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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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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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3
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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: 14] [Impact Index Per Article: 7.0] [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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4
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Lees NR, Han LC, Byrne MJ, Davies JA, Parnell AE, Moreland PEJ, Stach JEM, van der Kamp MW, Willis CL, Race PR. An Esterase-like Lyase Catalyzes Acetate Elimination in Spirotetronate/Spirotetramate Biosynthesis. Angew Chem Int Ed Engl 2019; 58:2305-2309. [PMID: 30664319 DOI: 10.1002/anie.201812105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Indexed: 11/09/2022]
Abstract
Spirotetronate and spirotetramate natural products include a multitude of compounds with potent antimicrobial and antitumor activities. Their biosynthesis incorporates many unusual biocatalytic steps, including regio- and stereo-specific modifications, cyclizations promoted by Diels-Alderases, and acetylation-elimination reactions. Here we focus on the acetate elimination catalyzed by AbyA5, implicated in the formation of the key Diels-Alder substrate to give the spirocyclic system of the antibiotic abyssomicin C. Using synthetic substrate analogues, it is shown that AbyA5 catalyzes stereospecific acetate elimination, establishing the (R)-tetronate acetate as a biosynthetic intermediate. The X-ray crystal structure of AbyA5, the first of an acetate-eliminating enzyme, reveals a deviant acetyl esterase fold. Molecular dynamics simulations and enzyme assays show the use of a His-Ser dyad to catalyze either elimination or hydrolysis, via disparate mechanisms, under substrate control.
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Affiliation(s)
- Nicholas R Lees
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol, BS8 1TQ, UK
| | - Li-Chen Han
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol, BS8 1TQ, UK
| | - Matthew J Byrne
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol, BS8 1TQ, UK
| | - Jonathan A Davies
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol, BS8 1TQ, UK
| | - Alice E Parnell
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol, BS8 1TQ, UK
| | - Pollyanna E J Moreland
- School of Biology, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.,Centre for Synthetic Biology and the Bioeconomy, Newcastle-upon-Tyne, NE2 4AX, UK
| | - James E M Stach
- School of Biology, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.,Centre for Synthetic Biology and the Bioeconomy, Newcastle-upon-Tyne, NE2 4AX, UK
| | - Marc W van der Kamp
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol, BS8 1TQ, UK
| | - Christine L Willis
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol, BS8 1TQ, UK
| | - Paul R Race
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol, BS8 1TQ, UK
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5
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Lees NR, Han LC, Byrne MJ, Davies JA, Parnell AE, Moreland PEJ, Stach JEM, van der Kamp MW, Willis CL, Race PR. An Esterase-like Lyase Catalyzes Acetate Elimination in Spirotetronate/Spirotetramate Biosynthesis. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Nicholas R. Lees
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
- BrisSynBio Synthetic Biology Research Centre; University of Bristol; Bristol BS8 1TQ UK
| | - Li-Chen Han
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
- BrisSynBio Synthetic Biology Research Centre; University of Bristol; Bristol BS8 1TQ UK
| | - Matthew J. Byrne
- School of Biochemistry; University of Bristol; Bristol BS8 1TD UK
- BrisSynBio Synthetic Biology Research Centre; University of Bristol; Bristol BS8 1TQ UK
| | - Jonathan A. Davies
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
- BrisSynBio Synthetic Biology Research Centre; University of Bristol; Bristol BS8 1TQ UK
| | - Alice E. Parnell
- School of Biochemistry; University of Bristol; Bristol BS8 1TD UK
- BrisSynBio Synthetic Biology Research Centre; University of Bristol; Bristol BS8 1TQ UK
| | - Pollyanna E. J. Moreland
- School of Biology; Newcastle University; Newcastle-upon-Tyne NE1 7RU UK
- Centre for Synthetic Biology and the Bioeconomy; Newcastle-upon-Tyne NE2 4AX UK
| | - James E. M. Stach
- School of Biology; Newcastle University; Newcastle-upon-Tyne NE1 7RU UK
- Centre for Synthetic Biology and the Bioeconomy; Newcastle-upon-Tyne NE2 4AX UK
| | - Marc W. van der Kamp
- School of Biochemistry; University of Bristol; Bristol BS8 1TD UK
- BrisSynBio Synthetic Biology Research Centre; University of Bristol; Bristol BS8 1TQ UK
| | - Christine L. Willis
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
- BrisSynBio Synthetic Biology Research Centre; University of Bristol; Bristol BS8 1TQ UK
| | - Paul R. Race
- School of Biochemistry; University of Bristol; Bristol BS8 1TD UK
- BrisSynBio Synthetic Biology Research Centre; University of Bristol; Bristol BS8 1TQ UK
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6
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Zheng K, Hong R. Stereoconfining macrocyclizations in the total synthesis of natural products. Nat Prod Rep 2019; 36:1546-1575. [DOI: 10.1039/c8np00094h] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This review covers selected examples of point chirality-forming macrocyclizations in natural product total synthesis in the past three decades.
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Affiliation(s)
- Kuan Zheng
- Key Laboratory of Synthetic Chemistry of Natural Substances
- Center for Excellence in Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
| | - Ran Hong
- Key Laboratory of Synthetic Chemistry of Natural Substances
- Center for Excellence in Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
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7
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Zheng Q, Gong Y, Guo Y, Zhao Z, Wu Z, Zhou Z, Chen D, Pan L, Liu W. Structural Insights into a Flavin-Dependent [4 + 2] Cyclase that Catalyzes trans-Decalin Formation in Pyrroindomycin Biosynthesis. Cell Chem Biol 2018; 25:718-727.e3. [DOI: 10.1016/j.chembiol.2018.03.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/28/2018] [Accepted: 03/12/2018] [Indexed: 12/13/2022]
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8
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Zheng Q, Fang H, Liu W. Post-translational modifications involved in the biosynthesis of thiopeptide antibiotics. Org Biomol Chem 2018; 15:3376-3390. [PMID: 28358161 DOI: 10.1039/c7ob00466d] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thiopeptide antibiotics are a class of typical ribosomally synthesized and post-translationally modified peptides (RiPPs) with complex chemical structures that are difficult to construct via chemical synthesis. To date, more than 100 thiopeptides have been discovered, and most of these compounds exhibit remarkable biological activities, such as antibacterial, antitumor and immunosuppressive activities. Therefore, studies of the biosynthesis of thiopeptides can contribute to the development of new drug leads and facilitate the understanding of the complex post-translational modifications (PTMs) of peptides and/or proteins. Since the biosynthetic gene clusters of thiopeptides were first discovered in 2009, several research studies regarding the biochemistry and enzymology of thiopeptide biosyntheses have been reported, indicating that their characteristic framework is constructed via a cascade of common PTMs and that additional specific PTMs diversify the molecules. In this review, we primarily summarize recent advances in understanding the biosynthesis of thiopeptide antibiotics and propose some potential applications based on our insights into the biosynthetic logic and machinery.
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Affiliation(s)
- Qingfei Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
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9
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Lv JM, Hu D, Gao H, Kushiro T, Awakawa T, Chen GD, Wang CX, Abe I, Yao XS. Biosynthesis of helvolic acid and identification of an unusual C-4-demethylation process distinct from sterol biosynthesis. Nat Commun 2017; 8:1644. [PMID: 29158519 PMCID: PMC5696383 DOI: 10.1038/s41467-017-01813-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 10/18/2017] [Indexed: 12/22/2022] Open
Abstract
Fusidane-type antibiotics represented by helvolic acid, fusidic acid and cephalosporin P1 are a class of bacteriostatic agents, which have drawn renewed attention because they have no cross-resistance to commonly used antibiotics. However, their biosynthesis is poorly understood. Here, we perform a stepwise introduction of the nine genes from the proposed gene cluster for helvolic acid into Aspergillus oryzae NSAR1, which enables us to isolate helvolic acid (~20 mg L-1) and its 21 derivatives. Anti-Staphylococcus aureus assay reveals that the antibacterial activity of three intermediates is even stronger than that of helvolic acid. Notably, we observe an unusual C-4 demethylation process mediated by a promiscuous short-chain dehydrogenase/reductase (HelC) and a cytochrome P450 enzyme (HelB1), which is distinct from the common sterol biosynthesis. These studies have set the stage for using biosynthetic approaches to expand chemical diversity of fusidane-type antibiotics.
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Affiliation(s)
- Jian-Ming Lv
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Hao Gao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou, 510632, People's Republic of China.
| | - Tetsuo Kushiro
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Guo-Dong Chen
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Chuan-Xi Wang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Xin-Sheng Yao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou, 510632, People's Republic of China.
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