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Zhang JX, Wei TT, Min D, Lv JL, Liu DF, Chen JJ, Yu YY, Yu HQ. Deciphering unique enzymatic pathways in sulfonamide biotransformation by direct ammonia oxidizer Alcaligenes ammonioxydans HO-1. WATER RESEARCH 2025; 273:123045. [PMID: 39733530 DOI: 10.1016/j.watres.2024.123045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 12/22/2024] [Accepted: 12/23/2024] [Indexed: 12/31/2024]
Abstract
Heterotrophic nitrification, similar to autotrophic nitrification, involves key enzymes and reactive nitrogen intermediates during ammonia oxidation, which may influence antibiotic transformation. However, the interference between antibiotic transformation products from ammonia oxidation and secondary metabolites in heterotrophic nitrifiers makes antibiotic transformation pathways more complicated. In this work, we observe that the heterotrophic nitrifier Alcaligenes ammonioxydans HO-1 can effectively convert sulfonamide antibiotics. Product analysis reveals the impacts of carbon and nitrogen concentrations as well as their ratio on the biotransformation of sulfamethazine (SMZ). The dnfABC gene cluster is identified as essential for mediating SMZ conversion. In vitro enzymatic activity reconstruction further confirms that DnfA exhibits N-oxygenase activity and can catalyze the conversion of various aryl-amines into aryl-nitro compounds. The results of this work not only expand our understanding of the functions of heterotrophic nitrifiers, but also provide a theoretical basis for developing efficient biotechnologies for treating antibiotics.
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Affiliation(s)
- Jia-Xin Zhang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Ting-Ting Wei
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Di Min
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
| | - Jun-Lu Lv
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Jie-Jie Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Yang-Yang Yu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Anhui University, Hefei 230601, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
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2
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Tahghighi A, Seyedhashemi E, Mohammadi J, Moradi A, Esmaeili A, Pornour M, Jafarifar K, Ganji SM. Epigenetic marvels: exploring the landscape of colorectal cancer treatment through cutting-edge epigenetic-based drug strategies. Clin Epigenetics 2025; 17:34. [PMID: 39987205 PMCID: PMC11847397 DOI: 10.1186/s13148-025-01844-w] [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: 09/01/2024] [Accepted: 02/14/2025] [Indexed: 02/24/2025] Open
Abstract
Epigenetics is currently considered the investigation of inheritable changes in gene expression that do not rely on DNA sequence alteration. Significant epigenetic procedures are involved, such as DNA methylations, histone modifications, and non-coding RNA actions. It is confirmed through several investigations that epigenetic changes are associated with the formation, development, and metastasis of various cancers, such as colorectal cancer (CRC). The difference between epigenetic changes and genetic mutations is that the former could be reversed or prevented; therefore, cancer treatment and prevention could be achieved by restoring abnormal epigenetic events within the neoplastic cells. These treatments, consequently, cause the anti-tumour effects augmentation, drug resistance reduction, and host immune response stimulation. In this article, we begin our survey by exploring basic epigenetic mechanisms to understand epigenetic tools and strategies for treating colorectal cancer in monotherapy and combination with chemotherapy or immunotherapy.
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Affiliation(s)
- Azar Tahghighi
- Medicinal Chemistry Laboratory, Clinical Research Department, Pasteur Institute of Iran, Tehran, Iran
| | - Effat Seyedhashemi
- Department of Molecular Medicine, Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-E Pajoohesh, Km 15, P.O. Box 14965/161, Tehran, Iran
| | - Javad Mohammadi
- Department of Molecular Medicine, Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-E Pajoohesh, Km 15, P.O. Box 14965/161, Tehran, Iran
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Arash Moradi
- Department of Molecular Medicine, Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-E Pajoohesh, Km 15, P.O. Box 14965/161, Tehran, Iran
| | - Aria Esmaeili
- Department of Molecular Medicine, Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-E Pajoohesh, Km 15, P.O. Box 14965/161, Tehran, Iran
| | - Majid Pornour
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, MD, USA
| | - Kimia Jafarifar
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Shahla Mohammad Ganji
- Department of Molecular Medicine, Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-E Pajoohesh, Km 15, P.O. Box 14965/161, Tehran, Iran.
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3
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Lenferink WB, Bakken LR, Jetten MSM, van Kessel MAHJ, Lücker S. Hydroxylamine production by Alcaligenes faecalis challenges the paradigm of heterotrophic nitrification. SCIENCE ADVANCES 2024; 10:eadl3587. [PMID: 38848370 PMCID: PMC11160463 DOI: 10.1126/sciadv.adl3587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
Abstract
Heterotrophic nitrifiers continue to be a hiatus in our understanding of the nitrogen cycle. Despite their discovery over 50 years ago, the physiology and environmental role of this enigmatic group remain elusive. The current theory is that heterotrophic nitrifiers are capable of converting ammonia to hydroxylamine, nitrite, nitric oxide, nitrous oxide, and dinitrogen gas via the subsequent actions of nitrification and denitrification. In addition, it was recently suggested that dinitrogen gas may be formed directly from ammonium. Here, we combine complementary high-resolution gas profiles, 15N isotope labeling studies, and transcriptomics data to show that hydroxylamine is the major product of nitrification in Alcaligenes faecalis. We demonstrated that denitrification and direct ammonium oxidation to dinitrogen gas did not occur under the conditions tested. Our results indicate that A. faecalis is capable of hydroxylamine production from an organic intermediate. These results fundamentally change our understanding of heterotrophic nitrification and have important implications for its biotechnological application.
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Affiliation(s)
- Wouter B. Lenferink
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
| | - Lars R. Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Mike S. M. Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
| | - Maartje A. H. J. van Kessel
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
| | - Sebastian Lücker
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
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4
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Liu J, Gao S, Miliordos E, Chen M. Asymmetric Syntheses of ( Z)- or ( E)-β,γ-Unsaturated Ketones via Silane-Controlled Enantiodivergent Catalysis. J Am Chem Soc 2023; 145:19542-19553. [PMID: 37639380 PMCID: PMC11144060 DOI: 10.1021/jacs.3c02595] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Cu-catalyzed highly stereoselective and enantiodivergent syntheses of (Z)- or (E)-β,γ-unsaturated ketones from 1,3-butadienyl silanes are developed. The nature of the silyl group of the dienes has a significant impact on the stereo- and enantioselectivity of the reactions. Under the developed catalytic systems, the reactions of acyl fluorides with phenyldiemthylsilyl-substituted 1,3-diene gave (Z)-β,γ-unsaturated ketones bearing an α-tertiary stereogenic center with excellent enantioselectivities and high Z-selectivities, where the reactions with triisopropylsilyl-substituted 1,3-butadiene formed (E)-β,γ-unsaturated ketones with high optical purities and excellent E-selectivities. The products generated from the reactions contain three functional groups with orthogonal chemical reactivities, which can undergo a variety of transformations to afford synthetically valuable intermediates.
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Affiliation(s)
- Jiaming Liu
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Shang Gao
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Evangelos Miliordos
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Ming Chen
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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5
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Nagata R, Nishiyama M, Kuzuyama T. Substrate Recognition Mechanism of a Trichostatin A-Forming Hydroxyamidotransferase. Biochemistry 2023. [PMID: 37167424 DOI: 10.1021/acs.biochem.3c00025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The hydroxyamidotransferase TsnB9 catalyzes hydroxylamine transfer from l-glutamic acid γ-monohydroxamate to the carboxyl group of trichostatic acid to produce the terminal hydroxamic acid group of trichostatin A, which is a potent inhibitor of histone deacetylase (HDAC). The reaction catalyzed by TsnB9 is similar to that catalyzed by glutamine-dependent asparagine synthetase, but the trichostatic acid recognition mechanism remains unclear. Here, we determine the crystal structure of TsnB9 composed of the N-terminal glutaminase domain and the C-terminal synthetase domain. Two consecutive phenylalanine residues, which are not found in glutamine-dependent asparagine synthetase, in the N-terminal glutaminase domain structurally form the bottom of the hydrophobic pocket in the C-terminal synthetase domain. Mutational and computational analyses of TsnB9 suggest five aromatic residues, including the two consecutive phenylalanine residues, in the hydrophobic pocket are important for the recognition of the dimethylaniline moiety of trichostatic acid. These insights lead us to the discovery of hydroxyamidotransferase to produce terminal hydroxamic acid group-containing HDAC inhibitors different from trichostatin A.
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Affiliation(s)
- Ryuhei Nagata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Makoto Nishiyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohisa Kuzuyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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6
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Ushimaru R, Abe I. Unusual Dioxygen-Dependent Reactions Catalyzed by Nonheme Iron Enzymes in Natural Product Biosynthesis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c05247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- ACT-X, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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7
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Gao Q, Deng S, Jiang T. Recent developments in the identification and biosynthesis of antitumor drugs derived from microorganisms. ENGINEERING MICROBIOLOGY 2022; 2:100047. [PMID: 39628704 PMCID: PMC11611020 DOI: 10.1016/j.engmic.2022.100047] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 12/06/2024]
Abstract
Secondary metabolites in microorganisms represent a resource for drug discovery and development. In particular, microbial-derived antitumor agents are in clinical use worldwide. Herein, we provide an overview of the development of classical antitumor drugs derived from microorganisms. Currently used drugs and drug candidates are comprehensively described in terms of pharmacological activities, mechanisms of action, microbial sources, and biosynthesis. We further discuss recent studies that have demonstrated the utility of gene-editing technologies and synthetic biology tools for the identification of new gene clusters, expansion of natural products, and elucidation of biosynthetic pathways. This review summarizes recent progress in the discovery and development of microbial-derived anticancer compounds with emphasis on biosynthesis.
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Affiliation(s)
- Qi Gao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Qingdao 266237, China
- School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Sizhe Deng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Qingdao 266237, China
- School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Tianyu Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Qingdao 266237, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518000, Guangdong, China
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8
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Ruzic D, Djoković N, Srdić-Rajić T, Echeverria C, Nikolic K, Santibanez JF. Targeting Histone Deacetylases: Opportunities for Cancer Treatment and Chemoprevention. Pharmaceutics 2022; 14:pharmaceutics14010209. [PMID: 35057104 PMCID: PMC8778744 DOI: 10.3390/pharmaceutics14010209] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/06/2022] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
The dysregulation of gene expression is a critical event involved in all steps of tumorigenesis. Aberrant histone and non-histone acetylation modifications of gene expression due to the abnormal activation of histone deacetylases (HDAC) have been reported in hematologic and solid types of cancer. In this sense, the cancer-associated epigenetic alterations are promising targets for anticancer therapy and chemoprevention. HDAC inhibitors (HDACi) induce histone hyperacetylation within target proteins, altering cell cycle and proliferation, cell differentiation, and the regulation of cell death programs. Over the last three decades, an increasing number of synthetic and naturally derived compounds, such as dietary-derived products, have been demonstrated to act as HDACi and have provided biological and molecular insights with regard to the role of HDAC in cancer. The first part of this review is focused on the biological roles of the Zinc-dependent HDAC family in malignant diseases. Accordingly, the small-molecules and natural products such as HDACi are described in terms of cancer therapy and chemoprevention. Furthermore, structural considerations are included to improve the HDACi selectivity and combinatory potential with other specific targeting agents in bifunctional inhibitors and proteolysis targeting chimeras. Additionally, clinical trials that combine HDACi with current therapies are discussed, which may open new avenues in terms of the feasibility of HDACi’s future clinical applications in precision cancer therapies.
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Affiliation(s)
- Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Nemanja Djoković
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Tatjana Srdić-Rajić
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia;
| | - Cesar Echeverria
- Facultad de Medicina, Universidad de Atacama, Copayapu 485, Copiapo 1531772, Chile;
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Juan F. Santibanez
- Group for Molecular Oncology, Institute for Medical Research, National Institute of the Republic of Serbia, University of Belgrade, Dr. Subotica 4, POB 102, 11129 Belgrade, Serbia
- Centro Integrativo de Biología y Química Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago 8370854, Chile
- Correspondence: ; Tel.: +381-11-2685-788; Fax: +381-11-2643-691
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9
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Mori Y, Kobayashi H, Fujita Y, Yatagawa M, Kato S, Kawanishi S, Murata M, Oikawa S. Mechanism of reactive oxygen species generation and oxidative DNA damage induced by acrylohydroxamic acid, a putative metabolite of acrylamide. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2022; 873:503420. [PMID: 35094805 DOI: 10.1016/j.mrgentox.2021.503420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 10/20/2022]
Abstract
Acrylamide is formed during the heating of food and is also found in cigarette smoke. It is classified by the International Agency for Research on Cancer as a probable human carcinogen (Group 2A). Glycidamide, an epoxide metabolite of acrylamide, is implicated in the mechanism of acrylamide carcinogenicity. Acrylamide causes oxidative DNA damage in target organs. We sought to clarify the mechanism of acrylamide-induced oxidative DNA damage by investigating site-specific DNA damage and reactive oxygen species (ROS) generation by a putative metabolite of acrylamide, acrylohydroxamic acid (AA). Our results, using 32P-5'-end-labeled DNA fragments, indicated that, although AA alone did not damage DNA, AA treated with amidase induced DNA damage in the presence of Cu(II). DNA cleavage occurred preferentially at T and C, and particularly at T in 5'-TG-3' sequences, and the DNA cleavage pattern was similar to that of hydroxylamine. The DNA damage was inhibited by methional, catalase, and Cu(I)-chelator bathocuproine, suggesting that H2O2 and Cu(I) are involved in the mechanism of DNA damage induced by AA treated with amidase. In addition, amidase-treated AA increased 8-oxo-7,8-dihydro-2'-deoxyguanosine formation in calf thymus DNA, an indicator of oxidative DNA damage, in a dose-dependent manner. In conclusion, hydroxylamine, possibly produced from AA treated with amidase, was autoxidized via the Cu(II)/Cu(I) redox cycle and H2O2 generation, suggesting that oxidative DNA damage induced by ROS plays an important role in acrylamide-related carcinogenesis.
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Affiliation(s)
- Yurie Mori
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Edobashi 2-174, Tsu, Mie, 514-8507, Japan; Faculty of Pharmacy, Gifu University of Medical Science, 4-3-3 Nijigaoka, Kani, Gifu, 509-0293, Japan
| | - Hatasu Kobayashi
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Edobashi 2-174, Tsu, Mie, 514-8507, Japan
| | - Yoshio Fujita
- Faculty of Pharmaceutical Science, Suzuka University of Medical Science, 3500-3, Minamitamagaki, Suzuka, Mie, 513-8670, Japan
| | - Minami Yatagawa
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Edobashi 2-174, Tsu, Mie, 514-8507, Japan
| | - Shinya Kato
- Radioisotope Experimental Facility, Advanced Science Research Promotion Center, Mie University, Edobashi 2-174, Tsu, Mie, 514-8507, Japan
| | - Shosuke Kawanishi
- Faculty of Pharmaceutical Science, Suzuka University of Medical Science, 3500-3, Minamitamagaki, Suzuka, Mie, 513-8670, Japan
| | - Mariko Murata
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Edobashi 2-174, Tsu, Mie, 514-8507, Japan
| | - Shinji Oikawa
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Edobashi 2-174, Tsu, Mie, 514-8507, Japan.
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10
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Hwang GJ, Jang M, Son S, Lee B, Jang JP, Lee JS, Ko SK, Hong YS, Ahn JS, Jang JH. Ulleunganilines A-C, Trichostatin Analogues Bearing a Modified Side Chain from Streptomyces sp. 13F051. JOURNAL OF NATURAL PRODUCTS 2021; 84:2420-2426. [PMID: 34455777 DOI: 10.1021/acs.jnatprod.1c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Three new trichostatin analogues, ulleunganilines A-C (1-3), and seven known trichostatins (4-10) were isolated from cultures of Streptomyces sp. 13F051. NMR, UV, and MS data indicated that the planar structures of 1-3 consisted of modified side chains in the trichostatic acid moiety. The absolute configuration of the 2,4-dimethyl-branched carbon chains in 1 and 2 was determined by the PGME method, while the amino acid group in 3 was identified by advanced Marfey's method. Based on the structure of the modified side chains, the origin of 1-3 is proposed. Further experiments indicated that 1 and 3 displayed moderate histone deacetylase inhibitory activity, suggesting that not only the hydroxamate group but also the N,N-dimethyl group were essential for the inhibitory activity.
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Affiliation(s)
- Gwi Ja Hwang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, South Korea
| | - Mina Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116, South Korea
| | - Sangkeun Son
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116, South Korea
| | - Byeongsan Lee
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116, South Korea
| | - Jun-Pil Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116, South Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, South Korea
| | - Sung-Kyun Ko
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116, South Korea
| | - Young-Soo Hong
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, South Korea
| | - Jong Seog Ahn
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, South Korea
| | - Jae-Hyuk Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, South Korea
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11
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He HY, Ryan KS. Glycine-derived nitronates bifurcate to O-methylation or denitrification in bacteria. Nat Chem 2021; 13:599-606. [PMID: 33782561 DOI: 10.1038/s41557-021-00656-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 02/08/2021] [Indexed: 02/01/2023]
Abstract
Natural products with rare functional groups are likely to be constructed by unique biosynthetic enzymes. One such rare functional group is the O-methyl nitronate, which can undergo [3 + 2] cycloaddition reactions with olefins in mild conditions. O-methyl nitronates are found in some natural products; however, how such O-methyl nitronates are assembled biosynthetically is unknown. Here we show that the assembly of the O-methyl nitronate in the natural product enteromycin carboxamide occurs via activation of glycine on a peptidyl carrier protein, followed by reaction with a diiron oxygenase to give a nitronate intermediate and then with a methyltransferase to give an O-methyl nitronate. Guided by the discovery of this pathway, we then identify related cryptic biosynthetic gene cassettes in other bacteria and show that these alternative gene cassettes can, instead, facilitate oxidative denitrification of glycine-derived nitronates. Altogether, our work reveals bifurcating pathways from a central glycine-derived nitronate intermediate in bacteria.
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Affiliation(s)
- Hai-Yan He
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.
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12
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Miura T, Oku N, Shiratori Y, Nagata Y, Murakami M. Stereo- and Enantioselective Synthesis of Propionate-Derived Trisubstituted Alkene Motifs. Chemistry 2021; 27:3861-3868. [PMID: 33277755 DOI: 10.1002/chem.202004930] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/03/2020] [Indexed: 12/14/2022]
Abstract
We report a new method for constructing propionate-derived trisubstituted alkene motifs in a stereoselective manner. 1-Substituted 1,1-di(pinacolatoboryl)-(E)-alk-2-enes are generated in situ from 1-substituted 1,1-di(pinacolatoboryl)alk-3-enes through ruthenium(II)-catalyzed double-bond transposition. These species undergo a chiral phosphoric acid catalyzed allylation reaction of aldehydes to produce the E isomers of anti-homoallylic alcohols. On the other hand, the corresponding Z isomers of anti-homoallylic alcohols are obtained when a dimeric palladium(I) complex is employed as the catalyst for this double-bond transposition. Thus, both E and Z isomers can be synthesized from the same starting materials. A B-C(sp2 ) bond remaining with the allylation product undergoes the Suzuki-Miyaura cross-coupling reaction to furnish a propionate-derived trisubstituted alkene motif in a stereo-defined form. The present method to construct the motifs with (E)- and (Z)-alkenes are successfully applied to the syntheses of (+)-isotrichostatic acid, (-)-isotrichostatin RK, and (+)-trichostatic acid, respectively.
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Affiliation(s)
- Tomoya Miura
- Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Kyoto, 615-8510, Japan
| | - Naoki Oku
- Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Kyoto, 615-8510, Japan
| | - Yota Shiratori
- Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Kyoto, 615-8510, Japan
| | - Yuuya Nagata
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido, 001-0021, Japan
| | - Masahiro Murakami
- Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Kyoto, 615-8510, Japan
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13
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Ran M, He J, Yan B, Liu W, Li Y, Fu Y, Li CJ, Yao Q. Catalyst-free generation of acyl radicals induced by visible light in water to construct C–N bonds. Org Biomol Chem 2021; 19:1970-1975. [DOI: 10.1039/d0ob02364g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new route to produce acyl radicals by the cleavage of Csp2–Csp2 bonds of α-diketones irradiated by visible light was developed and hydroxylamides or amides were selectively synthesized in water.
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Affiliation(s)
- Maogang Ran
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province
- Generic Drug Research Center of Guizhou Province
- Department of Pharmacy
- Zunyi Medical University
- Zunyi
| | - Jiaxin He
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province
- Generic Drug Research Center of Guizhou Province
- Department of Pharmacy
- Zunyi Medical University
- Zunyi
| | - Boyu Yan
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province
- Generic Drug Research Center of Guizhou Province
- Department of Pharmacy
- Zunyi Medical University
- Zunyi
| | - Wenbo Liu
- Department of Chemistry
- McGill University
- Montreal
- Canada
| | - Yi Li
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province
- Generic Drug Research Center of Guizhou Province
- Department of Pharmacy
- Zunyi Medical University
- Zunyi
| | - Yunfen Fu
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province
- Generic Drug Research Center of Guizhou Province
- Department of Pharmacy
- Zunyi Medical University
- Zunyi
| | - Chao-Jun Li
- Department of Chemistry
- McGill University
- Montreal
- Canada
| | - Qiuli Yao
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province
- Generic Drug Research Center of Guizhou Province
- Department of Pharmacy
- Zunyi Medical University
- Zunyi
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14
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Heterologous biosynthesis as a platform for producing new generation natural products. Curr Opin Biotechnol 2020; 66:123-130. [DOI: 10.1016/j.copbio.2020.06.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/27/2020] [Accepted: 06/30/2020] [Indexed: 12/18/2022]
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15
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Obermaier S, Müller M. Ibotenic Acid Biosynthesis in the Fly Agaric Is Initiated by Glutamate Hydroxylation. Angew Chem Int Ed Engl 2020; 59:12432-12435. [PMID: 32233056 PMCID: PMC7383597 DOI: 10.1002/anie.202001870] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Indexed: 11/09/2022]
Abstract
The fly agaric, Amanita muscaria, is widely known for its content of the psychoactive metabolites ibotenic acid and muscimol. However, their biosynthetic pathway and the respective enzymes are entirely unknown. 50 years ago, the biosynthesis was hypothesized to start with 3-hydroxyglutamate. Here, we build on this hypothesis by the identification and recombinant production of a glutamate hydroxylase from A. muscaria. The hydroxylase gene is surrounded by six further biosynthetic genes, which we link to the production of ibotenic acid and muscimol using recent genomic and transcriptomic data. Our results pinpoint the genetic basis for ibotenic acid formation and thus provide new insights into a decades-old question concerning a centuries-old drug.
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Affiliation(s)
- Sebastian Obermaier
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Michael Müller
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
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16
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Obermaier S, Müller M. Ibotenic Acid Biosynthesis in the Fly Agaric Is Initiated by Glutamate Hydroxylation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001870] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sebastian Obermaier
- Institute of Pharmaceutical Sciences Albert-Ludwigs-Universität Freiburg Albertstrasse 25 79104 Freiburg Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences Albert-Ludwigs-Universität Freiburg Albertstrasse 25 79104 Freiburg Germany
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17
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Komaki H, Hosoyama A, Igarashi Y, Tamura T. Streptomyces lydicamycinicus sp. nov. and Its Secondary Metabolite Biosynthetic Gene Clusters for Polyketide and Nonribosomal Peptide Compounds. Microorganisms 2020; 8:microorganisms8030370. [PMID: 32155704 PMCID: PMC7143880 DOI: 10.3390/microorganisms8030370] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/21/2020] [Accepted: 03/02/2020] [Indexed: 11/17/2022] Open
Abstract
(1) Background: Streptomyces sp. TP-A0598 derived from seawater produces lydicamycin and its congeners. We aimed to investigate its taxonomic status; (2) Methods: A polyphasic approach and whole genome analysis are employed; (3) Results: Strain TP-A0598 contained ll-diaminopimelic acid, glutamic acid, glycine, and alanine in its peptidoglycan. The predominant menaquinones were MK-9(H6) and MK-9(H8), and the major fatty acids were C16:0, iso-C15:0, iso-C16:0, and anteiso-C15:0. Streptomyces sp. TP-A0598 showed a 16S rDNA sequence similarity value of 99.93% (1 nucleottide difference) to Streptomyces angustmyceticus NRRL B-2347T. The digital DNA–DNA hybridisation value between Streptomyces sp. TP-A0598 and its closely related type strains was 25%–46%. Differences in phenotypic characteristics between Streptomyces sp. TP-A0598 and its phylogenetically closest relative, S. angustmyceticus NBRC 3934T, suggested strain TP-A0598 to be a novel species. Streptomyces sp. TP-A0598 and S. angustmyceticus NBRC 3934T harboured nine and 13 biosynthetic gene clusters for polyketides and nonribosomal peptides, respectively, among which only five clusters were shared between them, whereas the others are specific for each strain; and (4) Conclusions: For strain TP-A0598, the name Streptomyces lydicamycinicus sp. nov. is proposed; the type strain is TP-A0598T (=NBRC 110027T).
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Affiliation(s)
- Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan; (A.H.); (T.T.)
- Correspondence: ; Tel.: +81-438-20-5764
| | - Akira Hosoyama
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan; (A.H.); (T.T.)
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan;
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan; (A.H.); (T.T.)
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18
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He DH, Chen JX, Fu X, Guo DL, Xia B, Liu GH, Ding KY, Fang DM, Zhou Y. A 6/5/5/7 heterotetracyclic indole derivative alkaloid isolated from Typhonium giganteum. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2019.151497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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19
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Liu W, Jannu VG, Liu Z, Zhang Q, Jiang X, Ma L, Zhang W, Zhang C, Zhu Y. Heterologous expression of the trichostatin gene cluster and functional characterization ofN-methyltransferase TsnB8. Org Biomol Chem 2020; 18:3649-3653. [DOI: 10.1039/d0ob00617c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-Methyltransferase TsnB8 was demonstrated to catalyze successive methyltransfer reactions in the biosynthesis of trichostatin.
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Affiliation(s)
- Wei 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
| | - Vinay Gopal Jannu
- 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
| | - Zhiwen 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
| | - Qingbo 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
| | - Xiaodong Jiang
- 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
| | - Liang Ma
- 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
| | - Wenjun 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
| | - Changsheng 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
| | - Yiguang Zhu
- 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
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20
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Abstract
Natural nonproteinogenic amino acids vastly outnumber the well-known 22 proteinogenic amino acids. Such amino acids are generated in specialized metabolic pathways. In these pathways, diverse biosynthetic transformations, ranging from isomerizations to the stereospecific functionalization of C-H bonds, are employed to generate structural diversity. The resulting nonproteinogenic amino acids can be integrated into more complex natural products. Here we review recently discovered biosynthetic routes to freestanding nonproteinogenic α-amino acids, with an emphasis on work reported between 2013 and mid-2019.
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Affiliation(s)
- Jason B Hedges
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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21
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Guo YY, Li ZH, Xia TY, Du YL, Mao XM, Li YQ. Molecular mechanism of azoxy bond formation for azoxymycins biosynthesis. Nat Commun 2019; 10:4420. [PMID: 31594923 PMCID: PMC6783550 DOI: 10.1038/s41467-019-12250-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 08/27/2019] [Indexed: 01/07/2023] Open
Abstract
Azoxy bond is an important chemical bond and plays a crucial role in high energy density materials. However, the biosynthetic mechanism of azoxy bond remains enigmatic. Here we report that the azoxy bond biosynthesis of azoxymycins is an enzymatic and non-enzymatic coupling cascade reaction. In the first step, nonheme diiron N-oxygenase AzoC catalyzes the oxidization of amine to its nitroso analogue. Redox coenzyme pairs then facilitate the mutual conversion between nitroso group and hydroxylamine via the radical transient intermediates, which efficiently dimerize to azoxy bond. The deficiency of nucleophilic reactivity in AzoC is proposed to account for the enzyme's non-canonical oxidization of amine to nitroso product. Free nitrogen radicals induced by coenzyme pairs are proposed to be responsible for the efficient non-enzymatic azoxy bond formation. This mechanism study will provide molecular basis for the biosynthesis of azoxy high energy density materials and other valuable azoxy chemicals.
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Affiliation(s)
- Yuan-Yang Guo
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.,School of Chemistry and Chemical Engineering, Henan Normal University, 453007, Xinxiang, China
| | - Zhen-Hua Li
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Tian-Yu Xia
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Xu-Ming Mao
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
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22
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Ronan JL, Kadi N, McMahon SA, Naismith JH, Alkhalaf LM, Challis GL. Desferrioxamine biosynthesis: diverse hydroxamate assembly by substrate-tolerant acyl transferase DesC. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0068. [PMID: 29685972 DOI: 10.1098/rstb.2017.0068] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2017] [Indexed: 12/16/2022] Open
Abstract
Hydroxamate groups play key roles in the biological function of diverse natural products. Important examples include trichostatin A, which inhibits histone deacetylases via coordination of the active site zinc(II) ion with a hydroxamate group, and the desferrioxamines, which use three hydroxamate groups to chelate ferric iron. Desferrioxamine biosynthesis in Streptomyces species involves the DesD-catalysed condensation of various N-acylated derivatives of N-hydroxycadaverine with two molecules of N-succinyl-N-hydroxycadaverine to form a range of linear and macrocyclic tris-hydroxamates. However, the mechanism for assembly of the various N-acyl-N-hydroxycadaverine substrates of DesD from N-hydroxycadaverine has until now been unclear. Here we show that the desC gene of Streptomyces coelicolor encodes the acyl transferase responsible for this process. DesC catalyses the N-acylation of N-hydroxycadaverine with acetyl, succinyl and myristoyl-CoA, accounting for the diverse array of desferrioxamines produced by S. coelicolor The X-ray crystal structure of DesE, the ferrioxamine lipoprotein receptor, in complex with ferrioxamine B (which is derived from two units of N-succinyl-N-hydroxycadaverine and one of N-acetyl-N-hydroxycadaverine) was also determined. This showed that the acetyl group of ferrioxamine B is solvent exposed, suggesting that the corresponding acyl group in longer chain congeners can protrude from the binding pocket, providing insights into their likely function. This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- Jade L Ronan
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Nadia Kadi
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Stephen A McMahon
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
| | - James H Naismith
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
| | - Lona M Alkhalaf
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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23
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Zhi Y, Narindoshvili T, Bogomolnaya L, Talamantes M, El Saadi A, Andrews-Polymenis H, Raushel FM. Deciphering the Enzymatic Function of the Bovine Enteric Infection-Related Protein YfeJ from Salmonella enterica Serotype Typhimurium. Biochemistry 2019; 58:1236-1245. [PMID: 30715856 DOI: 10.1021/acs.biochem.8b01283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Non-typhoidal Salmonella can colonize the gastrointestinal system of cattle and can also cause significant food-borne disease in humans. The use of a library of single-gene deletions in Salmonella enterica serotype Typhimurium allowed identification of several proteins that are under selection in the intestine of cattle. STM2437 ( yfeJ) encodes one of these proteins, and it is currently annotated as a type I glutamine amidotransferase. STM2437 was purified to homogeneity, and its catalytic properties with a wide range of γ-glutamyl derivatives were determined. The catalytic efficiency toward the hydrolysis of l-glutamine was extremely weak with a kcat/ Km value of 20 M-1 s-1. γ-l-Glutamyl hydroxamate was identified as the best substrate for STM2437, with a kcat/ Km value of 9.6 × 104 M-1 s-1. A homology model of STM2437 was constructed on the basis of the known crystal structure of a protein of unknown function (Protein Data Bank entry 3L7N ), and γ-l-glutamyl hydroxamate was docked into the active site based on the binding of l-glutamine in the active site of carbamoyl phosphate synthetase. Acivicin was shown to inactivate the enzyme by reaction with the active site cysteine residue and the subsequent loss of HCl. Mutation of Cys91 to serine completely abolished catalytic activity. Inactivation of STM2437 did not affect the ability of this strain to colonize mice, but it inhibited the growth of S. enterica Typhimurium in bacteriologic media containing γ-l-glutamyl hydroxamate.
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Affiliation(s)
- Yuan Zhi
- Department of Biochemistry and Biophysics , Texas A&M University , College Station , Texas 77843 , United States
| | - Tamari Narindoshvili
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Lydia Bogomolnaya
- Department of Microbial Pathogenesis and Immunology, College of Medicine , Texas A&M University System Health Science Center , Bryan , Texas 77807 , United States
| | - Marissa Talamantes
- Department of Microbial Pathogenesis and Immunology, College of Medicine , Texas A&M University System Health Science Center , Bryan , Texas 77807 , United States
| | - Ahmed El Saadi
- Department of Microbial Pathogenesis and Immunology, College of Medicine , Texas A&M University System Health Science Center , Bryan , Texas 77807 , United States
| | - Helene Andrews-Polymenis
- Department of Microbial Pathogenesis and Immunology, College of Medicine , Texas A&M University System Health Science Center , Bryan , Texas 77807 , United States
| | - Frank M Raushel
- Department of Biochemistry and Biophysics , Texas A&M University , College Station , Texas 77843 , United States.,Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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24
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Tang C, Du Y, Liang Q, Cheng Z, Tian J. A selenium-containing selective histone deacetylase 6 inhibitor for targeted in vivo breast tumor imaging and therapy. J Mater Chem B 2019. [DOI: 10.1039/c9tb00383e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have developed a HDAC6-selective inhibitor, SelSA, which can be utilized as a target for the detection and treatment of ERα(+) breast cancer and TNBC. The biodistribution study showed that SelSA can specifically target the breast tumor and display potent antitumor effects in vivo. This result will help to better improve the treatment efficacy against breast cancer.
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Affiliation(s)
- Chu Tang
- Engineering Research Center of Molecular and Neuro Imaging Ministry of Education
- School of Life Science and Technology
- Xidian University
- Xi’an
- China
| | - Yang Du
- CAS Key Laboratory of Molecular Imaging
- The State Key Laboratory of Management and Control for Complex Systems
- Institute of Automation
- Chinese Academy of Sciences
- Beijing 100190
| | - Qian Liang
- CAS Key Laboratory of Molecular Imaging
- The State Key Laboratory of Management and Control for Complex Systems
- Institute of Automation
- Chinese Academy of Sciences
- Beijing 100190
| | - Zhen Cheng
- Molecular Imaging Program at Stanford (MIPS)
- Department of Radiology, and Bio-X Program
- Canary Center at Stanford for Cancer Early Detection
- Stanford University
- Stanford
| | - Jie Tian
- Engineering Research Center of Molecular and Neuro Imaging Ministry of Education
- School of Life Science and Technology
- Xidian University
- Xi’an
- China
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25
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Kaysser L. Built to bind: biosynthetic strategies for the formation of small-molecule protease inhibitors. Nat Prod Rep 2019; 36:1654-1686. [DOI: 10.1039/c8np00095f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The discovery and characterization of natural product protease inhibitors has inspired the development of numerous pharmaceutical agents.
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Affiliation(s)
- Leonard Kaysser
- Department of Pharmaceutical Biology
- University of Tübingen
- 72076 Tübingen
- Germany
- German Centre for Infection Research (DZIF)
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26
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Bai L, Ohnishi Y, Kim ES. A3 foresight network on natural products. J Ind Microbiol Biotechnol 2018; 46:313-317. [PMID: 30474768 DOI: 10.1007/s10295-018-2111-8] [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: 09/21/2018] [Accepted: 11/17/2018] [Indexed: 11/25/2022]
Abstract
Discovery and development of natural products (NPs) have played important roles in the fields of human medicine and other biotechnology fields for the past several decades. Recent genome-mining approaches for the isolation of novel and cryptic NP biosynthetic gene clusters (BGCs) have led to the growing interest in NP research communities including Asian NP researchers from China, Japan, and Korea. Recently, a three-nation government-sponsored program named 'A3 Foresight Network on Chemical and Synthetic Biology of NPs' has been launched with a goal of establishing an Asian hub for NP research-&-personnel exchange program. This brief commentary describes introduction, main researchers, and future perspective of A3 NP network program.
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Affiliation(s)
- Linquan Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University, Incheon, South Korea.
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27
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Wang KKA, Ng TL, Wang P, Huang Z, Balskus EP, van der Donk WA. Glutamic acid is a carrier for hydrazine during the biosyntheses of fosfazinomycin and kinamycin. Nat Commun 2018; 9:3687. [PMID: 30206228 PMCID: PMC6133997 DOI: 10.1038/s41467-018-06083-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 08/14/2018] [Indexed: 01/03/2023] Open
Abstract
Fosfazinomycin and kinamycin are natural products that contain nitrogen-nitrogen (N-N) bonds but that are otherwise structurally unrelated. Despite their considerable structural differences, their biosynthetic gene clusters share a set of genes predicted to facilitate N-N bond formation. In this study, we show that for both compounds, one of the nitrogen atoms in the N-N bond originates from nitrous acid. Furthermore, we show that for both compounds, an acetylhydrazine biosynthetic synthon is generated first and then funneled via a glutamyl carrier into the respective biosynthetic pathways. Therefore, unlike other pathways to N-N bond-containing natural products wherein the N-N bond is formed directly on a biosynthetic intermediate, during the biosyntheses of fosfazinomycin, kinamycin, and related compounds, the N-N bond is made in an independent pathway that forms a branch of a convergent route to structurally complex natural products.
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Affiliation(s)
- Kwo-Kwang A Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Tai L Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, 02138, MA, USA
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, 02138, MA, USA
- Red & Charline McCombs Institute for the Early Detection and Treatment of Cancer, University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Zedu Huang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Department of Chemistry, Fudan University, Shanghai, 200438-6789, China
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, 02138, MA, USA.
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
- Howard Hughes Medical Institute, Chevy Chase, 20815, MD, USA.
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28
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Natural product-derived compounds in HIV suppression, remission, and eradication strategies. Antiviral Res 2018; 158:63-77. [PMID: 30063970 DOI: 10.1016/j.antiviral.2018.07.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 07/10/2018] [Accepted: 07/21/2018] [Indexed: 12/12/2022]
Abstract
While combination antiretroviral therapy (cART) has successfully converted HIV to a chronic but manageable infection in many parts of the world, HIV continues to persist within latent cellular reservoirs, which can become reactivated at any time to produce infectious virus. New therapies are therefore needed not only for HIV suppression but also for containing or eliminating HIV reservoirs. Compounds derived from plant, marine, and other natural products have been found to combat HIV infection and/or target HIV reservoirs, and these discoveries have substantially guided current HIV therapy-based studies. Here we summarize the role of natural product-derived compounds in current HIV suppression, remission, and cure strategies.
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Wolf F, Leipoldt F, Kulik A, Wibberg D, Kalinowski J, Kaysser L. Characterization of the Actinonin Biosynthetic Gene Cluster. Chembiochem 2018; 19:1189-1195. [PMID: 29600569 DOI: 10.1002/cbic.201800116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Indexed: 11/05/2022]
Abstract
The hydroxamate moiety of the natural product actinonin mediates inhibition of metalloproteinases because of its chelating properties towards divalent cations in the active site of those enzymes. Owing to its antimicrobial activity, actinonin has served as a lead compound for the development of new antibiotic drug candidates. Recently, we identified a putative gene cluster for the biosynthesis of actinonin. Here, we confirm and characterize this cluster by heterologous pathway expression and gene-deletion experiments. We assigned the biosynthetic gene cluster to actinonin production and determine the cluster boundaries. Furthermore, we establish that ActI, an AurF-like oxygenase, is responsible for the N-hydroxylation reaction that forms the hydroxamate warhead. Our findings provide the basis for more detailed investigations of actinonin biosynthesis.
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Affiliation(s)
- Felix Wolf
- Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner site Tübingen
| | - Franziska Leipoldt
- Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner site Tübingen
| | - Andreas Kulik
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33594, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33594, Bielefeld, Germany
| | - Leonard Kaysser
- Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner site Tübingen
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Williams DE, Gunasekara NW, Ratnaweera PB, Zheng Z, Ellis S, Dada S, Patrick BO, Wijesundera RLC, Nanayakkara CM, Jefferies WA, de Silva ED, Andersen RJ. Serpulanines A to C, N-Oxidized Tyrosine Derivatives Isolated from the Sri Lankan Fungus Serpula sp.: Structure Elucidation, Synthesis, and Histone Deacetylase Inhibition. JOURNAL OF NATURAL PRODUCTS 2018; 81:78-84. [PMID: 29303267 DOI: 10.1021/acs.jnatprod.7b00680] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Serpulanines A (1), B (2), and C (3) have been isolated from extracts of the rare Sri Lankan macrofungus Serpula sp. The structures of 1, 2, and 3 were elucidated by a combination of spectroscopic and single-crystal X-ray diffraction analyses. Serpulanines A (1) and B (2) both contain the rare (E)-2-hydroxyimino hydroxamic acid functional group array. A proposed biogenesis for serpulanine B (2) suggests that its (E)-2-hydroxyimino hydroxamic acid moiety arises from a diketopiperazine precursor. Synthetic serpulanine A (1) inhibited class I/II histone deacetylases in murine metastatic lung carcinoma cells with an IC50 of 7 μM.
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Affiliation(s)
- David E Williams
- Departments of Chemistry and Earth, Ocean & Atmospheric Sciences, University of British Columbia , 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
| | - Niranjan W Gunasekara
- Departments of Chemistry and Plant Science, University of Colombo , Colombo 03, Sri Lanka
| | - Pamoda B Ratnaweera
- Departments of Chemistry and Earth, Ocean & Atmospheric Sciences, University of British Columbia , 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
- Departments of Chemistry and Plant Science, University of Colombo , Colombo 03, Sri Lanka
- Department of Science and Technology, Uva Wellassa University , Badulla, Sri Lanka
| | - Zehua Zheng
- Departments of Chemistry and Earth, Ocean & Atmospheric Sciences, University of British Columbia , 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
| | - Samantha Ellis
- The Michael Smith Laboratories; Vancouver Prostate Centre; Departments of Medical Genetics, Microbiology & Immunology, and Zoology; and The Centre for Blood Research and Djavad Mowafaghian Centre for Brain Health, University of British Columbia , Vancouver, BC, Canada
| | - Sarah Dada
- The Michael Smith Laboratories; Vancouver Prostate Centre; Departments of Medical Genetics, Microbiology & Immunology, and Zoology; and The Centre for Blood Research and Djavad Mowafaghian Centre for Brain Health, University of British Columbia , Vancouver, BC, Canada
| | - Brian O Patrick
- Department of Chemistry, University of British Columbia , 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
| | - Ravi L C Wijesundera
- Departments of Chemistry and Plant Science, University of Colombo , Colombo 03, Sri Lanka
| | | | - Wilfred A Jefferies
- The Michael Smith Laboratories; Vancouver Prostate Centre; Departments of Medical Genetics, Microbiology & Immunology, and Zoology; and The Centre for Blood Research and Djavad Mowafaghian Centre for Brain Health, University of British Columbia , Vancouver, BC, Canada
| | - E Dilip de Silva
- Departments of Chemistry and Plant Science, University of Colombo , Colombo 03, Sri Lanka
| | - Raymond J Andersen
- Departments of Chemistry and Earth, Ocean & Atmospheric Sciences, University of British Columbia , 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
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Warhead biosynthesis and the origin of structural diversity in hydroxamate metalloproteinase inhibitors. Nat Commun 2017; 8:1965. [PMID: 29213087 PMCID: PMC5719088 DOI: 10.1038/s41467-017-01975-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 10/27/2017] [Indexed: 11/09/2022] Open
Abstract
Metalloproteinase inhibitors often feature hydroxamate moieties to facilitate the chelation of metal ions in the catalytic center of target enzymes. Actinonin and matlystatins are potent metalloproteinase inhibitors that comprise rare N-hydroxy-2-pentyl-succinamic acid warheads. Here we report the identification and characterization of their biosynthetic pathways. By gene cluster comparison and a combination of precursor feeding studies, heterologous pathway expression and gene deletion experiments we are able to show that the N-hydroxy-alkyl-succinamic acid warhead is generated by an unprecedented variation of the ethylmalonyl-CoA pathway. Moreover, we present evidence that the remarkable structural diversity of matlystatin congeners originates from the activity of a decarboxylase-dehydrogenase enzyme with high similarity to enzymes that form epoxyketones. We further exploit this mechanism to direct the biosynthesis of non-natural matlystatin derivatives. Our work paves the way for follow-up studies on these fascinating pathways and allows the identification of new protease inhibitors by genome mining. Metalloproteinase inhibitors are leads for drug development, but their biosynthetic pathways are often unknown. Here the authors show that the acyl branched warhead of actinonin and matlystatins derives from an ethylmalonyl-CoA-like pathway and the structural diversity of matlystatins is due to the activity of a decarboxylase-dehydrogenase enzyme.
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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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