
- Center for Advanced Materials Research, Henan Key Laboratory of Functional Salt Materials, and School of Materials Electronics and Energy Storage, Zhongyuan University of Technology, Zhengzhou, 450007, P. R. China
| | - Jiaxing Cui
- Center for Advanced Materials Research, Henan Key Laboratory of Functional Salt Materials, and School of Materials Electronics and Energy Storage, Zhongyuan University of Technology, Zhengzhou, 450007, P. R. China
| | - Dandan Wang
- Center for Advanced Materials Research, Henan Key Laboratory of Functional Salt Materials, and School of Materials Electronics and Energy Storage, Zhongyuan University of Technology, Zhengzhou, 450007, P. R. China
| | - Peihong Wang
- School of Materials Science and Engineering, Anhui University, Hefei, 230601, P. R. China
| | - Ying-Ying Zhang
- Center for Advanced Materials Research, Henan Key Laboratory of Functional Salt Materials, and School of Materials Electronics and Energy Storage, Zhongyuan University of Technology, Zhengzhou, 450007, P. R. China
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5
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Xu H, Zhao J, Renata H. Discovery, Characterization and Synthetic Application of a Promiscuous Nonheme Iron Biocatalyst with Dual Hydroxylase/Desaturase Activity. Angew Chem Int Ed Engl 2024; 63:e202409143. [PMID: 39207909 DOI: 10.1002/anie.202409143] [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: 05/14/2024] [Revised: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
Alpha-ketoglutarate-dependent dioxygenases (αKGDs) have recently emerged as useful biocatalysts for C-H oxidation and functionalization. In this work, we characterized a new αKGD from aculene biosynthesis, AneA, which displays broad promiscuity toward a number of substrates with different ring systems. Unexpectedly, AneA was found to be capable of both desaturation and hydroxylation and require an amino ester motif on its substrate for productive catalysis. Insights gathered from the functional characterization and substrate-activity profiling of AneA enabled the development of a chemoenzymatic strategy toward several complex sesquiterpenoids.
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Affiliation(s)
- Hao Xu
- Department of Chemistry, Rice University Bioscience Research Collaborative, Houston, TX 77005, USA
| | - Jidong Zhao
- Department of Chemistry, Rice University Bioscience Research Collaborative, Houston, TX 77005, USA
| | - Hans Renata
- Department of Chemistry, Rice University Bioscience Research Collaborative, Houston, TX 77005, USA
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6
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Gu X, Zhang YA, Zhang S, Wang L, Ye X, Occhialini G, Barbour J, Pentelute BL, Wendlandt AE. Synthesis of non-canonical amino acids through dehydrogenative tailoring. Nature 2024; 634:352-358. [PMID: 39208846 DOI: 10.1038/s41586-024-07988-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Amino acids are essential building blocks in biology and chemistry. Whereas nature relies on a small number of amino acid structures, chemists desire access to a vast range of structurally diverse analogues1-3. The selective modification of amino acid side-chain residues represents an efficient strategy to access non-canonical derivatives of value in chemistry and biology. While semisynthetic methods leveraging the functional groups found in polar and aromatic amino acids have been extensively explored, highly selective and general approaches to transform unactivated C-H bonds in aliphatic amino acids remain less developed4,5. Here we disclose a stepwise dehydrogenative method to convert aliphatic amino acids into structurally diverse analogues. The key to the success of this approach lies in the development of a selective catalytic acceptorless dehydrogenation method driven by photochemical irradiation, which provides access to terminal alkene intermediates for downstream functionalization. Overall, this strategy enables the rapid synthesis of new amino acid building blocks and suggests possibilities for the late-stage modification of more complex oligopeptides.
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Affiliation(s)
- Xin Gu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yu-An Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shuo Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Leon Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xiyun Ye
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gino Occhialini
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonah Barbour
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alison E Wendlandt
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
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7
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Zhao Q, Chen Z, Soler J, Chen X, Rui J, Ji NT, Yu QE, Yang Y, Garcia-Borràs M, Huang X. Engineering non-haem iron enzymes for enantioselective C(sp3)-F bond formation via radical fluorine transfer. NATURE SYNTHESIS 2024; 3:958-966. [PMID: 39364063 PMCID: PMC11446476 DOI: 10.1038/s44160-024-00507-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/21/2024] [Indexed: 10/05/2024]
Abstract
In recent years there has been a surge in the development of methods for the synthesis of organofluorine compounds. However, enzymatic methods for C-F bond formation have been limited to nucleophilic fluoride substitution. Here, we report the incorporation of iron-catalysed radical fluorine transfer, a reaction mechanism that is not used in naturally occurring enzymes, into enzymatic catalysis for the development of biocatalytic enantioselective C(sp 3)-F bond formation. Using this strategy, we repurposed (S)-2-hydroxypropylphosphonate epoxidase from Streptomyces viridochromogenes (SvHppE) to catalyse an N-fluoroamide directed C(sp 3)-H fluorination. Directed evolution has enabled SvHppE to be optimized, forming diverse chiral benzylic fluoride products with turnover numbers of up to 180 and with excellent enantiocontrol (up to 94% e.e.). Mechanistic investigations showed that the N-F bond activation is the rate-determining step, and the strong preference for fluorination in the presence of excess NaN3 can be attributed to the spatial proximity of the carbon-centered radical to the iron-bound fluoride.
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Affiliation(s)
- Qun Zhao
- School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Zhenhong Chen
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jordi Soler
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Girona E-17071, Catalonia, Spain
| | - Xiahe Chen
- State Key Laboratory Breeding Base of Green Chemistry-Synthesis Technology, Key Laboratory of Green Chemistry-Synthesis Technology of Zhejiang Province, College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Jinyan Rui
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Nathan Tianlin Ji
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | - Yunfang Yang
- State Key Laboratory Breeding Base of Green Chemistry-Synthesis Technology, Key Laboratory of Green Chemistry-Synthesis Technology of Zhejiang Province, College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Marc Garcia-Borràs
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Girona E-17071, Catalonia, Spain
| | - Xiongyi Huang
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
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8
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Ehinger FJ, Hertweck C. Biosynthesis and recruitment of reactive amino acids in nonribosomal peptide assembly lines. Curr Opin Chem Biol 2024; 81:102494. [PMID: 38936328 DOI: 10.1016/j.cbpa.2024.102494] [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: 02/28/2024] [Revised: 05/29/2024] [Accepted: 06/05/2024] [Indexed: 06/29/2024]
Abstract
Reactive amino acid side chains play important roles in the binding of peptides to specific targets. In addition, their reactivity enables selective peptide conjugation and functionalization for pharmaceutical purposes. Diverse reactive amino acids are incorporated into nonribosomal peptides, which serve as a source for drug candidates. Notable examples include (poly)unsaturated (enamine, alkyne, and furyl) and halogenated residues, strained carbacycles (cyclopropyl and cyclopropanol), small heterocycles (oxirane and aziridine), and reactive N-N functionalities (hydrazones, diazo compounds, and diazeniumdiolates). Their biosynthesis requires diverse biocatalysts for sophisticated reaction mechanisms. Several avenues have been identified for their incorporation into peptides, the recruitment by adenylation domains or ligases, on-line modifications, and enzymatic tailoring reactions. Combined with protein engineering approaches, this knowledge provides new opportunities in synthetic biology and bioorthogonal chemistry.
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Affiliation(s)
- Friedrich Johannes Ehinger
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany; Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany.
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9
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Jain S, Ospina F, Hammer SC. A New Age of Biocatalysis Enabled by Generic Activation Modes. JACS AU 2024; 4:2068-2080. [PMID: 38938808 PMCID: PMC11200230 DOI: 10.1021/jacsau.4c00247] [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: 03/22/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 06/29/2024]
Abstract
Biocatalysis is currently undergoing a profound transformation. The field moves from relying on nature's chemical logic to a discipline that exploits generic activation modes, allowing for novel biocatalytic reactions and, in many instances, entirely new chemistry. Generic activation modes enable a wide range of reaction types and played a pivotal role in advancing the fields of organo- and photocatalysis. This perspective aims to summarize the principal activation modes harnessed in enzymes to develop new biocatalysts. Although extensively researched in the past, the highlighted activation modes, when applied within enzyme active sites, facilitate chemical transformations that have largely eluded efficient and selective catalysis. This advance is attributed to multiple tunable interactions in the substrate binding pocket that precisely control competing reaction pathways and transition states. We will highlight cases of new synthetic methodologies achieved by engineered enzymes and will provide insights into potential future developments in this rapidly evolving field.
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Affiliation(s)
| | | | - Stephan C. Hammer
- Research Group for Organic Chemistry
and Biocatalysis, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
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10
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Cheung-Lee WL, Kolev JN, McIntosh JA, Gil AA, Pan W, Xiao L, Velásquez JE, Gangam R, Winston MS, Li S, Abe K, Alwedi E, Dance ZEX, Fan H, Hiraga K, Kim J, Kosjek B, Le DN, Marzijarani NS, Mattern K, McMullen JP, Narsimhan K, Vikram A, Wang W, Yan JX, Yang RS, Zhang V, Zhong W, DiRocco DA, Morris WJ, Murphy GS, Maloney KM. Engineering Hydroxylase Activity, Selectivity, and Stability for a Scalable Concise Synthesis of a Key Intermediate to Belzutifan. Angew Chem Int Ed Engl 2024; 63:e202316133. [PMID: 38279624 DOI: 10.1002/anie.202316133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
Biocatalytic oxidations are an emerging technology for selective C-H bond activation. While promising for a range of selective oxidations, practical use of enzymes catalyzing aerobic hydroxylation is presently limited by their substrate scope and stability under industrially relevant conditions. Here, we report the engineering and practical application of a non-heme iron and α-ketoglutarate-dependent dioxygenase for the direct stereo- and regio-selective hydroxylation of a non-native fluoroindanone en route to the oncology treatment belzutifan, replacing a five-step chemical synthesis with a direct enantioselective hydroxylation. Mechanistic studies indicated that formation of the desired product was limited by enzyme stability and product overoxidation, with these properties subsequently improved by directed evolution, yielding a biocatalyst capable of >15,000 total turnovers. Highlighting the industrial utility of this biocatalyst, the high-yielding, green, and efficient oxidation was demonstrated at kilogram scale for the synthesis of belzutifan.
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Affiliation(s)
| | - Joshua N Kolev
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - John A McIntosh
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Agnieszka A Gil
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Weilan Pan
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Li Xiao
- Modeling & Informatics, Discovery Chemistry, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Juan E Velásquez
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Rekha Gangam
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Matthew S Winston
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Shasha Li
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Kotoe Abe
- Chemical Commercialization Technologies, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Embarek Alwedi
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Zachary E X Dance
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Haiyang Fan
- API Process Research & Development (Biocatalysis), Shanghai STA Pharmaceutical Co., Ltd., Shanghai, 201507, China
| | - Kaori Hiraga
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Jungchul Kim
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Birgit Kosjek
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Diane N Le
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Keith Mattern
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Karthik Narsimhan
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Ajit Vikram
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Wei Wang
- API Process Research & Development (Biocatalysis), Shanghai STA Pharmaceutical Co., Ltd., Shanghai, 201507, China
| | - Jia-Xuan Yan
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Rong-Sheng Yang
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Victoria Zhang
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Wendy Zhong
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Daniel A DiRocco
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - William J Morris
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Grant S Murphy
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Kevin M Maloney
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
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11
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Hooson JF, Tran HN, Bian KJ, West JG. Simple, catalytic C(sp 3)-H azidation using the C-H donor as the limiting reagent. Chem Commun (Camb) 2024. [PMID: 38477139 DOI: 10.1039/d3cc04728h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
C-N bonds play a critical role in pharmaceutical, agrochemical, and materials sciences, necessitating ever-better methods to forge this linkage. Here we report a simple procedure for direct C(sp3)-H azidation using iron or manganese catalysis and a nucleophilic azide source. All reagents are commercially available, the experimental procedure is simple, and we can use the C-H donor substrate as the limiting reagent, a challenge for many C-H azidation methods. Preliminary experiments are consistent with a hydrogen atom transfer (HAT)/radical ligand transfer (RLT) radical cascade mechanism and a wide variety of substrates can be azidated in moderate to high yields.
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Affiliation(s)
- James F Hooson
- Department of Chemistry, Rice University, 6500 Main St, Houston, TX, USA.
| | - Hai N Tran
- Department of Chemistry, Rice University, 6500 Main St, Houston, TX, USA.
| | - Kang-Jie Bian
- Department of Chemistry, Rice University, 6500 Main St, Houston, TX, USA.
| | - Julian G West
- Department of Chemistry, Rice University, 6500 Main St, Houston, TX, USA.
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Yin HN, Wang PC, Liu Z. Recent advances in biocatalytic C-N bond-forming reactions. Bioorg Chem 2024; 144:107108. [PMID: 38244379 DOI: 10.1016/j.bioorg.2024.107108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/25/2023] [Accepted: 01/06/2024] [Indexed: 01/22/2024]
Abstract
Molecules containing C-N bonds are of paramount importance in a diverse array of organic-based materials, natural products, pharmaceutical compounds, and agricultural chemicals. Biocatalytic C-N bond-forming reactions represent powerful strategies for producing these valuable targets, and their significance in the field of synthetic chemistry has steadily increased over the past decade. In this review, we provide a concise overview of recent advancements in the development of C-N bond-forming enzymes, with a particular emphasis on the inherent chemistry involved in these enzymatic processes. Overall, these enzymatic systems have proven their potential in addressing long-standing challenges in traditional small-molecule catalysis.
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Affiliation(s)
- Hong-Ning Yin
- National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Peng-Cheng Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Zhen Liu
- National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China.
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13
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Burke EJ, Copeland RA, Dixit Y, Krebs C, Bollinger JM. Steric Perturbation of the Grob-like Final Step of Ethylene-Forming Enzyme Enables 3-Hydroxypropionate and Propylene Production. J Am Chem Soc 2024; 146:1977-1983. [PMID: 38226594 DOI: 10.1021/jacs.3c09733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Ethylene-forming enzyme (EFE) is an iron(II)-dependent dioxygenase that fragments 2-oxoglutarate (2OG) to ethylene (from C3 and C4) and 3 equivs of carbon dioxide (from C1, C2, and C5). This major ethylene-forming pathway requires l-arginine as the effector and competes with a minor pathway that merely decarboxylates 2OG to succinate as it oxidatively fragments l-arginine. We previously proposed that ethylene forms in a polar-concerted (Grob-like) fragmentation of a (2-carboxyethyl)carbonatoiron(II) intermediate, formed by the coupling of a C3-C5-derived propion-3-yl radical to a C1-derived carbonate coordinated to the Fe(III) cofactor. Replacement of one or both C4 hydrogens of 2OG by fluorine, methyl, or hydroxyl favored the elimination products 2-(F1-2/Me/OH)-3-hydroxypropionate and CO2 over the expected olefin or carbonyl products, implying strict stereoelectronic requirements in the final step, as is known for Grob fragmentations. Here, we substituted active-site residues expected to interact sterically with the proposed Grob intermediate, aiming to disrupt or enable the antiperiplanar disposition of the carboxylate electrofuge and carbonate nucleofuge required for concerted fragmentation. The bulk-increasing A198L substitution barely affects the first partition between the major and minor pathways but then, as intended, markedly diminishes ethylene production in favor of 3-hydroxypropionate. Conversely, the bulk-diminishing L206V substitution enables propylene formation from (4R)-methyl-2OG, presumably by allowing the otherwise sterically disfavored antiperiplanar conformation of the Grob intermediate bearing the extra methyl group. The results provide additional evidence for a polar-concerted ethylene-yielding step and thus for the proposed radical-polar crossover via substrate-radical coupling to the Fe(III)-coordinated carbonate.
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Affiliation(s)
- Evan J Burke
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Rachelle A Copeland
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Yash Dixit
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - J Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Yadav V, Wen L, Yadav S, Siegler MA, Goldberg DP. Selective Radical Transfer in a Series of Nonheme Iron(III) Complexes. Inorg Chem 2023; 62:17830-17842. [PMID: 37857315 PMCID: PMC11296666 DOI: 10.1021/acs.inorgchem.3c02617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
A series of nonheme iron complexes, FeIII(BNPAPh2O)(Lax)(Leq) (Lax/eq = N3-, NCS-, NCO-, and Cl-) have been synthesized using the previously reported BNPAPh2O- ligand. The ferrous analogs FeII(BNPAPh2O)(Lax) (Lax = N3-, NCS-, and NCO-) were also prepared. The complexes were structurally characterized using single crystal X-ray diffraction, which shows that all the FeIII complexes are six-coordinate, with one anionic ligand (Lax) in the H-bonding axial site and the other anionic ligand (Leq) in the equatorial plane, cis to the Lax ligand. The reaction of FeIII(BNPAPh2O-)(Lax)(Leq) with Ph3C• shows that one ligand is selectively transferred in each case. A selectivity trend emerges that shows •N3 is the most favored for transfer in each case to the carbon radical, whereas Cl• is the least favored. The NCO and NCS ligands showed an intermediate propensity for radical transfer, with NCS > NCO. The overall order of selectivity is N3 > NCS > NCO > Cl. In addition, we also demonstrated that H-bonding has a small effect on governing product selectivity by using a non-H-bonded ligand (DPAPh2O-). This study demonstrates the inherent radical transfer selectivity of nonhydroxo-ligated nonheme iron(III) complexes, which could be useful for efforts in synthetic and (bio)catalytic C-H functionalization.
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Affiliation(s)
- Vishal Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Lyupeng Wen
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Sudha Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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Abstract
Verruculogens are rare fumitremorgin alkaloids that contain a highly unusual eight-membered endoperoxide. In this paper, we report a concise chemoenzymatic synthesis of 13-oxoverruculogen using enzymatic C-H peroxidation and rhodium-catalyzed C-C bond activation reactions to install the eight-membered endoperoxide and the pentacyclic core of the natural product, respectively. Our strategy involves the use of 13-epi-fumitremorgin B as a substrate analog for endoperoxidation by verruculogen synthase, FtmOx1. The resulting product, 13-epi-verruculogen, is the first unnatural endoperoxide generated by FtmOx1 and is used in the first synthesis of 13-oxoverruculogen. This strategy enables a 10-step synthesis of this natural product from commercially available starting materials and illustrates a hybrid approach utilizing biocatalytic and transition-metal-catalyzed reactions to access challenging alkaloid architectures. Moreover, this work demonstrates the use of native enzyme promiscuity as a viable strategy for the chemoenzymatic synthesis of natural products.
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Affiliation(s)
- Jun Yang
- Brandeis University, Edison-Lecks Laboratory, Waltham, Massachusetts 02453, United States
| | - Brandon Singh
- Brandeis University, Edison-Lecks Laboratory, Waltham, Massachusetts 02453, United States
| | - Gabriel Cohen
- Brandeis University, Edison-Lecks Laboratory, Waltham, Massachusetts 02453, United States
| | - Chi P Ting
- Brandeis University, Edison-Lecks Laboratory, Waltham, Massachusetts 02453, United States
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Zwick CR, Renata H. Overview of Amino Acid Modifications by Iron- and α-Ketoglutarate-Dependent Enzymes. ACS Catal 2023. [DOI: 10.1021/acscatal.3c00424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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