1
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Chao TH, Renata H. Chemoenzymatic Synthesis of 4,5-Dihydroxyisoleucine Fragment of α-Amanitin. Org Lett 2024; 26:3263-3266. [PMID: 38598422 DOI: 10.1021/acs.orglett.4c00901] [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: 04/12/2024]
Abstract
The ability of α-amanitin to potently inhibit RNA polymerase II (RNAP II) has elicited further research into its use as a novel payload for antibody-drug conjugates. Despite this promise, the de novo synthesis of α-amanitin is still a major challenge as it possesses an unusual bicyclic octapeptide structure that contains several oxidized amino acids, most notably 4,5-dihydroxy-l-isoleucine. Here, we report a concise chemoenzymatic synthesis of this key amino acid residue, which features two regioselective and diastereoselective enzymatic C-H oxidations on l-isoleucine.
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Affiliation(s)
- Tsung-Han Chao
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, Texas 77005, United States
| | - Hans Renata
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, Texas 77005, United States
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2
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Obydennik AY, Titov AA, Listratova AV, Borisova TN, Rybakov VB, Voskressensky LG, Varlamov AV. Concise and Free-Metal Access to Lactone-Annelated Pyrrolo[2,1- a]isoquinoline Derivatives via a 1,2-Rearrangement Step. Int J Mol Sci 2024; 25:1085. [PMID: 38256158 PMCID: PMC10816086 DOI: 10.3390/ijms25021085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Here, An efficient approach to obtaining previously unknown furo[2',3':2,3]pyrrolo[2,1-a]isoquinoline derivatives from readily available 1-R-1-ethynyl-2-vinylisoquinolines is described. The reaction features a simple procedure, occurs in hexaflouroisopropanol and does not require elevated temperatures. It has been found that the addition of glacial acetic acid significantly increases the yields of the target spirolactone products. Using trifluoroethanol instead of hexaflouroisopropanol results in the formation of pyrido[2,1-a]isoquinolines.
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Affiliation(s)
- Arina Y. Obydennik
- Organic Chemistry Department, Science Faculty, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, Moscow 117198, Russia; (A.Y.O.); (A.A.T.); (A.V.L.); (T.N.B.); (A.V.V.)
| | - Alexander A. Titov
- Organic Chemistry Department, Science Faculty, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, Moscow 117198, Russia; (A.Y.O.); (A.A.T.); (A.V.L.); (T.N.B.); (A.V.V.)
| | - Anna V. Listratova
- Organic Chemistry Department, Science Faculty, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, Moscow 117198, Russia; (A.Y.O.); (A.A.T.); (A.V.L.); (T.N.B.); (A.V.V.)
| | - Tatiana N. Borisova
- Organic Chemistry Department, Science Faculty, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, Moscow 117198, Russia; (A.Y.O.); (A.A.T.); (A.V.L.); (T.N.B.); (A.V.V.)
| | - Victor B. Rybakov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory, 1-3, Moscow 119991, Russia;
| | - Leonid G. Voskressensky
- Organic Chemistry Department, Science Faculty, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, Moscow 117198, Russia; (A.Y.O.); (A.A.T.); (A.V.L.); (T.N.B.); (A.V.V.)
| | - Alexey V. Varlamov
- Organic Chemistry Department, Science Faculty, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, Moscow 117198, Russia; (A.Y.O.); (A.A.T.); (A.V.L.); (T.N.B.); (A.V.V.)
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3
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Mori T, Abe I. Functional analysis of a fungal P450 enzyme. Methods Enzymol 2023; 693:171-190. [PMID: 37977730 DOI: 10.1016/bs.mie.2023.09.003] [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] [Indexed: 11/19/2023]
Abstract
Fungal cytochrome P450s participate in various physiological reactions, including the synthesis of internal cellular components, metabolic detoxification of xenobiotic compounds, and oxidative modification of natural products. Although functional analysis reports of fungal P450s continue to grow, there are still some difficulties as compared to prokaryotic P450s, because most of these fungal enzymes are transmembrane proteins. In this chapter, we will describe the methods for heterologous expression, in vivo analysis, enzyme preparation, and in vitro enzyme assays of the fungal P450 enzyme Trt6 and isomerase Trt14, which play important roles in the divergence of the biosynthetic pathway of terretonins, as a model for the functional analysis of fungal P450 enzymes.
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Affiliation(s)
- Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan; PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
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4
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Zwick CR, Renata H. Overview of Amino Acid Modifications by Iron- and α-Ketoglutarate-Dependent Enzymes. ACS Catal 2023. [DOI: 10.1021/acscatal.3c00424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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5
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Song Y, Wu C, Zhang J, Zhang W, Qin X, Yang Y, Kang G, Jiang J, Liu H. Switchable multipath cascade cyclization to synthesize bicyclic lactams and succinimides via chemodivergent reaction. Chem Commun (Camb) 2023; 59:3313-3316. [PMID: 36852458 DOI: 10.1039/d2cc06841a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Herein, a novel switchable multipath cascade cyclization via chemodivergent reaction between readily available ketoamides and deconjugated butenolides was developed to efficiently synthesize γ-lactone fused γ-lactams and succinimide fused hemiketals. The Aldol/aza-Michael reaction and Aldol/imidation/hemiketalization reaction were enabled by catalytic amounts of two bases, namely tetramethyl guanidine and NaOAc. A wide range of substrate scope with diverse functional group compatibility was demonstrated to deliver the corresponding products with good yield and excellent diastereoselectivity (>60 examples).
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Affiliation(s)
- Yimei Song
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, 325035, China.
| | - Chaofei Wu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, 325035, China.
| | - Jinhai Zhang
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, 325035, China.
| | - Wenhai Zhang
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, 325035, China.
| | - Xin Qin
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, 325035, China.
| | - Yixiao Yang
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, 325035, China.
| | - Guowei Kang
- Department of Chemistry, The Scripps Research Institute, North Torrey Pines Road, La Jolla 10550, USA.
| | - Jun Jiang
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, 325035, China.
| | - Hongxin Liu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, 325035, China. .,Institute of New Materials & Industrial Technology, Wenzhou University, Wenzhou, 325035, China.
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6
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Ohashi M, Tan D, Lu J, Jamieson CS, Kanayama D, Zhou J, Houk KN, Tang Y. Enzymatic cis-Decalin Formation in Natural Product Biosynthesis. J Am Chem Soc 2023; 145:3301-3305. [PMID: 36723171 PMCID: PMC9931682 DOI: 10.1021/jacs.2c12854] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Stereoselective synthesis of cis-decalin structures using [4 + 2] cycloaddition is challenging. We explored the biosynthetic pathway of the fungal natural product fischerin (1) to identify a new pericyclase FinI that can catalyze such a reaction. The cocrystal structure of FinI, a predicted O-methyltransferase, with the product and SAM provides insight into cis-decalin formation in nature.
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Affiliation(s)
- Masao Ohashi
- Departments of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
| | - Dan Tan
- Departments of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, People’s Republic of China
| | - Jiayan Lu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Cooper S. Jamieson
- Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Daiki Kanayama
- Departments of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
| | - Jiahai Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - K. N. Houk
- Departments of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
- Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Yi Tang
- Departments of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
- Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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7
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Chiang CY, Ohashi M, Tang Y. Deciphering chemical logic of fungal natural product biosynthesis through heterologous expression and genome mining. Nat Prod Rep 2023; 40:89-127. [PMID: 36125308 PMCID: PMC9906657 DOI: 10.1039/d2np00050d] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Covering: 2010 to 2022Heterologous expression of natural product biosynthetic gene clusters (BGCs) has become a widely used tool for genome mining of cryptic pathways, bottom-up investigation of biosynthetic enzymes, and engineered biosynthesis of new natural product variants. In the field of fungal natural products, heterologous expression of a complete pathway was first demonstrated in the biosynthesis of tenellin in Aspergillus oryzae in 2010. Since then, advances in genome sequencing, DNA synthesis, synthetic biology, etc. have led to mining, assignment, and characterization of many fungal BGCs using various heterologous hosts. In this review, we will highlight key examples in the last decade in integrating heterologous expression into genome mining and biosynthetic investigations. The review will cover the choice of heterologous hosts, prioritization of BGCs for structural novelty, and how shunt products from heterologous expression can reveal important insights into the chemical logic of biosynthesis. The review is not meant to be exhaustive but is rather a collection of examples from researchers in the field, including ours, that demonstrates the usefulness and pitfalls of heterologous biosynthesis in fungal natural product discovery.
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Affiliation(s)
- Chen-Yu Chiang
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Masao Ohashi
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Yi Tang
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
- Dept. of Chemistry and Biochemistry, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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8
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Recent Approaches for Downplaying Antibiotic Resistance: Molecular Mechanisms. BIOMED RESEARCH INTERNATIONAL 2023; 2023:5250040. [PMID: 36726844 PMCID: PMC9886476 DOI: 10.1155/2023/5250040] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/06/2022] [Accepted: 10/12/2022] [Indexed: 01/25/2023]
Abstract
Antimicrobial resistance (AMR) is a ubiquitous public health menace. AMR emergence causes complications in treating infections contributing to an upsurge in the mortality rate. The epidemic of AMR in sync with a high utilization rate of antimicrobial drugs signifies an alarming situation for the fleet recovery of both animals and humans. The emergence of resistant species calls for new treatments and therapeutics. Current records propose that health drug dependency, veterinary medicine, agricultural application, and vaccination reluctance are the primary etymology of AMR gene emergence and spread. Recently, several encouraging avenues have been presented to contest resistance, such as antivirulent therapy, passive immunization, antimicrobial peptides, vaccines, phage therapy, and botanical and liposomal nanoparticles. Most of these therapies are used as cutting-edge methodologies to downplay antibacterial drugs to subdue the resistance pressure, which is a featured motive of discussion in this review article. AMR can fade away through the potential use of current cutting-edge therapeutics, advancement in antimicrobial susceptibility testing, new diagnostic testing, prompt clinical response, and probing of new pharmacodynamic properties of antimicrobials. It also needs to promote future research on contemporary methods to maintain host homeostasis after infections caused by AMR. Referable to the microbial ability to break resistance, there is a great ultimatum for using not only appropriate and advanced antimicrobial drugs but also other neoteric diverse cutting-edge therapeutics.
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9
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Zhang T, Gu G, Liu G, Su J, Zhan Z, Zhao J, Qian J, Cai G, Cen S, Zhang D, Yu L. Late-stage cascade of oxidation reactions during the biosynthesis of oxalicine B in Penicillium oxalicum. Acta Pharm Sin B 2023; 13:256-270. [PMID: 36815048 PMCID: PMC9939320 DOI: 10.1016/j.apsb.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 11/01/2022] Open
Abstract
Oxalicine B (1) is an α-pyrone meroterpenoid with a unique bispirocyclic ring system derived from Penicillium oxalicum. The biosynthetic pathway of 15-deoxyoxalicine B (4) was preliminarily reported in Penicillium canescens, however, the genetic base and biochemical characterization of tailoring reactions for oxalicine B (1) has remained enigmatic. In this study, we characterized three oxygenases from the metabolic pathway of oxalicine B (1), including a cytochrome P450 hydroxylase OxaL, a hydroxylating Fe(II)/α-KG-dependent dioxygenase OxaK, and a multifunctional cytochrome P450 OxaB. Intriguingly, OxaK can catalyze various multicyclic intermediates or shunt products of oxalicines with impressive substrate promiscuity. OxaB was further proven via biochemical assays to have the ability to convert 15-hydroxdecaturin A (3) to 1 with a spiro-lactone core skeleton through oxidative rearrangement. We also solved the mystery of OxaL that controls C-15 hydroxylation. Chemical investigation of the wild-type strain and deletants enabled us to identify 10 metabolites including three new compounds, and the isolated compounds displayed potent anti-influenza A virus bioactivities exhibiting IC50 values in the range of 4.0-19.9 μmol/L. Our studies have allowed us to propose a late-stage biosynthetic pathway for oxalicine B (1) and create downstream derivatizations of oxalicines by employing enzymatic strategies.
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Affiliation(s)
- Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Guowei Gu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Jinhua Su
- The Third Medical Center, The General Hospital of People's Liberation Army, Beijing 100039, China
| | - Zhilai Zhan
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jianyuan Zhao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jinxiu Qian
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Guowei Cai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Dewu Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China,Corresponding authors. Tel./fax: +86 10 63187118.
| | - Liyan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China,Corresponding authors. Tel./fax: +86 10 63187118.
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10
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Tricyclic Fused Lactams by Mukaiyama Cyclisation of Phthalimides and Evaluation of their Biological Activity. Antibiotics (Basel) 2022; 12:antibiotics12010009. [PMID: 36671210 PMCID: PMC9854654 DOI: 10.3390/antibiotics12010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
We report that phthalimides may be cyclized using a Mukaiyama-type aldol coupling to give variously substituted fused lactam (1,2,3,9b-tetrahydro-5H-pyrrolo[2,1-a]isoindol-5-one) systems. This novel process shows a high level of regioselectivity for o-substituted phthalimides, dictated by steric and electronic factors, but not for m-substituted phthalimides. The initial aldol adduct is prone to elimination, giving 2,3-dihydro-5H-pyrrolo[2,1-a]isoindol-5-ones, and the initial cyclisation can be conducted in such a way that aldol cyclisation-elimination is achievable in a one-pot approach. The 2,3-dihydro-5H-pyrrolo[2,1-a]isoindol-5-ones possess cross conjugation and steric effects which significantly influence the reactivity of several functional groups, but conditions suitable for epoxidation, ester hydrolysis and amide formation, and reduction, which provide for ring manipulation, were identified. Many of the derived lactam systems, and especially the eliminated systems, show low solubility, which compromises biological activity, although in some cases, antibacterial and cytotoxic activity was found, and this new class of small molecule provides a useful skeleton for further elaboration and study.
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11
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Wang X, Kong D, Huang T, Xu F, Tang MC, Deng Z, Lin S. Flavoprotein StnP2 Catalyzes the β-Carboline Formation during the Streptonigrin Biosynthesis. ACS Chem Biol 2022; 17:3499-3506. [PMID: 36409520 DOI: 10.1021/acschembio.2c00704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
β-Carboline (βC) alkaloids constitute a large family of indole alkaloids that exhibit diverse pharmacological properties, such as antitumor, antiviral, antiparasitic, and antimicrobial activities. Here, we report that a flavoprotein StnP2 catalyzes the dehydrogenation at C1-N2 of a tetrahydro-β-carboline (THβC) generating a 3,4-dihydro-β-carboline (DHβC), and the DHβC subsequently undergoes a spontaneous dehydrogenation to βC formation involved in the biosynthesis of the antitumor agent streptonigrin. Biochemical characterization showed that StnP2 catalyzed the highly regio- and stereo-selective dehydrogenation, and StnP2 exhibits promiscuity toward different THβCs. This study provides an alternative kind of enzyme catalyzing the biosynthesis of βC alkaloids and enhances the importance of flavoproteins.
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Affiliation(s)
- Xiaozheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Dekun Kong
- Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Chongqing 400715, China
| | - Tingting Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Fei Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Man-Cheng Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.,Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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12
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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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Discovery and characterization of a terpene biosynthetic pathway featuring a norbornene-forming Diels-Alderase. Nat Commun 2022; 13:2568. [PMID: 35546152 PMCID: PMC9095873 DOI: 10.1038/s41467-022-30288-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
Pericyclases, enzymes that catalyze pericyclic reactions, form an expanding family of enzymes that have biocatalytic utility. Despite the increasing number of pericyclases discovered, the Diels-Alder cyclization between a cyclopentadiene and an olefinic dienophile to form norbornene, which is among the best-studied cycloadditions in synthetic chemistry, has surprisingly no enzymatic counterpart to date. Here we report the discovery of a pathway featuring a norbornene synthase SdnG for the biosynthesis of sordaricin-the terpene precursor of antifungal natural product sordarin. Full reconstitution of sordaricin biosynthesis reveals a concise oxidative strategy used by Nature to transform an entirely hydrocarbon precursor into the highly functionalized substrate of SdnG for intramolecular Diels-Alder cycloaddition. SdnG generates the norbornene core of sordaricin and accelerates this reaction to suppress host-mediated redox modifications of the activated dienophile. Findings from this work expand the scopes of pericyclase-catalyzed reactions and P450-mediated terpene maturation. Pericyclase enzymes are an expanding family of enzymes. Here, the authors identify the norbornene synthase SdnG, a pericyclase for the intramolecular Diels-Alder reaction between a cyclopentadiene and an olefinic dienophile to form the sordaricin norbornene structure, and reconstitute the sordaricin biosynthesis.
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14
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Watanabe K, Sato M, Osada H. Recent advances in the chemo-biological characterization of decalin natural products and unraveling of the workings of Diels-Alderases. Fungal Biol Biotechnol 2022; 9:9. [PMID: 35488322 PMCID: PMC9055775 DOI: 10.1186/s40694-022-00139-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/15/2022] [Indexed: 11/19/2022] Open
Abstract
The Diels–Alder (DA) reaction refers to a [4 + 2] cycloaddition reaction that falls under the category of pericyclic reactions. It is a reaction that allows regio- and stereo-selective construction of two carbon–carbon bonds simultaneously in a concerted manner to generate a six-membered ring structure through a six-electron cyclic transition state. The DA reaction is one of the most widely applied reactions in organic synthesis, yet its role in biological systems has been debated intensely over the last four decades. A survey of secondary metabolites produced by microorganisms suggests strongly that many of the compounds possess features that are likely formed through DA reactions, and most of them are considered to be catalyzed by enzymes that are commonly referred to as Diels–Alderases (DAases). In recent years, especially over the past 10 years or so, we have seen an accumulation of a substantial body of work that substantiates the argument that DAases indeed exist and play a critical role in the biosynthesis of complex metabolites. This review will cover the DAases involved in the biosynthesis of decalin moieties, which are found in many of the medicinally important natural products, especially those produced by fungi. In particular, we will focus on a subset of secondary metabolites referred to as pyrrolidine-2-one-bearing decalin compounds and discuss the decalin ring stereochemistry and the biological activities of those compounds. We will also look into the genes and enzymes that drive the biosynthetic construction of those complex natural products, and highlight the recent progress made on the structural and mechanistic understanding of DAases, especially regarding how those enzymes exert stereochemical control over the [4 + 2] cycloaddition reactions they catalyze.
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Affiliation(s)
- Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan.
| | - Michio Sato
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Hiroyuki Osada
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan. .,Chemical Resource Development Research Unit, RIKEN Center for Sustainable Resource Science, Wako-shi, 351-0198, Japan.
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15
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Skellam E. Biosynthesis of fungal polyketides by collaborating and trans-acting enzymes. Nat Prod Rep 2022; 39:754-783. [PMID: 34842268 DOI: 10.1039/d1np00056j] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Covering: 1999 up to 2021Fungal polyketides encompass a range of structurally diverse molecules with a wide variety of biological activities. The giant multifunctional enzymes that synthesize polyketide backbones remain enigmatic, as do many of the tailoring enzymes involved in functional modifications. Recent advances in elucidating biosynthetic gene clusters (BGCs) have revealed numerous examples of fungal polyketide synthases that require the action of collaborating enzymes to synthesize the carbon backbone. This review will discuss collaborating and trans-acting enzymes involved in loading, extending, and releasing polyketide intermediates from fungal polyketide synthases, and additional modifications introduced by trans-acting enzymes demonstrating the complexity encountered when investigating natural product biosynthesis in fungi.
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Affiliation(s)
- Elizabeth Skellam
- Department of Chemistry, BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA.
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16
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Moloney MG, Ibbotson LT, Christensen KE, Genov M, Pretsch A, Pretsch D. Skeletal Analogues of UCS1025A and B by Cyclization of Maleimides: Synthesis and Biological Activity. Synlett 2022. [DOI: 10.1055/s-0040-1719876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractApplication of a direct ring-closing approach which exploits an intramolecular aldol reaction with a ketene silyl acetal onto a remote imide function leading to the core skeleton of UCS1025A and B effectively provides access to small library of substituted analogues; of interest is their complete lack of antibacterial activity against MRSA (Gram+) and E. coli (Gram–) bacterial strains.
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Affiliation(s)
- Mark G. Moloney
- The Department of Chemistry, Chemistry Research Laboratory, University of Oxford
- Oxford Suzhou Centre for Advanced Research
| | - Lewis T. Ibbotson
- The Department of Chemistry, Chemistry Research Laboratory, University of Oxford
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17
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Gao Y, Xie M, Yu C, Zhang M, Huang J, Li Q, Zhang H, Li L. Heterologous Expression of Macrollins from Phytopathogenic Macrophomina phaseolina Revealed a Cytochrome P450 Mono-oxygenase in the Biosynthesis of β-Hydroxyl Tetramic Acid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15175-15183. [PMID: 34881573 DOI: 10.1021/acs.jafc.1c05304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Macrophomina phaseolina (M. phaseolina) is a crucial pathogenic fungus that can cause severe charcoal rot in economic crops and other plants. In this study, four new natural products, macrollins A-D, were discovered from M. phaseolina by the strategy of heterologous expression. To our knowledge, macrollins are the first reported polyketide-amino acid hybrids from the plant pathogen. Heterologous expression and in vitro reactions revealed a cytochrome P450 mono-oxygenase (MacC) catalyzing the hydroxylation at the β-carbon of tetramic acid molecules, which is different from P450s leading to the ring expansion in the biosynthesis of fungal 2-pyridones. Phylogenetic analysis of P450s involved in the fungal polyketide-amino acid hybrids showed that MacC was not classified in any known clades. The putative oxidative mechanisms of the P450s and the biosynthetic pathway of macrollins were also proposed.
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Affiliation(s)
- Yangle Gao
- Engineering Research Center of Industrial Microbiology, Fujian Normal University, Fuzhou, Fujian 350117, China
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Mengsi Xie
- Engineering Research Center of Industrial Microbiology, Fujian Normal University, Fuzhou, Fujian 350117, China
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Cui Yu
- Engineering Research Center of Industrial Microbiology, Fujian Normal University, Fuzhou, Fujian 350117, China
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Mingliang Zhang
- Engineering Research Center of Industrial Microbiology, Fujian Normal University, Fuzhou, Fujian 350117, China
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Jianzhong Huang
- Engineering Research Center of Industrial Microbiology, Fujian Normal University, Fuzhou, Fujian 350117, China
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Qin Li
- Engineering Research Center of Industrial Microbiology, Fujian Normal University, Fuzhou, Fujian 350117, China
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Huaidong Zhang
- Engineering Research Center of Industrial Microbiology, Fujian Normal University, Fuzhou, Fujian 350117, China
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Li Li
- Engineering Research Center of Industrial Microbiology, Fujian Normal University, Fuzhou, Fujian 350117, China
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, Fujian 361021, China
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18
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Enzymatic control of endo- and exo-stereoselective Diels–Alder reactions with broad substrate scope. Nat Catal 2021. [DOI: 10.1038/s41929-021-00717-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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19
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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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20
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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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21
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Yuan B, Wu Z, Ji W, Liu D, Guo X, Yang D, Fan A, Jia H, Ma M, Lin W. Discovery of cyclohexadepsipeptides with anti-Zika virus activities and biosynthesis of the nonproteinogenic building block (3S)-methyl-l-proline. J Biol Chem 2021; 297:100822. [PMID: 34029593 PMCID: PMC8233208 DOI: 10.1016/j.jbc.2021.100822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/28/2021] [Accepted: 05/20/2021] [Indexed: 11/23/2022] Open
Abstract
The fungal cyclohexadepsipeptides destruxins (DTXs), isaridins (ISDs), and isariins (ISRs) are nonribosomal peptides whose structures include a 19-membered ring composed of five amino acid residues and one α- or β-hydroxy acid residue. These cyclohexadepsipeptides contain unusual nonproteinogenic amino acid-building blocks and possess a range of antiviral, antibacterial, and other activities. The biosynthetic gene clusters for ISDs and ISRs have not been identified, and the biosynthesis of the nonproteinogenic (3S)-methyl-l-proline residue, which is found in DTXs, ISDs, and many other natural products, lacks full characterization. In an ongoing effort to identify compounds that can inhibit the Zika virus (ZIKV), we examined the extract of marine-derived fungus Beauveria felina SX-6-22 and discovered 30 DTXs, ISDs, and ISRs (1-30) including seven new compounds (1-7). The anti-ZIKV assays showed that 9-12 and 16-18 possess inhibitory activities against ZIKV RNA replication and NS5 (nonstructural protein 5) production in ZIKV-infected A549 cells. We sequenced the genome of B. felina SX-6-22 and identified three biosynthetic gene clusters detx, isd and isr, which are responsible for the biosynthesis of DTXs, ISDs, and ISRs, respectively. Comparative analyses of the three gene clusters clarified the biosynthetic relationships among these cyclohexadepsipeptides. Finally, we characterized the entire biosynthesis of nonproteinogenic building block (3S)-methyl-l-proline. The Δ1-pyrroline-5-carboxylate reductases (P5CRs), also used in the biosynthesis of l-proline, were demonstrated to catalyze the final reduction step in (3S)-methyl-l-proline formation, suggesting potential cross talk between primary and secondary metabolisms. These results provide opportunities for biosynthetic pathway engineering to generate new anti-ZIKV cyclohexadepsipeptides.
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Affiliation(s)
- Bochuan Yuan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Ziwei Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Wei Ji
- School of Basic Medical Sciences, Peking University, Beijing, China
| | - Dong Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Xiang Guo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Aili Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Hongli Jia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China.
| | - Wenhan Lin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China; Institute of Ocean Research, Peking University, Beijing, China.
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22
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Abstract
It has been proposed that biosyntheses of many natural products involve pericyclic reactions, including Diels-Alder (DA) reaction. However, only a small set of enzymes have been proposed to catalyze pericyclic reactions. Most surprisingly, there has been no formal identification of natural enzymes that can be defined to catalyze DA reactions (DAases), despite the wide application of the reaction in chemical syntheses of complex organic compounds. However, recent studies began to accumulate a growing body of evidence that supports the notion that enzymes that formally catalyze DA reactions, in fact exist. In this review, I will begin by describing a short history behind the discovery and characterization of macrophomate synthase, one of the earliest enzymes that was proposed to catalyze an intermolecular DA reaction during the biosynthesis of a substituted benzoic acid in a phytopathogenic fungus Macrophoma commelinae. Then, I will discuss representative enzymes that have been chemically authenticated to catalyze DA reactions, with emphasis on more recent discoveries of DAases involved mainly in fungal secondary metabolite biosynthesis except for one example from a marine streptomycete. The current success in identification of a series of DAases and enzymes that catalyze other pericyclic reactions owes to the combined efforts from both the experimental and theoretical approaches in discovering natural products. Such efforts typically involve identifying the chemical features derived from cycloaddition reactions, isolating the biosynthetic genes that encode enzymes that generate such chemical features and deciphering the reaction mechanisms for the enzyme-catalyzed pericyclic reactions.
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Affiliation(s)
- Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan.
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23
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Ohashi M, Kakule TB, Tang MC, Jamieson CS, Liu M, Zhao YL, Houk KN, Tang Y. Biosynthesis of para-Cyclophane-Containing Hirsutellone Family of Fungal Natural Products. J Am Chem Soc 2021; 143:5605-5609. [PMID: 33834778 DOI: 10.1021/jacs.1c00098] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hirsutellones are fungal natural products containing a macrocyclic para-cyclophane connected to a decahydrofluorene ring system. We have elucidated the biosynthetic pathway for pyrrocidine B (3) and GKK1032 A2 (4). Two small hypothetical proteins, an oxidoreductase and a lipocalin-like protein, function cooperatively in the oxidative cyclization of the cyclophane, while an additional hypothetical protein in the pyrrocidine pathway catalyzes the exo-specific cycloaddition to form the cis-fused decahydrofluorene.
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Affiliation(s)
| | | | | | | | | | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, MOE-LSB and MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Zhang H, Hantke V, Bruhnke P, Skellam EJ, Cox RJ. Chemical and Genetic Studies on the Formation of Pyrrolones During the Biosynthesis of Cytochalasans. Chemistry 2021; 27:3106-3113. [PMID: 33146923 PMCID: PMC7898483 DOI: 10.1002/chem.202004444] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Indexed: 01/17/2023]
Abstract
A key step during the biosynthesis of cytochalasans is a proposed Knoevenagel condensation to form the pyrrolone core, enabling the subsequent 4+2 cycloaddition reaction that results in the characteristic octahydroisoindolone motif of all cytochalasans. In this work, we investigate the role of the highly conserved α,β-hydrolase enzymes PyiE and ORFZ during the biosynthesis of pyrichalasin H and the ACE1 metabolite, respectively, using gene knockout and complementation techniques. Using synthetic aldehyde models we demonstrate that the Knoevenagel condensation proceeds spontaneously but results in the 1,3-dihydro-2H-pyrrol-2-one tautomer, rather than the required 1,5-dihydro-2H-pyrrol-2-one tautomer. Taken together our results suggest that the α,β-hydrolase enzymes are essential for first ring cyclisation, but the precise nature of the intermediates remains to be determined.
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Affiliation(s)
- Haili Zhang
- Institute for Organic ChemistryLeibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
- Biomolekulares Wirkstoff Zentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Verena Hantke
- Institute for Organic ChemistryLeibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
- Biomolekulares Wirkstoff Zentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Pia Bruhnke
- Institute for Organic ChemistryLeibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
- Biomolekulares Wirkstoff Zentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Elizabeth J. Skellam
- Institute for Organic ChemistryLeibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
- Biomolekulares Wirkstoff Zentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 3830167HannoverGermany
- Current Address: Department of ChemistryUniversity of North Texas1508 W Mulberry30167DentonTexasUSA
| | - Russell J. Cox
- Institute for Organic ChemistryLeibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
- Biomolekulares Wirkstoff Zentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 3830167HannoverGermany
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25
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Liu J, Liu A, Hu Y. Enzymatic dimerization in the biosynthetic pathway of microbial natural products. Nat Prod Rep 2021; 38:1469-1505. [PMID: 33404031 DOI: 10.1039/d0np00063a] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Covering: up to August 2020The dramatic increase in the identification of dimeric natural products generated by microorganisms and plants has played a significant role in drug discovery. The biosynthetic pathways of these products feature inherent dimerization reactions, which are valuable for biosynthetic applications and chemical transformations. The extraordinary mechanisms of the dimerization of secondary metabolites should advance our understanding of the uncommon chemical rules for natural product biosynthesis, which will, in turn, accelerate the discovery of dimeric reactions and molecules in nature and provide promising strategies for the total synthesis of natural products through dimerization. This review focuses on the enzymes involved in the dimerization in the biosynthetic pathway of microbial natural products, with an emphasis on cytochrome P450s, laccases, and intermolecular [4 + 2] cyclases, along with other atypical enzymes. The identification, characterization, and catalytic landscapes of these enzymes are also introduced.
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Affiliation(s)
- Jiawang Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
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26
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Renata H. Exploration of Iron- and a-Ketoglutarate-Dependent Dioxygenases as Practical Biocatalysts in Natural Product Synthesis. Synlett 2021; 32:775-784. [PMID: 34413574 PMCID: PMC8372184 DOI: 10.1055/s-0040-1707320] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Catalytic C─H oxidation is a powerful transformation with enormous promise to streamline access to complex molecules. In recent years, biocatalytic C─H oxidation strategies have received tremendous attention due to their potential to address unmet regio- and stereoselectivity challenges that are often encountered with the use of small-molecule-based catalysts. This Account provides an overview of recent contributions from our laboratory in this area, specifically in the use of iron- and α-ketoglutarate-dependent dioxygenases in the chemoenzymatic synthesis of complex natural products.
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Affiliation(s)
- Hans Renata
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
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27
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Zhang X, Guo J, Cheng F, Li S. Cytochrome P450 enzymes in fungal natural product biosynthesis. Nat Prod Rep 2021; 38:1072-1099. [PMID: 33710221 DOI: 10.1039/d1np00004g] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Covering: 2015 to the end of 2020 Fungal-derived polyketides, non-ribosomal peptides, terpenoids and their hybrids contribute significantly to the chemical space of total natural products. Cytochrome P450 enzymes play essential roles in fungal natural product biosynthesis with their broad substrate scope, great catalytic versatility and high frequency of involvement. Due to the membrane-bound nature, the functional and mechanistic understandings for fungal P450s have been limited for quite a long time. However, recent technical advances, such as the efficient and precise genome editing techniques and the development of several filamentous fungal strains as heterologous P450 expression hosts, have led to remarkable achievements in fungal P450 studies. Here, we provide a comprehensive review to cover the most recent progresses from 2015 to 2020 on catalytic functions and mechanisms, research methodologies and remaining challenges in the fast-growing field of fungal natural product biosynthetic P450s.
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Affiliation(s)
- Xingwang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China. and Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Jiawei Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Fangyuan Cheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China. and Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
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28
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Wu YT, Zhang R, Duan XY, Yu HF, Sun BY, Qi J. Access to dihydropyrano[3,2- b]pyrrol-5-ones skeletons by N-heterocyclic carbene-catalyzed [3+3] annulations. Chem Commun (Camb) 2020; 56:9854-9857. [PMID: 32840527 DOI: 10.1039/d0cc04661b] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A novel and efficient NHC-catalyzed [3+3] annulation of enals with pyrrol-4-ones was developed, thus providing the dihydropyrano[3,2-b]pyrrol-5-one core structures with broad scope and good to excellent enantioselectivities. Notably, this strategy could also expand to the synthesis of axially chiral compounds and polysubstituted indoles.
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Affiliation(s)
- Ya-Tong Wu
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, People's Republic of China.
| | - Rui Zhang
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, People's Republic of China.
| | - Xiao-Yong Duan
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, People's Republic of China. and Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Hebei University, Baoding 071002, People's Republic of China
| | - Hai-Fei Yu
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, People's Republic of China.
| | - Bo-Yu Sun
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, People's Republic of China.
| | - Jing Qi
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, People's Republic of China. and Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Hebei University, Baoding 071002, People's Republic of China
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29
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Minami A, Ugai T, Ozaki T, Oikawa H. Predicting the chemical space of fungal polyketides by phylogeny-based bioinformatics analysis of polyketide synthase-nonribosomal peptide synthetase and its modification enzymes. Sci Rep 2020; 10:13556. [PMID: 32782278 PMCID: PMC7421883 DOI: 10.1038/s41598-020-70177-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/24/2020] [Indexed: 11/10/2022] Open
Abstract
Fungal polyketide synthase (PKS)–nonribosomal peptide synthetase (NRPS) hybrids are key enzymes for synthesizing structurally diverse hybrid natural products (NPs) with characteristic biological activities. Predicting their chemical space is of particular importance in the field of natural product chemistry. However, the unexplored programming rule of the PKS module has prevented prediction of its chemical structure based on amino acid sequences. Here, we conducted a phylogenetic analysis of 884 PKS–NRPS hybrids and a modification enzyme analysis of the corresponding biosynthetic gene cluster, revealing a hidden relationship between its genealogy and core structures. This unexpected result allowed us to predict 18 biosynthetic gene cluster (BGC) groups producing known carbon skeletons (number of BGCs; 489) and 11 uncharacterized BGC groups (171). The limited number of carbon skeletons suggests that fungi tend to select PK skeletons for survival during their evolution. The possible involvement of a horizontal gene transfer event leading to the diverse distribution of PKS–NRPS genes among fungal species is also proposed. This study provides insight into the chemical space of fungal PKs and the distribution of their biosynthetic gene clusters.
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Affiliation(s)
- Atsushi Minami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
| | - Takahiro Ugai
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Taro Ozaki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
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30
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Zwick CR, Renata H. Harnessing the biocatalytic potential of iron- and α-ketoglutarate-dependent dioxygenases in natural product total synthesis. Nat Prod Rep 2020; 37:1065-1079. [PMID: 32055818 PMCID: PMC7426249 DOI: 10.1039/c9np00075e] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to the end of 2019Iron- and α-ketoglutarate-dependent dioxygenases (Fe/αKGs) represent a versatile and intriguing enzyme family by virtue of their ability to directly functionalize unactivated C-H bonds at the cost of αKG and O2. Fe/αKGs play an important role in the biosynthesis of natural products, valuable biologically active secondary metabolites frequently pursued as drug leads. The field of natural product total synthesis seeks to contruct these molecules as effeciently as possible, although natural products continue to challenge chemists due to their intricate structural complexity. Chemoenzymatic approaches seek to remedy the shortcomings of traditional synthetic methodology by combining Nature's biosynthetic machinery with traditional chemical methods to efficiently construct natural products. Although other oxygenase families have been widely employed for this purpose, Fe/αKGs remain underutilized. The following review will cover recent chemoenzymatic total syntheses involving Fe/αKG enzymes. Additionally, related information involving natural product biosynthesis, methods development, and non-chemoenzymatic total syntheses will be discussed to inform retrosynthetic logic and synthetic design.
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Affiliation(s)
- Christian R Zwick
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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31
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Chen M, Liu CT, Tang Y. Discovery and Biocatalytic Application of a PLP-Dependent Amino Acid γ-Substitution Enzyme That Catalyzes C-C Bond Formation. J Am Chem Soc 2020; 142:10506-10515. [PMID: 32434326 DOI: 10.1021/jacs.0c03535] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pyridoxal phosphate (PLP)-dependent enzymes can catalyze transformations of l-amino acids at α, β, and γ positions. These enzymes are frequently involved in the biosynthesis of nonproteinogenic amino acids as building blocks of natural products and are attractive biocatalysts. Here, we report the discovery of a two-step enzymatic synthesis of (2S,6S)-6-methyl pipecolate 1, from the biosynthetic pathway of citrinadin. The key enzyme CndF is PLP-dependent and catalyzes the synthesis of (S)-2-amino-6-oxoheptanoate 3 that is in equilibrium with the cyclic Schiff base. The second enzyme CndE is a stereoselective imine reductase that gives 1. Biochemical characterization of CndF showed this enzyme performs γ-elimination of O-acetyl-l-homoserine to generate the vinylglycine ketimine, which is subjected to nucleophilic attack by acetoacetate to form the new Cγ-Cδ bond in 3 and complete the γ-substitution reaction. CndF displays promiscuity toward different β-keto carboxylate and esters. With use of an Aspergillus strain expressing CndF and CndE, feeding various alkyl-β-keto esters led to the biosynthesis of 6-substituted l-pipecolates. The discovery of CndF expands the repertoire of reactions that can be catalyzed by PLP-dependent enzymes.
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Affiliation(s)
- Mengbin Chen
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Chun-Ting Liu
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
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32
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Gao L, Su C, Du X, Wang R, Chen S, Zhou Y, Liu C, Liu X, Tian R, Zhang L, Xie K, Chen S, Guo Q, Guo L, Hano Y, Shimazaki M, Minami A, Oikawa H, Huang N, Houk KN, Huang L, Dai J, Lei X. FAD-dependent enzyme-catalysed intermolecular [4+2] cycloaddition in natural product biosynthesis. Nat Chem 2020; 12:620-628. [DOI: 10.1038/s41557-020-0467-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/14/2020] [Indexed: 01/21/2023]
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Synthetic biology based construction of biological activity-related library of fungal decalin-containing diterpenoid pyrones. Nat Commun 2020; 11:1830. [PMID: 32286350 PMCID: PMC7156458 DOI: 10.1038/s41467-020-15664-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/19/2020] [Indexed: 12/12/2022] Open
Abstract
A synthetic biology method based on heterologous biosynthesis coupled with genome mining is a promising approach for increasing the opportunities to rationally access natural product with novel structures and biological activities through total biosynthesis and combinatorial biosynthesis. Here, we demonstrate the advantage of the synthetic biology method to explore biological activity-related chemical space through the comprehensive heterologous biosynthesis of fungal decalin-containing diterpenoid pyrones (DDPs). Genome mining reveals putative DDP biosynthetic gene clusters distributed in five fungal genera. In addition, we design extended DDP pathways by combinatorial biosynthesis. In total, ten DDP pathways, including five native pathways, four extended pathways and one shunt pathway, are heterologously reconstituted in a genetically tractable heterologous host, Aspergillus oryzae, resulting in the production of 22 DDPs, including 15 new analogues. We also demonstrate the advantage of expanding the diversity of DDPs to probe various bioactive molecules through a wide range of biological evaluations. Combining genome mining and heterologous expression in a genetically tractable host can lead to bioactive natural products discovery and production. Here, the authors employ this strategy for new decalin-containing diterpenoid pyrenes production by expressing native, extended, and shunt pathways in Aspergillus oryzae.
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34
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Fraley AE, Sherman DH. Enzyme evolution in fungal indole alkaloid biosynthesis. FEBS J 2020; 287:1381-1402. [PMID: 32118354 PMCID: PMC7317620 DOI: 10.1111/febs.15270] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/24/2019] [Accepted: 02/27/2020] [Indexed: 12/28/2022]
Abstract
The class of fungal indole alkaloids containing the bicyclo[2.2.2]diazaoctane ring is comprised of diverse molecules that display a range of biological activities. While much interest has been garnered due to their therapeutic potential, this class of molecules also displays unique chemical functionality, making them intriguing synthetic targets. Many elegant and intricate total syntheses have been developed to generate these alkaloids, but the selectivity required to produce them in high yield presents great barriers. Alternatively, if we can understand the molecular mechanisms behind how fungi make these complex molecules, we can leverage the power of nature to perform these chemical transformations. Here, we describe the various studies regarding the evolutionary development of enzymes involved in fungal indole alkaloid biosynthesis.
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Affiliation(s)
- Amy E. Fraley
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, United States
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35
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Koyanagi T, Siena PM, Przybyla DE, Rafie MI, Nagorski RW. N-(Hydroxybenzyl)benzamide Derivatives: Aqueous pH-Dependent Kinetics and Mechanistic Implications for the Aqueous Reactivity of Carbinolamides. J Org Chem 2020; 85:1115-1125. [PMID: 31830416 DOI: 10.1021/acs.joc.9b02812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rate constants for the aqueous reaction, between pH 0 and 14, have been determined for a series of amide substituted N-(hydroxybenzyl)benzamide derivatives, in H2O, at 25 °C, I = 1.0 M (KCl). The N-(hydroxybenzyl)benzamide derivatives were found to react via three distinct mechanisms with the kinetically dominant mechanism being dependent on the pH of the reaction solution. It has been shown that the carbinolamides react via a specific-base-catalyzed mechanism (E1cB-like) under basic and pH neutral conditions. At lower pH values, an acid-catalyzed mechanism was kinetically dominant and, last, a water reaction was postulated at pH values where neither the hydroxide-dependent nor the general-acid-catalyzed mechanism was dominant. Contrary to earlier studies with N-(hydroxymethyl)benzamide compounds, no evidence for mechanistic variation based upon the nature of the amidic substituent was observed for any of the N-(hydroxybenzyl)benzamide derivatives studied between pH values of 0-14. The rate for the acid-catalyzed reaction (kH, ρ = -1.17), the apparent second-order hydroxide rate constant (k1', ρ = 0.87), the hydroxide-independent rate (k1, ρ = 0.65), and the pKa's of the hydroxyl group of the carbinolamide (ρ = 0.23) are reported.
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Affiliation(s)
- Takaoki Koyanagi
- Department of Chemistry , Illinois State University , Normal , Illinois 61790-4160 , United States
| | - Paul M Siena
- Department of Chemistry , Illinois State University , Normal , Illinois 61790-4160 , United States
| | - David E Przybyla
- Department of Chemistry , Illinois State University , Normal , Illinois 61790-4160 , United States
| | - Mohammad I Rafie
- Department of Chemistry , Illinois State University , Normal , Illinois 61790-4160 , United States
| | - Richard W Nagorski
- Department of Chemistry , Illinois State University , Normal , Illinois 61790-4160 , United States
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36
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Wang X, Gao YL, Zhang ML, Zhang HD, Huang JZ, Li L. Genome mining and biosynthesis of the Acyl-CoA:cholesterol acyltransferase inhibitor beauveriolide I and III in Cordyceps militaris. J Biotechnol 2020; 309:85-91. [PMID: 31926180 DOI: 10.1016/j.jbiotec.2020.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 12/21/2019] [Accepted: 01/07/2020] [Indexed: 01/03/2023]
Abstract
Ascomycete fungi Cordyceps are widely used in traditional Chinese medicine, and numerous investigations have been carried out to uncover their biological activities. However, primary researches on the physiological effects of Cordyceps were committed using crude extracts. At present, there are only a few compounds which were comprehensively characterized from Cordyceps, partial owing to the low production. In order to scientifically take advantage of Cordyceps, we used the strategy of genome mining to discover bioactive compounds from Cordyceps militaris. We found the putative biosynthetic gene cluster of the acyl-CoA:cholesterol acyltransferase inhibitor beauveriolides in the genome of C. militaris, and produced the compounds by heterologous expression in Aspergillus nidulans. Production of beauveriolide I and III also was detected in both ferment mycelia and fruiting bodies of C. militaris. The possible biosynthetic pathway was proposed. Our studies unveil the active compounds of C. militaris against atherosclerosis and Alzheimer's disease and provide the enzyme resources for the biosynthesis of new cyclodepsipeptide molecules.
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Affiliation(s)
- Xue Wang
- Engineering Research Center of Industrial Microbiology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Yang-Le Gao
- Engineering Research Center of Industrial Microbiology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Ming-Liang Zhang
- Engineering Research Center of Industrial Microbiology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Huai-Dong Zhang
- Engineering Research Center of Industrial Microbiology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Jian-Zhong Huang
- Engineering Research Center of Industrial Microbiology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Li Li
- Engineering Research Center of Industrial Microbiology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
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37
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Zhang JM, Wang HH, Liu X, Hu CH, Zou Y. Heterologous and Engineered Biosynthesis of Nematocidal Polyketide–Nonribosomal Peptide Hybrid Macrolactone from Extreme Thermophilic Fungi. J Am Chem Soc 2020; 142:1957-1965. [DOI: 10.1021/jacs.9b11410] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Jin-Mei Zhang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Hang-Hang Wang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Xuan Liu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Chang-Hua Hu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Yi Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
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38
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Dan Q, Newmister SA, Klas KR, Fraley AE, McAfoos TJ, Somoza AD, Sunderhaus JD, Ye Y, Shende VV, Yu F, Sanders JN, Brown WC, Zhao L, Paton RS, Houk KN, Smith JL, Sherman DH, Williams RM. Fungal indole alkaloid biogenesis through evolution of a bifunctional reductase/Diels-Alderase. Nat Chem 2019; 11:972-980. [PMID: 31548667 PMCID: PMC6815239 DOI: 10.1038/s41557-019-0326-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 08/05/2019] [Indexed: 12/25/2022]
Abstract
Prenylated indole alkaloids such as the calmodulin-inhibitory malbrancheamides and anthelmintic paraherquamides possess great structural diversity and pharmaceutical utility. Here, we report complete elucidation of the malbrancheamide biosynthetic pathway accomplished through complementary approaches. These include a biomimetic total synthesis to access the natural alkaloid and biosynthetic intermediates in racemic form and in vitro enzymatic reconstitution to provide access to the natural antipode (+)-malbrancheamide. Reductive cleavage of an L-Pro-L-Trp dipeptide from the MalG non-ribosomal peptide synthetase (NRPS) followed by reverse prenylation and a cascade of post-NRPS reactions culminates in an intramolecular [4+2] hetero-Diels-Alder (IMDA) cyclization to furnish the bicyclo[2.2.2]diazaoctane scaffold. Enzymatic assembly of optically pure (+)-premalbrancheamide involves an unexpected zwitterionic intermediate where MalC catalyses enantioselective cycloaddition as a bifunctional NADPH-dependent reductase/Diels-Alderase. The crystal structures of substrate and product complexes together with site-directed mutagenesis and molecular dynamics simulations demonstrate how MalC and PhqE (its homologue from the paraherquamide pathway) catalyse diastereo- and enantioselective cyclization in the construction of this important class of secondary metabolites.
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Affiliation(s)
- Qingyun Dan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Sean A Newmister
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Kimberly R Klas
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Amy E Fraley
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Timothy J McAfoos
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Amber D Somoza
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - James D Sunderhaus
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Ying Ye
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Vikram V Shende
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Fengan Yu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - W Clay Brown
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Le Zhao
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Robert S Paton
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Robert M Williams
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
- University of Colorado Cancer Center, Aurora, CO, USA.
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39
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Chen Q, Gao J, Jamieson C, Liu J, Ohashi M, Bai J, Yan D, Liu B, Che Y, Wang Y, Houk KN, Hu Y. Enzymatic Intermolecular Hetero-Diels-Alder Reaction in the Biosynthesis of Tropolonic Sesquiterpenes. J Am Chem Soc 2019; 141:14052-14056. [PMID: 31461283 PMCID: PMC6944466 DOI: 10.1021/jacs.9b06592] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Diels-Alder reactions are among the most powerful synthetic transformations to construct complex natural products. Despite that increasing of enzymatic intramolecular Diels-Alder reactions have been discovered, natural intermolecular Diels-Alderases are rarely described. Here, we report an intermolecular hetero-Diels-Alder reaction in the biosynthesis of tropolonic sesquiterpenes and functionally characterize EupfF as the first fungal intermolecular hetero-Diels-Alderase. We demonstrate that EupfF catalyzed the dehydration of a hydroxymethyl-containing tropolone (5) to generate a reactive tropolone o-quinone methide (6) and might further stereoselectively control the subsequent intermolecular hetero-Diels-Alder reaction with (1E,4E,8Z)-humulenol (8) to produce enantiomerically pure neosetophomone B (1). Our results reveal the biosynthetic pathway of 1 and expand the repertoire of activities of Diels-Alder cyclases.
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Affiliation(s)
- Qibin Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
| | - Jie Gao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
| | - Cooper Jamieson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Jiawang Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
| | - Masao Ohashi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
| | - Jian Bai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
| | - Daojian Yan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
| | - Bingyu Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
| | - Yongsheng Che
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
| | - Yanan Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Youcai Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
- NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
- CAMS Key Laboratory of Enzyme and Catalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P.R. China
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40
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Niu G, Li W. Next-Generation Drug Discovery to Combat Antimicrobial Resistance. Trends Biochem Sci 2019; 44:961-972. [PMID: 31256981 DOI: 10.1016/j.tibs.2019.05.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 12/16/2022]
Abstract
The widespread emergence of antibiotic-resistant pathogens poses a severe threat to public health. This problem becomes even worse with a coincident decline in the supply of new antibiotics. Conventional bioactivity-guided natural product discovery has failed to meet the urgent need for new antibiotics, largely due to limited resources and high rediscovery rates. Recent advances in cultivation techniques, analytical technologies, and genomics-based approaches have greatly expanded our access to previously underexploited microbial sources. These strategies will enable us to access new reservoirs of microorganisms and unleash their chemical potentials, thus opening new opportunities for the discovery of next-generation drugs to address the growing concerns of antimicrobial resistance.
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Affiliation(s)
- Guoqing Niu
- Biotechnology Research Center, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Southwest University, Chongqing 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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41
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Zeng H, Yin G, Wei Q, Li D, Wang Y, Hu Y, Hu C, Zou Y. Unprecedented [5.5.5.6]Dioxafenestrane Ring Construction in Fungal Insecticidal Sesquiterpene Biosynthesis. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Haichun Zeng
- College of Pharmaceutical SciencesSouthwest University Chongqing 400715 China
| | - Guoping Yin
- College of Pharmaceutical SciencesSouthwest University Chongqing 400715 China
| | - Qian Wei
- College of Pharmaceutical SciencesSouthwest University Chongqing 400715 China
| | - Dehai Li
- Laboratory for Marine Drugs and Bioproducts of Qingdao, National Laboratory for Marine Science and Technology Qingdao 266237 China
| | - Yi Wang
- State Key Laboratory of Silkworm Genome BiologySouthwest University Chongqing 400715 China
| | - Youcai Hu
- State Key Laboratory of Bioactive Substance and Function of Natural MedicinesInstitute of Materia MedicaChinese Academy of Medical Sciences & Peking Union Medical College Beijing 100050 China
| | - Changhua Hu
- College of Pharmaceutical SciencesSouthwest University Chongqing 400715 China
| | - Yi Zou
- College of Pharmaceutical SciencesSouthwest University Chongqing 400715 China
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42
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Zeng H, Yin G, Wei Q, Li D, Wang Y, Hu Y, Hu C, Zou Y. Unprecedented [5.5.5.6]Dioxafenestrane Ring Construction in Fungal Insecticidal Sesquiterpene Biosynthesis. Angew Chem Int Ed Engl 2019; 58:6569-6573. [PMID: 30908782 DOI: 10.1002/anie.201813722] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 03/11/2019] [Indexed: 11/09/2022]
Abstract
Fenestranes, a specific class of natural products, contain four fused rings that share a central quaternary carbon atom. The fungal natural product penifulvin A (1) is a potent insecticidal sesquiterpene that features the [5.5.5.6]dioxafenestrane ring. Although the chemical synthesis of 1 has been achieved recently, the enzymes catalysing the cyclization and oxidation of FPP to 1 remain unknown. In this work, we identified a concise pathway that uses only three enzymes to produce 1. A new sesquiterpene cyclase (PeniA) generates the angular triquinane scaffold silphinene (6). A cytochrome P450 (PeniB) and a flavin-dependent monooxygenase (PeniC) catalyse a series of oxidation reactions to transform 6 into 1, including oxidation of the C15 methyl group to a carboxylate moiety, oxidative coupling of the C15 carboxylate and the C1-C2 olefin to form a γ-lactone, and Baeyer-Villiger oxidation to form a δ-lactone. Our results demonstrate the highly concise and efficient ways in which fungal biosynthetic pathways can generate complex sesquiterpene scaffolds.
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Affiliation(s)
- Haichun Zeng
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Guoping Yin
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Qian Wei
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Dehai Li
- Laboratory for Marine Drugs and Bioproducts of Qingdao, National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yi Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Youcai Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Changhua Hu
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Yi Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
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43
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Zhang X, Renata H. Efficient Chemoenzymatic Synthesis of (2 S,3 R)-3-Hydroxy-3-Methylproline, a Key Fragment in Polyoxypeptin A and FR225659. Tetrahedron 2019; 75:3253-3257. [PMID: 31885405 DOI: 10.1016/j.tet.2019.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report an efficient synthesis of protected (2S,3R)-3-hydroxy-3-methylproline that proceeds in three steps with complete stereoselectivity. This route represents a significant improvement over previous approaches to this noncanonical amino acid. Key to this success is the development of a one-pot chemoenzymatic procedure for the preparation of (2S,3S)-3- methylproline from L-isoleucine. This work lays the foundation for future chemoenzymatic syntheses of polyoxypeptin A and FR225659.
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Affiliation(s)
- Xiao Zhang
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Hans Renata
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458
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44
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Shi J, Liu CL, Zhang B, Guo WJ, Zhu J, Chang CY, Zhao EJ, Jiao RH, Tan RX, Ge HM. Genome mining and biosynthesis of kitacinnamycins as a STING activator. Chem Sci 2019; 10:4839-4846. [PMID: 31160959 PMCID: PMC6510318 DOI: 10.1039/c9sc00815b] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 04/01/2019] [Indexed: 01/08/2023] Open
Abstract
Genome mining targeting unique type II PKS and NRPS led to the identification of a novel class of glycopeptides named kitacinnamycins.
Cinnamoyl-containing nonribosomal peptides (CCNPs) are a small group of secondary metabolites with potent biological activities produced by actinobacteria. Two remarkable features in the biosynthesis of CCNPs include the nonribosomal peptide synthases (NRPSs) for assembly of the depsipeptide backbone and the type II polyketide synthases (PKSs) for N-terminal cinnamoyl moiety construction. Here, we present a genome mining approach targeting both NRPS and type II PKS for discovery of new CCNPs, which led to the identification of 51 putative CCNP gene clusters from public bacterial genome databases. After strain prioritization, a novel class of CCNP-type glycopeptides named kitacinnamycins, one of which showing potent activation ability towards the stimulator of interferon genes (STING) protein, was identified. Bioinformatic, genetic and biochemical analysis revealed the use of the NRPS assembly line to form the macrocyclic peptide backbone, followed by a P450 monooxygenase to generate terminal oxidized groups. A glycosyltransferase with relatively broad substrate specificity transfers sugars to the newly generated OH/COOH group. The protein crystallographic study further provided structural insights into this glycosylation. Our results not only demonstrated the feasibility of genome mining and strain prioritization for the discovery of new bioactive natural products but also disclosed the biosynthetic pathway for kitacinnamycins.
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Affiliation(s)
- Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , School of Life Sciences , Nanjing University , 210023 , P. R. China . ;
| | - Cheng Li Liu
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , School of Life Sciences , Nanjing University , 210023 , P. R. China . ;
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , School of Life Sciences , Nanjing University , 210023 , P. R. China . ;
| | - Wen Jie Guo
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , School of Life Sciences , Nanjing University , 210023 , P. R. China . ;
| | - Jiapeng Zhu
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy , Nanjing University of Chinese Medicine , Nanjing 210023 , P. R. China
| | - Chin-Yuan Chang
- Department of Biological Science and Technology , National Chiao Tung University , Hsinchu , Republic of China
| | - Er Juan Zhao
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , School of Life Sciences , Nanjing University , 210023 , P. R. China . ;
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , School of Life Sciences , Nanjing University , 210023 , P. R. China . ;
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , School of Life Sciences , Nanjing University , 210023 , P. R. China . ; .,State Key Laboratory Cultivation Base for TCM Quality and Efficacy , Nanjing University of Chinese Medicine , Nanjing 210023 , P. R. China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , School of Life Sciences , Nanjing University , 210023 , P. R. China . ;
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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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46
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Li H, Gilchrist CLM, Lacey HJ, Crombie A, Vuong D, Pitt JI, Lacey E, Chooi YH, Piggott AM. Discovery and Heterologous Biosynthesis of the Burnettramic Acids: Rare PKS-NRPS-Derived Bolaamphiphilic Pyrrolizidinediones from an Australian Fungus, Aspergillus burnettii. Org Lett 2019; 21:1287-1291. [DOI: 10.1021/acs.orglett.8b04042] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hang Li
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Cameron L. M. Gilchrist
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Heather J. Lacey
- Microbial Screening Technologies Pty. Ltd., Smithfield, New South Wales 2164, Australia
| | - Andrew Crombie
- Microbial Screening Technologies Pty. Ltd., Smithfield, New South Wales 2164, Australia
| | - Daniel Vuong
- Microbial Screening Technologies Pty. Ltd., Smithfield, New South Wales 2164, Australia
| | - John I. Pitt
- Commonwealth Scientific and Industrial Research Organisation, North Ryde, New South Wales 2113, Australia
| | - Ernest Lacey
- Microbial Screening Technologies Pty. Ltd., Smithfield, New South Wales 2164, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Andrew M. Piggott
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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47
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Parvez A, Giri S, Bisht R, Saxena P. New Insights on Cyclization Specificity of Fungal Type III Polyketide Synthase, PKSIII Nc in Neurospora crassa. Indian J Microbiol 2018; 58:268-277. [PMID: 30013270 PMCID: PMC6023819 DOI: 10.1007/s12088-018-0738-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 05/03/2018] [Indexed: 12/13/2022] Open
Abstract
Type III polyketide synthases (PKSs) biosynthesize varied classes of metabolites with diverse bio-functionalities. Inherent promiscuous substrate specificity, multiple elongations of reaction intermediates and several modes of ring-closure, confer the proteins with the ability to generate unique scaffolds from limited substrate pools. Structural studies have identified crucial amino acid residues that dictate type III PKS functioning, though cyclization specific residues need further investigation. PKSIIINc, a functionally and structurally characterized type III PKS from the fungus, Neurospora crassa, is known to biosynthesize alkyl-resorcinol, alkyl-triketide- and alkyl-tetraketide-α-pyrone products. In this study, we attempted to identify residue positions governing cyclization specificity in PKSIIINc through comparative structural analysis. Structural comparisons with other type III PKSs revealed a motif with conserved hydroxyl/thiol groups that could dictate PKSIIINc catalysis. Site-directed mutagenesis of Cys120 and Ser186 to Ser and Cys, respectively, altered product profiles of mutant proteins. While both C120S and S186C proteins retained wild-type PKSIIINc product activity, S186C favoured lactonization and yielded higher amounts of the α-pyrone products. Notably, C120S gained new cyclization capability and biosynthesized acyl-phloroglucinol in addition to wild-type PKSIIINc products. Generation of alkyl-resorcinol and acyl-phloroglucinol by a single protein is a unique observation in fungal type III PKS family. Mutation of Cys120 to bulky Phe side-chain abrogated formation of tetraketide products and adversely affected overall protein stability as revealed by molecular dynamics simulation studies. Our investigations identify residue positions governing cyclization programming in PKSIIINc protein and provide insights on how subtle variations in protein cores dictate product profiles in type III PKS family.
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Affiliation(s)
- Amreesh Parvez
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
| | - Samir Giri
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
- Present Address: Department of Ecology, School of Biology, University of Osnabrück, Osnabrück, 49076 Germany
| | - Renu Bisht
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
| | - Priti Saxena
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
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48
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Kato N, Nogawa T, Takita R, Kinugasa K, Kanai M, Uchiyama M, Osada H, Takahashi S. Control of the Stereochemical Course of [4+2] Cycloaddition during trans
-Decalin Formation by Fsa2-Family Enzymes. Angew Chem Int Ed Engl 2018; 57:9754-9758. [DOI: 10.1002/anie.201805050] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Naoki Kato
- Natural Product Biosynthesis Research Unit; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Toshihiko Nogawa
- Chemical Biology Research Group; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Ryo Takita
- Advanced Elements Chemistry Research Team; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Kiyomi Kinugasa
- Natural Product Biosynthesis Research Unit; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Misae Kanai
- Advanced Elements Chemistry Research Team; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Masanobu Uchiyama
- Advanced Elements Chemistry Research Team; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
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49
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Kato N, Nogawa T, Takita R, Kinugasa K, Kanai M, Uchiyama M, Osada H, Takahashi S. Control of the Stereochemical Course of [4+2] Cycloaddition during trans
-Decalin Formation by Fsa2-Family Enzymes. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805050] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Naoki Kato
- Natural Product Biosynthesis Research Unit; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Toshihiko Nogawa
- Chemical Biology Research Group; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Ryo Takita
- Advanced Elements Chemistry Research Team; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Kiyomi Kinugasa
- Natural Product Biosynthesis Research Unit; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Misae Kanai
- Advanced Elements Chemistry Research Team; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Masanobu Uchiyama
- Advanced Elements Chemistry Research Team; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
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50
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Hill RA, Sutherland A. Hot off the press. Nat Prod Rep 2018. [DOI: 10.1039/c8np90008f] [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 tundrenone from Methylobacter tundripaludum.
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