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Yu MZ, Yuan Y, Li ZJ, Kunthic T, Wang HX, Xu C, Xiang Z. An Artificial Enzyme for Asymmetric Nitrocyclopropanation of α,β-Unsaturated Aldehydes-Design and Evolution. Angew Chem Int Ed Engl 2024; 63:e202401635. [PMID: 38597773 DOI: 10.1002/anie.202401635] [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: 01/23/2024] [Revised: 03/24/2024] [Accepted: 04/08/2024] [Indexed: 04/11/2024]
Abstract
The introduction of an abiological catalytic group into the binding pocket of a protein host allows for the expansion of enzyme chemistries. Here, we report the generation of an artificial enzyme by genetic encoding of a non-canonical amino acid that contains a secondary amine side chain. The non-canonical amino acid and the binding pocket function synergistically to catalyze the asymmetric nitrocyclopropanation of α,β-unsaturated aldehydes by the iminium activation mechanism. The designer enzyme was evolved to an optimal variant that catalyzes the reaction at high conversions with high diastereo- and enantioselectivity. This work demonstrates the application of genetic code expansion in enzyme design and expands the scope of enzyme-catalyzed abiological reactions.
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Affiliation(s)
- Ming-Zhu Yu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School, University Town of Shenzhen, Nanshan District, 518055, Shenzhen, P. R. China
| | - Ye Yuan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School, University Town of Shenzhen, Nanshan District, 518055, Shenzhen, P. R. China
| | - Zhen-Jie Li
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology Nanshan District, 518055, Shenzhen, P. R. China
| | - Thittaya Kunthic
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School, University Town of Shenzhen, Nanshan District, 518055, Shenzhen, P. R. China
| | - He-Xiang Wang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School, University Town of Shenzhen, Nanshan District, 518055, Shenzhen, P. R. China
| | - Chen Xu
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology Nanshan District, 518055, Shenzhen, P. R. China
| | - Zheng Xiang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School, University Town of Shenzhen, Nanshan District, 518055, Shenzhen, P. R. China
- Institute of Chemical Biology, Shenzhen Bay Laboratory Gaoke Innovation Center, Guangqiao Road, Guangming District, 518132, Shenzhen, P. R. China
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2
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Chen KY, Wang HQ, Yuan Y, Mou SB, Xiang Z. Chemoenzymatic Synthesis of Cylindrocyclophanes A and F and Merocyclophanes A and D. Angew Chem Int Ed Engl 2023; 62:e202307602. [PMID: 37771066 DOI: 10.1002/anie.202307602] [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: 05/30/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023]
Abstract
Incorporating enzymatic reactions into natural product synthesis can significantly improve synthetic efficiency and selectivity. In contrast to the increasing applications of biocatalytic functional-group interconversions, the use of enzymatic C-C bond formation reactions in natural product synthesis is underexplored. Herein, we report a concise and efficient approach for the synthesis of [7.7]paracyclophane natural products, a family of polyketides with diverse biological activities. By using enzymatic Friedel-Crafts alkylation, cylindrocyclophanes A and F and merocyclophanes A and D were synthesized in six to eight steps in the longest linear sequence. This study demonstrates the power of combining enzymatic reactions with contemporary synthetic methodologies and provides opportunities for the structure-activity relationship studies of [7.7]paracyclophane natural products.
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Affiliation(s)
- Kai-Yue Chen
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, University Town of Shenzhen, Nanshan District, 518055, Shenzhen, P. R. China
| | - Hua-Qi Wang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, University Town of Shenzhen, Nanshan District, 518055, Shenzhen, P. R. China
| | - Ye Yuan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, University Town of Shenzhen, Nanshan District, 518055, Shenzhen, P. R. China
| | - Shu-Bin Mou
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, University Town of Shenzhen, Nanshan District, 518055, Shenzhen, P. R. China
| | - Zheng Xiang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, University Town of Shenzhen, Nanshan District, 518055, Shenzhen, P. R. China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, 518132, Shenzhen, P. R. China
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3
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Yu MZ, Chen KY, Zhang YB, Zhang CX, Xiang Z. Enantioselective conjugate addition of malonates to α,β-unsaturated aldehydes catalysed by 4-oxalocrotonate tautomerase. Org Biomol Chem 2023; 21:2086-2090. [PMID: 36806856 DOI: 10.1039/d3ob00111c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The enantioselective conjugate addition of malonates to α,β-unsaturated aldehydes catalysed by 4-oxalocrotonate tautomerase is described. High conversions, high enantioselectivities, and good isolation yields were achieved for a range of substrates. We further completed a four-step synthesis of the antidepressant (+)-femoxetine by utilizing this reaction and an enzymatic reductive amination reaction.
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Affiliation(s)
- Ming-Zhu Yu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Kai-Yue Chen
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Yi-Bin Zhang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Chang-Xuan Zhang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Zheng Xiang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China. .,Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China.,AI for Science (AI4S) Preferred Program, Peking University Shenzhen Graduate School, Shenzhen 518055, China
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Dai J, Philbin CS, Wakano C, Yoshida WY, Williams PG. New Nostocyclophanes from Nostoc linckia. Mar Drugs 2023; 21:md21020101. [PMID: 36827142 PMCID: PMC9967113 DOI: 10.3390/md21020101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 02/01/2023] Open
Abstract
Six new nostocyclophanes and four known compounds have been isolated from Nostoc linckia (Nostocaceae) cyanobacterial strain UTEX B1932. The new compounds, nostocyclophanes E-J (1-6), were characterized by NMR and MS techniques. The known compounds were nostocyclophanes B-D, previously isolated from this strain, and dedichloronostocyclophane D. Structural modifications on the new [7.7]paracyclophane analogs 1-5, isolated from the 80% methanol fraction, range from simple changes such as the lack of methylation or halogenation to more unusual modifications such as those seen in nostocyclophane H (4), in which the exocyclic alkyl chains are of different length; this is the first time this modification has been observed in this family of natural products. In addition, nostocyclophane J (6) is a linear analog in which C-20 is chlorinated in preparation for the presumed enzymatic Friedel-Craft cyclization needed to form the final ring structure, analogous to the biosynthesis of the related cylindrocyclophanes. Nostocyclophane D, dedichloronostocyclophane D, and nostocyclophanes E-J demonstrated moderate to weak growth inhibition against MDA-MB-231 breast cancer cells.
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Affiliation(s)
- Jingqiu Dai
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Casey S. Philbin
- Department of Chemistry, University of Nevada Reno, Reno, NV 89557, USA
| | - Clay Wakano
- Center for Biomedical Research, The Queen’s Medical Center, Honolulu, HI 96813, USA
| | - Wesley Y. Yoshida
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Philip G. Williams
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Department of Chemistry, University of Nevada Reno, Reno, NV 89557, USA
- Correspondence: ; Tel.: +1-808-956-5720
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Leveson‐Gower RB, Roelfes G. Biocatalytic Friedel-Crafts Reactions. ChemCatChem 2022; 14:e202200636. [PMID: 36606067 PMCID: PMC9804301 DOI: 10.1002/cctc.202200636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/10/2022] [Indexed: 01/07/2023]
Abstract
Friedel-Crafts alkylation and acylation reactions are important methodologies in synthetic and industrial chemistry for the construction of aryl-alkyl and aryl-acyl linkages that are ubiquitous in bioactive molecules. Nature also exploits these reactions in many biosynthetic processes. Much work has been done to expand the synthetic application of these enzymes to unnatural substrates through directed evolution. The promise of such biocatalysts is their potential to supersede inefficient and toxic chemical approaches to these reactions, with mild operating conditions - the hallmark of enzymes. Complementary work has created many bio-hybrid Friedel-Crafts catalysts consisting of chemical catalysts anchored into biomolecular scaffolds, which display many of the same desirable characteristics. In this Review, we summarise these efforts, focussing on both mechanistic aspects and synthetic considerations, concluding with an overview of the frontiers of this field and routes towards more efficient and benign Friedel-Crafts reactions for the future of humankind.
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Affiliation(s)
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of Groningen9747 AGGroningenThe Netherlands
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Kumar V, Turnbull WB, Kumar A. Review on Recent Developments in Biocatalysts for Friedel–Crafts Reactions. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Vajinder Kumar
- Department of Chemistry, Akal University, Talwandi Sabo, Bathinda, Punjab 151302, India
| | - W. Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Avneesh Kumar
- Department of Botany, Akal University, Talwandi Sabo, Bathinda, Punjab 151302, India
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Braffman NR, Ruskoski TB, Davis KM, Glasser NR, Johnson C, Okafor CD, Boal AK, Balskus EP. Structural basis for an unprecedented enzymatic alkylation in cylindrocyclophane biosynthesis. eLife 2022; 11:75761. [PMID: 35212625 PMCID: PMC8916777 DOI: 10.7554/elife.75761] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
The cyanobacterial enzyme CylK assembles the cylindrocyclophane natural products by performing two unusual alkylation reactions, forming new carbon–carbon bonds between aromatic rings and secondary alkyl halide substrates. This transformation is unprecedented in biology, and the structure and mechanism of CylK are unknown. Here, we report X-ray crystal structures of CylK, revealing a distinctive fusion of a Ca2+-binding domain and a β-propeller fold. We use a mutagenic screening approach to locate CylK’s active site at its domain interface, identifying two residues, Arg105 and Tyr473, that are required for catalysis. Anomalous diffraction datasets collected with bound bromide ions, a product analog, suggest that these residues interact with the alkyl halide electrophile. Additional mutagenesis and molecular dynamics simulations implicate Asp440 in activating the nucleophilic aromatic ring. Bioinformatic analysis of CylK homologs from other cyanobacteria establishes that they conserve these key catalytic amino acids, but they are likely associated with divergent reactivity and altered secondary metabolism. By gaining a molecular understanding of this unusual biosynthetic transformation, this work fills a gap in our understanding of how alkyl halides are activated and used by enzymes as biosynthetic intermediates, informing enzyme engineering, catalyst design, and natural product discovery.
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Affiliation(s)
- Nathaniel R Braffman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Terry B Ruskoski
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, United States
| | - Katherine M Davis
- Department of Chemistry, Pennsylvania State University, University Park, United States
| | - Nathaniel R Glasser
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Cassidy Johnson
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - C Denise Okafor
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, United States
| | - Amie K Boal
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, United States
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
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