1
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Zhu J, Liu S, Dai L, Yu F, Zhou T, Chen J, Xu J, Yu B, Tang S, Liu Q, Yang XL, Han XL. Elucidating the interaction between equisetin and human serum albumin: A comprehensive study using spectroscopy, microcalorimetry and molecular docking approaches. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123409. [PMID: 37729815 DOI: 10.1016/j.saa.2023.123409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/28/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
Equisetin, a bioactive compound of marine origin, offers compelling inhibitory properties against HIV-1 transcriptase. To gain comprehensive insights into the interaction of Equisetin with human serum albumin (HSA), we utilized a multipronged approach involving spectroscopy, isothermal titration calorimetry (ITC) and molecular docking. Our fluorescence analyses confirmed that the interaction between Equisetin and HSA results in a significant quenching of HSA's fluorescence, primarily achieved through a dynamic mechanism aided by hydrogen bonding and van der Waals forces. Isothermal titration calorimetry (ITC) measurements revealed an impressive binding affinity of Equisetin for HSA, quantified to be 4.3 × 107 mol L-1. Molecular docking studies illustrated that Equisetin binds at site III of HSA, with specific amino acid residues, GLN-104 and LYS-106, playing a pivotal role. Further, our study discovered that the interaction induces slight unfolding of HSA's polypeptide chain and significant alterations in its secondary structure, thereby triggering the exposure of previously concealed hydrophobic regions. This comprehensive study enhances our understanding of Equisetin's interaction with serum proteins, potentially influencing its pharmacokinetics and pharmacodynamics, and opening avenues for future research and therapeutic applications.
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Affiliation(s)
- Jiahua Zhu
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, School of Chemistry and Materials Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Shuzhi Liu
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, PR China
| | - Le Dai
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, School of Chemistry and Materials Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Fan Yu
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, School of Chemistry and Materials Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Tao Zhou
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, School of Chemistry and Materials Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Jiang Chen
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, School of Chemistry and Materials Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Jianming Xu
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, School of Chemistry and Materials Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Boren Yu
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, School of Chemistry and Materials Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Shuoya Tang
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, School of Chemistry and Materials Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Qingpei Liu
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, PR China
| | - Xiao-Long Yang
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, PR China
| | - Xiao-Le Han
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, School of Chemistry and Materials Science, South-Central Minzu University, Wuhan 430074, PR China.
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2
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Ju Z, Li Z, Li M, Xu S, Kaliaperumal K, Chen FE. A Chemo-Enzymatic Approach for Preparing Efinaconazole with High Optical Yield. J Org Chem 2023; 88:14803-14808. [PMID: 37792295 DOI: 10.1021/acs.joc.3c01641] [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: 10/05/2023]
Abstract
Herein, we present a novel and ecofriendly biocatalytic approach for synthesizing efinaconazole (7), a clinically used antifungal agent. This method involves utilizing benzaldehyde lyase (BAL) to catalyze the crucial benzoin condensation step in the ketone precursor. Treating 2,4-difluorobenzaldehyde with BAL in the presence of thiamin-diphosphate (ThDP) and Mg2+ resulted in the formation of α-hydroxy ketone which then underwent the preparation of 7. This innovative approach not only provides a greener alternative but also offers significant advantages over the traditional chemical process. Through our efforts and development work, we have established efficient and scalable procedures that enable the production of 7 in a moderate 38% yield.
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Affiliation(s)
- Zhiran Ju
- Institute of Pharmaceutical Science and Technology, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zhiyun Li
- Institute of Pharmaceutical Science and Technology, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Menglan Li
- Institute of Pharmaceutical Science and Technology, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Saili Xu
- Institute of Pharmaceutical Science and Technology, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | | | - Fen-Er Chen
- Institute of Pharmaceutical Science and Technology, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai 200433, China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China
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3
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Kariya T, Hasegawa H, Udagawa T, Inada Y, Nishiyama K, Tsuji M, Hirayama T, Suzutani T, Kato N, Nagano S, Nagasawa H. Elucidation of the stereocontrol mechanisms of the chemical and biosynthetic intramolecular Diels-Alder cycloaddition for the formation of bioactive decalins. RSC Adv 2023; 13:27828-27838. [PMID: 37731829 PMCID: PMC10508222 DOI: 10.1039/d3ra04406h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023] Open
Abstract
The intramolecular Diels-Alder reaction (IMDA) is a powerful method for regioselective and stereoselective construction of functionalised decalin skeletons, and the recent discovery of enzymes that catalyse IMDA cycloaddition in biosynthesis has generated considerable interest. This study focused on the role of the absolute configuration of the C-6 carbon of the substrate polyene in the stereocontrol of the IMDA reaction catalysed by Fsa2 and Phm7, which construct different enantiomeric decalin skeletons. Their enantiomeric precursor polyenes were synthesised and subjected to enzymatic or thermal IMDA reactions to isolate various diastereomeric decalines and determine their absolute configuration. Furthermore, density functional theory calculations were performed to elucidate the stereocontrol mechanism underlying the formation of decalin. The results showed that Fsa2 exhibits the same equisetin-type stereoselectivity for enantiomeric substrates regardless of the 6-methyl group configuration of the substrate, while Phm7 shows two types of stereoselectivity depending on the configuration of the 6-methyl group. We also found a unique stereochemistry-activity relationship in antibacterial activity for decalin diastereomers, including new derivatives. This study provides new insights into the stereoselectivity of DAase, which is important in the synthesis of natural product skeletons.
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Affiliation(s)
- Takumi Kariya
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University 1-25-4 Daigaku-nishi Gifu 501-1196 Japan
| | - Hayato Hasegawa
- Department of Engineering, Graduate School of Sustainability Science, Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan
| | - Taro Udagawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University 1-1 Yanagido Gifu 501-1193 Japan
| | - Yusaku Inada
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University 1-25-4 Daigaku-nishi Gifu 501-1196 Japan
| | - Kyoko Nishiyama
- Department of Microbiology, Fukushima Medical University 1 Hikarigaoka Fukushima 960-1295 Japan
| | - Mieko Tsuji
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University 1-25-4 Daigaku-nishi Gifu 501-1196 Japan
| | - Tasuku Hirayama
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University 1-25-4 Daigaku-nishi Gifu 501-1196 Japan
| | - Tatsuo Suzutani
- Department of Microbiology, Fukushima Medical University 1 Hikarigaoka Fukushima 960-1295 Japan
| | - Naoki Kato
- Faculty of Agriculture, Setsunan University 45-1 Nagaotoge-cho, Hirakata Osaka 573-0101 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
| | - Hideko Nagasawa
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University 1-25-4 Daigaku-nishi Gifu 501-1196 Japan
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4
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Yu C, Chen L, Gao YL, Liu J, Li PL, Zhang ML, Li Q, Zhang HD, Tang MC, Li L. Discovery and biosynthesis of macrophasetins from the plant pathogen fungus Macrophomina phaseolina. Front Microbiol 2022; 13:1056392. [PMID: 36452919 PMCID: PMC9701702 DOI: 10.3389/fmicb.2022.1056392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/17/2022] [Indexed: 09/16/2023] Open
Abstract
3-Decalinoyltetramic acids (DTAs) are a class of natural products with chemical diversity and potent bioactivities. In fungal species there is a general biosynthetic route to synthesize this type of compounds, which usually features a polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) and a lipocalin-like Diels-Alderase (LLDAse). Using a synthetic biology approach, combining the bioinformatics analysis prediction and heterologous expression, we mined a PKS-NRPS and LLDAse encoding gene cluster from the plant pathogenic fungus Macrophomina phaseolina and characterized the cluster to be responsible for the biosynthesis of novel DTAs, macrophasetins. In addition, we investigated the biosynthesis of these compounds and validated the accuracy of the phylogeny-guided bioinformatics analysis prediction. Our results provided a proof of concept example to this approach, which may facilitate the discovery of novel DTAs from the fungal kingdom.
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Affiliation(s)
- Cui Yu
- Engineering Research Center of Industrial Microbiology (Ministry of Education) and College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Lin Chen
- 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, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Le Gao
- Engineering Research Center of Industrial Microbiology (Ministry of Education) and College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jia Liu
- Engineering Research Center of Industrial Microbiology (Ministry of Education) and College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Pei Lin Li
- Engineering Research Center of Industrial Microbiology (Ministry of Education) and College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Ming Liang Zhang
- Engineering Research Center of Industrial Microbiology (Ministry of Education) and College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Qin Li
- Engineering Research Center of Industrial Microbiology (Ministry of Education) and College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Huai Dong Zhang
- Engineering Research Center of Industrial Microbiology (Ministry of Education) and College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Man Cheng Tang
- 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, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China
| | - Li Li
- Engineering Research Center of Industrial Microbiology (Ministry of Education) and College of Life Sciences, Fujian Normal University, Fuzhou, China
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5
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Tian J, Chen S, Liu F, Zhu Q, Shen J, Lin W, Zhu K. Equisetin Targets Intracellular Staphylococcus aureus through a Host Acting Strategy. Mar Drugs 2022; 20:656. [PMID: 36354979 PMCID: PMC9694014 DOI: 10.3390/md20110656] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/15/2022] [Accepted: 10/16/2022] [Indexed: 09/22/2023] Open
Abstract
Mammalian cells act as reservoirs of internalized bacteria to circumvent extracellular antibacterial compounds, resulting in relapse and reinfection diseases. The intracellular persistence of Staphylococcus aureus renders most traditional antibiotics useless, due to their inadequate subcellular accumulation. To replenish our antibiotic arsenal, we found that a marine-derived compound, equisetin, efficiently eliminates intracellular S. aureus by potentiating the host autophagy and inducing mitochondrial-mediated ROS generation to clear the invading S. aureus. The remarkable anti-infection activity of equisetin was validated in a peritonitis-infected mouse model. The marine product equisetin utilizes a unique dual mechanism to modulate the host-pathogen interaction in the clearance of intracellular bacteria. Thus, equisetin is an inspiring host-acting candidate for overcoming intracellular pathogens.
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Affiliation(s)
- Jiayao Tian
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shang Chen
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Fei Liu
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Qian Zhu
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Jianzhong Shen
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Wenhan Lin
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Kui Zhu
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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6
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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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7
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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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8
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Chi C, Wang Z, Liu T, Zhang Z, Zhou H, Li A, Jin H, Jia H, Yin F, Yang D, Ma M. Crystal Structures of Fsa2 and Phm7 Catalyzing [4 + 2] Cycloaddition Reactions with Reverse Stereoselectivities in Equisetin and Phomasetin Biosynthesis. ACS OMEGA 2021; 6:12913-12922. [PMID: 34056443 PMCID: PMC8154222 DOI: 10.1021/acsomega.1c01593] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Fsa2 and Phm7 are a unique pair of pericyclases catalyzing [4 + 2] cycloaddition reactions with reverse stereoselectivities in the biosynthesis of equisetin and phomasetin, both of which are potent HIV-1 integrase inhibitors. We here solve the crystal structures of Fsa2 and Phm7, both of which possess unusual "two-β barrel" folds. Different residues are evident between the active sites of Fsa2 and Phm7, and modeling experiments provide key structural information determining the reverse stereoselectivities. These results provide a better understanding of how natural pericyclases control the catalytic stereoselectivities and benefit the protein engineering in future.
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Affiliation(s)
- Changbiao Chi
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Zhengdong Wang
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Tan Liu
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Zhongyi Zhang
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Huan Zhou
- Shanghai
Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 239 Zhangheng Road, Pudong District, Shanghai 201204, China
| | - Annan Li
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Hongwei Jin
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Hongli Jia
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Fuling Yin
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Donghui Yang
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, 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
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9
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An interpreted atlas of biosynthetic gene clusters from 1,000 fungal genomes. Proc Natl Acad Sci U S A 2021; 118:2020230118. [PMID: 33941694 DOI: 10.1073/pnas.2020230118] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Fungi are prolific producers of natural products, compounds which have had a large societal impact as pharmaceuticals, mycotoxins, and agrochemicals. Despite the availability of over 1,000 fungal genomes and several decades of compound discovery efforts from fungi, the biosynthetic gene clusters (BGCs) encoded by these genomes and the associated chemical space have yet to be analyzed systematically. Here, we provide detailed annotation and analyses of fungal biosynthetic and chemical space to enable genome mining and discovery of fungal natural products. Using 1,037 genomes from species across the fungal kingdom (e.g., Ascomycota, Basidiomycota, and non-Dikarya taxa), 36,399 predicted BGCs were organized into a network of 12,067 gene cluster families (GCFs). Anchoring these GCFs with reference BGCs enabled automated annotation of 2,026 BGCs with predicted metabolite scaffolds. We performed parallel analyses of the chemical repertoire of fungi, organizing 15,213 fungal compounds into 2,945 molecular families (MFs). The taxonomic landscape of fungal GCFs is largely species specific, though select families such as the equisetin GCF are present across vast phylogenetic distances with parallel diversifications in the GCF and MF. We compare these fungal datasets with a set of 5,453 bacterial genomes and their BGCs and 9,382 bacterial compounds, revealing dramatic differences between bacterial and fungal biosynthetic logic and chemical space. These genomics and cheminformatics analyses reveal the large extent to which fungal and bacterial sources represent distinct compound reservoirs. With a >10-fold increase in the number of interpreted strains and annotated BGCs, this work better regularizes the biosynthetic potential of fungi for rational compound discovery.
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10
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Chen S, Liu D, Zhang Q, Guo P, Ding S, Shen J, Zhu K, Lin W. A Marine Antibiotic Kills Multidrug-Resistant Bacteria without Detectable High-Level Resistance. ACS Infect Dis 2021; 7:884-893. [PMID: 33653026 DOI: 10.1021/acsinfecdis.0c00913] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Antibiotic resistance nowadays is spreading much faster than the introduction of new antibiotics into clinical practice. There is an urgent need for potential compounds to combat multidrug-resistant (MDR) bacteria. Marine fungi provide a promising source for chemical diversity with antibiotic-like molecules. To identify structurally distinct compounds that effectively eradicate MDR pathogens and to control the development of antibiotic resistance, we have reinvestigated equisetin, a previously reported meroterpenoid isolated from a marine sponge-derived fungus. Equisetin exerted efficient antibacterial activities against either MRSA or VRE without detectable high-level resistance. Meanwhile, equisetin, as an antibiotic adjuvant, restores colistin susceptibility to colistin-resistant bacteria toward diverse Gram-negative pathogens. Intriguingly, the low-level equisetin-resistant Staphylococcus aureus displayed collateral sensitivity to multiple classes of existing antibiotics with decreased capacity to produce biofilm. Lastly, equisetin showed efficacy with MRSA in three infected animal models. This work suggests that equisetin derived from marine natural products is a promising lead to overcome antibiotic resistance, providing new insight in future antibiotic discovery and development.
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Affiliation(s)
- Shang Chen
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing 100193, China
| | - Dong Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Qi Zhang
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Peng Guo
- Pharmacology and Toxicology Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Shuangyang Ding
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing 100193, China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing 100193, China
| | - Kui Zhu
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing 100193, China
| | - Wenhan Lin
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
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11
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Zhang W, Kaplan AR, Davison EK, Freeman JL, Brimble MA, Wuest WM. Building trans-bicyclo[4.4.0]decanes/decenes in complex multifunctional frameworks: the case for antibiotic development. Nat Prod Rep 2021; 38:880-889. [PMID: 33206093 DOI: 10.1039/d0np00052c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: 2000 to 2020. trans-Bicyclo[4.4.0]decane/decene (such as trans-decalin and trans-octalin)-containing natural products display a wide range of structural diversity and frequently exhibit potent and selective antibacterial activities. With one of the major factors in combatting antibiotic resistance being the discovery of novel scaffolds, the efficient construction of these natural products is an attractive pursuit in the development of novel antibiotics. This highlight aims to provide a critical analysis on how the presence of dense architectural and stereochemical complexity necessitated special strategies in the synthetic pursuits of these natural trans-bicyclo[4.4.0]decane/decene antibiotics.
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Affiliation(s)
- Wanli Zhang
- Department of Chemistry, Emory University, USA.
| | | | - Emma K Davison
- School of Chemical Sciences, University of Auckland, 23 Symonds St., Auckland, 1010, New Zealand and School of Biological Sciences, University of Auckland, 23 Symonds St., Auckland, 1010, New Zealand and The Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Jared L Freeman
- School of Chemical Sciences, University of Auckland, 23 Symonds St., Auckland, 1010, New Zealand and The Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, University of Auckland, 23 Symonds St., Auckland, 1010, New Zealand and School of Biological Sciences, University of Auckland, 23 Symonds St., Auckland, 1010, New Zealand and The Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - William M Wuest
- Department of Chemistry, Emory University, USA. and Emory Antibiotic Resistance Center, Emory School of Medicine, USA
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12
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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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13
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Yuan J, Rao CB, Liang Y, Zhang R, Zhang Q, Hou L, Dong D. Copper‐Catalyzed Regioselective Oxidative Cycloamidation of
α
‐[(
β
‐Dimethylamino)propenoyl]‐Alkylamides: Synthetic Route to Substituted Pyrrolidine‐2,4‐diones. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201801237] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Jingwen Yuan
- Key Laboratory of High Performance Synthetic Rubber and its Composites, Changchun Institute of Applied ChemistryChinese Academy of Sciences Changchun 130022 People's Republic of China
- University of the Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Chitturi Bhujanga Rao
- Key Laboratory of High Performance Synthetic Rubber and its Composites, Changchun Institute of Applied ChemistryChinese Academy of Sciences Changchun 130022 People's Republic of China
| | - Yongjiu Liang
- Key Laboratory of High Performance Synthetic Rubber and its Composites, Changchun Institute of Applied ChemistryChinese Academy of Sciences Changchun 130022 People's Republic of China
| | - Rui Zhang
- Key Laboratory of High Performance Synthetic Rubber and its Composites, Changchun Institute of Applied ChemistryChinese Academy of Sciences Changchun 130022 People's Republic of China
| | - Qian Zhang
- Key Laboratory of High Performance Synthetic Rubber and its Composites, Changchun Institute of Applied ChemistryChinese Academy of Sciences Changchun 130022 People's Republic of China
| | - Liman Hou
- Key Laboratory of High Performance Synthetic Rubber and its Composites, Changchun Institute of Applied ChemistryChinese Academy of Sciences Changchun 130022 People's Republic of China
| | - Dewen Dong
- Key Laboratory of High Performance Synthetic Rubber and its Composites, Changchun Institute of Applied ChemistryChinese Academy of Sciences Changchun 130022 People's Republic of China
- University of the Chinese Academy of Sciences Beijing 100049 People's Republic of China
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14
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Fusopoltide A and fusosterede A, A polyketide with a pentaleno[1,2- c ]pyran ring system and A degraded steride, from the fungus Fusarium solani. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.05.082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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15
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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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16
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Yang B, Gao S. Recent advances in the application of Diels–Alder reactions involving o-quinodimethanes, aza-o-quinone methides and o-quinone methides in natural product total synthesis. Chem Soc Rev 2018; 47:7926-7953. [DOI: 10.1039/c8cs00274f] [Citation(s) in RCA: 240] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This review summarizes recent advances in Diels–Alder reactions involving o-QDMs, o-QMs and aza-o-QMs. The power and potential of this strategy in organic synthesis and natural product total synthesis is highlighted.
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Affiliation(s)
- Baochao Yang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
- China
| | - Shuanhu Gao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
- China
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17
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Hill RA, Sutherland A. Hot off the Press. Nat Prod Rep 2017; 34:940-944. [PMID: 28717803 DOI: 10.1039/c7np90028g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as svetamycin B from a Streptomyces species.
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Affiliation(s)
- Robert A Hill
- School of Chemistry, Glasgow University, Glasgow, G12 8QQ, UK.
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