1
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Wu Z, Xia Z, Tang Z, Li J, Liu W. Mutasynthesis generates nine new pyrroindomycins. Org Biomol Chem 2024; 22:2813-2818. [PMID: 38511276 DOI: 10.1039/d4ob00239c] [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: 03/22/2024]
Abstract
Pyrroindomycins (PYRs) represent the only spirotetramate natural products discovered in nature, and possess potent activities against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium. Their unique structure and impressive biological activities make them attractive targets for synthesis and biosynthesis; however, the discovery and generation of new PYRs remains challenging. To date, only the initial components A and B have been reported. Herein, we report a mutasynthesis approach for the generation of nine new PYRs with varying acyl modifications on their deoxy-trisaccharide moieties. This was achieved by blocking the formation of the acyl group 1,8-dihydropyrrolo[2,3-b]indole (DHPI) via gene pyrK1 inactivation and supplying chemical acyl precursors. The gene pyrK1 encodes a DUF1864 family protein that probably catalyzes the oxidative transformation of L-tryptophan to DHPI, and its deletion results in the abolishment of DHPI-containing PYRs and the accumulation of three new PYRs either without acyl modification or with DHPI replaced by benzoic acid and pyrrole-2-carboxylic acid. Capitalizing on the capacity of the ΔpyrK1 mutant to produce new PYRs, we have successfully developed a mutasynthesis strategy for the generation of six novel PYR analogs with various aromatic acid modifications on their deoxy-trisaccharide moieties, showcasing the potential for generating structurally diverse PYRs. Overall, this research contributes significantly to understanding the biosynthesis of PYRs and offers valuable perspectives on their structural diversity.
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Affiliation(s)
- Zhuhua Wu
- National key Laboratory of Lead druggability Research, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Copernicus Road, Shanghai 201203, China.
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Zhengxiang Xia
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
- Department of Pharmacy, Stomatological Hospital and Dental School of Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, 399 Middle Yan Chang Road, Shanghai, 200072, China
| | - Zhijun Tang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Ji'an Li
- National key Laboratory of Lead druggability Research, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Copernicus Road, Shanghai 201203, China.
| | - Wen Liu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
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2
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Ding Q, Guo N, Gao L, McKee M, Wu D, Yang J, Fan J, Weng JK, Lei X. The evolutionary origin of naturally occurring intermolecular Diels-Alderases from Morus alba. Nat Commun 2024; 15:2492. [PMID: 38509059 PMCID: PMC10954736 DOI: 10.1038/s41467-024-46845-0] [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: 11/18/2023] [Accepted: 03/12/2024] [Indexed: 03/22/2024] Open
Abstract
Biosynthetic enzymes evolutionarily gain novel functions, thereby expanding the structural diversity of natural products to the benefit of host organisms. Diels-Alderases (DAs), functionally unique enzymes catalysing [4 + 2] cycloaddition reactions, have received considerable research interest. However, their evolutionary mechanisms remain obscure. Here, we investigate the evolutionary origins of the intermolecular DAs in the biosynthesis of Moraceae plant-derived Diels-Alder-type secondary metabolites. Our findings suggest that these DAs have evolved from an ancestor functioning as a flavin adenine dinucleotide (FAD)-dependent oxidocyclase (OC), which catalyses the oxidative cyclisation reactions of isoprenoid-substituted phenolic compounds. Through crystal structure determination, computational calculations, and site-directed mutagenesis experiments, we identified several critical substitutions, including S348L, A357L, D389E and H418R that alter the substrate-binding mode and enable the OCs to gain intermolecular DA activity during evolution. This work provides mechanistic insights into the evolutionary rationale of DAs and paves the way for mining and engineering new DAs from other protein families.
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Affiliation(s)
- Qi Ding
- School of Life Science, Tsinghua University, Beijing, 100084, China
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Nianxin Guo
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Lei Gao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
| | - Michelle McKee
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Dongshan Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Jun Yang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Junping Fan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
- Institute for Plant-Human Interface, Northeastern University, Boston, MA, 02120, USA
- Department of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, MA, 02120, USA
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
- Institute for Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518107, China.
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3
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Zhang X, Pang X, Zhang L, Li Y, Song Y, Xiao H, Liu Y, Wang J, Yan Y. Genome Mining Uncovers a Flavoenzyme-Catalyzed Isomerization Process during the Maturation of Pyrenophorol Dilactones. Org Lett 2024; 26:1612-1617. [PMID: 38377309 DOI: 10.1021/acs.orglett.4c00008] [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: 02/22/2024]
Abstract
The biosynthetic gene cluster responsible for the production of C2-asymmetric 16-membered dilactones, including pyrenophorol and its derivatives, was discovered through genome mining of polyketides from a sponge-derived fungus. The biosynthetic pathway of the pyrenophorol dilactones was subsequently elucidated. A distinctive flavoenzyme PylE was identified to catalyze the isomerization of the 4-alcohol-2,3-unsaturated moiety within the dilactone scaffold, resulting in the formation of a 1,4-diketone. Further insights into the catalytic mechanism of PylE were obtained through mutagenesis experiments combined with molecular docking.
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Affiliation(s)
- Xiufeng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Xiaoyan Pang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing 100049, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing 100049, China
| | - Yanqin Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Yongxiang Song
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Hua Xiao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Yonghong Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing 100049, China
| | - Junfeng Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Yan Yan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
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4
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Zorn K, Back CR, Barringer R, Chadimová V, Manzo‐Ruiz M, Mbatha SZ, Mobarec J, Williams SE, van der Kamp MW, Race PR, Willis CL, Hayes MA. Interrogation of an Enzyme Library Reveals the Catalytic Plasticity of Naturally Evolved [4+2] Cyclases. Chembiochem 2023; 24:e202300382. [PMID: 37305956 PMCID: PMC10946715 DOI: 10.1002/cbic.202300382] [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: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/13/2023]
Abstract
Stereoselective carbon-carbon bond forming reactions are quintessential transformations in organic synthesis. One example is the Diels-Alder reaction, a [4+2] cycloaddition between a conjugated diene and a dienophile to form cyclohexenes. The development of biocatalysts for this reaction is paramount for unlocking sustainable routes to a plethora of important molecules. To obtain a comprehensive understanding of naturally evolved [4+2] cyclases, and to identify hitherto uncharacterised biocatalysts for this reaction, we constructed a library comprising forty-five enzymes with reported or predicted [4+2] cycloaddition activity. Thirty-one library members were successfully produced in recombinant form. In vitro assays employing a synthetic substrate incorporating a diene and a dienophile revealed broad-ranging cycloaddition activity amongst these polypeptides. The hypothetical protein Cyc15 was found to catalyse an intramolecular cycloaddition to generate a novel spirotetronate. The crystal structure of this enzyme, along with docking studies, establishes the basis for stereoselectivity in Cyc15, as compared to other spirotetronate cyclases.
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Affiliation(s)
- Katja Zorn
- Compound Synthesis and Management, Discovery SciencesBiopharmaceuticals R&DAstraZenecaPepparedsleden 1431 83MölndalSweden
| | | | - Rob Barringer
- School of BiochemistryUniversity of BristolBristolBS8 1TDUK
| | - Veronika Chadimová
- Compound Synthesis and Management, Discovery SciencesBiopharmaceuticals R&DAstraZenecaPepparedsleden 1431 83MölndalSweden
| | | | | | - Juan‐Carlos Mobarec
- Mechanistic and Structural BiologyBiopharmaceuticals R&DAstraZenecaCambridgeCB21 6GHUK
| | | | | | - Paul R. Race
- School of BiochemistryUniversity of BristolBristolBS8 1TDUK
| | | | - Martin A. Hayes
- Compound Synthesis and Management, Discovery SciencesBiopharmaceuticals R&DAstraZenecaPepparedsleden 1431 83MölndalSweden
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5
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Niwa K, Ohashi M, Xie K, Chiang CY, Jamieson CS, Sato M, Watanabe K, Liu F, Houk K, Tang Y. Biosynthesis of Polycyclic Natural Products from Conjugated Polyenes via Tandem Isomerization and Pericyclic Reactions. J Am Chem Soc 2023; 145:13520-13525. [PMID: 37310230 PMCID: PMC10871872 DOI: 10.1021/jacs.3c02380] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We report biosynthetic pathways that can synthesize and transform conjugated octaenes and nonaenes to complex natural products. The biosynthesis of (-)-PF1018 involves an enzyme PfB that can control the regio-, stereo-, and periselectivity of multiple reactions starting from a conjugated octaene. Using PfB as a lead, we discovered a homologous enzyme, BruB, that facilitates diene isomerization, tandem 8π-6π-electrocyclization, and a 1,2-divinylcyclobutane Cope rearrangement to generate a new-to-nature compound.
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Affiliation(s)
- Kanji Niwa
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | - Masao Ohashi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | - Kaili Xie
- College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Chen-Yu Chiang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | - Cooper S. Jamieson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Michio Sato
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Fang Liu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - K.N. Houk
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
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6
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Liu J, Lu J, Zhang C, Zhou Q, Jamieson CS, Shang C, Houk KN, Zhou J, Hu Y. Tandem intermolecular [4 + 2] cycloadditions are catalysed by glycosylated enzymes for natural product biosynthesis. Nat Chem 2023:10.1038/s41557-023-01260-8. [PMID: 37365335 DOI: 10.1038/s41557-023-01260-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/26/2023] [Indexed: 06/28/2023]
Abstract
Tandem Diels-Alder reactions are frequently used in the construction of polycyclic ring systems in complex organic compounds. Unlike the many Diels-Alderases (DAases) that catalyse a single cycloaddition, enzymes for multiple Diels-Alder reactions are rare. Here we demonstrate that two calcium-ion-dependent glycosylated enzymes, EupfF and PycR1, independently catalyse sequential, intermolecular Diels-Alder reactions in the biosynthesis of bistropolone-sesquiterpenes. We elucidate the origins of catalysis and stereoselectivity within these DAases through analysis of enzyme co-crystal structures, together with computational and mutational studies. These enzymes are secreted as glycoproteins with diverse N-glycans. The N-glycan at N211 in PycR1 significantly increases the affinity to the calcium ion, which in turn regulates the active cavity, making it specifically interact with substrates to accelerate the tandem [4 + 2] cycloaddition. The synergistic effect of the calcium ion and N-glycan on the catalytic centre of enzymes involved in secondary metabolism, especially for complex tandem reactions, can extend our understanding of protein evolution and improve the artificial design of biocatalysts.
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Affiliation(s)
- Jiawang Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Jiayan Lu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, People's Republic of China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Chen Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Qingyang Zhou
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Cooper S Jamieson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Changhui Shang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA.
| | - Jiahai Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.
| | - Youcai Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China.
- NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China.
- CAMS Key Laboratory of Enzyme and Catalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China.
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7
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Liu Z, Rivera S, Newmister SA, Sanders JN, Nie Q, Liu S, Zhao F, Ferrara JD, Shih HW, Patil S, Xu W, Miller MD, Phillips GN, Houk KN, Sherman DH, Gao X. An NmrA-like enzyme-catalysed redox-mediated Diels-Alder cycloaddition with anti-selectivity. Nat Chem 2023; 15:526-534. [PMID: 36635598 PMCID: PMC10073347 DOI: 10.1038/s41557-022-01117-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 11/22/2022] [Indexed: 01/14/2023]
Abstract
The Diels-Alder cycloaddition is one of the most powerful approaches in organic synthesis and is often used in the synthesis of important pharmaceuticals. Yet, strictly controlling the stereoselectivity of the Diels-Alder reactions is challenging, and great efforts are needed to construct complex molecules with desired chirality via organocatalysis or transition-metal strategies. Nature has evolved different types of enzymes to exquisitely control cyclization stereochemistry; however, most of the reported Diels-Alderases have been shown to only facilitate the energetically favourable diastereoselective cycloadditions. Here we report the discovery and characterization of CtdP, a member of a new class of bifunctional oxidoreductase/Diels-Alderase, which was previously annotated as an NmrA-like transcriptional regulator. We demonstrate that CtdP catalyses the inherently disfavoured cycloaddition to form the bicyclo[2.2.2]diazaoctane scaffold with a strict α-anti-selectivity. Guided by computational studies, we reveal a NADP+/NADPH-dependent redox mechanism for the CtdP-catalysed inverse electron demand Diels-Alder cycloaddition, which serves as the first example of a bifunctional Diels-Alderase that utilizes this mechanism.
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Affiliation(s)
- Zhiwen Liu
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Sebastian Rivera
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sean A Newmister
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Qiuyue Nie
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Shuai Liu
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Fanglong Zhao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | | | - Hao-Wei Shih
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Siddhant Patil
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Weijun Xu
- Department of Biosciences, Rice University, Houston, TX, USA
| | | | - George N Phillips
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA.
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.
- Department of Chemistry, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
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8
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Selective cycloadditions. Nat Chem 2023; 15:167-169. [PMID: 36717614 DOI: 10.1038/s41557-022-01123-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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9
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Wang H, Zou Y, Li M, Tang Z, Wang J, Tian Z, Strassner N, Yang Q, Zheng Q, Guo Y, Liu W, Pan L, Houk KN. A cyclase that catalyses competing 2 + 2 and 4 + 2 cycloadditions. Nat Chem 2023; 15:177-184. [PMID: 36690833 DOI: 10.1038/s41557-022-01104-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 11/01/2022] [Indexed: 01/24/2023]
Abstract
Cycloaddition reactions are among the most widely used reactions in chemical synthesis. Nature achieves these cyclization reactions with a variety of enzymes, including Diels-Alderases that catalyse concerted 4 + 2 cycloadditions, but biosynthetic enzymes with 2 + 2 cyclase activity have yet to be discovered. Here we report that PloI4, a β-barrel-fold protein homologous to the exo-selective 4 + 2 cyclase that functions in the biosynthesis of pyrroindomycins, catalyses competitive 2 + 2 and 4 + 2 cycloaddition reactions. PloI4 is believed to catalyse an endo-4 + 2 cycloaddition in the biosynthesis of pyrrolosporin A; however, when the substrate precursor of pyrroindomycins was treated with PloI4, an exo-2 + 2 adduct was produced in addition to the exo- and endo-4 + 2 adducts. Biochemical characterizations, computational analyses, (co)crystal structures and mutagenesis outcomes have allowed the catalytic versatility of PloI4 to be rationalized. Mechanistic studies involved the directed engineering of PloI4 to variants that produced the exo-4 + 2, endo-4 + 2 or exo-2 + 2 product preferentially. This work illustrates an enzymatic thermal 2 + 2 cycloaddition and provides evidence of a process through which an enzyme evolves along with its substrate for specialization and activity improvement.
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Affiliation(s)
- Hongbo Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Yike Zou
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Miao Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China.,School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Zhijun Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Jiabao Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China.,Department of Chemistry, Shanghai Normal University, Shanghai, China
| | - Zhenhua Tian
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China.,Abiochem Biotechnology Co., Ltd, Shanghai, China
| | - Nina Strassner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Qian Yang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Qingfei Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Yujiao Guo
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China. .,Department of Chemistry, Shanghai Normal University, Shanghai, China.
| | - Lifeng Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China. .,School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA.
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10
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Mastachi-Loza S, Ramírez-Candelero TI, Benítez-Puebla LJ, Fuentes-Benítes A, González-Romero C, Vázquez MA. Chalcones, a Privileged Scaffold: Highly Versatile Molecules in [4+2] Cycloadditions. Chem Asian J 2022; 17:e202200706. [PMID: 35976743 DOI: 10.1002/asia.202200706] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/14/2022] [Indexed: 11/09/2022]
Abstract
Chalcones are aromatic ketones found in nature as the central core of many biological compounds. They have a wide range of biological activity and are biogenetic precursors of other important molecules such as flavonoids. Their pharmacological relevance makes them a privileged scaffold, advantageous for seeking alternative therapies in medicinal chemistry. Due to their structural diversity and ease of synthesis, they are often employed as building blocks for chemical transformations. Chalcones have a carbonyl conjugated system with two electrophilic centers that are commonly used for nucleophilic additions, as described in numerous articles. They can also participate in Diels-Alder reactions, which are [4+2] cycloadditions between a diene and a dienophile. This microreview presents a chronological survey of studies on chalcones as dienes and dienophiles in Diels-Alder cycloadditions. Although these reactions occur in nature, isolation of chalcones from plants yields very small quantities. Contrarily, synthesis leads to large quantities at a low cost. Hence, novel methodologies have been developed for [4+2] cycloadditions, with chalcones serving as a 2π or 4π electron system.
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Affiliation(s)
- Salvador Mastachi-Loza
- Universidad de Guanajuato Division de Ciencias Naturales y Exactas, Departamento de Química, MEXICO
| | - Tania I Ramírez-Candelero
- Universidad Autonoma del Estado de Mexico Facultad de Quimica, Departamento de Química Orgánica, MEXICO
| | - Luis J Benítez-Puebla
- Universidad de Guanajuato Division de Ciencias Naturales y Exactas, Departamento de Química, MEXICO
| | - Aydee Fuentes-Benítes
- Universidad Autonoma del Estado de Mexico Facultad de Quimica, Departamento de Química Orgánica, MEXICO
| | - Carlos González-Romero
- Universidad Autonoma del Estado de Mexico Facultad de Quimica, Departamento de Química Orgánica, MEXICO
| | - Miguel A Vázquez
- Universidad de Guanajuato Division de Ciencias Naturales y Exactas, CHEMISTRY, NORIA ALTA S/N, 36050, GUANAJUATO, MEXICO
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11
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Liu SH, Sun JL, Hu YL, Zhang L, Zhang X, Yan ZY, Guo X, Guo ZK, Jiao RH, Zhang B, Tan RX, Ge HM. Biosynthesis of Sordarin Revealing a Diels–Alderase for the Formation of the Norbornene Skeleton. Angew Chem Int Ed Engl 2022; 61:e202205577. [DOI: 10.1002/anie.202205577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Shuang He Liu
- State Key Laboratory of Pharmaceutical Biotechnology Institute of Functional Biomolecules Chemistry and Biomedicine Innovation Center (ChemBIC) School of Life Sciences Nanjing University Nanjing 210023 China
| | - Jia Li Sun
- State Key Laboratory of Pharmaceutical Biotechnology Institute of Functional Biomolecules Chemistry and Biomedicine Innovation Center (ChemBIC) School of Life Sciences Nanjing University Nanjing 210023 China
| | - Yi Ling Hu
- State Key Laboratory of Pharmaceutical Biotechnology Institute of Functional Biomolecules Chemistry and Biomedicine Innovation Center (ChemBIC) School of Life Sciences Nanjing University Nanjing 210023 China
| | - Li Zhang
- State Key Laboratory of Pharmaceutical Biotechnology Institute of Functional Biomolecules Chemistry and Biomedicine Innovation Center (ChemBIC) School of Life Sciences Nanjing University Nanjing 210023 China
| | - Xuan Zhang
- State Key Laboratory of Pharmaceutical Biotechnology Institute of Functional Biomolecules Chemistry and Biomedicine Innovation Center (ChemBIC) School of Life Sciences Nanjing University Nanjing 210023 China
| | - Zhang Yuan Yan
- State Key Laboratory of Pharmaceutical Biotechnology Institute of Functional Biomolecules Chemistry and Biomedicine Innovation Center (ChemBIC) School of Life Sciences Nanjing University Nanjing 210023 China
| | - Xing Guo
- State Key Laboratory of Pharmaceutical Biotechnology Institute of Functional Biomolecules Chemistry and Biomedicine Innovation Center (ChemBIC) School of Life Sciences Nanjing University Nanjing 210023 China
| | - Zhi Kai Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops Ministry of Agriculture Institute of Tropical Bioscience and Bio-technology Chinese Academy of Tropical Agricultural Sciences Haikou 571101 China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology Institute of Functional Biomolecules Chemistry and Biomedicine Innovation Center (ChemBIC) School of Life Sciences Nanjing University Nanjing 210023 China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology Institute of Functional Biomolecules Chemistry and Biomedicine Innovation Center (ChemBIC) School of Life Sciences Nanjing University Nanjing 210023 China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology Institute of Functional Biomolecules Chemistry and Biomedicine Innovation Center (ChemBIC) School of Life Sciences Nanjing University Nanjing 210023 China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology Institute of Functional Biomolecules Chemistry and Biomedicine Innovation Center (ChemBIC) School of Life Sciences Nanjing University Nanjing 210023 China
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12
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Zhu HJ, Zhang B, Wei W, Liu SH, Xiang L, Zhu J, Jiao RH, Igarashi Y, Bashiri G, Liang Y, Tan RX, Ge HM. AvmM catalyses macrocyclization through dehydration/Michael-type addition in alchivemycin A biosynthesis. Nat Commun 2022; 13:4499. [PMID: 35922406 PMCID: PMC9349299 DOI: 10.1038/s41467-022-32088-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 07/15/2022] [Indexed: 11/21/2022] Open
Abstract
Macrocyclization is an important process that affords morphed scaffold in biosynthesis of bioactive natural products. Nature has adapted diverse biosynthetic strategies to form macrocycles. In this work, we report the identification and characterization of a small enzyme AvmM that can catalyze the construction of a 16-membered macrocyclic ring in the biosynthesis of alchivemycin A (1). We show through in vivo gene deletion, in vitro biochemical assay and isotope labelling experiments that AvmM catalyzes tandem dehydration and Michael-type addition to generate the core scaffold of 1. Mechanistic studies by crystallography, DFT calculations and MD simulations of AvmM reveal that the reactions are achieved with assistance from the special tenuazonic acid like moiety of substrate. Our results thus uncover an uncharacterized macrocyclization strategy in natural product biosynthesis. Macrocyclization is an important process in bioactive natural product synthesis. Here, the authors report on the study of a macrocyclic ring constructing enzyme in the biosynthesis of alchivemycin A and using gene deletion, biochemical assays and isotope labelling show the enzyme catalyses tandem dehydration and Michael-type addition.
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Affiliation(s)
- Hong Jie Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Centre, Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Centre, Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Wanqing Wei
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Centre, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Shuang He Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Centre, Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Lang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Centre, Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jiapeng Zhu
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Medicine and Life Sciences, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Centre, Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama, 939-0398, Japan
| | - Ghader Bashiri
- Laboratory of Molecular and Microbial Biochemistry, School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Centre, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China.
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Centre, Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Centre, Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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13
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Sun C, Tian W, Lin Z, Qu X. Biosynthesis of pyrroloindoline-containing natural products. Nat Prod Rep 2022; 39:1721-1765. [PMID: 35762180 DOI: 10.1039/d2np00030j] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: up to 2022Pyrroloindoline is a privileged tricyclic indoline motif widely present in many biologically active and medicinally valuable natural products. Thus, understanding the biosynthesis of this molecule is critical for developing convenient synthetic routes, which is highly challenging for its chemical synthesis due to the presence of rich chiral centers in this molecule, especially the fully substituted chiral carbon center at the C3-position of its rigid tricyclic structure. In recent years, progress has been made in elucidating the biosynthetic pathways and enzymatic mechanisms of pyrroloindoline-containing natural products (PiNPs). This article reviews the main advances in the past few decades based on the different substitutions on the C3 position of PiNPs, especially the various key enzymatic mechanisms involved in the biosynthesis of different types of PiNPs.
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Affiliation(s)
- Chenghai Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Wenya Tian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Zhi Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xudong Qu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
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14
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Ge HM, Liu SH, Sun JL, Hu YL, Zhang L, Zhang X, Yan ZY, Guo X, Guo ZK, Jiao RH, Zhang B, Tan RX. Biosynthesis of Sordarin Revealing a Diels‐Alderase for the Formation of the Norbornene Skeleton. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Hui Ming Ge
- Nanjing University School of Lifescience 22 Hankou Road 210093 Nanjing CHINA
| | | | - Jia Li Sun
- Nanjing University School of Life Science CHINA
| | - Yi Ling Hu
- Nanjing University School of Life Science CHINA
| | - Li Zhang
- Nanjing University School of Life Science CHINA
| | - Xuan Zhang
- Nanjing University School of Life Science CHINA
| | | | - Xing Guo
- Nanjing University School of Life Science CHINA
| | - Zhi Kai Guo
- Chinese Academy of Tropical Agricultural Sciences Key Laboratory of Biology and Genetic Resources of Tropical Crops CHINA
| | | | - Bo Zhang
- Nanjing University School of Life Science xianlin No163, Jiangsu, ChinaJiangsu, China 210023 nanjing CHINA
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15
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Discovery and characterization of a terpene biosynthetic pathway featuring a norbornene-forming Diels-Alderase. Nat Commun 2022; 13:2568. [PMID: 35546152 PMCID: PMC9095873 DOI: 10.1038/s41467-022-30288-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
Pericyclases, enzymes that catalyze pericyclic reactions, form an expanding family of enzymes that have biocatalytic utility. Despite the increasing number of pericyclases discovered, the Diels-Alder cyclization between a cyclopentadiene and an olefinic dienophile to form norbornene, which is among the best-studied cycloadditions in synthetic chemistry, has surprisingly no enzymatic counterpart to date. Here we report the discovery of a pathway featuring a norbornene synthase SdnG for the biosynthesis of sordaricin-the terpene precursor of antifungal natural product sordarin. Full reconstitution of sordaricin biosynthesis reveals a concise oxidative strategy used by Nature to transform an entirely hydrocarbon precursor into the highly functionalized substrate of SdnG for intramolecular Diels-Alder cycloaddition. SdnG generates the norbornene core of sordaricin and accelerates this reaction to suppress host-mediated redox modifications of the activated dienophile. Findings from this work expand the scopes of pericyclase-catalyzed reactions and P450-mediated terpene maturation. Pericyclase enzymes are an expanding family of enzymes. Here, the authors identify the norbornene synthase SdnG, a pericyclase for the intramolecular Diels-Alder reaction between a cyclopentadiene and an olefinic dienophile to form the sordaricin norbornene structure, and reconstitute the sordaricin biosynthesis.
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16
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Mori T, Nakashima Y, Chen H, Hoshino S, Mitsuhashi T, Abe I. Structure-based redesign of Fe(II)/2-oxoglutarate-dependent oxygenase AndA to catalyze spiro-ring formation. Chem Commun (Camb) 2022; 58:5510-5513. [PMID: 35420093 DOI: 10.1039/d2cc00736c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Structure- and mechanism-based redesign of the Fe(II)/2-oxoglutarate-dependent oxygenase AndA was performed. The function of AndA was expanded to catalyze a spiro-ring formation reaction from an isomerization reaction. The redesigned AndA variants produced two unnatural novel spiro-ring containing compounds through two and three consecutive oxidation reactions.
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Affiliation(s)
- Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.,PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Yu Nakashima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Heping Chen
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Shotaro Hoshino
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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17
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I2/PhI(OAc)2-assisted oxidative C-H amination protocols toward metal-free pragmatic synthesis of pyrrolo[2,3-b]indoles. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.05.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Li B, Guan X, Yang S, Zou Y, Liu W, Houk KN. Mechanism of the Stereoselective Catalysis of Diels-Alderase PyrE3 Involved in Pyrroindomycin Biosynthesis. J Am Chem Soc 2022; 144:5099-5107. [PMID: 35258962 DOI: 10.1021/jacs.2c00015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The biosynthesis of pyrroindomycins A and B features a complexity-building [4 + 2] cycloaddition cascade, which generates the spirotetramate core under the catalytic effects of monofunctional Diels-Alderases PyrE3 and PyrI4. We recently showed that the main functions of PyrI4 include acid catalysis and induced-fit/conformational selection. We now present quantum mechanical and molecular dynamics studies implicating a different mode of action by PyrE3, which prearranges an anionic polyene substrate into a high-energy reactive conformation at which an inverse-electron-demand Diels-Alder reaction can occur with a low barrier. Stereoselection is realized by strong binding interactions at the endo stereochemical relationship and a local steric constraint on the endo-1,3-diene unit. These findings, illustrating distinct mechanisms for PyrE3 and PyrI4, highlight how nature has evolved multiple ways to catalyze Diels-Alder reactions.
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Affiliation(s)
- Bo Li
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Xingyi Guan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Song Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Yike Zou
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
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19
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Pu DB, Guo SQ, Ni DX, Lin J, Gao JB, Li XN, Zhang RH, Li XL, Luo C, Chen SJ, Xiao WL. Spiroarborin, an ent-Clerodane Homodimer from Callicarpa arborea as an Inhibitor of the Eleven-Nineteen Leukemia (ENL) Protein by Targeting the YEATS Domain. JOURNAL OF NATURAL PRODUCTS 2022; 85:317-326. [PMID: 35029993 DOI: 10.1021/acs.jnatprod.1c00775] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A spiro ent-clerodane homodimer with a rare 6/6/6/6/6-fused pentacyclic scaffold, spiroarborin (1), together with four new monomeric analogues (2-5), were isolated from Callicarpa arborea. Their structures were elucidated by comprehensive spectroscopic data analysis, quantum-chemical calculations, and X-ray diffraction. A plausible biosynthetic pathway of 1 was proposed, and a biomimetic synthesis of its derivative was accomplished. Compound 1 showed a potent inhibitory effect by directly binding to the YEATS domain of the 11-19 leukemia (ENL) protein with an IC50 value of 7.3 μM. This gave a KD value of 5.0 μM, as recorded by a surface plasmon resonance binding assay.
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Affiliation(s)
- De-Bing Pu
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming 650091, People's Republic of China
| | - Si-Qi Guo
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
- School of Pharmacy, Nanchang University, Nanchang 330006, People's Republic of China
| | - Dong-Xuan Ni
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming 650091, People's Republic of China
| | - Jing Lin
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming 650091, People's Republic of China
| | - Jun-Bo Gao
- State Key Laboratory of CAD&CG, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Xiao-Ning Li
- School of Pharmaceutical Sciences, Yunnan University of Chinese Medicine, Kunming 650500, People's Republic of China
| | - Rui-Han Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming 650091, People's Republic of China
| | - Xiao-Li Li
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming 650091, People's Republic of China
| | - Cheng Luo
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Shi-Jie Chen
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Wei-Lie Xiao
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming 650091, People's Republic of China
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20
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Jeon BS, Huang TY, Ruszczycky MW, Choi SH, Kim N, Franklin JL, Hung SC, Liu HW. Byproduct formation during the biosynthesis of spinosyn A and evidence for an enzymatic interplay to prevent its formation. Tetrahedron 2022; 103. [PMID: 35685987 DOI: 10.1016/j.tet.2021.132569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Biosynthesis of spinosyn A in Saccharopolyspora spinosa involves a 1,4-dehydration followed by an intramolecular [4 + 2]-cycloaddition catalyzed by SpnM and SpnF, respectively. The cycloaddition also takes place in the absence of SpnF leading to questions regarding its mechanism of catalysis and biosynthetic role. Substrate analogs were prepared with an unactivated dienophile or an acyclic structure and found to be unreactive consistent with the importance of these features for cyclization. The SpnM-catalyzed dehydration reaction was also found to yield a byproduct corresponding to the C11 = C12 cis isomer of the SpnF substrate. This byproduct is stable both in the presence and absence of SpnF; however, relative production of the SpnM product and byproduct could be shifted in favor of the former by including SpnF or the dehydrogenase SpnJ in the reaction. This result suggests a potential interplay between the enzymes of spinosyn A biosynthesis that may help to improve the efficiency of the pathway.
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Affiliation(s)
- Byung-Sun Jeon
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Teng-Yi Huang
- Genomics Research Center, Academia Sinica, 128, Section 2, Academia Road, Taipei, 11529, Taiwan
| | - Mark W Ruszczycky
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX, 78712, USA
| | - Sei-Hyun Choi
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Namho Kim
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX, 78712, USA
| | - Joseph Livy Franklin
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX, 78712, USA
| | - Shang-Cheng Hung
- Genomics Research Center, Academia Sinica, 128, Section 2, Academia Road, Taipei, 11529, Taiwan
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.,Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX, 78712, USA
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21
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Zhou T, Zheng A, Huo L, Li C, Tan H, Wang S, Chen H. Total syntheses of ericifolione and its analogues via a biomimetic inverse-electron-demand Diels-Alder reaction. Chem Commun (Camb) 2021; 58:270-273. [PMID: 34878459 DOI: 10.1039/d1cc06361h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Driven by bioinspiration and appreciation of the structure of ericifolione, a biomimetic tautomerization/intermolecular inverse-electron-demand hetero Diels-Alder reaction cascade sequence promoted by sodium acetate to rapidly construct sterically hindered dihydropyran scaffolds was established, which allowed the first straightforward biomimetic total syntheses of ericifolione and its analogues with high simplicity. Moreover, this methodology set the stage for the preparation of relevant natural products or derivatives.
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Affiliation(s)
- Tingting Zhou
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, People's Republic of China. .,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, People's Republic of China.
| | - Anquan Zheng
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, People's Republic of China. .,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, People's Republic of China.
| | - Luqiong Huo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, People's Republic of China.
| | - Changgeng Li
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, People's Republic of China.
| | - Haibo Tan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, People's Republic of China.
| | - Sasa Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, People's Republic of China. .,Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Centre for Chemistry and Engineering of Forest Products, Guangxi University for Nationalities, Nanning 530006, People's Republic of China
| | - Huiyu Chen
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, People's Republic of China. .,School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, People's Republic of China
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22
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Enzymatic control of endo- and exo-stereoselective Diels–Alder reactions with broad substrate scope. Nat Catal 2021. [DOI: 10.1038/s41929-021-00717-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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23
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Fujiyama K, Kato N, Re S, Kinugasa K, Watanabe K, Takita R, Nogawa T, Hino T, Osada H, Sugita Y, Takahashi S, Nagano S. Molecular Basis for Two Stereoselective Diels–Alderases that Produce Decalin Skeletons**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Keisuke Fujiyama
- Department of Chemistry and Biotechnology Graduate School of Engineering Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
- Current address: Dormancy and Adaptation Research Unit RIKEN Center for Sustainable Resource Science 1-7-22 Suehiro, Tsurumi Yokohama Kanagawa 230-0045 Japan
| | - Naoki Kato
- Natural Product Biosynthesis Research Unit RIKEN Center for Sustainable Research Science 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Faculty of Agriculture Setsunan University 45-1 Nagaotoge-cho, Hirakata Osaka 573-0101 Japan
| | - Suyong Re
- Laboratory for Biomolecular Function Simulation RIKEN Center for Biosystems Dynamics Research 2-2-3 Minatojima-minami-machi, Chuo-ku Kobe Hyogo 650-0047 Japan
- Artificial Intelligence Center for Health and Biomedical Research National Institutes of Biomedical Innovation, Health, and Nutrition 7-6-8, Saito-Asagi, Ibaraki Osaka 567-0085 Japan
| | - Kiyomi Kinugasa
- Natural Product Biosynthesis Research Unit RIKEN Center for Sustainable Research Science 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Kohei Watanabe
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Ryo Takita
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Toshihiko Nogawa
- Chemical Biology Research Group RIKEN Center for Sustainable Research Science 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Tomoya Hino
- Department of Chemistry and Biotechnology Graduate School of Engineering Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
- Center for Research on Green Sustainable Chemistry Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group RIKEN Center for Sustainable Research Science 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function Simulation RIKEN Center for Biosystems Dynamics Research 2-2-3 Minatojima-minami-machi, Chuo-ku Kobe Hyogo 650-0047 Japan
- Theoretical Molecular Science Laboratory RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Computational Biophysics Research Team RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi Chuo-ku Kobe, Hyogo 650-0047 Japan
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit RIKEN Center for Sustainable Research Science 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Shingo Nagano
- Department of Chemistry and Biotechnology Graduate School of Engineering Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
- Center for Research on Green Sustainable Chemistry Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
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24
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Fujiyama K, Kato N, Re S, Kinugasa K, Watanabe K, Takita R, Nogawa T, Hino T, Osada H, Sugita Y, Takahashi S, Nagano S. Molecular Basis for Two Stereoselective Diels-Alderases that Produce Decalin Skeletons*. Angew Chem Int Ed Engl 2021; 60:22401-22410. [PMID: 34121297 PMCID: PMC8518865 DOI: 10.1002/anie.202106186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Indexed: 12/02/2022]
Abstract
Enzymes catalyzing [4+2] cycloaddition have attracted increasing attention because of their key roles in natural product biosynthesis. Here, we solved the X-ray crystal structures of a pair of decalin synthases, Fsa2 and Phm7, that catalyze intramolecular [4+2] cycloadditions to form enantiomeric decalin scaffolds during biosynthesis of the HIV-1 integrase inhibitor equisetin and its stereochemical opposite, phomasetin. Computational modeling, using molecular dynamics simulations as well as quantum chemical calculations, demonstrates that the reactions proceed through synergetic conformational constraints assuring transition state-like substrates folds and their stabilization by specific protein-substrate interactions. Site-directed mutagenesis experiments verified the binding models. Intriguingly, the flexibility of bound substrates is largely different in two enzymes, suggesting the distinctive mechanism of dynamics regulation behind these stereoselective reactions. The proposed reaction mechanism herein deepens the basic understanding how these enzymes work but also provides a guiding principle to create artificial enzymes.
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Affiliation(s)
- Keisuke Fujiyama
- Department of Chemistry and BiotechnologyGraduate School of EngineeringTottori University4-101 Koyama-choMinamiTottori680-8552Japan
- Current address: Dormancy and Adaptation Research UnitRIKEN Center for Sustainable Resource Science1-7-22 Suehiro, TsurumiYokohamaKanagawa230-0045Japan
| | - Naoki Kato
- Natural Product Biosynthesis Research UnitRIKEN Center for Sustainable Research Science2-1 HirosawaWakoSaitama351-0198Japan
- Faculty of AgricultureSetsunan University45-1 Nagaotoge-cho, HirakataOsaka573-0101Japan
| | - Suyong Re
- Laboratory for Biomolecular Function SimulationRIKEN Center for Biosystems Dynamics Research2-2-3 Minatojima-minami-machi, Chuo-kuKobeHyogo650-0047Japan
- Artificial Intelligence Center for Health and Biomedical ResearchNational Institutes of Biomedical Innovation, Health, and Nutrition7-6-8, Saito-Asagi, IbarakiOsaka567-0085Japan
| | - Kiyomi Kinugasa
- Natural Product Biosynthesis Research UnitRIKEN Center for Sustainable Research Science2-1 HirosawaWakoSaitama351-0198Japan
| | - Kohei Watanabe
- Graduate School of Pharmaceutical SciencesThe University of Tokyo7-3-1 Hongo, Bunkyo-kuTokyo113-0033Japan
| | - Ryo Takita
- Graduate School of Pharmaceutical SciencesThe University of Tokyo7-3-1 Hongo, Bunkyo-kuTokyo113-0033Japan
| | - Toshihiko Nogawa
- Chemical Biology Research GroupRIKEN Center for Sustainable Research Science2-1 HirosawaWakoSaitama351-0198Japan
| | - Tomoya Hino
- Department of Chemistry and BiotechnologyGraduate School of EngineeringTottori University4-101 Koyama-choMinamiTottori680-8552Japan
- Center for Research on Green Sustainable ChemistryTottori University4-101 Koyama-choMinamiTottori680-8552Japan
| | - Hiroyuki Osada
- Chemical Biology Research GroupRIKEN Center for Sustainable Research Science2-1 HirosawaWakoSaitama351-0198Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function SimulationRIKEN Center for Biosystems Dynamics Research2-2-3 Minatojima-minami-machi, Chuo-kuKobeHyogo650-0047Japan
- Theoretical Molecular Science LaboratoryRIKEN Cluster for Pioneering Research2-1 HirosawaWakoSaitama351-0198Japan
- Computational Biophysics Research TeamRIKEN Center for Computational Science7-1-26 Minatojima-minami-machiChuo-kuKobe, Hyogo650-0047Japan
| | - Shunji Takahashi
- Natural Product Biosynthesis Research UnitRIKEN Center for Sustainable Research Science2-1 HirosawaWakoSaitama351-0198Japan
| | - Shingo Nagano
- Department of Chemistry and BiotechnologyGraduate School of EngineeringTottori University4-101 Koyama-choMinamiTottori680-8552Japan
- Center for Research on Green Sustainable ChemistryTottori University4-101 Koyama-choMinamiTottori680-8552Japan
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25
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Houk KN, Xue X, Liu F, Chen Y, Chen X, Jamieson C. Computations on Pericyclic Reactions Reveal the Richness of Ambimodal Transition States and Pericyclases. Isr J Chem 2021. [DOI: 10.1002/ijch.202100071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- K. N. Houk
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90095-1569 USA
| | - Xiao‐Song Xue
- Department of Chemistry Nankai University Tianjin 300071 China
| | - Fang Liu
- College of Sciences Nanjing Agricultural University Nanjing Jiangsu 210095 China
| | - Yu Chen
- School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
| | - Xiangyang Chen
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90095-1569 USA
| | - Cooper Jamieson
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90095-1569 USA
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26
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Ding W, Chi C, Wei X, Sun C, Tu J, Ma M, Li Q, Ju J. Enzymatic Synthesis of a Diastereomer of Neoabyssomicin Derivative Using the
Diels‐Alderase AbyU. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wenjuan Ding
- CAS Key Laboratory of Tropical Marine Bio‐Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences 164 West Xingang Road Guangzhou Guangdong 510301 China
- College of Oceanology, University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
| | - Changbiao Chi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China
| | - Xiaoyi Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences Guangzhou Guangdong 510650 China
| | - Changli Sun
- CAS Key Laboratory of Tropical Marine Bio‐Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences 164 West Xingang Road Guangzhou Guangdong 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) No. 1119, Haibin Rd., Nansha District Guangzhou Guangdong 510301 China
| | - Jiajia Tu
- CAS Key Laboratory of Tropical Marine Bio‐Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences 164 West Xingang Road Guangzhou Guangdong 510301 China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China
| | - Qinglian Li
- CAS Key Laboratory of Tropical Marine Bio‐Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences 164 West Xingang Road Guangzhou Guangdong 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) No. 1119, Haibin Rd., Nansha District Guangzhou Guangdong 510301 China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio‐Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences 164 West Xingang Road Guangzhou Guangdong 510301 China
- College of Oceanology, University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) No. 1119, Haibin Rd., Nansha District Guangzhou Guangdong 510301 China
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27
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Li H, Zhang M, Li H, Yu H, Chen S, Wu W, Sun P. Discovery of Venturicidin Congeners and Identification of the Biosynthetic Gene Cluster from Streptomyces sp. NRRL S-4. JOURNAL OF NATURAL PRODUCTS 2021; 84:110-119. [PMID: 33356258 DOI: 10.1021/acs.jnatprod.0c01177] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chemical screening of Streptomyces sp. NRRL S-4 with liquid chromatography-mass spectrometry (LC-MS) and the following chromatographic isolation led to the discovery of four 20-membered macrolides, venturicidin A (4) and three new congeners venturicidins D-F (1-3). Genome sequencing of strain S-4 revealed the presence of a biosynthetic gene cluster (BGC) encoding glycosylated type I polyketides (PKS). The BGC designated to venturicidin biosynthesis (ven) was supported by the proposed biosynthetic pathway and confirmed by inactivation of the core PKS gene of venK. Bioinformatic analyses on the conserved motifs and known stereospecificities in PKS modules are consistent with the structure and absolute configuration. This is the first report of venturicidin BGC since the discovery of the macrolide in 1961. In the biological assays, venturicidin A (4) and E (2) displayed a high selective cytotoxicity against acute monocytic leukemia MV-4-11 cells with IC50 values of 0.09 and 0.94 μM, respectively. Venturicidin A (4) also showed a weak inhibitory activity on FMS-like-tyrosine kinase.
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Affiliation(s)
- Huanhuan Li
- School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai 200433, People's Republic of China
- College of Food Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, People's Republic of China
| | - Mengxue Zhang
- School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai 200433, People's Republic of China
- College of Food Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, People's Republic of China
| | - Hongji Li
- School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai 200433, People's Republic of China
| | - Hai Yu
- School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai 200433, People's Republic of China
| | - Shuo Chen
- School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai 200433, People's Republic of China
- College of Food Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, People's Republic of China
| | - Wenhui Wu
- College of Food Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, People's Republic of China
| | - Peng Sun
- School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai 200433, People's Republic of China
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28
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Lu J, Li Y, Bai Z, Lv H, Wang H. Enzymatic macrocyclization of ribosomally synthesized and posttranslational modified peptides via C-S and C-C bond formation. Nat Prod Rep 2021; 38:981-992. [PMID: 33185226 DOI: 10.1039/d0np00044b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 2000 to 2020 Ribosomally synthesized and posttranslational modified peptides (RiPPs) are a rapidly growing class of bioactive natural products. Many members of RiPPs contain macrocyclic structural units constructed by modification enzymes through macrocyclization of linear precursor peptides. In this study, we summarize recent progress in the macrocyclization of RiPPs by C-S and C-C bond formation with a focus on the current understanding of the enzymatic mechanisms.
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Affiliation(s)
- Jingxia Lu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
| | - Yuqing Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
| | - Zengbing Bai
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
| | - Hongmei Lv
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
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29
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Zou Y, Yang S, Sanders JN, Li W, Yu P, Wang H, Tang Z, Liu W, Houk KN. Computational Investigation of the Mechanism of Diels-Alderase PyrI4. J Am Chem Soc 2020; 142:20232-20239. [PMID: 33190496 DOI: 10.1021/jacs.0c10813] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We studied the mechanisms of activation and stereoselectivity of a monofunctional Diels-Alderase (PyrI4)-catalyzed intramolecular Diels-Alder reaction that leads to formation of the key spiro-tetramate moiety in the biosynthesis of the pyrroindomycin family of natural products. Key activation effects of PyrI4 include acid catalysis and an induced-fit mechanism that cooperate with the unique "lid" feature of PyrI4 to stabilize the Diels-Alder transition state. PyrI4 enhances the intrinsic Diels-Alder stereoselectivity of the substrate and leads to stereospecific formation of the product.
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Affiliation(s)
- Yike Zou
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Song Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Wei Li
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Peiyuan Yu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Hongbo Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Zhijun Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
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30
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Abstract
An ongoing challenge in chemical research is to design catalysts that select the outcomes of the reactions of complex molecules. Chemists rely on organo- or transition metal catalysts to control stereo-, regio-, and periselectivity (selectivity among possible pericyclic reactions). Nature achieves these types of selectivity with a variety of enzymes such as the recently discovered pericyclases – a family of enzymes that catalyze pericyclic reactions.1 To date, the majority of characterized enzymatic pericyclic reactions are cycloadditions and it has been difficult to rationalize how observed selectivities are achieved.2-13 We report here the discovery of two homologous groups of pericyclases that catalyze distinct reactions: one group catalyzes an Alder-ene reaction, previously unknown in biology; the second catalyzes a stereoselective hetero-Diels–Alder reaction. Guided by computational studies, we rationalized the observed differences in reactivities and designed mutants that reverse periselectivities from Alder-ene to hetero-Diels–Alder and vice versa. A combination of in vitro biochemical characterizations, computational studies, enzyme co-crystal structures, and mutational studies provide a picture of how high regio- and periselectivities are achieved in nearly identical active sites.
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31
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The biosynthetic pathway to tetromadurin (SF2487/A80577), a polyether tetronate antibiotic. PLoS One 2020; 15:e0239054. [PMID: 32925967 PMCID: PMC7489565 DOI: 10.1371/journal.pone.0239054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/30/2020] [Indexed: 12/03/2022] Open
Abstract
The type I polyketide SF2487/A80577 (herein referred to as tetromadurin) is a polyether tetronate ionophore antibiotic produced by the terrestrial Gram-positive bacterium Actinomadura verrucosospora. Tetromadurin is closely related to the polyether tetronates tetronasin (M139603) and tetronomycin, all of which are characterised by containing a tetronate, cyclohexane, tetrahydropyran, and at least one tetrahydrofuran ring. We have sequenced the genome of Actinomadura verrucosospora to identify the biosynthetic gene cluster responsible for tetromadurin biosynthesis (the mad gene cluster). Based on bioinformatic analysis of the 32 genes present within the cluster a plausible biosynthetic pathway for tetromadurin biosynthesis is proposed. Functional confirmation of the mad gene cluster is obtained by performing in-frame deletions in each of the genes mad10 and mad31, which encode putative cyclase enzymes responsible for cyclohexane and tetrahydropyran formation, respectively. Furthermore, the A. verrucosospora Δmad10 mutant produces a novel tetromadurin metabolite that according to mass spectrometry analysis is analogous to the recently characterised partially cyclised tetronasin intermediate lacking its cyclohexane and tetrahydropyran rings. Our results therefore elucidate the biosynthetic machinery of tetromadurin biosynthesis and lend support for a conserved mechanism of cyclohexane and tetrahydropyran biosynthesis across polyether tetronates.
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32
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Clinger JA, Wang X, Cai W, Zhu Y, Miller MD, Zhan CG, Van Lanen SG, Thorson JS, Phillips GN. The crystal structure of AbsH3: A putative flavin adenine dinucleotide-dependent reductase in the abyssomicin biosynthesis pathway. Proteins 2020; 89:132-137. [PMID: 32852843 DOI: 10.1002/prot.25994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/01/2020] [Accepted: 07/26/2020] [Indexed: 11/06/2022]
Abstract
Natural products and natural product-derived compounds have been widely used for pharmaceuticals for many years, and the search for new natural products that may have interesting activity is ongoing. Abyssomicins are natural product molecules that have antibiotic activity via inhibition of the folate synthesis pathway in microbiota. These compounds also appear to undergo a required [4 + 2] cycloaddition in their biosynthetic pathway. Here we report the structure of an flavin adenine dinucleotide-dependent reductase, AbsH3, from the biosynthetic gene cluster of novel abyssomicins found in Streptomyces sp. LC-6-2.
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Affiliation(s)
| | - Xiachang Wang
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Wenlong Cai
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Yanyan Zhu
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | | | - Chang-Guo Zhan
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Steven G Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Jon S Thorson
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas, USA.,Department of Chemistry, Rice University, Houston, Texas, USA
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33
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Li Y, Zhang J, Zheng J, Guan H, Liu W, Tan H. Co-expression of a SARP Family Activator ChlF2 and a Type II Thioesterase ChlK Led to High Production of Chlorothricin in Streptomyces antibioticus DSM 40725. Front Bioeng Biotechnol 2020; 8:1013. [PMID: 32974326 PMCID: PMC7471628 DOI: 10.3389/fbioe.2020.01013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/03/2020] [Indexed: 11/20/2022] Open
Abstract
Chlorothricin (CHL), produced by Streptomyces antibioticus DSM 40725 (wild-type strain, WT), belongs to a growing family of spirotetronate antibiotics that have biological activities inhibiting pyruvate carboxylase and malate dehydrogenase. ChlF2, a cluster-situated SARP regulator, can activate the transcription of chlJ, chlC3, chlC6, chlE1, chlM, and chlL to control CHL biosynthesis. Co-expression of chlF2 and chlK encoding type II thioesterase in WT strain under the control of Pkan led to high production of chlorothricin by 840% in comparison with that of WT. Since the inhibitory activity of CHL against several Gram-positive bacteria is higher than des-CHL, combinatorial strategies were applied to promote the conversion of des-CHL to CHL. Over-expression of chlB4, encoding a halogenase, combining with the supplementation of sodium chloride led to further 41% increase of CHL production compared to that of F2OE, a chlF2 over-expression strain. These findings provide new insights into the fine-tuned regulation of spirotetronate family of antibiotics and the construction of high-yield engineered strains.
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Affiliation(s)
- Yue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiazhen Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hanye Guan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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34
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Li Q, Ding W, Tu J, Chi C, Huang H, Ji X, Yao Z, Ma M, Ju J. Nonspecific Heme-Binding Cyclase, AbmU, Catalyzes [4 + 2] Cycloaddition during Neoabyssomicin Biosynthesis. ACS OMEGA 2020; 5:20548-20557. [PMID: 32832808 PMCID: PMC7439702 DOI: 10.1021/acsomega.0c02776] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/27/2020] [Indexed: 05/05/2023]
Abstract
Diels-Alder (DA) [4 + 2]-cycloaddition reactions rank among the most powerful transformations in synthetic organic chemistry; biosynthetic examples, however, are few and far between. We report here a heme-binding cyclase, AbmU, that catalyzes an essential [4 + 2] cycloaddition during neoabyssomicin scaffold assembly. In vivo genetic and in vitro biochemical analyses strongly suggest that AbmU catalyzes an intramolecular and stereoselective [4 + 2] cycloaddition to form a spirotetronate skeleton from an acyclic substrate featuring both a terminal 1,3-diene and an exo-methylene group. Biochemical assays and X-ray diffraction analyses reveal that AbmU binds nonspecifically to a heme b cofactor and that this association does not play a catalytic role in AbmU catalysis. A detailed study of the AbmU crystal structure reveals a unique mode of substrate binding and reaction catalysis; His160 forms a H-bond with the C-1 carbonyl O-atom of the acyclic substrate, and the imidazole of the same amino acid directs the tetronate moiety of acyclic substrate toward the terminal Δ10,11, Δ12,13-diene moiety, thereby facilitating intramolecular DA chemistry. Our findings expand upon what is known about mechanistic diversities available to biosynthetic [4 + 2] cyclases and help to lay the foundation for the use of AbmU in possible industrial applications.
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Affiliation(s)
- Qinglian Li
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia
Medica, RNAM Center for Marine Microbiology, South China Sea Institute
of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Wenjuan Ding
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia
Medica, RNAM Center for Marine Microbiology, South China Sea Institute
of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- College
of Oceanology, University of Chinese Academy
of Sciences, 19 Yuquan
Road, Beijing 100049, China
| | - Jiajia Tu
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia
Medica, RNAM Center for Marine Microbiology, South China Sea Institute
of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Changbiao Chi
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Hongbo Huang
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia
Medica, RNAM Center for Marine Microbiology, South China Sea Institute
of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Xiaoqi Ji
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia
Medica, RNAM Center for Marine Microbiology, South China Sea Institute
of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- College
of Oceanology, University of Chinese Academy
of Sciences, 19 Yuquan
Road, Beijing 100049, China
| | - Ziwei Yao
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia
Medica, RNAM Center for Marine Microbiology, South China Sea Institute
of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- College
of Oceanology, University of Chinese Academy
of Sciences, 19 Yuquan
Road, Beijing 100049, China
| | - Ming Ma
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Jianhua Ju
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia
Medica, RNAM Center for Marine Microbiology, South China Sea Institute
of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- College
of Oceanology, University of Chinese Academy
of Sciences, 19 Yuquan
Road, Beijing 100049, China
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35
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Gao L, Su C, Du X, Wang R, Chen S, Zhou Y, Liu C, Liu X, Tian R, Zhang L, Xie K, Chen S, Guo Q, Guo L, Hano Y, Shimazaki M, Minami A, Oikawa H, Huang N, Houk KN, Huang L, Dai J, Lei X. FAD-dependent enzyme-catalysed intermolecular [4+2] cycloaddition in natural product biosynthesis. Nat Chem 2020; 12:620-628. [DOI: 10.1038/s41557-020-0467-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/14/2020] [Indexed: 01/21/2023]
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36
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Fraley AE, Sherman DH. Enzyme evolution in fungal indole alkaloid biosynthesis. FEBS J 2020; 287:1381-1402. [PMID: 32118354 PMCID: PMC7317620 DOI: 10.1111/febs.15270] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/24/2019] [Accepted: 02/27/2020] [Indexed: 12/28/2022]
Abstract
The class of fungal indole alkaloids containing the bicyclo[2.2.2]diazaoctane ring is comprised of diverse molecules that display a range of biological activities. While much interest has been garnered due to their therapeutic potential, this class of molecules also displays unique chemical functionality, making them intriguing synthetic targets. Many elegant and intricate total syntheses have been developed to generate these alkaloids, but the selectivity required to produce them in high yield presents great barriers. Alternatively, if we can understand the molecular mechanisms behind how fungi make these complex molecules, we can leverage the power of nature to perform these chemical transformations. Here, we describe the various studies regarding the evolutionary development of enzymes involved in fungal indole alkaloid biosynthesis.
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Affiliation(s)
- Amy E. Fraley
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, United States
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37
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Tan B, Chen S, Zhang Q, Chen Y, Zhu Y, Khan I, Zhang W, Zhang C. Heterologous Expression Leads to Discovery of Diversified Lobophorin Analogues and a Flexible Glycosyltransferase. Org Lett 2020; 22:1062-1066. [PMID: 31971807 DOI: 10.1021/acs.orglett.9b04597] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Bin Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Institution of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siqiang Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Institution of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Institution of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Yuchan Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Guangzhou 510070, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Institution of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Imran Khan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Institution of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Guangzhou 510070, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Institution of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
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38
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Han WB, Wang GY, Tang JJ, Wang WJ, Liu H, Gil RR, Navarro-Vázquez A, Lei X, Gao JM. Herpotrichones A and B, Two Intermolecular [4 + 2] Adducts with Anti-Neuroinflammatory Activity from a Herpotrichia Species. Org Lett 2019; 22:405-409. [DOI: 10.1021/acs.orglett.9b04099] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wen-Bo Han
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
| | - Guang-Yi Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
| | - Jiang-Jiang Tang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
| | - Wen-Ji Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
| | - Han Liu
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, Hubei 430074, People’s Republic of China
| | - Roberto R. Gil
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Avenida Professor Moraes Rego, 1235, Cidade Universitária, Recife, Pernambuco 50670-901, Brazil
| | - Xinxiang Lei
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, Hubei 430074, People’s Republic of China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
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39
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Jamieson CS, Ohashi M, Liu F, Tang Y, Houk KN. The expanding world of biosynthetic pericyclases: cooperation of experiment and theory for discovery. Nat Prod Rep 2019; 36:698-713. [PMID: 30311924 DOI: 10.1039/c8np00075a] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: 2000 to 2018 Pericyclic reactions are a distinct class of reactions that have wide synthetic utility. Before the recent discoveries described in this review, enzyme-catalyzed pericyclic reactions were not widely known to be involved in biosynthesis. This situation is changing rapidly. We define the scope of pericyclic reactions, give a historical account of their discoveries as biosynthetic reactions, and provide evidence that there are many enzymes in nature that catalyze pericyclic reactions. These enzymes, the "pericyclases," are the subject of this review.
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Affiliation(s)
- Cooper S Jamieson
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA.
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40
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Dan Q, Newmister SA, Klas KR, Fraley AE, McAfoos TJ, Somoza AD, Sunderhaus JD, Ye Y, Shende VV, Yu F, Sanders JN, Brown WC, Zhao L, Paton RS, Houk KN, Smith JL, Sherman DH, Williams RM. Fungal indole alkaloid biogenesis through evolution of a bifunctional reductase/Diels-Alderase. Nat Chem 2019; 11:972-980. [PMID: 31548667 PMCID: PMC6815239 DOI: 10.1038/s41557-019-0326-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 08/05/2019] [Indexed: 12/25/2022]
Abstract
Prenylated indole alkaloids such as the calmodulin-inhibitory malbrancheamides and anthelmintic paraherquamides possess great structural diversity and pharmaceutical utility. Here, we report complete elucidation of the malbrancheamide biosynthetic pathway accomplished through complementary approaches. These include a biomimetic total synthesis to access the natural alkaloid and biosynthetic intermediates in racemic form and in vitro enzymatic reconstitution to provide access to the natural antipode (+)-malbrancheamide. Reductive cleavage of an L-Pro-L-Trp dipeptide from the MalG non-ribosomal peptide synthetase (NRPS) followed by reverse prenylation and a cascade of post-NRPS reactions culminates in an intramolecular [4+2] hetero-Diels-Alder (IMDA) cyclization to furnish the bicyclo[2.2.2]diazaoctane scaffold. Enzymatic assembly of optically pure (+)-premalbrancheamide involves an unexpected zwitterionic intermediate where MalC catalyses enantioselective cycloaddition as a bifunctional NADPH-dependent reductase/Diels-Alderase. The crystal structures of substrate and product complexes together with site-directed mutagenesis and molecular dynamics simulations demonstrate how MalC and PhqE (its homologue from the paraherquamide pathway) catalyse diastereo- and enantioselective cyclization in the construction of this important class of secondary metabolites.
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Affiliation(s)
- Qingyun Dan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Sean A Newmister
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Kimberly R Klas
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Amy E Fraley
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Timothy J McAfoos
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Amber D Somoza
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - James D Sunderhaus
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Ying Ye
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Vikram V Shende
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Fengan Yu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - W Clay Brown
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Le Zhao
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Robert S Paton
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Robert M Williams
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
- University of Colorado Cancer Center, Aurora, CO, USA.
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41
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Little R, Paiva FCR, Jenkins R, Hong H, Sun Y, Demydchuk Y, Samborskyy M, Tosin M, Leeper FJ, Dias MVB, Leadlay PF. Unexpected enzyme-catalysed [4+2] cycloaddition and rearrangement in polyether antibiotic biosynthesis. Nat Catal 2019. [DOI: 10.1038/s41929-019-0351-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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42
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Chen Q, Gao J, Jamieson C, Liu J, Ohashi M, Bai J, Yan D, Liu B, Che Y, Wang Y, Houk KN, Hu Y. Enzymatic Intermolecular Hetero-Diels-Alder Reaction in the Biosynthesis of Tropolonic Sesquiterpenes. J Am Chem Soc 2019; 141:14052-14056. [PMID: 31461283 PMCID: PMC6944466 DOI: 10.1021/jacs.9b06592] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Diels-Alder reactions are among the most powerful synthetic transformations to construct complex natural products. Despite that increasing of enzymatic intramolecular Diels-Alder reactions have been discovered, natural intermolecular Diels-Alderases are rarely described. Here, we report an intermolecular hetero-Diels-Alder reaction in the biosynthesis of tropolonic sesquiterpenes and functionally characterize EupfF as the first fungal intermolecular hetero-Diels-Alderase. We demonstrate that EupfF catalyzed the dehydration of a hydroxymethyl-containing tropolone (5) to generate a reactive tropolone o-quinone methide (6) and might further stereoselectively control the subsequent intermolecular hetero-Diels-Alder reaction with (1E,4E,8Z)-humulenol (8) to produce enantiomerically pure neosetophomone B (1). Our results reveal the biosynthetic pathway of 1 and expand the repertoire of activities of Diels-Alder cyclases.
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Affiliation(s)
- Qibin Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
| | - Jie Gao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
| | - Cooper Jamieson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Jiawang Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
| | - Masao Ohashi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
| | - Jian Bai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
| | - Daojian Yan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
| | - Bingyu Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
| | - Yongsheng Che
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
| | - Yanan Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Youcai Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
- NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
- CAMS Key Laboratory of Enzyme and Catalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
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43
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Yi X, Zhao Q, Tian Z, Jia X, Cao W, Liu W, He Q. Insights into the Functionalization of the Methylsalicyclic Moiety during the Biosynthesis of Chlorothricin by Comparative Kinetic Assays of the Activities of Two KAS III‐like Acyltransferases. CHINESE J CHEM 2019. [DOI: 10.1002/cjoc.201900134] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xuan Yi
- Department of Chemistry, Innovative Drug Research CenterShanghai University 99 Shangda Road, Shanghai 200444 China
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
| | - Qunfei Zhao
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
| | - Zhenhua Tian
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
| | - Xinying Jia
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
| | - Weiguo Cao
- Department of Chemistry, Innovative Drug Research CenterShanghai University 99 Shangda Road, Shanghai 200444 China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
- Huzhou Center of Bio‐Synthetic Innovation 1366 Hongfeng Road, Huzhou, Zhejiang 313000 China
| | - Qing‐Li He
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine 1200 Cai Lun Road, Shanghai 201203 China
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44
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Abstract
Bacterial natural products display astounding structural diversity, which, in turn, endows them with a remarkable range of biological activities that are of significant value to modern society. Such structural features are generated by biosynthetic enzymes that construct core scaffolds or perform peripheral modifications, and can thus define natural product families, introduce pharmacophores and permit metabolic diversification. Modern genomics approaches have greatly enhanced our ability to access and characterize natural product pathways via sequence-similarity-based bioinformatics discovery strategies. However, many biosynthetic enzymes catalyse exceptional, unprecedented transformations that continue to defy functional prediction and remain hidden from us in bacterial (meta)genomic sequence data. In this Review, we highlight exciting examples of unusual enzymology that have been uncovered recently in the context of natural product biosynthesis. These suggest that much of the natural product diversity, including entire substance classes, awaits discovery. New approaches to lift the veil on the cryptic chemistries of the natural product universe are also discussed.
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45
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Zhong W, Wang J, Wei X, Fu T, Chen Y, Zeng Q, Huang Z, Huang X, Zhang W, Zhang S, Long L, Wang F. Three Pairs of New Spirocyclic Alkaloid Enantiomers From the Marine-Derived Fungus Eurotium sp. SCSIO F452. Front Chem 2019; 7:350. [PMID: 31165062 PMCID: PMC6536037 DOI: 10.3389/fchem.2019.00350] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 04/29/2019] [Indexed: 11/13/2022] Open
Abstract
Three pairs of new spirocyclic alkaloid enantiomers eurotinoids A-C (1-3), as well as a known biogenetically related racemate dihydrocryptoechinulin D (4) were isolated from a marine-derived fungus Eurotium sp. SCSIO F452. Their structures were determined by spectroscopic analyses and electronic circular dichroism (ECD) calculations. Compounds 1 and 2 represent the first two "meta" products from a non-stereoselective [4 + 2] Diels-Alder cycloaddition presumably between an enone group of a diketopiperazine alkaloid and a diene group of a benzaldehyde derivative via a new head-to-tail coupling mode biosynthetically, while 3 and 4 were "ortho" products. Their enantiomers exhibited different antioxidative and cytotoxic activities. The modes of action were investigated by a preliminary molecular docking study.
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Affiliation(s)
- Weimao Zhong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Junfeng Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaoyi Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Tingdan Fu
- Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuchan Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Qi Zeng
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhonghui Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xinan Huang
- Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Lijuan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Fazuo Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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46
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Abstract
Enzyme-mediated cascade reactions are widespread in biosynthesis. To facilitate comparison with the mechanistic categorizations of cascade reactions by synthetic chemists and delineate the common underlying chemistry, we discuss four types of enzymatic cascade reactions: those involving nucleophilic, electrophilic, pericyclic, and radical reactions. Two subtypes of enzymes that generate radical cascades exist at opposite ends of the oxygen abundance spectrum. Iron-based enzymes use O2 to generate high valent iron-oxo species to homolyze unactivated C-H bonds in substrates to initiate skeletal rearrangements. At anaerobic end, enzymes reversibly cleave S-adenosylmethionine (SAM) to generate the 5'-deoxyadenosyl radical as a powerful oxidant to initiate C-H bond homolysis in bound substrates. The latter enzymes are termed radical SAM enzymes. We categorize the former as "thwarted oxygenases".
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Affiliation(s)
- Christopher T Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (CheM-H), Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
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47
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Chang M, Zhou Y, Wang H, Liu Z, Zhang Y, Feng Y. Crystal structure of the multifunctional SAM-dependent enzyme LepI provides insights into its catalytic mechanism. Biochem Biophys Res Commun 2019; 515:255-260. [PMID: 31101338 DOI: 10.1016/j.bbrc.2019.05.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 05/03/2019] [Indexed: 01/13/2023]
Abstract
Pericyclic reactions are among the most powerful synthetic transformations widely applied in the synthesis of multiple regioselective and stereoselective carbon-carbon bonds. LepI is a recently identified S-adenosyl-l-methionine (SAM)-dependent enzyme, which could catalyze dehydration, Diels-Alder reaction, and the retro-Claisen rearrangement reactions. However, the mechanism underlying these reactions by LepI remains elusive. Here we report the structure of LepI in complex with SAM as its co-factor, which adopts a typical class I methyltransferase fold. Docking studies are performed to investigate the binding modes of various substrates/products and provide insights into the catalytic mechanism of the multiple reactions catalyzed by LepI. Our study suggests that the dehydration reaction may start from the deprotonation of the hydroxyl group on the pyridone ring of the substrate by LepIH133, during which R295 and D296 play important roles in substrate binding and stabilizing the reaction intermediate. The stereoselective dehydration is accomplished through the trans-conformer of the leaving alcohol group which is trapped by nearby residues. The pericyclic reactions following dehydration are facilitated by the hydrophobic and hydrophilic interactions in the binding pocket. H133 and R295, two residues not conserved in other methyltransferases, might account for the unique activity of LepI among the SAM-dependent methyltransferase family. Together, this study provides important structural insights into the unique reactions catalyzed by LepI and will shed light on the knowledge of mechanisms of pericyclic reactions.
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Affiliation(s)
- Min Chang
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Yu Zhou
- National Institute of Biological Sciences, Beijing, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, PR China
| | - Hao Wang
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Zihe Liu
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Yi Zhang
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Yue Feng
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China.
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Zhang Z, Jamieson CS, Zhao YL, Li D, Ohashi M, Houk KN, Tang Y. Enzyme-Catalyzed Inverse-Electron Demand Diels-Alder Reaction in the Biosynthesis of Antifungal Ilicicolin H. J Am Chem Soc 2019; 141:5659-5663. [PMID: 30905148 DOI: 10.1021/jacs.9b02204] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The pericyclases are a growing superfamily of enzymes that catalyze pericyclic reactions. We report a pericyclase IccD catalyzing an inverse-electron demand Diels-Alder (IEDDA) reaction with a rate acceleration of 3 × 105-fold in the biosynthesis of fungal natural product ilicicolin H. We demonstrate IccD is highly periselective toward the IEDDA cycloaddition over a competing normal electron demand Diels-Alder (NEDDA) reaction from an ambimodal transition state. A predicted flavoenzyme IccE was identified to epimerize the IEDDA product 8- epi-ilicicolin H to ilicicolin H, a step that is critical for the observed antifungal activity of ilicicolin H. Our results reveal the ilicicolin H biosynthetic pathway and add to the collection of pericyclic reactions that are catalyzed by pericyclases.
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Affiliation(s)
| | | | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, MOE-LSB and MOE-LSC, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology , Ocean University of China , Qingdao 266003 , China
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49
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Enzyme-catalysed [6+4] cycloadditions in the biosynthesis of natural products. Nature 2019; 568:122-126. [PMID: 30867595 DOI: 10.1038/s41586-019-1021-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/07/2019] [Indexed: 01/01/2023]
Abstract
Pericyclic reactions are powerful transformations for the construction of carbon-carbon and carbon-heteroatom bonds in organic synthesis. Their role in biosynthesis is increasingly apparent, and mechanisms by which pericyclases can catalyse reactions are of major interest1. [4+2] cycloadditions (Diels-Alder reactions) have been widely used in organic synthesis2 for the formation of six-membered rings and are now well-established in biosynthesis3-6. [6+4] and other 'higher-order' cycloadditions were predicted7 in 1965, and are now increasingly common in the laboratory despite challenges arising from the generation of a highly strained ten-membered ring system8,9. However, although enzyme-catalysed [6+4] cycloadditions have been proposed10-12, they have not been proven to occur. Here we demonstrate a group of enzymes that catalyse a pericyclic [6+4] cycloaddition, which is a crucial step in the biosynthesis of streptoseomycin-type natural products. This type of pericyclase catalyses [6+4] and [4+2] cycloadditions through a single ambimodal transition state, which is consistent with previous proposals11,12. The [6+4] product is transformed to a less stable [4+2] adduct via a facile Cope rearrangement, and the [4+2] adduct is converted into the natural product enzymatically. Crystal structures of three pericyclases, computational simulations of potential energies and molecular dynamics, and site-directed mutagenesis establish the mechanism of this transformation. This work shows how enzymes are able to catalyse concerted pericyclic reactions involving ambimodal transition states.
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50
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Lichman BR, O'Connor SE, Kries H. Biocatalytic Strategies towards [4+2] Cycloadditions. Chemistry 2019; 25:6864-6877. [DOI: 10.1002/chem.201805412] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/17/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Benjamin R. Lichman
- Department of Biological Chemistry; The John Innes Centre; Colney Lane Norwich UK
- Current address: Department of Biology; University of York; York YO10 5YW UK
| | - Sarah E. O'Connor
- Department of Biological Chemistry; The John Innes Centre; Colney Lane Norwich UK
| | - Hajo Kries
- Independent Junior Research Group, Biosynthetic Design of Natural Products; Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI Jena); Beutenbergstr. 11a 07745 Jena Germany
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