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Jiang Y, Chang Z, Xu Y, Zhan X, Wang Y, Gao M. Advances in molecular enzymology of β-1,3-glucanases: A comprehensive review. Int J Biol Macromol 2024; 279:135349. [PMID: 39242004 DOI: 10.1016/j.ijbiomac.2024.135349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 08/14/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
β-1,3-Glucanases are essential enzymes involved in the hydrolysis of β-1,3-glucans, with significant biological and industrial relevance. These enzymes are derived from diverse sources, including bacteria, fungi, plants, and animals, each exhibiting unique substrate specificities and biochemical properties. This review provides an in-depth analysis of the natural sources and ecological roles of β-1,3-glucanases, exploring their enzymatic properties such as optimal pH, temperature, molecular weight, isoelectric points, and kinetic parameters, which are crucial for understanding their functionality and stability. Advances in molecular enzymology are discussed, focusing on gene cloning, expression in systems like Escherichia coli and Pichia pastoris, and structural-functional relationships. The reaction mechanisms and the role of non-catalytic carbohydrate-binding modules in enhancing substrate hydrolysis are examined. Industrial applications of β-1,3-glucanases are highlighted, including the production of β-1,3-glucooligosaccharides, uses in the food industry, biological control of plant pathogens, and nutritional roles. This review aims to provide a foundation for future research, improving the efficiency and robustness of β-1,3-glucanases for various industrial applications.
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Affiliation(s)
- Yun Jiang
- School of Biotechnology and Key Laboratory of Carbohydrate Chemistry and Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Zepeng Chang
- School of Biotechnology and Key Laboratory of Carbohydrate Chemistry and Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Ying Xu
- School of Biotechnology and Key Laboratory of Carbohydrate Chemistry and Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiaobei Zhan
- School of Biotechnology and Key Laboratory of Carbohydrate Chemistry and Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yuying Wang
- School of Biotechnology and Key Laboratory of Carbohydrate Chemistry and Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China.
| | - Minjie Gao
- School of Biotechnology and Key Laboratory of Carbohydrate Chemistry and Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China.
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2
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Kumari M, Checker VG, Kathpalia R, Srivastava V, Singh IK, Singh A. Metabolic engineering for enhanced terpenoid production: Leveraging new horizons with an old technique. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108511. [PMID: 38593484 DOI: 10.1016/j.plaphy.2024.108511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/06/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
Terpenoids are a vast class of plant specialized metabolites (PSMs) manufactured by plants and are involved in their interactions with environment. In addition, they add health benefits to human nutrition and are widely used as pharmaceutically active compounds. However, native plants produce a limited amount of terpenes restricting metabolite yield of terpene-related metabolites. Exponential growth in the plant metabolome data and the requirement of alternative approaches for producing the desired amount of terpenoids, has redirected plant biotechnology research to plant metabolic engineering, which requires in-depth knowledge and precise expertise about dynamic plant metabolic pathways and cellular physiology. Metabolic engineering is an assuring tool for enhancing the concentration of terpenes by adopting specific strategies such as overexpression of the key genes associated with the biosynthesis of targeted metabolites, controlling the modulation of transcription factors, downregulation of competitive pathways (RNAi), co-expression of the biosynthetic pathway genes in heterologous system and other combinatorial approaches. Microorganisms, fast-growing host plants (such as Nicotiana benthamiana), and cell suspension/callus cultures have provided better means for producing valuable terpenoids. Manipulation in the biosynthetic pathways responsible for synthesis of terpenoids can provide opportunities to enhance the content of desired terpenoids and open up new avenues to enhance their production. This review deliberates the worth of metabolic engineering in medicinal plants to resolve issues associated with terpenoid production at a commercial scale. However, to bring the revolution through metabolic engineering, further implementation of genome editing, elucidation of metabolic pathways using omics approaches, system biology approaches, and synthetic biology tactics are essentially needed.
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Affiliation(s)
- Megha Kumari
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India; Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India
| | | | - Renu Kathpalia
- Department of Botany, Kirori Mal College, University of Delhi, Delhi, 110007, India
| | - Vikas Srivastava
- Department of Botany, School of Life Sciences, Central University of Jammu, Samba, 181143, India
| | - Indrakant Kumar Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Archana Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India; Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India; Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, Delhi, India.
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3
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Gu X, Fu L, Wang Z, Cao Z, Zhao L, Seswita-Zilda D, Zhang A, Zhang Q, Li J. A Novel Bifunctional Alginate Lyase and Antioxidant Activity of the Enzymatic Hydrolysates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4116-4126. [PMID: 38372665 DOI: 10.1021/acs.jafc.3c08638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Alginate lyase Aly448, a potential new member of the polysaccharide lyase (PL) 7 family, which was cloned and identified from the macroalgae-associated bacterial metagenomic library, showed bifunctionality. The molecular docking results revealed that Aly448 has two completely different binding sites for alginate (polyMG), poly-α-l-guluronic acid (polyG), and poly-β-d-mannuronic acid (polyM) substrates, respectively, which might be the molecular basis for the enzyme's bifunctionality. Truncational results confirmed that predicted key residues affected the bifunctionality of Aly448, but did not wholly explain. Besides, Aly448 presented excellent biochemical characteristics, such as higher thermal stability and pH tolerance. Degradation of polyMG, polyM, and polyG substrates by Aly448 produced tetrasaccharide (DP4), disaccharide (DP2), and galactose (DP1), which exhibited excellent antioxidant activity. These findings provide novel insights into the substrate recognition mechanism of bifunctional alginate lyases and pave a new path for the exploitation of natural antioxidant agents.
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Affiliation(s)
- Xiaoqian Gu
- Key Lab of Ecological Environment Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Liping Fu
- Key Lab of Ecological Environment Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Zhiyan Wang
- Key Lab of Ecological Environment Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Zhe Cao
- Key Lab of Ecological Environment Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Luying Zhao
- Key Lab of Ecological Environment Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Dewi Seswita-Zilda
- Research Center for Deep Sea, Earth Sciences and Maritime Research Organization, National Research and Innovation Agency (BRIN), Jl. Pasir Putih Raya, Pademangan, North Jakarta City, Jakarta 14430, Indonesia
| | - Ao Zhang
- Chemical Engineering Institute, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Qian Zhang
- Key Lab of Ecological Environment Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Jiang Li
- Key Lab of Ecological Environment Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
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4
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Yñigez-Gutierrez AE, Wurm JE, Froese JT, Rosenthal NE, Bachmann BO. Characterization of Dichloroisoeverninic Acid Biosynthesis and Chemoenzymatic Synthesis of New Orthosomycins. ACS Chem Biol 2024; 19:526-535. [PMID: 38289021 DOI: 10.1021/acschembio.3c00693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
The orthosomycins are highly modified oligosaccharide natural products with a broad spectrum and potent antimicrobial activities. These include everninomicins and avilamycins, which inhibit protein translation by binding a unique site on the bacterial ribosome. Notably, ribosomal bound structures reveal a network of interactions between the 50S subunit and dichloroisoeverninic acid (DCIE), the aromatic A1-ring conserved across orthosomycins, but the relationship of these interactions to their antimicrobial activity remains undetermined. Genetic functional analysis of three genes putatively associated with DCIE biosynthesis in the everninomicin producer Micromonospora carbonacea delineates the native biosynthetic pathway and provides previously unreported advanced biosynthetic intermediates. Subsequent in vitro biochemical analyses demonstrate the complete DCIE biosynthetic pathway and provide access to novel everninomicin analogs. In addition to the orsellinate synthase EvdD3 and a flavin-dependent halogenase EvdD2, our results identified a key acyltransferase, EvdD1, responsible for transferring orsellinate from the acyl carrier protein domain of EvdD3 to a heptasaccharide orthosomycin biosynthetic intermediate. We have also shown that EvdD1 is able to transfer unnatural aryl groups via their N-acyl cysteamine thioesters to the everninomicin scaffold and used this as a biocatalyst to generate a panel of unnatural aryl analogs. The impact of diverse aryl functional group substitution on both ribosome inhibition and antibacterial activities demonstrates the importance of the DCIE moiety in the pharmacology of orthosomycins, notably revealing an uncoupling between ribosomal engagement and antibiotic activity. Control of A1-ring functionality in this class of molecules provides a potential handle to explore and address pharmacological roles of the DCIE ring in this potent and unique class of antibiotics.
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Affiliation(s)
| | - Jennifer E Wurm
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Chemical and Physical Biology Graduate Program, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jordan T Froese
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Nicholas E Rosenthal
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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Huang X, Zheng L, Zhou Y, Hu S, Ning W, Li S, Lin Z, Huang S. Controllable Adaptive Molybdate-Oligosaccharide Nanoparticles Regulate M2 Macrophage Mitochondrial Function and Promote Angiogenesis via PI3K/HIF-1α/VEGF Pathway to Accelerate Diabetic Wound Healing. Adv Healthc Mater 2024; 13:e2302256. [PMID: 37922497 DOI: 10.1002/adhm.202302256] [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: 07/16/2023] [Revised: 10/22/2023] [Indexed: 11/05/2023]
Abstract
The complex wound environment of diabetic wounds leads to poor treatment efficacy, and the inflammatory disorders and vascular injury are the primary causes of death in such patients. Herein, a sprayable, controllable adaptive, pH-responsive nanosystem of molybdate and oligosaccharide (CMO) is specially developed as an immunomodulatory and angiogenesis-promotion material for diabetic wound healing. CMO exhibited pH-responsive release of Mo2+ and oligosaccharide (COS), specifically in response to the alkalescent environment observed in diabetic wounds. CMO provide an anti-inflammatory environment by promoting M2 polarization through significantly stimulating macrophage mitochondrial function. Specifically, CMO with a certain concentration reduce reactive oxygen species (ROS) and tumor necrosis factor α (TNF-α) expression, and upregulated mitochondrial membrane potential (MMP), superoxide dismutase (SOD), and interleukin 10 (IL-10) expression in macrophages. Moreover, CMO facilitate angiogenesis via upregulating the PI3K/HIF-1α/VEGF pathway-a critical process for the formation of new blood vessels that supply nutrients and oxygen to the healing tissue. Remarkably, CMO promote cell viability and migration of endothelial cells, and enhance the expression of angiogenic genes. In vitro and in vivo studies suggest this simple but powerful nanosystem targeting mitochondrial function has the potential to become an effective treatment for diabetic wound healing.
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Affiliation(s)
- Xiuhong Huang
- Department of Preventive Dentistry, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, 510280, China
| | - Liqin Zheng
- Department of The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510405, China
| | - Yueshan Zhou
- Department of Preventive Dentistry, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, 510280, China
| | - Shaonan Hu
- Department of Preventive Dentistry, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, 510280, China
| | - Wancheng Ning
- Department of Preventive Dentistry, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, 510280, China
| | - Simin Li
- Department of Preventive Dentistry, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, 510280, China
| | - Ziling Lin
- Department of Orthopedic Trauma, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510405, China
| | - Shaohong Huang
- Department of Preventive Dentistry, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, 510280, China
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Zhang H, Ren X, Xu H, Qi H, Du S, Huang J, Zhang J, Wang J. Phenopyrrolizins A and B, Two Novel Pyrrolizine Alkaloids from Marine-Derived Actinomycetes Micromonospora sp. HU138. Molecules 2023; 28:7672. [PMID: 38005394 PMCID: PMC10675482 DOI: 10.3390/molecules28227672] [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: 11/03/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Two previously undescribed pyrrolizine alkaloids, named phenopyrrolizins A and B (1 and 2), were obtained from the fermentation broth of marine-derived Micromonospora sp. HU138. Their structures were established by extensive spectroscopic analysis, including 1D and 2D NMR spectra as well as HRESIMS data. The structure of 1 was confirmed by single-crystal diffraction analysis and its racemization mechanism was proposed. The antifungal activity assay showed that 2 could inhibit the mycelial growth of Botrytis cinerea with the inhibitory rates of 18.9% and 35.9% at 20 μg/disc and 40 μg/disc, respectively.
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Affiliation(s)
- Hui Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China; (H.Z.); (X.R.); (H.Q.); (J.H.)
- Key Laboratory of Horticultural Biotechnology of Taizhou, School of Agriculture and Bioengineering, Taizhou Vocational College of Science and Technology, Taizhou 318020, China;
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, China;
| | - Xiaohan Ren
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China; (H.Z.); (X.R.); (H.Q.); (J.H.)
| | - Haiju Xu
- Key Laboratory of Horticultural Biotechnology of Taizhou, School of Agriculture and Bioengineering, Taizhou Vocational College of Science and Technology, Taizhou 318020, China;
| | - Huan Qi
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China; (H.Z.); (X.R.); (H.Q.); (J.H.)
| | - Shihua Du
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, China;
| | - Jun Huang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China; (H.Z.); (X.R.); (H.Q.); (J.H.)
- Zhejiang Makohs Biotech Co., Ltd., Taizhou 318000, China
| | - Ji Zhang
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, China;
| | - Jidong Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China; (H.Z.); (X.R.); (H.Q.); (J.H.)
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7
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Kalinovskii AP, Sintsova OV, Gladkikh IN, Leychenko EV. Natural Inhibitors of Mammalian α-Amylases as Promising Drugs for the Treatment of Metabolic Diseases. Int J Mol Sci 2023; 24:16514. [PMID: 38003703 PMCID: PMC10671682 DOI: 10.3390/ijms242216514] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
α-Amylase is a generally acknowledged molecular target of a distinct class of antidiabetic drugs named α-glucosidase inhibitors. This class of medications is scarce and rather underutilized, and treatment with current commercial drugs is accompanied by unpleasant adverse effects. However, mammalian α-amylase inhibitors are abundant in nature and form an extensive pool of high-affinity ligands that are available for drug discovery. Individual compounds and natural extracts and preparations are promising therapeutic agents for conditions associated with impaired starch metabolism, e.g., diabetes mellitus, obesity, and other metabolic disorders. This review focuses on the structural diversity and action mechanisms of active natural products with inhibitory activity toward mammalian α-amylases, and emphasizes proteinaceous inhibitors as more effective compounds with significant potential for clinical use.
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Affiliation(s)
- Aleksandr P. Kalinovskii
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Oksana V. Sintsova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690022, Russia; (O.V.S.); (I.N.G.)
| | - Irina N. Gladkikh
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690022, Russia; (O.V.S.); (I.N.G.)
| | - Elena V. Leychenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690022, Russia; (O.V.S.); (I.N.G.)
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Zhu M, Wang L, Zhang H, Zhang L, Tan B, Huang Q, Zhu Y, Zhang C. Biosynthesis and Engineered Overproduction of Everninomicins with Promising Activity against Multidrug-Resistant Bacteria. ACS Synth Biol 2023; 12:1520-1532. [PMID: 37084337 DOI: 10.1021/acssynbio.3c00055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
Ribosome-targeting oligosaccharides, everninomicins (EVNs), are promising drug leads with a unique mode of action distinct from that of currently used antibiotics in human therapy. However, the low yields in natural microbial producers hamper an efficient preparation of EVNs for detailed structure-activity relationship analysis. Herein, we enhance the production of EVNs by duplicating the biosynthetic gene cluster (BGC) in Micromonospora sp. SCSIO 07395 and thus obtain multiple EVNs that are sufficient for bioactivity evaluation. EVNs (1-5) are shown to significantly inhibit the growth of multidrug-resistant Gram-positive staphylococcal, enterococcal, and streptococcal strains and Gram-negative pathogens Acinetobacter baumannii and Vibrio cholerae, with micromolar to nanomolar potency, which are comparable or superior to vancomycin, linezolid, and daptomycin. Furthermore, the BGC duplication strategy is proven effective in stepwisely improving titers of the bioactive EVN M (5) from the trace amount to 98.6 mg L-1. Our findings demonstrate the utility of a bioengineering approach for enhanced production and chemical diversification of the medicinally promising EVNs.
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Affiliation(s)
- Mengyi Zhu
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Lijuan Wang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Haibo Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Bin Tan
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Qi Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, College of Veterinary Medicine, Wuhan 430070, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
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Zhang S, Chen Y, Zhu J, Lu Q, Cryle MJ, Zhang Y, Yan F. Structural diversity, biosynthesis, and biological functions of lipopeptides from Streptomyces. Nat Prod Rep 2023; 40:557-594. [PMID: 36484454 DOI: 10.1039/d2np00044j] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2022Streptomyces are ubiquitous in terrestrial and marine environments, where they display a fascinating metabolic diversity. As a result, these bacteria are a prolific source of active natural products. One important class of these natural products is the nonribosomal lipopeptides, which have diverse biological activities and play important roles in the lifestyle of Streptomyces. The importance of this class is highlighted by the use of related antibiotics in the clinic, such as daptomycin (tradename Cubicin). By virtue of recent advances spanning chemistry and biology, significant progress has been made in biosynthetic studies on the lipopeptide antibiotics produced by Streptomyces. This review will serve as a comprehensive guide for researchers working in this multidisciplinary field, providing a summary of recent progress regarding the investigation of lipopeptides from Streptomyces. In particular, we highlight the structures, properties, biosynthetic mechanisms, chemical and chemoenzymatic synthesis, and biological functions of lipopeptides. In addition, the application of genome mining techniques to Streptomyces that have led to the discovery of many novel lipopeptides is discussed, further demonstrating the potential of lipopeptides from Streptomyces for future development in modern medicine.
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Affiliation(s)
- Songya Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yunliang Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- The Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 1000050, China.
| | - Jing Zhu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Qiujie Lu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800 Australia
- EMBL Australia, Monash University, Clayton, Victoria, 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria, 3800 Australia
| | - Youming Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Fu Yan
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
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10
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Sharma S, Hegde P, Panda S, Orimoloye MO, Aldrich CC. Drugging the microbiome: targeting small microbiome molecules. Curr Opin Microbiol 2023; 71:102234. [PMID: 36399893 DOI: 10.1016/j.mib.2022.102234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022]
Abstract
The human microbiome represents a large and diverse collection of microbes that plays an integral role in human physiology and pathophysiology through interactions with the host and within the microbial community. While early work exploring links between microbiome signatures and diseases states has been associative, emerging evidence demonstrates the metabolic products of the human microbiome have more proximal causal effects on disease phenotypes. The therapeutic implications of this shift are profound as manipulation of the microbiome by the administration of live biotherapeutics, ongoing, can now be pursued alongside research efforts toward describing inhibitors of key microbiome enzymes involved in the biosynthesis of metabolites implicated in various disease states and processing of host-derived metabolites. With growing interest in 'drugging the microbiome', we review few notable microbial metabolites for which traditional drug-development campaigns have yielded compounds with therapeutic promise.
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Affiliation(s)
- Sachin Sharma
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Subhankar Panda
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Moyosore O Orimoloye
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA.
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11
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Mukherji A, Rotta MKV, Sarmah BK, Kancharla PK. Influence of Various Silyl Protecting Groups on Stereoselective 2-Deoxyrhamnosylation. J Org Chem 2023; 88:245-260. [PMID: 36524596 DOI: 10.1021/acs.joc.2c02285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The influence of various silyl protecting groups on 2-deoxyrhamnosylation using 2-deoxyrhamnosyl acetates, thioglycosides, and (p-methoxyphenyl)vinylbenzoate (PMPVB) donors has been presented. C-Glycosylation reactions reveal that tert-butyldimethylsilyl (TBDMS), triisopropylsilyl (TIPS), and tert-butyldiphenylsilyl (TBDPS) silyl protected rhamnosyl oxocarbenium ions have no facial selectivity except for the conformationally (4H3) locked tetraisopropyldisiloxane (TIPDS) protected rhamnose donor, which provides complete α-selectivity. However, TBDPS protected rhamnosyl donors are found to be superior protecting groups for α-stereoselective O-glycosylation reactions with various acceptors. The observed results are found consistent across donors and donor activation conditions. Most importantly, the study was conducted at room temperature unlike the other energy-intensive low-temperature studies and was bound to have more practical utility. The outcomes have been explained using kinetic and thermodynamic analyses.
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Affiliation(s)
- Ananya Mukherji
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Mahendra K V Rotta
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Bikash K Sarmah
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Pavan K Kancharla
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
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12
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Gribble GW. Naturally Occurring Organohalogen Compounds-A Comprehensive Review. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2023; 121:1-546. [PMID: 37488466 DOI: 10.1007/978-3-031-26629-4_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.
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Affiliation(s)
- Gordon W Gribble
- Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA.
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13
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Tsunoda T, Asamizu S, Mahmud T. Biochemical Characterization of GacI, a Bifunctional Glycosyltransferase-Phosphatase Enzyme Involved in Acarbose Biosynthesis in Streptomyces glaucescens GLA.O. Biochemistry 2022; 61:2628-2635. [PMID: 36288494 PMCID: PMC9669214 DOI: 10.1021/acs.biochem.2c00473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acarbose, a pseudotetrasaccharide produced by several strains of Actinoplanes and Streptomyces, is an α-glucosidase inhibitor clinically used to control type II diabetes. Bioinformatic analysis of the biosynthetic gene clusters of acarbose in Actinoplanes sp. SE50/110 (the acb cluster) and Streptomyces glaucescens GLA.O (the gac cluster) revealed their distinct genetic organizations and presumably biosynthetic pathways. However, to date, only the acarbose pathway in the SE50/110 strain has been extensively studied. Here, we report that GacI, one of the proteins that appear to be different between the two pathways, is a bifunctional glycosyltransferase family 5 (GT5)-phosphatase (PP) enzyme that functions at two different steps in acarbose biosynthesis in S. glaucescens GLA.O. In the acb pathway, the GT and the PP reactions are performed by two different enzymes. Truncated GacI proteins having only the GT or the PP domain showed comparable catalytic activity with the full-length GacI, indicating that domain separation does not significantly affect their respective catalytic activity. GacI, which is widely distributed in many Streptomyces, represents the first example of naturally occurring GT5-PP bifunctional enzymes biochemically characterized.
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Affiliation(s)
- Takeshi Tsunoda
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Shumpei Asamizu
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
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14
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Mangano K, Marks J, Klepacki D, Saha CK, Atkinson GC, Vázquez-Laslop N, Mankin AS. Context-based sensing of orthosomycin antibiotics by the translating ribosome. Nat Chem Biol 2022; 18:1277-1286. [PMID: 36138139 DOI: 10.1038/s41589-022-01138-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 08/10/2022] [Indexed: 11/09/2022]
Abstract
Orthosomycin antibiotics inhibit protein synthesis by binding to the large ribosomal subunit in the tRNA accommodation corridor, which is traversed by incoming aminoacyl-tRNAs. Structural and biochemical studies suggested that orthosomycins block accommodation of any aminoacyl-tRNAs in the ribosomal A-site. However, the mode of action of orthosomycins in vivo remained unknown. Here, by carrying out genome-wide analysis of antibiotic action in bacterial cells, we discovered that orthosomycins primarily inhibit the ribosomes engaged in translation of specific amino acid sequences. Our results reveal that the predominant sites of orthosomycin-induced translation arrest are defined by the nature of the incoming aminoacyl-tRNA and likely by the identity of the two C-terminal amino acid residues of the nascent protein. We show that nature exploits this antibiotic-sensing mechanism for directing programmed ribosome stalling within the regulatory open reading frame, which may control expression of an orthosomycin-resistance gene in a variety of bacterial species.
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Affiliation(s)
- Kyle Mangano
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.,Amgen Research, Thousand Oaks, CA, USA
| | - James Marks
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.,National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, USA
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Chayan Kumar Saha
- Department of Experimental Medicine, Lund University, Lund, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Gemma C Atkinson
- Department of Experimental Medicine, Lund University, Lund, Sweden
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA. .,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA. .,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.
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15
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Yan S, Zeng M, Wang H, Zhang H. Micromonospora: A Prolific Source of Bioactive Secondary Metabolites with Therapeutic Potential. J Med Chem 2022; 65:8735-8771. [PMID: 35766919 DOI: 10.1021/acs.jmedchem.2c00626] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Micromonospora, one of the most important actinomycetes genera, is well-known as the treasure trove of bioactive secondary metabolites (SMs). Herein, together with an in-depth genomic analysis of the reported Micromonospora strains, all SMs from this genus are comprehensively summarized, containing structural features, bioactive properties, and mode of actions as well as their biosynthetic and chemical synthesis pathways. The perspective enables a detailed view of Micromonospora-derived SMs, which will enrich the chemical diversity of natural products and inspire new drug discovery in the pharmaceutical industry.
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Affiliation(s)
- Suqi Yan
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Mingyuan Zeng
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hong Wang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
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16
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Della-Felice F, de Andrade Bartolomeu A, Pilli RA. The phosphate ester group in secondary metabolites. Nat Prod Rep 2022; 39:1066-1107. [PMID: 35420073 DOI: 10.1039/d1np00078k] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2000 to mid-2021The phosphate ester is a versatile, widespread functional group involved in a plethora of biological activities. Its presence in secondary metabolites, however, is relatively rare compared to other functionalities and thus is part of a rather unexplored chemical space. Herein, the chemistry of secondary metabolites containing the phosphate ester group is discussed. The text emphasizes their structural diversity, biological and pharmacological profiles, and synthetic approaches employed in the phosphorylation step during total synthesis campaigns, covering the literature from 2000 to mid-2021.
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Affiliation(s)
- Franco Della-Felice
- Institute of Chemistry, University of Campinas (UNICAMP), P.O. Box 6154, CEP 13083-970 Campinas, Sao Paulo, Brazil.,Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007 Tarragona, Spain.
| | | | - Ronaldo Aloise Pilli
- Institute of Chemistry, University of Campinas (UNICAMP), P.O. Box 6154, CEP 13083-970 Campinas, Sao Paulo, Brazil
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17
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Sun Q, Xin X, An Z, Hu Y, Feng Q. Therapeutic Potential of Natural Plants Against Non-Alcoholic Fatty Liver Disease: Targeting the Interplay Between Gut Microbiota and Bile Acids. Front Cell Infect Microbiol 2022; 12:854879. [PMID: 35356532 PMCID: PMC8959594 DOI: 10.3389/fcimb.2022.854879] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/16/2022] [Indexed: 12/12/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) remains a common disease with a significant health and economic burden worldwide. The gut microbiota (GM) and bile acids (BAs), which play important roles in the gut-liver axis, have been confirmed to jointly participate in the development of NAFLD. GM not only regulate bile acids’ synthesis, transport, and reabsorption by regulating other metabolites (such as trimetlyl amine oxide, butyrate), but also regulate dehydrogenation, dehydroxylation and desulfurization of bile acids. Meanwhile, disordered bile acids influence the gut microbiota mainly through promoting the bacterial death and lowering the microbial diversity. Although weight loss and lifestyle changes are effective in the treatment of NAFLD, the acceptability and compliance of patients are poor. Recently, increasing natural plants and their active ingredients have been proved to alleviate NAFLD by modulating the joint action of gut microbiota and bile acids, and considered to be promising potential candidates. In this review, we discuss the efficacy of natural plants in treating NAFLD in the context of their regulation of the complex interplay between the gut microbiota and bile acids, the crosstalk of which has been shown to significantly promote the progression of NAFLD. Herein, we summarize the prior work on this topic and further suggest future research directions in the field.
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Affiliation(s)
- QinMei Sun
- Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xin Xin
- Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - ZiMing An
- Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - YiYang Hu
- Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shanghai, China
- Key Laboratory of Liver and Kidney Diseases, Shanghai University of Traditional Chinese Medicine, Ministry of Education, Shanghai, China
- *Correspondence: YiYang Hu, ; Qin Feng,
| | - Qin Feng
- Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shanghai, China
- Key Laboratory of Liver and Kidney Diseases, Shanghai University of Traditional Chinese Medicine, Ministry of Education, Shanghai, China
- *Correspondence: YiYang Hu, ; Qin Feng,
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18
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Xu J, Liu Z, Feng Z, Ren Y, Liu H, Wang Y. Rapid Mining of Novel α-Glucosidase and Lipase Inhibitors from Streptomyces sp. HO1518 Using UPLC-QTOF-MS/MS. Mar Drugs 2022; 20:md20030189. [PMID: 35323488 PMCID: PMC8955712 DOI: 10.3390/md20030189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 02/01/2023] Open
Abstract
A rapid and sensitive method using ultra-high performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS/MS) was applied for the analysis of the metabolic profile of acarviostatin-containing aminooligosaccharides derived from Streptomyces sp. HO1518. A total of ninety-eight aminooligosaccharides, including eighty potential new compounds, were detected mainly based on the characteristic fragment ions originating from quinovosidic bond cleavages in their molecules. Following an LC-MS-guided separation technique, seven new aminooligosaccharides (10–16) along with four known related compounds (17–20) were obtained directly from the crude extract of strain HO1518. Compounds 10–13 represent the first examples of aminooligosaccharides with a rare acarviostatin II02-type structure. In addition, all isolates displayed considerable inhibitory effects on three digestive enzymes, which revealed that the number of the pseudo-trisaccharide core(s), the feasible length of the oligosaccharides, and acyl side chain exerted a crucial influence on their bioactivities. These results demonstrated that the UPLC-QTOF-MS/MS-based metabolomics approach could be applied for the rapid identification of aminooligosaccharides and other similar structures in complex samples. Furthermore, this study highlights the potential of acylated aminooligosaccharides with conspicuous α-glucosidase and lipase inhibition for the future development of multi-target anti-diabetic drugs.
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Affiliation(s)
- Jianlin Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (J.X.); (Y.R.)
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (Z.L.); (Z.F.)
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhifeng Liu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (Z.L.); (Z.F.)
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhanguang Feng
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (Z.L.); (Z.F.)
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yuhong Ren
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (J.X.); (Y.R.)
| | - Haili Liu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (Z.L.); (Z.F.)
- Correspondence: (H.L.); (Y.W.); Tel.: +86-021-5492-4295 (Y.W.)
| | - Yong Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (J.X.); (Y.R.)
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (Z.L.); (Z.F.)
- Correspondence: (H.L.); (Y.W.); Tel.: +86-021-5492-4295 (Y.W.)
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19
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Salama S, Habib MH, Hatti-Kaul R, Gaber Y. Reviewing a plethora of oxidative-type reactions catalyzed by whole cells of Streptomyces species. RSC Adv 2022; 12:6974-7001. [PMID: 35424663 PMCID: PMC8982256 DOI: 10.1039/d1ra08816e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/17/2022] [Indexed: 11/21/2022] Open
Abstract
Selective oxidation reactions represent a challenging task for conventional organic chemistry. Whole-cell biocatalysis provides a very convenient, easy to apply method to carry out different selective oxidation reactions including chemo-, regio-, and enantio-selective reactions. Streptomyces species are important biocatalysts as they can catalyze these selective reactions very efficiently owing to the wide diversity of enzymes and enzymatic cascades in their cell niche. In this review, we present and analyze most of the examples reported to date of oxidative reactions catalyzed by Streptomyces species as whole-cell biocatalysts. We discuss 33 different Streptomyces species and strains and the role they play in different oxidative reactions over the past five decades. The oxidative reactions have been classified into seven categories that include: hydroxylation of steroids/non-steroids, asymmetric sulfoxidations, oxidation of aldehydes, multi-step oxidations, oxidative cleavage, and N-oxidations. The role played by Streptomyces species as recombinant hosts catalyzing bio-oxidations has also been highlighted.
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Affiliation(s)
- Sara Salama
- Biotechnology and Life Sciences Department, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University Beni-Suef 62517 Egypt
| | - Mohamed H Habib
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
| | - Rajni Hatti-Kaul
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University Sweden
| | - Yasser Gaber
- Department of Pharmaceutical Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University Beni-Suef 62511 Egypt
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Mutah University Al-Karak 61710 Jordan
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20
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Genome Mining of Pseudomonas Species: Diversity and Evolution of Metabolic and Biosynthetic Potential. Molecules 2021; 26:molecules26247524. [PMID: 34946606 PMCID: PMC8704066 DOI: 10.3390/molecules26247524] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022] Open
Abstract
Microbial genome sequencing has uncovered a myriad of natural products (NPs) that have yet to be explored. Bacteria in the genus Pseudomonas serve as pathogens, plant growth promoters, and therapeutically, industrially, and environmentally important microorganisms. Though most species of Pseudomonas have a large number of NP biosynthetic gene clusters (BGCs) in their genomes, it is difficult to link many of these BGCs with products under current laboratory conditions. In order to gain new insights into the diversity, distribution, and evolution of these BGCs in Pseudomonas for the discovery of unexplored NPs, we applied several bioinformatic programming approaches to characterize BGCs from Pseudomonas reference genome sequences available in public databases along with phylogenetic and genomic comparison. Our research revealed that most BGCs in the genomes of Pseudomonas species have a high diversity for NPs at the species and subspecies levels and built the correlation of species with BGC taxonomic ranges. These data will pave the way for the algorithmic detection of species- and subspecies-specific pathways for NP development.
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21
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Barpuzary B, Kim M, Rhee YH. Synthetic Study toward Saccharomicin Based upon Asymmetric Metal Catalysis. Org Lett 2021; 23:5969-5972. [PMID: 34292756 DOI: 10.1021/acs.orglett.1c02060] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we report a de novo metal-catalyzed approach toward the stereoselective glycosidic bond formation in saccharomicin. The signature step is highlighted by the Pd-catalyzed asymmetric coupling of ene-alkoxyallenes and highly functionalized alcohol substrates. The reaction showed high chemo-, regio-, and ligand-driven diastereoselectivity. In combination with the ring-closing metathesis and late-stage functionalization, this method led to highly efficient synthesis of saccharosamine-rhamnose and rhamnose-fucose fragments.
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Affiliation(s)
- Bhawna Barpuzary
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Hyoja-dong San 31, Pohang 790-784, Republic of Korea
| | - Mijin Kim
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Hyoja-dong San 31, Pohang 790-784, Republic of Korea
| | - Young Ho Rhee
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Hyoja-dong San 31, Pohang 790-784, Republic of Korea
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22
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Microbial Oligosaccharides with Biomedical Applications. Mar Drugs 2021; 19:md19060350. [PMID: 34205503 PMCID: PMC8234114 DOI: 10.3390/md19060350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 11/17/2022] Open
Abstract
Microbial oligosaccharides have been regarded as one of the most appealing natural products attributable to their potent and selective bioactivities, such as antimicrobial activity, inhibition of α-glucosidases and lipase, interference of cellular recognition and signal transduction, and disruption of cell wall biosynthesis. Accordingly, a handful of bioactive oligosaccharides have been developed for the treatment of bacterial infections and type II diabetes mellitus. Given that naturally occurring oligosaccharides have increasingly gained recognition in recent years, a comprehensive review is needed. The current review highlights the chemical structures, biological activities and divergent biosynthetic origins of three subgroups of oligomers including the acarviosine-containing oligosaccharides, saccharomicins, and orthosomycins.
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23
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Abstract
A new synthetic approach toward oligosaccharides consisting only of 2,3,6-trideoxypyranoglycosides is reported. The key feature is highlighted by the convergent approach that allows the introduction of the aglycon moiety in the late stage of the synthesis. As an illustrative example, the tetrasaccharide portion of cervimycin K was prepared as cyclohexyl glycoside.
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Affiliation(s)
- Jihun Kang
- Department of Chemistry, POSTECH, 77 Cheongam-Ro, Nam-Gu, Pohang, Kyungbuk, Republic of Korea
| | - Young Ho Rhee
- Department of Chemistry, POSTECH, 77 Cheongam-Ro, Nam-Gu, Pohang, Kyungbuk, Republic of Korea
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24
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Zhao J, Mo T, Li X, Ding W, Zhang Q. Dissection of the Glycosylation in the Biosynthesis of the Heptadecaglycoside Antibiotic Saccharomicin A. J Org Chem 2021; 86:11117-11124. [PMID: 33724024 DOI: 10.1021/acs.joc.0c03056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Oligosaccharide natural products have diverse biological activities and represent a potentially important source for drug development. In this study, we focus on the glycosylation pathway in the biosynthesis of saccharomicin A (SA-A), an oligosaccharide antibiotic containing 17 sugar moieties. By extensive gene-knockout studies with comparative metabolic profile analysis, we established a complete pathway in assembling the heptadecasaccharide chain of SA-A, the longest saccharide chain found in natural products.
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Affiliation(s)
- Junfeng Zhao
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Tianlu Mo
- Department of Chemistry, Fudan University, Shanghai 200433, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinhui Li
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
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25
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Nóbile ML, Stricker AM, Marchesano L, Iribarren AM, Lewkowicz ES. N-oxygenation of amino compounds: Early stages in its application to the biocatalyzed preparation of bioactive compounds. Biotechnol Adv 2021; 51:107726. [PMID: 33675955 DOI: 10.1016/j.biotechadv.2021.107726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 10/22/2022]
Abstract
Among the compounds that contain unusual functional groups, nitro is perhaps one of the most interesting due to the valuable properties it confers on pharmaceuticals and explosives. Traditional chemistry has for many years used environmentally unfriendly strategies; in contrast, the biocatalyzed production of this type of products offers a promising alternative. The small family of enzymes formed by N-oxygenases allows the conversion of an amino group to a nitro through the sequential addition of oxygen. These enzymes also make it possible to obtain other less oxidized N-O functions, such as hydroxylamine or nitroso, present in intermediate or final products. The current substrates on which these enzymes are reported to work encompass a few aromatic molecules and sugars. The unique characteristics of N-oxygenases and the great economic value of the products that they could generate, place them in a position of very high scientific and industrial interest. The most important and best studied N-oxygenases will be presented here.
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Affiliation(s)
- Matías L Nóbile
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina.
| | - Abigail M Stricker
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina
| | - Lucas Marchesano
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina
| | - Adolfo M Iribarren
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina
| | - Elizabeth S Lewkowicz
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina
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26
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Nóbile ML, Stricker AM, Iribarren AM, Lewkowicz ES. Streptomyces griseus: A new biocatalyst with N-oxygenase activity. J Biotechnol 2020; 327:36-42. [PMID: 33373628 DOI: 10.1016/j.jbiotec.2020.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/21/2022]
Abstract
Aromatic nitro compounds are key building blocks for many industrial syntheses and are also components of explosives, drugs and pesticides. Due to the environmentally unfriendly experimental conditions involved in their chemical syntheses, industrial processes would benefit from the use of biocatalysts. Among potentially useful enzymes, N-oxygenases, whose role is to oxygenate primary amines, are becoming relevant. These enzymes are involved in different secondary metabolic pathways in Streptomyces and in few other bacteria, forming part of the enzyme pools implicated in antibiotic synthesis. In this work, a group of Streptomyces strains, whose biomass was obtained from simple and novel culture media, were identified as new sources of N-oxygenase activity. Furthermore, the use of unspecific metabolic stimulation strategies allowed substantial improvements in the activity of whole cells as biocatalysts. It is remarkable the 6 to 50-fold increase in nitro compound yields compared to the biotransformation under standard conditions when Streptomyces griseus was the biocatalyst. In addition, biocatalyst substrate acceptance was studied in order to determine the biocatalytic potential of this enzyme.
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Affiliation(s)
- Matías L Nóbile
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, LBB, Roque Sáenz Peña 352, Quilmes, 1876, Argentina.
| | - Abigail M Stricker
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, LBB, Roque Sáenz Peña 352, Quilmes, 1876, Argentina
| | - Adolfo M Iribarren
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, LBB, Roque Sáenz Peña 352, Quilmes, 1876, Argentina
| | - Elizabeth S Lewkowicz
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, LBB, Roque Sáenz Peña 352, Quilmes, 1876, Argentina
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27
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Pal KB, Guo A, Das M, Lee J, Báti G, Yip BRP, Loh TP, Liu XW. Iridium-promoted deoxyglycoside synthesis: stereoselectivity and mechanistic insight. Chem Sci 2020; 12:2209-2216. [PMID: 34163986 PMCID: PMC8179265 DOI: 10.1039/d0sc06529c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Herein, we devised a method for stereoselective O-glycosylation using an Ir(i)-catalyst which enables both hydroalkoxylation and nucleophilic substitution of glycals with varying substituents at the C3 position. In this transformation, 2-deoxy-α-O-glycosides were acquired when glycals equipped with a notoriously poor leaving group at C3 were used; in contrast 2,3-unsaturated-α-O-glycosides were produced from glycals that bear a good leaving group at C3. Mechanistic studies indicate that both reactions proceed via the directing mechanism, through which the acceptor coordinates to the Ir(i) metal in the α-face-coordinated Ir(i)-glycal π-complex and then attacks the glycal that contains the O-glycosidic bond in a syn-addition manner. This protocol exhibits good functional group tolerance and is exemplified with the preparation of a library of oligosaccharides in moderate to high yields and with excellent stereoselectivities. Ir(i)-catalyzed α-selective O-glycosylation of glycals provided an access to both 2-deoxyglycosides and 2,3-unsaturated glycosides with a broad substrate scope. The underlying rationale of α-selectivity has been illustrated by the DFT study.![]()
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Affiliation(s)
- Kumar Bhaskar Pal
- Institute of Advanced Synthesis, Northwestern Polytechnical University Xi'an 710072 China.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371
| | - Aoxin Guo
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371
| | - Mrinmoy Das
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371
| | - Jiande Lee
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371 .,Nanyang Environment and Water Research Institute, Nanyang Technological University 1 Cleantech Loop Singapore 637141
| | - Gábor Báti
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371
| | - Benjamin Rui Peng Yip
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371
| | - Teck-Peng Loh
- Institute of Advanced Synthesis, Northwestern Polytechnical University Xi'an 710072 China.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371 .,Yangtze River Delta Research Institute of Northwestern Polytechnical University Taicang Jiangsu 215400 China
| | - Xue-Wei Liu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371
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28
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Liu M, Liu K, Xiong D, Zhang H, Li T, Li B, Qin X, Bai J, Ye X. Stereoselective Electro‐2‐deoxyglycosylation from Glycals. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006115] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Miao Liu
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
| | - Kai‐Meng Liu
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
| | - De‐Cai Xiong
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
- Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology Shandong University 27 Shanda Nanlu Jinan Shandong 250100 China
| | - Hanyu Zhang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
| | - Tian Li
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
| | - Bohan Li
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
| | - Xianjin Qin
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
| | - Jinhe Bai
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
| | - Xin‐Shan Ye
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
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29
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Niu K, Liu Z, Feng Y, Gao T, Wang Z, Zhang P, Du Z, Gao D, Fang X. A novel strategy for efficient disaccharides synthesis from glucose by β-glucosidase. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00334-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
AbstractOligosaccharides have important therapeutic applications. A useful route for oligosaccharides synthesis is reverse hydrolysis by β-glucosidase. However, the low conversion efficiency of disaccharides from monosaccharides limits its large-scale production because the equilibrium is biased in the direction of hydrolysis. Based on the analysis of the docking results, we hypothesized that the hydropathy index of key amino acid residues in the catalytic site is closely related with disaccharide synthesis and more hydrophilic residues located in the catalytic site would enhance reverse hydrolysis activity. In this study, positive variants TrCel1bI177S, TrCel1bI177S/I174S, and TrCel1bI177S/I174S/W173H, and one negative variant TrCel1bN240I were designed according to the Hydropathy Index For Enzyme Activity (HIFEA) strategy. The reverse hydrolysis with TrCel1bI177S/I174S/W173H was accelerated and then the maximum total production (195.8 mg/mL/mg enzyme) of the synthesized disaccharides was increased by 3.5-fold compared to that of wild type. On the contrary, TrCel1bN240I lost reverse hydrolysis activity. The results demonstrate that the average hydropathy index of the key amino acid residues in the catalytic site of TrCel1b is an important factor for the synthesis of laminaribiose, sophorose, and cellobiose. The HIFEA strategy provides a new perspective for the rational design of β-glucosidases used for the synthesis of oligosaccharides.
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30
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Liu M, Liu KM, Xiong DC, Zhang H, Li T, Li B, Qin X, Bai J, Ye XS. Stereoselective Electro-2-deoxyglycosylation from Glycals. Angew Chem Int Ed Engl 2020; 59:15204-15208. [PMID: 32394599 DOI: 10.1002/anie.202006115] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Indexed: 11/09/2022]
Abstract
We report a novel and highly stereoselective electro-2-deoxyglycosylation from glycals. This method features excellent stereoselectivity, scope, and functional-group tolerance. This process can also be applied to the modification of a wide range of natural products and drugs. Furthermore, a scalable synthesis of glycosylated podophyllotoxin and a one-pot trisaccharide synthesis through iterative electroglycosylations were achieved.
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Affiliation(s)
- Miao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road No. 38, Beijing, 100191, China
| | - Kai-Meng Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road No. 38, Beijing, 100191, China
| | - De-Cai Xiong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road No. 38, Beijing, 100191, China.,Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 27 Shanda Nanlu, Jinan, Shandong, 250100, China
| | - Hanyu Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road No. 38, Beijing, 100191, China
| | - Tian Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road No. 38, Beijing, 100191, China
| | - Bohan Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road No. 38, Beijing, 100191, China
| | - Xianjin Qin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road No. 38, Beijing, 100191, China
| | - Jinhe Bai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road No. 38, Beijing, 100191, China
| | - Xin-Shan Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road No. 38, Beijing, 100191, China
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31
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Yalamanchili S, Miller W, Chen X, Bennett CS. Rapid de Novo Preparation of 2,6-Dideoxy Sugar Libraries through Gold-Catalyzed Homopropargyl Orthoester Cyclization. Org Lett 2019; 21:9646-9651. [PMID: 31755271 PMCID: PMC6956608 DOI: 10.1021/acs.orglett.9b03812] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A flexible de novo route capable of producing libraries of 2,6-dideoxy sugars is described. We have found that Au(JackiePhos)SbF6MeCN promotes the conversion of homopropargyl orthoesters into functionalized 2,3-dihydro-4H-pyran-4-ones in good to excellent yields (71-90%). These latter compounds can be easily converted into a number of otherwise difficult to access 2,6-dideoxy sugars.
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Affiliation(s)
- Subbarao Yalamanchili
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - William Miller
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Xizhao Chen
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Clay S. Bennett
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
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32
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Li C, Wen Y, He Y, Zhu J, Yin X, Yang J, Zhang L, Song L, Xia X, Yu R. Purification and characterization of a novel β-1,3-glucanase from Arca inflata and its immune-enhancing effects. Food Chem 2019; 290:1-9. [DOI: 10.1016/j.foodchem.2019.03.131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 01/25/2023]
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33
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Liao L, Su S, Zhao B, Fan C, Zhang J, Li H, Chen B. Biosynthetic Potential of a Novel Antarctic Actinobacterium Marisediminicola antarctica ZS314 T Revealed by Genomic Data Mining and Pigment Characterization. Mar Drugs 2019; 17:md17070388. [PMID: 31266176 PMCID: PMC6669644 DOI: 10.3390/md17070388] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 11/24/2022] Open
Abstract
Rare actinobacterial species are considered as potential resources of new natural products. Marisediminicola antarctica ZS314T is the only type strain of the novel actinobacterial genus Marisediminicola isolated from intertidal sediments in East Antarctica. The strain ZS314T was able to produce reddish orange pigments at low temperatures, showing characteristics of carotenoids. To understand the biosynthetic potential of this strain, the genome was completely sequenced for data mining. The complete genome had 3,352,609 base pairs (bp), much smaller than most genomes of actinomycetes. Five biosynthetic gene clusters (BGCs) were predicted in the genome, including a gene cluster responsible for the biosynthesis of C50 carotenoid, and four additional BGCs of unknown oligosaccharide, salinixanthin, alkylresorcinol derivatives, and NRPS (non-ribosomal peptide synthetase) or amino acid-derived compounds. Further experimental characterization indicated that the strain may produce C.p.450-like carotenoids, supporting the genomic data analysis. A new xanthorhodopsin gene was discovered along with the analysis of the salinixanthin biosynthetic gene cluster. Since little is known about this genus, this work improves our understanding of its biosynthetic potential and provides opportunities for further investigation of natural products and strategies for adaptation to the extreme Antarctic environment.
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Affiliation(s)
- Li Liao
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai 200136, China.
| | - Shiyuan Su
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai 200136, China
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Bin Zhao
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai 200136, China
- School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Chengqi Fan
- Key Laboratory of East China Sea & Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
| | - Jin Zhang
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai 200136, China
| | - Huirong Li
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai 200136, China
| | - Bo Chen
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai 200136, China.
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34
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Gandeepan P, Koeller J, Korvorapun K, Mohr J, Ackermann L. Visible-Light-Enabled Ruthenium-Catalyzed meta-C-H Alkylation at Room Temperature. Angew Chem Int Ed Engl 2019; 58:9820-9825. [PMID: 31075177 DOI: 10.1002/anie.201902258] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/19/2019] [Indexed: 11/08/2022]
Abstract
Visible-light-induced ruthenium catalysis has enabled remote C-H alkylations with excellent levels of position control under exceedingly mild conditions at room temperature. The metallaphotocatalysis occurred under exogenous-photosensitizer-free conditions and features an ample substrate scope. The robust nature of the photo-induced mild meta-C-H functionalization is reflected by the broad functional group tolerance, and the reaction can be carried out in an operationally simple manner, setting the stage for challenging secondary and tertiary meta-C-H alkylations by ruthenaphotoredox catalysis.
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Affiliation(s)
- Parthasarathy Gandeepan
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstrasse 2, 37077, Göttingen, Germany
| | - Julian Koeller
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstrasse 2, 37077, Göttingen, Germany
| | - Korkit Korvorapun
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstrasse 2, 37077, Göttingen, Germany
| | - Jens Mohr
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstrasse 2, 37077, Göttingen, Germany
| | - Lutz Ackermann
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstrasse 2, 37077, Göttingen, Germany
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35
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Gandeepan P, Koeller J, Korvorapun K, Mohr J, Ackermann L. Sichtbares Licht ermöglicht Ruthenium‐katalysierte
meta
‐C‐H‐Alkylierung bei Raumtemperatur. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902258] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Parthasarathy Gandeepan
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität Göttingen Tammannstraße 2 37077 Göttingen Deutschland
| | - Julian Koeller
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität Göttingen Tammannstraße 2 37077 Göttingen Deutschland
| | - Korkit Korvorapun
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität Göttingen Tammannstraße 2 37077 Göttingen Deutschland
| | - Jens Mohr
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität Göttingen Tammannstraße 2 37077 Göttingen Deutschland
| | - Lutz Ackermann
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität Göttingen Tammannstraße 2 37077 Göttingen Deutschland
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36
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Matsumoto Y, Ishii M, Hasegawa S, Sekimizu K. Enterococcus faecalis YM0831 suppresses sucrose-induced hyperglycemia in a silkworm model and in humans. Commun Biol 2019; 2:157. [PMID: 31069266 PMCID: PMC6497652 DOI: 10.1038/s42003-019-0407-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 03/25/2019] [Indexed: 12/12/2022] Open
Abstract
Hyperglycemia caused by excessive intake of sucrose leads to lifestyle-related diseases such as diabetes. Administration of a lactic acid bacterial strain to mice suppresses sucrose-induced hyperglycemia, but evidence for a similar effect in humans is lacking. Here we show that Enterococcus faecalis YM0831, identified using an in vivo screening system with silkworms, suppressed sucrose-induced hyperglycemia in humans. E. faecalis YM0831 also suppressed glucose-induced hyperglycemia in silkworms. E. faecalis YM0831 inhibited glucose uptake by the human intestinal epithelial cell line Caco-2. A transposon insertion mutant of E. faecalis YM0831, which showed decreased inhibitory activity against glucose uptake by Caco-2 cells, also exhibited decreased inhibitory activity against both sucrose-induced and glucose-induced hyperglycemia in silkworms. In human clinical trials, oral ingestion of E. faecalis YM0831 suppressed the increase in blood glucose in a sucrose tolerance test. These findings suggest that E. faecalis YM0831 inhibits intestinal glucose transport and suppresses sucrose-induced hyperglycemia in humans.
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Affiliation(s)
- Yasuhiko Matsumoto
- Teikyo University Institute of Medical Mycology, 359 Otsuka, Hachioji, Tokyo, 192-0395 Japan
- Department of Microbiology, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo, 204-8588 Japan
| | - Masaki Ishii
- Molecular Cell Biology Laboratory, Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi Nishitokyo-shi, Tokyo, 202-8585 Japan
- Genome Pharmaceuticals Institute Co. Ltd., 3-4-5-2D Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Setsuo Hasegawa
- Pharmaspur Inc., Toyo building, 1-2-10 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Kazuhisa Sekimizu
- Teikyo University Institute of Medical Mycology, 359 Otsuka, Hachioji, Tokyo, 192-0395 Japan
- Genome Pharmaceuticals Institute Co. Ltd., 3-4-5-2D Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
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37
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Bihari Mishra K, Kandasamy J. Tris(Pentafluorophenyl)Borane‐Driven Stereoselective
O
‐Glycosylation with Glycal Donors under Mild Condition. ASIAN J ORG CHEM 2019. [DOI: 10.1002/ajoc.201900055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Kunj Bihari Mishra
- Department of chemistryIndian Institute of Technology, IIT BHU Varanasi- 221005
| | - Jeyakumar Kandasamy
- Department of chemistryIndian Institute of Technology, IIT BHU Varanasi- 221005
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38
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József J, Juhász L, Somsák L. Thio-click reaction of 2-deoxy-exo-glycals towards new glycomimetics: stereoselective synthesis of C-2-deoxy-d-glycopyranosyl compounds. NEW J CHEM 2019. [DOI: 10.1039/c8nj06138f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Photoinitiated addition of thiols to 2-deoxy-exo-glycals obtained from endo-glycals of d-arabino, d-lyxo, d-erythro and d-threo configurations resulted in highly regio- and stereoselective formation of glycosylmethyl sulfide type glycomimetics.
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Affiliation(s)
- János József
- University of Debrecen
- Department of Organic Chemistry
- Hungary
| | - László Juhász
- University of Debrecen
- Department of Organic Chemistry
- Hungary
| | - László Somsák
- University of Debrecen
- Department of Organic Chemistry
- Hungary
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39
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Zhao C, Yang C, Wai STC, Zhang Y, P. Portillo M, Paoli P, Wu Y, San Cheang W, Liu B, Carpéné C, Xiao J, Cao H. Regulation of glucose metabolism by bioactive phytochemicals for the management of type 2 diabetes mellitus. Crit Rev Food Sci Nutr 2018; 59:830-847. [PMID: 30501400 DOI: 10.1080/10408398.2018.1501658] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Chao Zhao
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Chemistry, University of California, Davis, CA, USA
| | - Chengfeng Yang
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Sydney Tang Chi Wai
- Department of Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Yanbo Zhang
- School Chinese Medicine, University of Hong Kong, Hong Kong, China
| | - Maria P. Portillo
- Department of Nutrition and Food Science, Faculty of Pharmacy, University of Basque Country (UPV/EHU) and Lucio Lascaray Research Center, Vitoria, Spain
- CIBEROBN Physiopathology of Obesity and Nutrition, Institute of Health Carlos III (ISCIII), Spain
| | - Paolo Paoli
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Yijing Wu
- Institute of Oceanography, Minjiang University, Fuzhou, China
- College of Food Science and Nutritional Engineering, China Agricultural University, China
| | - Wai San Cheang
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Control in Chinese Medicine, University of Macau, Macau SAR, China
| | - Bin Liu
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Christian Carpéné
- Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Institut National de la Santé et de la Recherche Médicale (INSERM U1048)/Université Paul Sabatier, Bât. L4, CHU Rangueil, Toulouse cedex 4, France
| | - Jianbo Xiao
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Control in Chinese Medicine, University of Macau, Macau SAR, China
| | - Hui Cao
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Control in Chinese Medicine, University of Macau, Macau SAR, China
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40
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Oligosaccharides Derived from Red Seaweed: Production, Properties, and Potential Health and Cosmetic Applications. Molecules 2018; 23:molecules23102451. [PMID: 30257445 PMCID: PMC6222765 DOI: 10.3390/molecules23102451] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/17/2018] [Accepted: 09/21/2018] [Indexed: 12/30/2022] Open
Abstract
Because of their potential use as functional ingredients in human nutrition, oligosaccharides derived from natural sources are receiving paramount consideration. Red seaweed, a proven rich source of agar and carrageenan, is one of the most abundantly present sources of such oligosaccharides. Agaro-oligosaccharides (AOS) and carrageenan-oligosaccharides (COS) are produced from agar and carrageenan, respectively, through chemical and enzymatic hydrolyses. Enzymatic hydrolysis of agar and carrageenan into oligosaccharides is preferred in industrial production because of certain problems associated with chemical hydrolysis, including the release of high amounts of monosaccharides and undesirable toxic products, such as furfural. AOS and COS possess many biological activities, including prebiotic, immuno-modulatory, anti-oxidant, and anti-tumor activities. These activities are related to their chemical structure, molecular weight, degree of polymerization, and the flexibility of the glycosidic linkages. Therefore, the structure–function relationship and the mechanisms occurring during the specific biological applications of AOS and COS are discussed herein. Moreover, the chromatographic separation, purification, and characterization of AOS and COS are also part of this review. This piece of writing strives to create a new perspective on the potential applications of AOS and COS in the functional food and pharmaceutical industry.
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Abstract
Pseudo-oligosaccharides are microbial-derived secondary metabolites whose chemical structures contain pseudosugars (glycomimetics). Due to their high resemblance to the molecules of life (carbohydrates), most pseudo-oligosaccharides show significant biological activities. Some of them have been used as drugs to treat human and plant diseases. Because of their significant economic value, efforts have been put into understanding their biosynthesis, optimizing their fermentation conditions, and engineering their metabolic pathways to obtain better production yields. A number of unusual enzymes participating in diverse biosynthetic pathways to pseudo-oligosaccharides have been reported. Various methods and conditions to improve the production yields of the target compounds and eliminate byproducts have also been developed. This review article describes recent studies on the biosynthesis, fermentation optimization, and metabolic engineering of high-value pseudo-oligosaccharides.
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Meng S, Tang GL, Pan HX. Enzymatic Formation of Oxygen-Containing Heterocycles in Natural Product Biosynthesis. Chembiochem 2018; 19:2002-2022. [PMID: 30039582 DOI: 10.1002/cbic.201800225] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Indexed: 01/12/2023]
Abstract
Oxygen-containing heterocycles are widely encountered in natural products that display diverse pharmacological properties and have potential benefits to human health. The formation of O-heterocycles catalyzed by different types of enzymes in the biosynthesis of natural products not only contributes to the structural diversity of these compounds, but also enriches our understanding of nature's ability to construct complex molecules. This minireview focuses on the various modes of enzymatic O-heterocyclization identified in natural product biosynthesis and summarizes the possible mechanisms involved in ring closure.
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Affiliation(s)
- Song Meng
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Hai-Xue Pan
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
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Jin W, Ren L, Liu B, Zhang Q, Zhong W. Structural Features of Sulfated Glucuronomannan Oligosaccharides and Their Antioxidant Activity. Mar Drugs 2018; 16:E291. [PMID: 30134603 PMCID: PMC6165275 DOI: 10.3390/md16090291] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/16/2018] [Accepted: 08/16/2018] [Indexed: 12/18/2022] Open
Abstract
Glucuronomannan oligosaccharides (Gs) were derived from fucoidan, which was extracted from the brown alga Sargassum thunbergii. Sulfated glucuronomannan oligosaccharides (SGs) were obtained by the sulfation of Gs. NMR techniques were used to reveal that the order of sulfation was Man-C6 > Man-C4 > Man-C1R > GlcA-C3 > Man-C3 > GlcA-C2. Finally, the antioxidant activities (hydroxyl radical scavenging activity, superoxide radical scavenging activity, reducing power and DPPH radical scavenging activity) of Gs and SGs were determined. The findings showed that the higher the degree of polymerization, the better the activity, except for the hydroxyl radical scavenging activity. In addition, the higher the sulfate content, the lower the activities for the reducing power and DPPH radical scavenging activity. Opposite results were found for the superoxide radical scavenging activity. Finally, compared with fucoidan, most Gs and SGs had higher antioxidant activity, suggesting that they might be good candidates for antioxidants.
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Affiliation(s)
- Weihua Jin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Langlang Ren
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Bing Liu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Quanbin Zhang
- Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266000, China.
| | - Weihong Zhong
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310023, China.
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Epstein SC, Charkoudian LK, Medema MH. A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences. Stand Genomic Sci 2018; 13:16. [PMID: 30008988 PMCID: PMC6042397 DOI: 10.1186/s40793-018-0318-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 06/04/2018] [Indexed: 11/18/2022] Open
Abstract
Microorganisms utilize complex enzymatic pathways to biosynthesize structurally complex and pharmacologically relevant molecules. These pathways are encoded by gene clusters and are found in a diverse set of organisms. The Minimum Information about a Biosynthetic Gene cluster repository facilitates standardized and centralized storage of experimental data on these gene clusters and their molecular products, by utilizing user-submitted data to translate scientific discoveries into a format that can be analyzed computationally. This accelerates the processes of connecting genes to chemical structures, understanding biosynthetic gene clusters in the context of environmental diversity, and performing computer-assisted design of synthetic gene clusters. Here, we present a Standard Operating Procedure, Excel templates, a tutorial video, and a collection of relevant review literature to support scientists in their efforts to submit data into MiBIG. Further, we provide tools to integrate gene cluster annotation projects into the classroom environment, including workflows and assessment materials.
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Affiliation(s)
- Samuel C. Epstein
- Department of Chemistry, Haverford College, Haverford, PA 19041-1391 USA
| | | | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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Matsuda Y, Bai T, Phippen CBW, Nødvig CS, Kjærbølling I, Vesth TC, Andersen MR, Mortensen UH, Gotfredsen CH, Abe I, Larsen TO. Novofumigatonin biosynthesis involves a non-heme iron-dependent endoperoxide isomerase for orthoester formation. Nat Commun 2018; 9:2587. [PMID: 29968715 PMCID: PMC6030086 DOI: 10.1038/s41467-018-04983-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/04/2018] [Indexed: 12/11/2022] Open
Abstract
Novofumigatonin (1), isolated from the fungus Aspergillus novofumigatus, is a heavily oxygenated meroterpenoid containing a unique orthoester moiety. Despite the wide distribution of orthoesters in nature and their biological importance, little is known about the biogenesis of orthoesters. Here we show the elucidation of the biosynthetic pathway of 1 and the identification of key enzymes for the orthoester formation by a series of CRISPR-Cas9-based gene-deletion experiments and in vivo and in vitro reconstitutions of the biosynthesis. The novofumigatonin pathway involves endoperoxy compounds as key precursors for the orthoester synthesis, in which the Fe(II)/α-ketoglutarate-dependent enzyme NvfI performs the endoperoxidation. NvfE, the enzyme catalyzing the orthoester synthesis, is an Fe(II)-dependent, but cosubstrate-free, endoperoxide isomerase, despite the fact that NvfE shares sequence homology with the known Fe(II)/α-ketoglutarate-dependent dioxygenases. NvfE thus belongs to a class of enzymes that gained an isomerase activity by losing the α-ketoglutarate-binding ability.
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Affiliation(s)
- Yudai Matsuda
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark.
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Department of Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, China.
| | - Tongxuan Bai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Christopher B W Phippen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark
| | - Christina S Nødvig
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark
| | - Inge Kjærbølling
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark
| | - Tammi C Vesth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark
| | - Mikael R Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark
| | - Uffe H Mortensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark
| | - Charlotte H Gotfredsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Thomas O Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark.
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Lloyd D, Bennett CS. An Improved Approach to the Direct Construction of 2-Deoxy-β-Linked Sugars: Applications to Oligosaccharide Synthesis. Chemistry 2018; 24:7610-7614. [PMID: 29572995 DOI: 10.1002/chem.201800736] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/19/2018] [Indexed: 02/05/2023]
Abstract
A next-generation reagent-controlled approach for the synthesis of 2,6-dideoxy and 2,3,6-trideoxy sugar donors in good yield and high β-selectivity is reported. The use of p-toluenesulfonyl chloride and potassium hexamethyldisilazide (KHMDS) greatly simplifies deoxy-sugar glycoside construction, and can be used for gram-scale glycosylation reactions. The development of this approach and its application to the construction of β-linked deoxy-sugar oligosaccharides are described.
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Affiliation(s)
- Dina Lloyd
- Department Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA, 02155, USA
| | - Clay S Bennett
- Department Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA, 02155, USA
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Zhao G, Wang T. Stereoselective Synthesis of 2‐Deoxyglycosides from Glycals by Visible‐Light‐Induced Photoacid Catalysis. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800909] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Gaoyuan Zhao
- Department of Chemistry University at Albany, State University of New York 1400 Washington Avenue Albany NY 12222 USA
| | - Ting Wang
- Department of Chemistry University at Albany, State University of New York 1400 Washington Avenue Albany NY 12222 USA
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48
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Zhao G, Wang T. Stereoselective Synthesis of 2‐Deoxyglycosides from Glycals by Visible‐Light‐Induced Photoacid Catalysis. Angew Chem Int Ed Engl 2018; 57:6120-6124. [DOI: 10.1002/anie.201800909] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/07/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Gaoyuan Zhao
- Department of Chemistry University at Albany, State University of New York 1400 Washington Avenue Albany NY 12222 USA
| | - Ting Wang
- Department of Chemistry University at Albany, State University of New York 1400 Washington Avenue Albany NY 12222 USA
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Zheng J, Yuan X, Cheng G, Jiao S, Feng C, Zhao X, Yin H, Du Y, Liu H. Chitosan oligosaccharides improve the disturbance in glucose metabolism and reverse the dysbiosis of gut microbiota in diabetic mice. Carbohydr Polym 2018; 190:77-86. [PMID: 29628262 DOI: 10.1016/j.carbpol.2018.02.058] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/20/2018] [Accepted: 02/20/2018] [Indexed: 12/11/2022]
Abstract
The aim of this study is to investigate the effect of chitosan oligosaccharides (COS) on type 2 diabetes mellitus. Wild type C57BL/6J mice or diabetic db/db mice were treated with vehicle or COS for three months. COS treatment significantly decreased the blood glucose (P < 0.01) and reversed the insulin resistance (P < 0.05) in db/db mice, which was accompanied by suppressing the inflammation mediators (P < 0.05), down-regulating the lipogenesis (P < 0.01) and inhibiting the adipocyte differentiation (P < 0.05) in white adipose tissue. Additionally, COS treatment inhibited the reduction of occludin (P < 0.01) and relieved the gut dysbiosis in diabetic mice by promoting Akkermansia (P < 0.01) and suppressing Helicobacter (P < 0.05). Spearman's correlation analysis indicates that the COS-modulated bacteria are positively correlated with inflammation, hyperglycemia and dyslipidemia. The functional profiling based on the microbiota composition implicated that COS treatment may regulate the metabolic pathways of gut microbiota. In summary, COS treatment remarkably improved the glucose metabolism and reshaped the unbalanced gut microbiota of diabetic mice. Our study provided the evidence for application of COS to the treatment of diabetes mellitus.
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Affiliation(s)
- Junping Zheng
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; State Key Laboratory of Biochemical Engineering and Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Xubing Yuan
- University of Chinese Academy of Sciences, Beijing 100049, PR China; State Key Laboratory of Biochemical Engineering and Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Gong Cheng
- State Key Laboratory of Biochemical Engineering and Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Siming Jiao
- State Key Laboratory of Biochemical Engineering and Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Cui Feng
- State Key Laboratory of Biochemical Engineering and Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Xiaoming Zhao
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China
| | - Heng Yin
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China
| | - Yuguang Du
- State Key Laboratory of Biochemical Engineering and Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China.
| | - Hongtao Liu
- State Key Laboratory of Biochemical Engineering and Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; Zhengzhou Institute of Emerging Industrial Technology, Zhengzhou 450000, PR China.
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50
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Tracanna V, de Jong A, Medema MH, Kuipers OP. Mining prokaryotes for antimicrobial compounds: from diversity to function. FEMS Microbiol Rev 2018; 41:417-429. [PMID: 28402441 DOI: 10.1093/femsre/fux014] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/02/2017] [Indexed: 01/03/2023] Open
Abstract
The bacterial kingdom provides a major source of antimicrobials that can either be directly applied or used as scaffolds to further improve their functionality in the host. The rapidly increasing amount of bacterial genomic, metabolomic and transcriptomic data offers unique opportunities to apply a variety of approaches to mine for existing and novel antimicrobials. Here, we discuss several powerful mining approaches to identify novel molecules with antimicrobial activity across structurally diverse natural products, including ribosomally synthesized and posttranslationally modified peptides, nonribosomal peptides and polyketides. We not only discuss the direct mining of genomes based on identification of biosynthetic gene clusters, but also describe more advanced and integrative approaches in ecology-based mining, functionality-based mining and mode-of-action-based mining. These efforts are likely to accelerate the discovery and development of novel antimicrobial drugs.
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Affiliation(s)
- Vittorio Tracanna
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, Radix West, Building 107, 6708 PB Wageningen, The Netherlands
| | - Anne de Jong
- Molecular Genetics, University of Groningen, Nijenborgh 7, 9726AG Groningen, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, Radix West, Building 107, 6708 PB Wageningen, The Netherlands
| | - Oscar P Kuipers
- Molecular Genetics, University of Groningen, Nijenborgh 7, 9726AG Groningen, The Netherlands
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