1
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Yu Y, van der Donk WA. PEARL-Catalyzed Peptide Bond Formation after Chain Reversal by Ureido-Forming Condensation Domains. ACS CENTRAL SCIENCE 2024; 10:1242-1250. [PMID: 38947204 PMCID: PMC11212132 DOI: 10.1021/acscentsci.4c00044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 07/02/2024]
Abstract
A subset of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are encoded in their biosynthetic gene clusters (BGCs) with enzymes annotated as lantibiotic dehydratases. The functions of these putative lantibiotic dehydratases remain unknown. Here, we characterize an NRPS-PKS BGC with a putative lantibiotic dehydratase from the bacterium Stackebrandtia nassauensis (sna). Heterologous expression revealed several metabolites produced by the BGC, and the omission of selected biosynthetic enzymes revealed the biosynthetic pathway toward these compounds. The final product is a bisarginyl ureidopeptide with an enone electrophile. The putative lantibiotic dehydratase catalyzes peptide bond formation to a Thr that extends the peptide scaffold opposite to the NRPS and PKS biosynthetic direction. The condensation domain of the NRPS SnaA catalyzes the formation of a ureido group, and bioinformatics analysis revealed a distinct active site signature EHHXXHDG of ureido-generating condensation (Curea) domains. This work demonstrates that the annotated lantibiotic dehydratase serves as a separate amide bond-forming machinery in addition to the NRPS, and that the lantibiotic dehydratase enzyme family possesses diverse catalytic activities in the biosynthesis of both ribosomal and nonribosomal natural products.
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Affiliation(s)
- Yue Yu
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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2
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Castaldi A, Truong BN, Vu QT, Le THM, Marie A, Le Pennec G, Rouvier F, Brunel JM, Longeon A, Pham VC, Doan TMH, Bourguet-Kondracki ML. Computational Methods Reveal a Series of Cyclic and Linear Lichenysins and Surfactins from the Vietnamese Marine Sediment-Derived Streptomyces Strain G222. Molecules 2024; 29:1458. [PMID: 38611738 PMCID: PMC11012875 DOI: 10.3390/molecules29071458] [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: 02/20/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
The Streptomyces strain G222, isolated from a Vietnamese marine sediment, was confidently identified by 16S rRNA gene sequencing. Its AcOEt crude extract was successfully analyzed using non-targeted LC-MS/MS analysis, and molecular networking, leading to a putative annotation of its chemical diversity thanks to spectral libraries from GNPS and in silico metabolite structure prediction obtained from SIRIUS combined with the bioinformatics tool conCISE (Consensus Annotation Propagation of in silico Elucidations). This dereplication strategy allowed the identification of an interesting cluster of a series of putative cyclic and linear lipopeptides of the lichenysin and surfactin families. Lichenysins (3-7) were isolated from the sub-fraction, which showed significant anti-biofilm activity against Pseudomonas aeruginosa MUC-N1. Their structures were confirmed by detailed 1D and 2D NMR spectroscopy (COSY, HSQC, HMBC, TOCSY, ROESY) recorded in CD3OH, and their absolute configurations were determined using the modified Marfey's method. The isolated lichenysins showed anti-biofilm activity at a minimum concentration of 100 µM. When evaluated for antibacterial activity against a panel of Gram-positive and Gram-negative strains, two isolated lichenysins exhibited selective activity against the MRSA strain without affecting its growth curve and without membranotropic activity. This study highlights the power of the MS/MS spectral similarity strategy using computational methods to obtain a cross-validation of the annotated molecules from the complex metabolic profile of a marine sediment-derived Streptomyces extract. This work provides the first report from a Streptomyces strain of combined cyclic and linear lichenysins and surfactins, known to be characteristic compounds of the genus Bacillus.
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Affiliation(s)
- Andrea Castaldi
- Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS, Muséum National d’Histoire Naturelle, 57 rue Cuvier (CP54), 75005 Paris, France; (A.C.); (A.M.); (A.L.)
| | - Bich Ngan Truong
- Institute of Marine Biochemistry (IMBC), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi 100000, Vietnam; (B.N.T.); (Q.T.V.); (T.H.M.L.); (V.C.P.)
| | - Quyen Thi Vu
- Institute of Marine Biochemistry (IMBC), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi 100000, Vietnam; (B.N.T.); (Q.T.V.); (T.H.M.L.); (V.C.P.)
| | - Thi Hong Minh Le
- Institute of Marine Biochemistry (IMBC), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi 100000, Vietnam; (B.N.T.); (Q.T.V.); (T.H.M.L.); (V.C.P.)
| | - Arul Marie
- Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS, Muséum National d’Histoire Naturelle, 57 rue Cuvier (CP54), 75005 Paris, France; (A.C.); (A.M.); (A.L.)
| | - Gaël Le Pennec
- Laboratoire de Biotechnologie et Chimie Marines, Université Bretagne Sud, EMR CNRS 6076, IUEM, 56100 Lorient, France;
| | - Florent Rouvier
- UMR MD1 “Membranes et Cibles Thérapeutiques”, U1261 INSERM, Aix-Marseille Université, Faculté de Pharmacie, 27 Bd Jean Moulin, CEDEX 5, 13385 Marseille, France; (F.R.); (J.-M.B.)
| | - Jean-Michel Brunel
- UMR MD1 “Membranes et Cibles Thérapeutiques”, U1261 INSERM, Aix-Marseille Université, Faculté de Pharmacie, 27 Bd Jean Moulin, CEDEX 5, 13385 Marseille, France; (F.R.); (J.-M.B.)
| | - Arlette Longeon
- Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS, Muséum National d’Histoire Naturelle, 57 rue Cuvier (CP54), 75005 Paris, France; (A.C.); (A.M.); (A.L.)
| | - Van Cuong Pham
- Institute of Marine Biochemistry (IMBC), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi 100000, Vietnam; (B.N.T.); (Q.T.V.); (T.H.M.L.); (V.C.P.)
| | - Thi Mai Huong Doan
- Institute of Marine Biochemistry (IMBC), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi 100000, Vietnam; (B.N.T.); (Q.T.V.); (T.H.M.L.); (V.C.P.)
| | - Marie-Lise Bourguet-Kondracki
- Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS, Muséum National d’Histoire Naturelle, 57 rue Cuvier (CP54), 75005 Paris, France; (A.C.); (A.M.); (A.L.)
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3
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Li Q, Li S, Li S, Hao X, Wang A, Si S, Xu Y, Shu J, Gan M. Antimicrobial and Anti-inflammatory Cyclic Tetrapeptides from the Co-cultures of Two Marine-Derived Fungi. JOURNAL OF NATURAL PRODUCTS 2024; 87:365-370. [PMID: 38276888 DOI: 10.1021/acs.jnatprod.3c01115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Violaceotides B-E (1-4), four new cyclic tetrapeptides, along with seven known compounds, were identified from the sponge-associated Aspergillus insulicola IMB18-072 co-cultivated with the marine-derived Alternaria angustiovoidea IMB20-805. Their structures were elucidated by extensive analysis of spectroscopic data, including HRESIMS, 1D and 2D NMR, and MS/MS data. The absolute configurations were determined by the advanced Marfey's method. Compounds 2, 3, and violaceotide A (5) displayed selective antimicrobial activities against the aquatic pathogenic bacteria Edwardsiella tarda and E. ictaluri. In addition, compounds 1-5 showed inhibitory activities against the LPS-induced expression of the inflammatory mediator IL-6 in RAW264.7 cells at a concentration of 10 μM.
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Affiliation(s)
- Qin Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
- Key Laboratory of Modern Preparation of Traditional Chinese Medicines, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, People's Republic of China
| | - Shasha Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Shunwang Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Xiaomeng Hao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Anqi Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Shuyi Si
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Yanni Xu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Jicheng Shu
- Key Laboratory of Modern Preparation of Traditional Chinese Medicines, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, People's Republic of China
| | - Maoluo Gan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
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4
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Ma Z, Zuo P, Sheng J, Liu Q, Qin X, Ke C. Characterization and Production of a Biosurfactant Viscosin from Pseudomonas sp. HN11 and its Application on Enhanced oil Recovery During oily Sludge Cleaning. Appl Biochem Biotechnol 2023; 195:7668-7684. [PMID: 37084032 DOI: 10.1007/s12010-023-04503-z] [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] [Accepted: 04/11/2023] [Indexed: 04/22/2023]
Abstract
Biosurfactants are renewable resources with versatile applications on environmental bioremediation and industrial processes. Pseudomonas species are one of the promising biosurfactant producers. However, besides rhamnolipids, little is known about Pseudomonas-derived biosurfactants on solubilization of polycyclic aromatic hydrocarbons (PAHs) and oily sludge treatment. In this study, Pseudomonas sp. HN11-derived biosurfactant was purified by chromatographic methods and was characterized as viscosin via bioinformatic analysis, spectrometric and spectroscopic analyses, Marfey's method and (C-H)α NMR fingerprint matching approach. Viscosin is a potent biosurfactant with critical micelle concentration of 5.79 mg/L and is stable under various stresses. Moreover, viscosin was produced at 0.42 g/L at 48 h of liquid fermentation. Further data have shown that emulsifying agent viscosin is capable of promoting the solubilization of PAHs and displays enhanced oil recovery during oily sludge treatment. More specifically, viscosin has shown significantly enhanced solubilization on fluoranthene compared with control (0.04 mg/L), 2.21 mg/L and 1.27 mg/L fluoranthene was recovered from 100 mg/L and 200 mg/L viscosin treatment, respectively. However, only 200 mg/L viscosin has significantly enhanced the solubilization of phenanthrene (0.75 mg/L) and benzo[a]pyrene (0.51 mg/L) compared to each control (0.23 mg/L for phenanthrene and 0.09 mg/L for benzo[a]pyrene). Viscosin treatment of oily sludge (recovering of 0.58 g oil) has shown a significant oil recovery compared to that of control (recovering of 0.42 g oil). This study shows the great potential of viscosin-type biosurfactant on oily sludge treatment.
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Affiliation(s)
- Zongwang Ma
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China.
| | - Pingcheng Zuo
- School of Mechanical Engineering, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Jun Sheng
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Qian Liu
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Xiao Qin
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Congyu Ke
- Shaanxi Province Key Laboratory of Environmental Pollution Control and Reservoir Protection Technology of Oilfields, Xi'an Shiyou University, Xi'an, 710065, China
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5
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Yoshimura A, Saeki R, Nakada R, Tomimoto S, Jomori T, Suganuma K, Wakimoto T. Membrane-Vesicle-Mediated Interbacterial Communication Activates Silent Secondary Metabolite Production. Angew Chem Int Ed Engl 2023; 62:e202307304. [PMID: 37449463 DOI: 10.1002/anie.202307304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Most bacterial biosynthetic gene clusters (BGCs) are "silent BGCs" that are expressed poorly or not at all under normal culture conditions. However, silent BGCs, even in part, may be conditionally expressed in response to external stimuli in the original bacterial habitats. The growing knowledge of bacterial membrane vesicles (MVs) suggests that they could be promising imitators of the exogenous stimulants, especially given their functions as signaling mediators in bacterial cell-to-cell communication. Therefore, we envisioned that MVs added to bacterial cultures could activate diverse silent BGCs. Herein, we employed Burkholderia multivorans MVs, which induced silent metabolites in a wide range of bacteria in Actinobacteria, Bacteroidetes and Proteobacteria phyla. A mechanistic analysis of MV-induced metabolite production in Xenorhabdus innexi suggested that the B. multivorans MVs activate silent metabolite production by inhibiting quorum sensing in X. innexi. In turn, the X. innexi MVs carrying some MV-induced peptides suppressed the growth of B. multivorans, highlighting the interspecies communication between B. multivorans and X. innexi through MV exchange.
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Affiliation(s)
- Aya Yoshimura
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Rio Saeki
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Ryusuke Nakada
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Shota Tomimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Takahiro Jomori
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
- Faculty of Science, University of the Ryukyus, 1-Senbaru, Nishihara, Nakagami, Okinawa, 903-0213, Japan
| | - Keisuke Suganuma
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, 080-8555, Japan
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine Inada, Obihiro, 080-8555, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
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6
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Gomez JS, Shaikhet M, Loganathan AK, Darnowski MG, Boddy CN, McMullin DR, Avis TJ. Characterization of Arthropeptide B, an Antifungal Cyclic Tetrapeptide from Arthrobacter humicola. J Chem Ecol 2023; 49:528-536. [PMID: 37322383 DOI: 10.1007/s10886-023-01438-x] [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: 04/30/2023] [Revised: 06/04/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023]
Abstract
Disease suppressive composts are known, yet little information on the potential role of specific microbial antagonist within are available. Arthrobacter humicola isolate M9-1A has been obtained from a compost prepared from marine residues and peat moss. The bacterium is a non-filamentous actinomycete with antagonistic activity against plant pathogenic fungi and oomycetes sharing its ecological niche in agri-food microecosystems. Our objective was to identify and characterize compounds with antifungal activity produced by A. humicola M9-1A. Arthrobacter humicola culture filtrates were tested for antifungal activity in vitro and in vivo and a bioassay-guided approach was used to identify potential chemical determinants of its observed activity against molds. The filtrates reduced the development of lesions of Alternaria rot on tomatoes and the ethyl acetate extract inhibited growth of Alternaria alternata. A compound, arthropeptide B [cyclo-(L-Leu, L-Phe, L-Ala, L-Tyr)], was purified from the ethyl acetate extract of the bacterium. Arthropeptide B is a new chemical structure reported for the first time and has shown antifungal activity against A. alternata spore germination and mycelial growth.
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Affiliation(s)
| | - Michael Shaikhet
- Institute of Biochemistry, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | | | - Michael G Darnowski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - David R McMullin
- Department of Chemistry, Carleton University, Ottawa, ON, K1S 5B6, Canada
- Institute of Biochemistry, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Tyler J Avis
- Department of Chemistry, Carleton University, Ottawa, ON, K1S 5B6, Canada.
- Institute of Biochemistry, Carleton University, Ottawa, ON, K1S 5B6, Canada.
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7
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Salim AA, Hussein WM, Dewapriya P, Hoang HN, Zhou Y, Samarasekera K, Khalil ZG, Fairlie DP, Capon RJ. Talarolides Revisited: Cyclic Heptapeptides from an Australian Marine Tunicate-Associated Fungus, Talaromyces sp. CMB-TU011. Mar Drugs 2023; 21:487. [PMID: 37755100 PMCID: PMC10533135 DOI: 10.3390/md21090487] [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] [Received: 08/11/2023] [Revised: 09/06/2023] [Accepted: 09/06/2023] [Indexed: 09/28/2023] Open
Abstract
Application of a miniaturized 24-well plate system for cultivation profiling (MATRIX) permitted optimization of the cultivation conditions for the marine-derived fungus Talaromyces sp. CMB-TU011, facilitating access to the rare cycloheptapeptide talarolide A (1) along with three new analogues, B-D (2-4). Detailed spectroscopic analysis supported by Marfey's analysis methodology was refined to resolve N-Me-l-Ala from N-Me-d-Ala, l-allo-Ile from l-Ile and l-Leu, and partial and total syntheses of 2, and permitted unambiguous assignment of structures for 1 (revised) and 2-4. Consideration of diagnostic ROESY correlations for the hydroxamates 1 and 3-4, and a calculated solution structure for 1, revealed how cross-ring H-bonding to the hydroxamate moiety influences (defines/stabilizes) the cyclic peptide conformation. Such knowledge draws attention to the prospect that hydroxamates may be used as molecular bridges to access new cyclic peptide conformations, offering the prospect of new biological properties, including enhanced oral bioavailability.
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Affiliation(s)
- Angela A. Salim
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.A.S.); (W.M.H.); (P.D.); (H.N.H.); (Y.Z.); (K.S.); (Z.G.K.); (D.P.F.)
| | - Waleed M. Hussein
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.A.S.); (W.M.H.); (P.D.); (H.N.H.); (Y.Z.); (K.S.); (Z.G.K.); (D.P.F.)
| | - Pradeep Dewapriya
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.A.S.); (W.M.H.); (P.D.); (H.N.H.); (Y.Z.); (K.S.); (Z.G.K.); (D.P.F.)
| | - Huy N. Hoang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.A.S.); (W.M.H.); (P.D.); (H.N.H.); (Y.Z.); (K.S.); (Z.G.K.); (D.P.F.)
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Yahao Zhou
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.A.S.); (W.M.H.); (P.D.); (H.N.H.); (Y.Z.); (K.S.); (Z.G.K.); (D.P.F.)
| | - Kaumadi Samarasekera
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.A.S.); (W.M.H.); (P.D.); (H.N.H.); (Y.Z.); (K.S.); (Z.G.K.); (D.P.F.)
| | - Zeinab G. Khalil
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.A.S.); (W.M.H.); (P.D.); (H.N.H.); (Y.Z.); (K.S.); (Z.G.K.); (D.P.F.)
| | - David P. Fairlie
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.A.S.); (W.M.H.); (P.D.); (H.N.H.); (Y.Z.); (K.S.); (Z.G.K.); (D.P.F.)
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Robert J. Capon
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (A.A.S.); (W.M.H.); (P.D.); (H.N.H.); (Y.Z.); (K.S.); (Z.G.K.); (D.P.F.)
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8
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Jin Y, Lee KT, Kim T, Kim J, Lee JW, Shim SH. New secondary metabolites produced by Paraphoma radicina FB55 as potential antifungal agents. J Antibiot (Tokyo) 2023; 76:474-480. [PMID: 37198338 DOI: 10.1038/s41429-023-00626-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/16/2023] [Accepted: 04/17/2023] [Indexed: 05/19/2023]
Abstract
Microorganisms in specific environments are rich sources of bioactive natural products as they produce compounds that can aid their survival in harsh environments. In an effort to investigate antifungal compounds produced by microorganisms, the fungal strain Paraphoma radicia FB55, isolated from a marine sediment of the Beaufort Sea, north of Alaska, was subjected to chemical investigation. Chromatography of the culture extracts yielded two new compounds (1 and 2) and eight known compounds (3-10). Their structures were determined using spectroscopic and chemical methods. Compound 1 was a new analog of the known compound (3) with an isobenzofuranone skeleton. The absolute configuration of the chiral center in 1 was established by comparison of its ECD and specific rotation values with those for a known analogue. Compound 2 is a polyketide-amino acid hybrid. Comprehensive Nuclear Magnetic Resonance (NMR) analysis indicated that 2 consisted of two substructures:5-methyl-6-oxo-2,4-heptadienoic acid and isoleucinol. The absolute configuration of the isoleucinol moiety in 2 was determined to be D using Marfey's method. All the isolated compounds were evaluated for antifungal activities. Although the antifungal activity of the isolated compounds was not potent, co-treatment of compounds 7 and 8 with a clinically available amphotericin B (AmB) lowered the IC50 values of AmB by synergism against human pathogenic yeast.
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Affiliation(s)
- Yeongwoon Jin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 01369, Republic of Korea
| | - Kyung-Tae Lee
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Jeonbuk, Republic of Korea
| | - Taeyeon Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 01369, Republic of Korea
| | - Jaekyeong Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 01369, Republic of Korea
| | - Jin Woo Lee
- College of Pharmacy, Duksung Women's University, Seoul, 01369, Republic of Korea
| | - Sang Hee Shim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 01369, Republic of Korea.
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9
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Gaudêncio SP, Bayram E, Lukić Bilela L, Cueto M, Díaz-Marrero AR, Haznedaroglu BZ, Jimenez C, Mandalakis M, Pereira F, Reyes F, Tasdemir D. Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation. Mar Drugs 2023; 21:md21050308. [PMID: 37233502 DOI: 10.3390/md21050308] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023] Open
Abstract
Natural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particularly the determination of the absolute configuration of metabolites with stereogenic centers. This review comprehensively focuses on recent technological and instrumental advances, highlighting the development of methods that alleviate these obstacles, paving the way for accelerating NP discovery towards biotechnological applications. Herein, we emphasize the most innovative high-throughput tools and methods for advancing bioactivity screening, NP chemical analysis, dereplication, metabolite profiling, metabolomics, genome sequencing and/or genomics approaches, databases, bioinformatics, chemoinformatics, and three-dimensional NP structure elucidation.
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Affiliation(s)
- Susana P Gaudêncio
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Engin Bayram
- Institute of Environmental Sciences, Room HKC-202, Hisar Campus, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Lada Lukić Bilela
- Department of Biology, Faculty of Science, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina
| | - Mercedes Cueto
- Instituto de Productos Naturales y Agrobiología-CSIC, 38206 La Laguna, Spain
| | - Ana R Díaz-Marrero
- Instituto de Productos Naturales y Agrobiología-CSIC, 38206 La Laguna, Spain
- Instituto Universitario de Bio-Orgánica (IUBO), Universidad de La Laguna, 38206 La Laguna, Spain
| | - Berat Z Haznedaroglu
- Institute of Environmental Sciences, Room HKC-202, Hisar Campus, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Carlos Jimenez
- CICA- Centro Interdisciplinar de Química e Bioloxía, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain
| | - Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, HCMR Thalassocosmos, 71500 Gournes, Crete, Greece
| | - Florbela Pereira
- LAQV, REQUIMTE, Chemistry Department, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Fernando Reyes
- Fundación MEDINA, Avda. del Conocimiento 34, 18016 Armilla, Spain
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
- Faculty of Mathematics and Natural Science, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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10
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Ma Z, Sheng J. Pseudophomins A-D Produced from Pseudomonas sp. HN8-3 Using an OSMAC Approach and Their Roles in Biocontrol of Phytophthora capsici in Cucumbers. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6268-6276. [PMID: 37068136 DOI: 10.1021/acs.jafc.3c00137] [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: 05/03/2023]
Abstract
In this study, two new cyclic lipopeptides (CLPs) pseudophomins C (3) and D (4) and two known CLPs pseudophomins A (1) and B (2) were produced and characterized from the bacterial supernatant of Pseudomonas sp. HN8-3 by an OSMAC (one strain-many compounds) approach. OSMAC is a strategy that involves feeding of a single microorganism with divergent substrates to stimulate the production of new secondary metabolites. These pseudophomins were purified and identified via chromatographic methods, droplet collapse assay, genome mining, spectroscopic and spectrometric analyses, and single-crystal X-ray diffraction (XRD). Moreover, bioactivity tests showed that pseudophomins could lyse the zoospores of Phytophthora capsici in vitro, and coapplication of pseudophomins with zoospores of P. capsici further reduced the incidence of P. capsici on cucumber leaves. Collectively, these results indicated that pseudophomins have the potential to be developed as biopesticides for controlling P. capsici in cucumber.
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Affiliation(s)
- Zongwang Ma
- College of Life Science, Northwest Normal University, East Anning Road 967, 730070 Lanzhou, China
| | - Jun Sheng
- College of Life Science, Northwest Normal University, East Anning Road 967, 730070 Lanzhou, China
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11
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Pistorius D, Buntin K, Richard E, Rust M, Bouquet C, Wollbrett S, Weber E, Dietschin D, Bruccoleri R, Oakeley E, Petersen F. Valhidepsin Lipopeptides from Chromobacterium vaccinii: Structures, Biosynthesis, and Coregulation with FR900359 Production. JOURNAL OF NATURAL PRODUCTS 2023; 86:246-255. [PMID: 36745695 DOI: 10.1021/acs.jnatprod.2c00825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Microbial secondary metabolites continue to provide a valuable source of both chemical matter and inspiration for drug discovery in a broad range of therapeutic areas. Beyond this, the corresponding microorganisms represent a sustainable modality for biotechnological production of structurally complex molecules at the quantities required for drug development or even commercial manufacturing. Chromobacterium vaccinii, which has recently been reported as a producer of the pharmacologically highly important Gq inhibitor FR900359 (FR), represents such an example. The characterization of an orphan biosynthetic gene cluster (BGC) located directly downstream of the frs BCG led to the discovery of eight new lipopeptides, valhidepsins A-H (1-8), produced by C. vaccinii. Their chemical structures were elucidated through analysis of 1D and 2D NMR data and high-resolution MS/MS fragmentation methods. The valhidepsins did not display significant antibiotic nor cytotoxic activities but showed surfactant properties. The cluster-compound correlation was demonstrated by generation of a knockout mutant, which abolished production of valhidepsins. This knockout mutant yielded a significantly increased isolated yield of FR.
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Affiliation(s)
- Dominik Pistorius
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Kathrin Buntin
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Etienne Richard
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Michael Rust
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Caroline Bouquet
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Séverine Wollbrett
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Eric Weber
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Daniele Dietschin
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | | | - Edward Oakeley
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Frank Petersen
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
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12
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Fang Y, Wang J, Tang Y, Guo Z, Bai J, Wu L, Su J, Cen S, Yu L, Zhang D. Geninthiocins E and F, two new cyclic thiopeptides with antiviral activities from soil-derived Streptomyces sp. CPCC 200267 using OSMAC strategy. J Antibiot (Tokyo) 2023; 76:101-104. [PMID: 36434277 DOI: 10.1038/s41429-022-00580-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/23/2022] [Accepted: 10/23/2022] [Indexed: 11/26/2022]
Abstract
On the basis of the one strain-many compounds (OSMAC) strategy, two new cyclic thiopeptides, geninthiocins E and F, together with four known geninthiocin derivatives, geninthiocins A, B, C, and val-geninthiocin were isolated from Streptomyces sp. CPCC 200267. Their structures and absolute configurations were elucidated by extensive spectroscopic analyses and Marfey's method. Geninthiocin E (1), val-geninthiocin (3), geninthiocin A (4), and geninthiocin B (5) exhibited significant anti-influenza A virus activities with the IC50 values of 28.7, 15.3, 7.3, and 18.3 μM, respectively. Compounds 3 and 4 showed moderate antibacterial activities against Staphylococcus aureus.
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Affiliation(s)
- Yuan Fang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Tang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- School of Pharmacy, Yantai University, Yantai, China
| | - Zhe Guo
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jinglin Bai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Linzhuan Wu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Su
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liyan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Dewu Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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13
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Ma Z. Genome mining and chemical characterization of a new cyclic lipopeptide associated with MDN-0066 from Pseudomonas moraviensis HN2 cultured in a valine-rich medium. J Antibiot (Tokyo) 2023; 76:244-248. [PMID: 36702935 DOI: 10.1038/s41429-023-00597-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/27/2022] [Accepted: 01/11/2023] [Indexed: 01/27/2023]
Abstract
A new cyclic lipopeptide (CLP) MDN-0066-β (1) and MDN-0066 (2) were isolated and characterized from the bacterial cultures of P. moraviensis HN2 in this study. The CLPs were purified by solid-phase extraction (SPE) and reversed-phase high performance liquid chromatography (RP-HPLC). Moreover, chemical structures of two CLPs were characterized by genome mining and analysis, nuclear magnetic resonance (NMR), high-resolution mass spectrometry (HR-MS), Marfey's method and (C-H)α NMR fingerprint matching approach. MDN-0066 (2) has an amino acid sequence of L-Leu1, D-Glu2, D-allo-Thr3, D-Leu4, D-Leu5, D-Ser6, L-Leu7, L-Ile8 linked to a saturated C10 β-hydroxyl fatty acid moiety (R-configuration for 3-OH). The new CLP MDN-0066-β (1) differs MDN-0066 (2) in the 8th position of L-valine in its peptide moiety, this variation in structure could be attributed to the supplement of L-valine in the cultural medium during liquid fermentation. Further antimicrobial tests showed that the two CLPs display moderate antagonistic activity against Staphylococcus aureus and Escherichia coli.
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Affiliation(s)
- Zongwang Ma
- College of Life Science, Northwest Normal University, 967 East Anning Road, 730070, Lanzhou, China.
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14
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Absolute Stereochemistry Determination of Bioactive Marine-Derived Cyclopeptides by Liquid Chromatography Methods: An Update Review (2018-2022). MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020615. [PMID: 36677673 PMCID: PMC9867211 DOI: 10.3390/molecules28020615] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023]
Abstract
Cyclopeptides are considered as one of the most important classes of compounds derived from marine sources, due to their structural diversity and a myriad of their biological and pharmacological activities. Since marine-derived cyclopeptides consist of different amino acids, many of which are non-proteinogenic, they possess various stereogenic centers. In this respect, the structure elucidation of new molecular scaffolds obtained from natural sources, including marine-derived cyclopeptides, can become a very challenging task. The determination of the absolute configurations of the amino acid residues is accomplished, in most cases, by performing acidic hydrolysis, followed by analyses by liquid chromatography (LC). In a continuation with the authors' previous publication, and to analyze the current trends, the present review covers recently published works (from January 2018 to November 2022) regarding new cyclopeptides from marine organisms, with a special focus on their biological/pharmacological activities and the absolute stereochemical assignment of the amino acid residues. Ninety-one unreported marine-derived cyclopeptides were identified during this period, most of which displayed anticancer or antimicrobial activities. Marfey's method, which involves LC, was found to be the most frequently used for this purpose.
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15
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Bracegirdle J, Casandra D, Rocca JR, Adams JH, Baker BJ. Highly N-Methylated Peptides from the Antarctic Sponge Inflatella coelosphaeroides Are Active against Plasmodium falciparum. JOURNAL OF NATURAL PRODUCTS 2022; 85:2454-2460. [PMID: 36178104 DOI: 10.1021/acs.jnatprod.2c00684] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Malaria, caused by the parasite Plasmodium falciparum, continues to threaten much of the world's population, and there is a pressing need for expanding treatment options. Natural products have been a vital source of such drugs, and here we report seven new highly N-methylated linear peptides, friomaramide B (2) and shagamides A-F (3-8) from the marine sponge Inflatella coelosphaeroides, collected in Antarctic waters, which demonstrate activity against three strains of blood-stage P. falciparum. The planar structures of these metabolites were solved by interpreting NMR data, as well as HRESIMS/MS fragmentation patterns, while Marfey's analysis was used to establish the configurations of the amino acids. Reisolation of the previously reported compound friomaramide A (1) allowed us to revise its structure. The panel of isolated compounds allowed establishing structure/activity relationships and provided information for future structure optimization for this class of P. falciparum inhibitory metabolites.
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Affiliation(s)
- Joe Bracegirdle
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620, United States
| | - Debora Casandra
- Center for Global Health and Infectious Disease Research, College of Public Health, University of South Florida, Tampa, Florida 33612, United States
| | - James R Rocca
- AMRIS, McKnight Brain Institute, University of Florida, P.O. Box 100015, Gainesville, Florida 32610, United States
| | - John H Adams
- Center for Global Health and Infectious Disease Research, College of Public Health, University of South Florida, Tampa, Florida 33612, United States
| | - Bill J Baker
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620, United States
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16
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Zhou B, Shetye G, Wolf NM, Chen SN, Qader M, Ray GJ, Lankin DC, Cho S, Cheng J, Suh JW, Franzblau SG, McAlpine JB, Pauli GF. New Rufomycins from Streptomyces atratus MJM3502 Expand Anti- Mycobacterium tuberculosis Structure-Activity Relationships. Org Lett 2022; 24:7265-7270. [PMID: 36194676 PMCID: PMC9588618 DOI: 10.1021/acs.orglett.2c02493] [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: 11/30/2022]
Abstract
Four new rufomycins, compounds 1-4, named rufomycins 56, 57, 58, and 61, respectively, exhibiting new skeletal features, were obtained from Streptomyces atratus strain MJM3502 and were fully characterized. Compounds 1 and 2 possess a 4-imidazolidinone ring not previously encountered in this family of cyclopeptides, thereby resulting in a [5,17] bicyclic framework. The in vitro anti-Mycobacterium tuberculosis potency of compounds 3 and 4 is remarkable, with minimum inhibitory concentration values of 8.5 and 130 nM, respectively.
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Affiliation(s)
- Bin Zhou
- Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Gauri Shetye
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Nina M. Wolf
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Shao-Nong Chen
- Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Mallique Qader
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - G. Joseph Ray
- Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - David C. Lankin
- Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Sanghyun Cho
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Jinhua Cheng
- Myongji Bioefficacy Research Center, Myongji University, 116 Myongji-ro, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Joo-Won Suh
- Myongji Bioefficacy Research Center, Myongji University, 116 Myongji-ro, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Scott G. Franzblau
- Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - James B. McAlpine
- Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Guido F. Pauli
- Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
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17
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Pérez-Victoria I, Crespo G, Reyes F. Expanding the utility of Marfey's analysis by using HPLC-SPE-NMR to determine the C β configuration of threonine and isoleucine residues in natural peptides. Anal Bioanal Chem 2022; 414:8063-8070. [PMID: 36194241 DOI: 10.1007/s00216-022-04339-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/01/2022]
Abstract
The determination of amino acid chirality in natural peptides is typically addressed by Marfey's analysis. This approach relies on the complete hydrolysis of the peptide followed by the reaction of the resulting amino acid pool with Marfey's reagent, a chiral derivatizing agent which turns amino acid enantiomers into diastereomeric pairs which can be resolved by conventional reversed-phase HPLC. However, for certain amino acids possessing a second chiral centre at Cβ, the discrimination between the two possible epimers may still be challenging due to the lack of chromatographic resolution. Such is the case of isoleucine and threonine which can also be found in natural nonribosomal peptides as their allo-diastereomers. We describe a new approach based on the extension of Marfey's analysis using HPLC-SPE-NMR to sort out this challenge. Marfey's derivatives of these epimeric amino acids at Cβ can be differentiated by their distinct NMR spectra. Thus, simple comparison of the NMR spectra of trapped HPLC peaks with the corresponding spectra of standards enables the unambiguous assignment of the absolute configuration at the second chiral centre in such cases. The general applicability of this approach is showcased for two model cyclic peptides bearing L-Ile and L-Thr.
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Affiliation(s)
- Ignacio Pérez-Victoria
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016, Armilla, Granada, Spain.
| | - Gloria Crespo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016, Armilla, Granada, Spain
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016, Armilla, Granada, Spain
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18
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Xiao W, Satoh Y, Ogasawara Y, Dairi T. Biosynthetic Gene Cluster of linaridin Peptides Contain Epimerase Gene. Chembiochem 2022; 23:e202100705. [PMID: 35460155 DOI: 10.1002/cbic.202100705] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/24/2022] [Indexed: 11/10/2022]
Abstract
Salinipeptins belong to the type-A linaridin class of ribosomally synthesized and post-translationally modified peptides (RiPPs) comprising 22 amino acid residues with multiple D-amino acids. Although chirality of other type-A linaridins, such as grisemycin and cypemycin, has not been reported, the biosynthetic gene clusters of type-A linaridins have identical gene organization. Here, we report heterologous expression of grisemycin biosynthetic gene cluster ( grm ) and show that grisemycin contained multiple D-amino acids, similar to salinipeptins. The heterologous expression experiments also confirmed involvement of a novel peptide epimerase in grisemycin biosynthesis. Gene-deletion experiments indicated that grmL , a sole gene with unknown function, was indispensable for grisemycin production. We also show that the presence of D-amino acids is likely a common feature of linaridin natural products by analyzing two other type-A linaridin clusters.
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Affiliation(s)
- Wanlu Xiao
- Hokkaido University: Hokkaido Daigaku, Graduate School of Chemical Sciences and Engineering, JAPAN
| | - Yasuharu Satoh
- Hokkaido University: Hokkaido Daigaku, Graduate School of Engineering, JAPAN
| | - Yasushi Ogasawara
- Hokkaido University: Hokkaido Daigaku, Graduate School of Engineering, N13 W8, Kita-ku, 060-8628, Sapporo, JAPAN
| | - Tohru Dairi
- Hokkaido University, Graduate School of Engineering, N 13 W 8, Kita, 060-8628, Sapporo, JAPAN
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19
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Luo M, Chang S, Li Y, Xi X, Chen M, He N, Wang M, Zhao W, Xie Y. Molecular Networking-Based Screening Led to the Discovery of a Cyclic Heptadepsipeptide from an Endolichenic Xylaria sp. JOURNAL OF NATURAL PRODUCTS 2022; 85:972-979. [PMID: 35385664 DOI: 10.1021/acs.jnatprod.1c01108] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
MS/MS-based molecular networking strain prioritization led to the discovery of a group of cyclic depsipeptides from an endolichenic Xylaria sp. The main component, xylaroamide A (1), was obtained by LC-MS-guided isolation. The planar structure of compound 1 was elucidated via 1D and 2D NMR, as well as MS/MS data. The configurations were fully determined by the combination of advanced Marfey's analysis, partial hydrolysis, Mosher's reaction, and GIAO NMR calculation based on a restricted conformational search. A plausible biosynthetic pathway for xylaroamide A (1) involving a rare trans-acting N-methyltransferase is proposed based on bioinformatics analysis. Xylaroamide A (1) exhibited inhibitory activity against cancer cell lines BT-549 and RKO with IC50 values of 2.5 and 9.5 μM, respectively.
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20
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Mohamed OG, Khalil ZG, Santiago V, Capon RJ. Metarhizides A–C and metarhizosides A–B: PKS-NRPS macrolides and aromatic glycosides from an Australian fish gut-derived fungus, Metarhizium sp. CMB-F624. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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Sarksian R, Hegemann JD, Simon MA, Acedo JZ, van der Donk WA. Unexpected Methyllanthionine Stereochemistry in the Morphogenetic Lanthipeptide SapT. J Am Chem Soc 2022; 144:6373-6382. [PMID: 35352944 PMCID: PMC9011353 DOI: 10.1021/jacs.2c00517] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
Lanthipeptides are
polycyclic peptides characterized by the presence
of lanthionine (Lan) and/or methyllanthionine (MeLan). They are members
of the ribosomally synthesized and post-translationally modified peptides (RiPPs). The stereochemical
configuration of (Me)Lan cross-links is important for the bioactivity
of lanthipeptides. To date, MeLan residues in characterized lanthipeptides
have either the 2S,3S or 2R,3R stereochemistry. Herein, we reconstituted
in Escherichia coli the biosynthetic pathway toward
SapT, a class I lanthipeptide that exhibits morphogenetic activity.
Through the synthesis of standards, the heterologously produced peptide
was shown to possess three MeLan residues with the 2S,3R stereochemistry (d-allo-l-MeLan), the first time such stereochemistry has been
observed in a lanthipeptide. Bioinformatic analysis of the biosynthetic
enzymes suggests this stereochemistry may also be present in other
lanthipeptides. Analysis of another gene cluster in Streptomyces
coelicolor that is widespread in actinobacteria confirmed
another example of d-allo-l-MeLan
and verified the bioinformatic prediction. We propose a mechanism
for the origin of the unexpected stereochemistry and provide support
using site-directed mutagenesis.
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Affiliation(s)
- Raymond Sarksian
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Max A Simon
- Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States
| | - Jeella Z Acedo
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States
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22
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Le TC, Pulat S, Lee J, Kim GJ, Kim H, Lee EY, Hillman PF, Choi H, Yang I, Oh DC, Kim H, Nam SJ, Fenical W. Marine Depsipeptide Nobilamide I Inhibits Cancer Cell Motility and Tumorigenicity via Suppressing Epithelial-Mesenchymal Transition and MMP2/9 Expression. ACS OMEGA 2022; 7:1722-1732. [PMID: 35071867 PMCID: PMC8771697 DOI: 10.1021/acsomega.1c04520] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/22/2021] [Indexed: 05/11/2023]
Abstract
A cyclic depsipeptide, nobilamide I (1), along with the known peptide A-3302-B/TL-119 (2), was isolated from the saline cultivation of the marine-derived bacterium Saccharomonospora sp., strain CNQ-490. The planar structure of 1 was elucidated by interpretation of 1D and 2D NMR and MS spectroscopic data. The absolute configurations of the amino acids in 1 were assigned by using the C3 Marfey's analysis and comparing them with those of 2 based on their biosynthetic pathways. Nobilamide I (1) decreased cell motility by inhibiting epithelial-mesenchymal transition markers in A549 (lung cancer), AGS (gastric cancer), and Caco2 (colorectal cancer) cell lines. In addition, 1 modulated the expression of the matrix metalloproteinase (MMP) family (MMP2 and MMP9) in the three cell lines.
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Affiliation(s)
- Tu Cam Le
- College
of Pharmacy, Hong Bang International University, Hoa Binh, Hoa Thanh Ward, Tan Phu
District, Ho Chi Minh City72006, Vietnam
| | - Sultan Pulat
- College
of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon-si, Jeonnam57922, Republic of Korea
| | - Jihye Lee
- Department
of Chemistry and Nanoscience, Ewha Womans
University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul03760, Republic of Korea
| | - Geum Jin Kim
- College
of Pharmacy, Yeungnam University, 280, Daehak-ro, Gyeongsan-si, Gyeongsangbukdo38541, Republic of Korea
| | - Haerin Kim
- The
Graduate School of Industrial Pharmaceutical Sciences, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul03760, Republic
of Korea
| | - Eun-Young Lee
- Department
of Chemistry and Nanoscience, Ewha Womans
University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul03760, Republic of Korea
| | - Prima F. Hillman
- Department
of Chemistry and Nanoscience, Ewha Womans
University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul03760, Republic of Korea
| | - Hyukjae Choi
- College
of Pharmacy, Yeungnam University, 280, Daehak-ro, Gyeongsan-si, Gyeongsangbukdo38541, Republic of Korea
| | - Inho Yang
- Department
of Convergence Study on the Ocean Science and Technology, Korea Maritime and Ocean University, 727, Taejong-ro, Yeongdo-gu, Busan49112, Republic
of Korea
| | - Dong-Chan Oh
- Natural
Products Research Institute College of Pharmacy, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul08826, Republic of Korea
| | - Hangun Kim
- College
of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon-si, Jeonnam57922, Republic of Korea
- . Phone: +82
53 810 2824
| | - Sang-Jip Nam
- Department
of Chemistry and Nanoscience, Ewha Womans
University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul03760, Republic of Korea
- . Phone: +82 2 3277 6805
| | - William Fenical
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, California92093-0204, United States
- . Phone: +1 858 259 3839
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23
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Calderón C, Lämmerhofer M. Enantioselective metabolomics by liquid chromatography-mass spectrometry. J Pharm Biomed Anal 2022; 207:114430. [PMID: 34757254 DOI: 10.1016/j.jpba.2021.114430] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022]
Abstract
Metabolomics strives to capture the entirety of the metabolites in a biological system by comprehensive analysis, often by liquid chromatography hyphenated to mass spectrometry. A particular challenge thereby is the differentiation of structural isomers. Common achiral targeted and untargeted assays do not distinguish between enantiomers. This may lead to information loss. An increasing number of publications demonstrate that the enantiomeric ratio of certain metabolites can be meaningful biomarkers of certain diseases emphasizing the importance of introducing enantioselective analytical procedures in metabolomics. In this work, the state-of-the-art in the field of LC-MS based metabolomics is summarized with focus on developments in the recent decade. Methodologies, tagging strategies, workflows and general concepts are outlined. Selected biological applications in which enantioselective metabolomics has documented its usefulness are briefly discussed. In general, targeted enantioselective metabolomics assays are often based on a direct approach using chiral stationary phases (CSP) with polysaccharide derivatives, macrocyclic antibiotics, chiral crown ethers, chiral ion exchangers, donor-acceptor phases as chiral selectors. Rarely, these targeted assays focus on more than 20 analytes and usually are restricted to a certain metabolite class. In a variety of cases, pre-column derivatization of metabolites has been performed, especially for amino acids, to improve separation and detection sensitivity. Triple quadrupole instruments are the detection methods of first choice in targeted assays. Here, issues like matrix effect, absence of blank matrix impair accuracy of results. In selected applications, multiple heart cutting 2D-LC (RP followed by chiral separation) has been pursued to overcome this problem and alleviate bias due to interferences. Non-targeted assays, on the other hand, are based on indirect approach involving tagging with a chiral derivatizing agent (CDA). Besides classical CDAs numerous innovative reagents and workflows have been proposed and are discussed. Thereby, a critical issue for the accuracy is often neglected, viz. the validation of the enantiomeric impurity in the CDA. The majority of applications focus on amino acids, hydroxy acids, oxidized fatty acids and oxylipins. Some potential clinical applications are highlighted.
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Affiliation(s)
- Carlos Calderón
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany; Escuela de Química, Universidad de Costa Rica, San José 11501-2060, Costa Rica
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
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24
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Nartey AP, Dofuor AK, Owusu KBA, Camas AS, Deng H, Jaspars M, Kyeremeh K. Digyalipopeptide A, an antiparasitic cyclic peptide from the Ghanaian Bacillus sp. strain DE2B. Beilstein J Org Chem 2022; 18:1763-1771. [PMID: 36632531 PMCID: PMC9811306 DOI: 10.3762/bjoc.18.185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/07/2022] [Indexed: 12/29/2022] Open
Abstract
During the continued isolation of different bacteria from highly diverse, low human activity environments in Ghana and the subsequent characterization and biological activity studies of their secondary metabolites, we found both Gram-positive and Gram-negative Bacillus strains to be ubiquitous and widespread. One of such strains, the Ghanaian novel Bacillus sp. strain DE2B was isolated from rhizosphere soils collected from the Digya National Park in Ghana. Chromatographic purifications of the fermented culture extract of the strain DE2B, led to the isolation of a cyclic lipopeptide, digyalipopeptide A (1). Using 1D and 2D NMR data, mass spectrometry sequence tagging, advanced Marfey's analysis, and the GNPS molecular networking we solved the full structure of digyalipopeptide A (1). We found that compound 1 is a member of a somewhat homologous series of peptides produced as a mixture by the strain containing the same amino acid sequence in the cyclic peptide backbone but differing only by the length of aliphatic fatty acid side chains. When tested against Trypanosoma brucei subsp. brucei strain GUTat 3.1 and Leishmania donovani (Laveran and Mesnil) Ross (D10), digyalipopeptide A (1) gave IC50 values of 12.89 µM (suramin IC50 0.96 µM) and 4.85 µM (amphotericin B IC50 4.87 µM), respectively. Furthermore, digyalipopeptide A (1) produced IC50 values of 10.07 µM (ampicillin IC50 0.18 µM) and 10.01 µM (ampicillin IC50 1.53 µM) for Staphylococcus aureus and Shigella sonnei, respectively. The selectivity and toxicity profile of compound 1 was investigated using normal cell lines, macrophages RAW 264.7. When tested against normal macrophages, compound 1 gave an IC50 value of 71.32 μM. Selectivity indices (SI) were obtained by calculating the ratio of the IC50 in RAW 264.7 to the IC50 in the respective microbe and neglected parasite. In the presence of RAW 264.7 cell lines, compound 1 was particularly selective towards Leishmania donovani (Laveran and Mesnil) Ross (D10) with an SI value of 14.71. The bioactivity studies conducted confirm the role of these cyclic lipopeptides as defense chemicals in their natural environment and their ability to be biologically active across different species.
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Affiliation(s)
- Adwoa P Nartey
- Marine and Plant Research Laboratory of Ghana, Department of Chemistry, University of Ghana, P.O. Box LG 56 Legon-Accra, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P.O. Box LG 54 Legon-Accra, Ghana
| | - Aboagye K Dofuor
- Department of Biological, Physical and Mathematical Sciences, University of Environment and Sustainable Development, PMB, Somanya, Ghana
| | - Kofi B A Owusu
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, P.O. Box LG 581, Legon-Accra, Ghana
| | - Anil S Camas
- Department of Biomedical Engineering, Faculty of Engineering, University of Samsun, Ballica Campus 55420, Samsun, Turkey
| | - Hai Deng
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
| | - Kwaku Kyeremeh
- Marine and Plant Research Laboratory of Ghana, Department of Chemistry, University of Ghana, P.O. Box LG 56 Legon-Accra, Ghana
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25
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Development and application of highly sensitive labeling reagents for amino acids. Methods Enzymol 2022; 665:105-133. [DOI: 10.1016/bs.mie.2021.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Ramlawi S, Aitken A, Abusharkh S, McMullin DR, Avis TJ. Arthropeptide A, an antifungal cyclic tetrapeptide from Arthrobacter psychrophenolicus isolated from disease suppressive compost. Nat Prod Res 2021; 36:5715-5723. [PMID: 34933636 DOI: 10.1080/14786419.2021.2018434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
In an effort to describe bioactive antifungal compounds from antagonistic bacteria with potential for biocontrol of plant pathogens, a strain of Arthrobacter psychrophenolicus was collected from plant disease suppressive compost prepared from composted material of marine origin. Few natural products have been characterized from the non-filamentous Actinobacteria genus Arthrobacter. A new cyclic tetrapeptide, cyclo-(L-Pro-L-Leu-L-γHyp-L-Tyr); arthropeptide A (1), was isolated from the EtOAc soluble culture filtrate extract of A. psychrophenolicus M9-17 grown in MOLP broth. Its structure was confirmed by HRMS, interpretation of NMR data, and a modified Marfey's method. Arthropeptide A (1) displayed antifungal activity towards Alternaria alternata, the causal agent of disease in numerous host plant species, which had shown the previous susceptibility to A. psychrophenolicus. The newly identified compound may be responsible, in part, for the inhibitory activity of the bacterium against fungal plant pathogens.
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Affiliation(s)
- Serine Ramlawi
- Department of Chemistry, Carleton University, Ottawa, ON, Canada
| | - Alex Aitken
- Department of Chemistry, Carleton University, Ottawa, ON, Canada
| | - Sawsan Abusharkh
- Department of Chemistry, Carleton University, Ottawa, ON, Canada
| | - David R McMullin
- Department of Chemistry, Carleton University, Ottawa, ON, Canada.,Institute of Biochemistry, Carleton University, Ottawa, ON, Canada
| | - Tyler J Avis
- Department of Chemistry, Carleton University, Ottawa, ON, Canada.,Institute of Biochemistry, Carleton University, Ottawa, ON, Canada
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27
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De BC, Zhang W, Zhang G, Liu Z, Tan B, Zhang Q, Zhang L, Zhang H, Zhu Y, Zhang C. Host-dependent heterologous expression of berninamycin gene cluster leads to linear thiopeptide antibiotics. Org Biomol Chem 2021; 19:8940-8946. [PMID: 34617948 DOI: 10.1039/d1ob01759d] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Berninamycins are a class of thiopeptide antibiotics with potent activity against Gram-positive bacteria. Heterologous expression of the berninamycin (ber) biosynthetic gene cluster from marine-derived Streptomyces sp. SCSIO 11878 in different terrestrial model Streptomyces hosts led to the production of berninamycins A (1) and B (2) in Streptomyces lividans SBT18 and Streptomyces coelicolor M1154, while two new linearized berninamycins J (3) and K (4) were obtained in Streptomyces albus J1074. Their structures were elucidated by detailed interpretation of NMR data and Marfey's method. Bioactivity assays showed that the linear thiopeptides 3 and 4 were less potent than 1 and 2 in antibacterial activity. This work indicates that undefined host-dependent enzymes might be responsible for generating the linear thiopeptides 3 and 4 in S. albus J1074.
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Affiliation(s)
- Bidhan Chandra De
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China. .,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China. .,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd., Nansha District, Guangzhou 511458, China
| | - Guangtao Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China. .,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd., Nansha District, Guangzhou 511458, China
| | - Zhiwen Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
| | - Bin Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China. .,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd., Nansha District, Guangzhou 511458, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China. .,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd., Nansha District, Guangzhou 511458, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China. .,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd., Nansha District, Guangzhou 511458, China
| | - Haibo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China. .,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd., Nansha District, Guangzhou 511458, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China. .,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd., Nansha District, Guangzhou 511458, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China. .,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd., Nansha District, Guangzhou 511458, China
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28
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Paulus C, Zapp J, Luzhetskyy A. New Scabimycins A-C Isolated from Streptomyces acidiscabies (Lu19992). Molecules 2021; 26:5922. [PMID: 34641466 PMCID: PMC8513078 DOI: 10.3390/molecules26195922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 11/16/2022] Open
Abstract
Peptide natural products displaying a wide range of biological activities have become important drug candidates over the years. Microorganisms have been a powerful source of such bioactive peptides, and Streptomyces have yielded many novel natural products thus far. In an effort to uncover such new, meaningful compounds, the metabolome of Streptomyces acidiscabies was analyzed thoroughly. Three new compounds, scabimycins A-C (1-3), were discovered, and their chemical structures were elucidated by NMR spectroscopy. The relative and absolute configurations were determined using ROESY NMR experiments and advanced Marfey's method.
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Affiliation(s)
- Constanze Paulus
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany;
| | - Josef Zapp
- Department of Pharmaceutical Biology, Saarland University, 66123 Saarbrücken, Germany;
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany;
- AMEG Department, Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbrücken, Germany
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29
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Chemical Investigation of Diketopiperazines and N-Phenethylacetamide Isolated from Aquimarina sp. MC085 and Their Effect on TGF-β-Induced Epithelial–Mesenchymal Transition. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11198866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chemical investigations of Aquimarina sp. MC085, which suppressed TGF-β-induced epithelial–mesenchymal transition (EMT) in A549 human lung cancer cells, led to the isolation of compounds 1–3. Structural characterization using spectroscopic data analyses in combination with Marfey’s analysis revealed that they were two diketopiperazines [cyclo(l-Pro-l-Leu) (1) and cyclo(l-Pro-l-Ile) (2)] and one N-phenethylacetamide (3). Cyclo(l-Pro-l-Leu) (1) and N-phenethylactamide (3) inhibited the TGF-β/Smad pathway and suppressed the metastasis of A549 cells by affecting TGF-β-induced EMT. However, cyclo(l-Pro-l-Ile) (2) downregulated mesenchymal factors via a non-Smad-mediated signaling pathway.
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30
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Kim S, Lee CW, Park SY, Asolkar RN, Kim H, Kim GJ, Oh SJ, Kim Y, Lee EY, Oh DC, Yang I, Paik MJ, Choi H, Kim H, Nam SJ, Fenical W. Acremonamide, a Cyclic Pentadepsipeptide with Wound-Healing Properties Isolated from a Marine-Derived Fungus of the Genus Acremonium. JOURNAL OF NATURAL PRODUCTS 2021; 84:2249-2255. [PMID: 34387477 DOI: 10.1021/acs.jnatprod.1c00305] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Acremonamide (1) was isolated from a marine-derived fungus belonging to the genus Acremonium. The chemical structure of 1 was established using MS, UV, and NMR spectroscopic data analyses. Acremonamide (1) was found to contain N-Me-Phe, N-Me-Ala, Val, Phe, and 2-hydroxyisovaleric acid. The absolute configurations of the four aforementioned amino acids were determined through acid hydrolysis followed by the advanced Marfey's method, whereas the absolute configuration of 2-hydroxyisovaleric acid was determined through GC-MS analysis after formation of the O-pentafluoropropionylated derivative of the (-)-menthyl ester of 2-hydroxyisovaleric acid. As an intrinsic biological activity, acremonamide (1) did not exert cytotoxicity to cancer and noncancer cells and increased the migration and invasion. Based on these activities, the wound healing properties of acremonamide (1) were confirmed in vitro and in vivo.
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Affiliation(s)
- Sojeong Kim
- College of Pharmacy, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Chang Wook Lee
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam 57922, Republic of Korea
| | - So-Yeon Park
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam 57922, Republic of Korea
| | - Ratnakar N Asolkar
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, California 92093-0204, United States
| | - Haerin Kim
- College of Pharmacy, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Geum Jin Kim
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Republic of Korea
| | - Song Jin Oh
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam 57922, Republic of Korea
| | - Youngbae Kim
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam 57922, Republic of Korea
| | - Eun-Young Lee
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Inho Yang
- Ocean Science and Technology School, Korea Maritime and Ocean University, Busan 49112, Republic of Korea
| | - Man Jeong Paik
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam 57922, Republic of Korea
| | - Hyukjae Choi
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Republic of Korea
| | - Hangun Kim
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam 57922, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, California 92093-0204, United States
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31
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Ekanayake D, Perlatti B, Swenson DC, Põldmaa K, Bills GF, Gloer JB. Broomeanamides: Cyclic Octapeptides from an Isolate of the Fungicolous Ascomycete Sphaerostilbella broomeana from India. JOURNAL OF NATURAL PRODUCTS 2021; 84:2028-2034. [PMID: 34191504 PMCID: PMC8314271 DOI: 10.1021/acs.jnatprod.1c00414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Indexed: 06/13/2023]
Abstract
The genus Sphaerostilbella comprises fungi that colonize basidiomata of wood-inhabiting fungi, including important forest pathogens. Studies of fermentation cultures of an isolate (TFC201724) collected on the foothills of Himalayas, and closely related to S. broomeana isolates from Europe, led to the identification of a new cyclic octapeptide along with two closely related analogues (1-3) and four dioxopiperazines (4-7). The structure of the lead compound, broomeanamide A (1), was assigned mainly by analysis of 2D NMR and HRESIMS data. The structure consisted of one unit each of N-MeVal, Ala, N-MePhe, Pro, Val, and Ile and two N-MeLeu units. The amino acid sequence was determined on the basis of 2D NMR and HRESIMSMS data. NMR and HRMS data revealed that the other two new peptides have the same amino acid composition except that the Ile unit was replaced with Val in one instance (2) and the N-MeVal unit was replaced with Val in the other (3). The absolute configuration of 1 was assigned by analysis of the acid hydrolysate by application of Marfey's method using both C18 and C3 bonded-phase columns. Broomeanamide A (1) showed antifungal activity against Cryptococcus neoformans and Candida albicans, with MIC values of 8.0 and 64 μg/mL, respectively.
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Affiliation(s)
| | - Bruno Perlatti
- Texas
Therapeutic Institute, The Brown Foundation Institute of Molecular
Medicine, University of Texas Health Science
Center, 1881 East Road, Houston, Texas 77054, United
States
| | - Dale C. Swenson
- Department
of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Kadri Põldmaa
- Department
of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, EE-51005 Tartu, Estonia
| | - Gerald F. Bills
- Texas
Therapeutic Institute, The Brown Foundation Institute of Molecular
Medicine, University of Texas Health Science
Center, 1881 East Road, Houston, Texas 77054, United
States
| | - James B. Gloer
- Department
of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
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32
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Kanki D, Nakamukai S, Ogura Y, Takikawa H, Ise Y, Morii Y, Yamawaki N, Takatani T, Arakawa O, Okada S, Matsunaga S. Homophymamide A, Heterodetic Cyclic Tetrapeptide from a Homophymia sp. Marine Sponge: A Cautionary Note on Configurational Assignment of Peptides That Contain a Ureido Linkage. JOURNAL OF NATURAL PRODUCTS 2021; 84:1848-1853. [PMID: 34081460 DOI: 10.1021/acs.jnatprod.1c00336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A previously unreported heterodetic cyclic peptide, homophymamide A (1), was isolated from a Homophymia sp. marine sponge. The structure of homophymamide A was determined to be a lower homologue of anabaenopeptins by spectroscopic analysis, chemical degradation, and chemical synthesis. Analysis of the acidic hydrolysate showed that the racemization of Lys took place, leading us to pose a cautionary note on the configurational assignment of peptides that contain a ureido bond.
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Affiliation(s)
- Daichi Kanki
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shohei Nakamukai
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yusuke Ogura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hirosato Takikawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yuji Ise
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
| | - Yasuhiro Morii
- Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, Nagasaki 852-8521, Japan
| | - Nobuhiro Yamawaki
- Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, Nagasaki 852-8521, Japan
| | - Tomohiro Takatani
- Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, Nagasaki 852-8521, Japan
| | - Osamu Arakawa
- Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, Nagasaki 852-8521, Japan
| | - Shigeru Okada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Bunkyo-ku, Tokyo 113-8657, Japan
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Abstract
Lanthipeptides are a class of ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products characterized by the presence of lanthionine and methyllanthionine. During the maturation of select lanthipeptides, five different alterations have been observed to the chemical structure of the peptide backbone. First, dehydratases generate dehydroalanine and dehydrobutyrine from Ser or Thr residues, respectively. A second example of introduction of unsaturation is the oxidative decarboxylation of C-terminal Cys residues catalyzed by the decarboxylase LanD. Both modifications result in loss of chirality at the α-carbon of the amino acid residues. Attack of a cysteine thiol onto a dehydrated amino acid results in thioether crosslink formation with either inversion or retention of the l-stereochemical configuration at the α-carbon of former Ser and Thr residues. A fourth modification of the protein backbone is the hydrogenation of dehydroamino acids to afford d-amino acids catalyzed by NAD(P)H-dependent reductases. A fifth modification is the conversion of Asp to isoAsp. Herein, the methods used to produce and characterize the lanthipeptide bicereucin will be described in detail along with a brief overview of other lanthipeptides.
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Affiliation(s)
- Richard S Ayikpoe
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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34
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Fusaristatins D–F and (7S,8R)-(−)-chlamydospordiol from Fusarium sp. BZCB-CA, an endophyte of Bothriospermum chinense. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Pérez-Victoria I. Co-occurring Congeners Reveal the Position of Enantiomeric Amino Acids in Nonribosomal Peptides. Chembiochem 2021; 22:2087-2092. [PMID: 33440038 DOI: 10.1002/cbic.202000805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/11/2021] [Indexed: 11/09/2022]
Abstract
The absolute configuration of the constituent amino acids in microbial nonribosomal peptides is typically determined by Marfey's method after total hydrolysis of the peptide. A challenge to structure elucidation arises when both d and l enantiomeric configurations of an amino acid are present. Determining the actual position of each amino acid enantiomer within the peptide sequence typically requires laborious approaches based on peptide partial hydrolysis or even total synthesis of the possible diastereomers. Herein, an alternative solution is discussed based on the homogeneous backbone chirality that governs all peptides biosynthesized by a common nonribosomal peptide synthetase. The information on configuration provided by Marfey's analysis of co-occurring minor congeners can reveal unequivocally the stereochemical sequence of the whole peptide family.
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Affiliation(s)
- Ignacio Pérez-Victoria
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016, Armilla, Granada, Spain
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36
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Primahana G, Risdian C, Mozef T, Wink J, Surup F, Stadler M. Amycolatomycins A and B, Cyclic Hexapeptides Isolated from an Amycolatopsis sp. 195334CR. Antibiotics (Basel) 2021; 10:261. [PMID: 33807584 PMCID: PMC8002008 DOI: 10.3390/antibiotics10030261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 11/16/2022] Open
Abstract
The rare actinobacterium Amycolatopsis sp. strain 195334CR was found to produce previously undescribed cyclic hexapeptides, which we named amycolatomycin A and B (1 and 2). Their planar structures were determined by high-resolution mass spectrometry as well as extensive 1D and 2D NMR spectroscopy, while the absolute stereochemistry of its amino acids were determined by Marfey's method. Moreover, 1 and 2 differ by the incorporation of l-Ile and l-allo-Ile, respectively, whose FDVA (Nα-(2,4-Dinitro-5-fluorphenyl)-L-valinamide) derivatives were separated on a C4 column. Their hallmark in common is a unique 2,6-dichloro-tryptophan amino acid unit. Amycolatomycin A (1) exhibited weak activity against Bacillus subtilis DSM 10 (minimum inhibitory concentration (MIC) = 33.4 µg/mL).
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Affiliation(s)
- Gian Primahana
- Department Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany; (G.P.); (F.S.)
- Research Center for Chemistry, Indonesian Institute of Sciences (LIPI), Kawasan Puspiptek, Serpong, Tangerang Selatan 15314, Indonesia;
| | - Chandra Risdian
- Working Group Microbial Strain Collection, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany; (C.R.); (J.W.)
- Research Unit for Clean Technology, Indonesian Institute of Sciences (LIPI), Bandung 40135, Indonesia
| | - Tjandrawati Mozef
- Research Center for Chemistry, Indonesian Institute of Sciences (LIPI), Kawasan Puspiptek, Serpong, Tangerang Selatan 15314, Indonesia;
| | - Joachim Wink
- Working Group Microbial Strain Collection, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany; (C.R.); (J.W.)
| | - Frank Surup
- Department Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany; (G.P.); (F.S.)
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany; (G.P.); (F.S.)
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37
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Zhou T, Katsuragawa M, Xing T, Fukaya K, Okuda T, Tokiwa T, Tashiro E, Imoto M, Oku N, Urabe D, Igarashi Y. Cyclopeptides from the Mushroom Pathogen Fungus Cladobotryum varium. JOURNAL OF NATURAL PRODUCTS 2021; 84:327-338. [PMID: 33439652 DOI: 10.1021/acs.jnatprod.0c00980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Three new cyclopeptides with serial Phe residues were identified with the aid of HPLC-DAD analysis, from the culture broth of Cladobotryum varium, a fungal pathogen causing mushroom cobweb disease. Cladoamides A (1) and B (2) have two consecutive N-methylphenylalanine units in the destruxin class cyclic depsipentapeptide framework, while cladoamide C (3) has a three consecutive Phe motif in a cyclopentapeptide structure. Of these three cyclopeptides, 1 showed potent autophagy-inducing activity at 10 μg/mL, comparable to a positive control, rapamycin. For the determination of the absolute configurations of the Ile residues in 1 and 3, new conditions for separating Ile and allo-Ile, using a pentafluorophenyl-bonded solid phase and methanolic solvent, were established within the analytical scheme of the advanced Marfey's method, thus offering a convenient alternative to the C3 Marfey's method, which requires elution with a three-solvent mixture. The sequence of two d-Phe and one l-Phe in 3 was determined through NMR chemical shift prediction by DFT-based calculations and chemical synthesis, which demonstrated the significance of noncovalent interactions in the accurate calculation of stable conformers for peptides with multiple aromatic rings.
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Affiliation(s)
- Tao Zhou
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Misaki Katsuragawa
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Tian Xing
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Keisuke Fukaya
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Toru Okuda
- HyphaGenesis, Inc., 2-18-28 Tamagawa-Gakuen, Machida, Tokyo 194-0041, Japan
| | - Toshiyuki Tokiwa
- Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Etsu Tashiro
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Masaya Imoto
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Naoya Oku
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Daisuke Urabe
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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38
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Jiang Y, Matsumoto T, Kuranaga T, Lu S, Wang W, Onaka H, Kakeya H. Longicatenamides A-D, Two Diastereomeric Pairs of Cyclic Hexapeptides Produced by Combined-culture of Streptomyces sp. KUSC_F05 and Tsukamurella pulmonis TP-B0596. J Antibiot (Tokyo) 2021; 74:307-316. [PMID: 33483628 DOI: 10.1038/s41429-020-00400-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 12/16/2020] [Indexed: 12/21/2022]
Abstract
Longicatenamides A-D, two diastereomeric pairs of new cyclic hexapeptides, were isolated from the combined-culture of Streptomyces sp. KUSC_F05 and Tsukamurella pulmonis TP-B0596. Their planar structures were determined by spectroscopic analysis including extensive 2D NMR and MS analysis. The absolute configurations of their component amino acids were determined by the use of highly sensitive reagents we recently developed; the highly sensitive-advanced Marfey's method (HS-advanced Marfey's method), which led us to reduce the sample loss and prevent incorrect structural determination. Particularly, the Cβ-stereochemistry of hyGlu in longicatenamides A and C was assigned without any use of Cβ-Marfey's methods. Longicatenamide A exhibited weak but preferential antimicrobial activity against Bacillus subtilis.
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Affiliation(s)
- Yulu Jiang
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Takumi Matsumoto
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Takefumi Kuranaga
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shan Lu
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan.,Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Okinawa, 903-0213, Japan
| | - Weicheng Wang
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hiroyasu Onaka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan.
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39
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Hashizume H, Harada S, Sawa R, Iijima K, Kubota Y, Shibuya Y, Nagasaka R, Hatano M, Igarashi M. New chloptosins B and C from an Embleya strain exhibit synergistic activity against methicillin-resistant Staphylococcus aureus when combined with co-producing compound L-156,602. J Antibiot (Tokyo) 2021; 74:80-85. [PMID: 32796954 DOI: 10.1038/s41429-020-0361-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/13/2020] [Accepted: 07/20/2020] [Indexed: 11/09/2022]
Abstract
Two new dimeric cyclohexapeptides, chloptosins B and C, were discovered from the culture broth of Embleya sp. MM621-AF10 together with the known compounds chloptosin and L-156,602. The structures of the new chloptosins were determined by spectroscopic studies and advanced Marfey's methods. The stereo structure of the constituent isoleucine was determined by C3 Marfey's analysis. Chloptosins demonstrated potent antimicrobial activity against Gram-positive bacteria including drug-resistant strains of methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci with MICs of 0.5-2 µg ml-1. The antimicrobial activities of chloptosins were enhanced by addition of co-producing compound L-156,602, as shown by checkerboard analysis.
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Affiliation(s)
- Hideki Hashizume
- Laboratory of Microbiology, Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan.
| | - Shigeko Harada
- Laboratory of Microbiology, Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Ryuichi Sawa
- Laboratory of Molecular Structure Analysis, Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Kiyoko Iijima
- Laboratory of Molecular Structure Analysis, Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Yumiko Kubota
- Laboratory of Molecular Structure Analysis, Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Yuko Shibuya
- Laboratory of Microbiology, Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Ryoko Nagasaka
- Laboratory of Microbiology, Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Masaki Hatano
- Laboratory of Microbiology, Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Masayuki Igarashi
- Laboratory of Microbiology, Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
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40
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Liu Y, Zhao X, Wang H, Liu H, Sui Z, Yan B, Du Y. Total Synthesis of the Proposed Microcyclamides MZ602 and MZ568. J Org Chem 2021; 86:1065-1073. [PMID: 33295775 DOI: 10.1021/acs.joc.0c02541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The first convergent total synthesis for the proposed structures of microcyclamides MZ602 (1) and MZ568 (2) has been accomplished in 11 linear steps with 12.5 and 16.8% overall yield, respectively. Key features of the syntheses include a one-pot cascade reaction to construct core Boc-l-Ile-Thz-OAllyl fragment 5, and a removable pseudoproline (ΨMe,Me pro) inducer assisted cyclization of thiazole-containing all-l linear peptides. The spectral data (1H NMR, 13C NMR, and HRMS) of synthetic MZ602 (1) were quite similar to those of the proposed natural microcyclamide MZ602, except to an opposite sign of the optical rotation value. Surprisingly, the synthetic MZ568 (2) presented large discrepancies in characteristic spectral data from those of the reported natural product, although the absolute configuration of key intermediate 36 was unambiguously determined by single-crystal X-ray analysis in our work. These findings revealed that the proposed structures of natural microcyclamides MZ602 and MZ568 required revision.
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Affiliation(s)
- Yi Liu
- School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
| | - Xiangyun Zhao
- School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
| | - Hongbo Wang
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Yantai University, Yantai 264005, China
| | - Huili Liu
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Yantai University, Yantai 264005, China
| | - Zhuyin Sui
- School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
| | - Bingfei Yan
- School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
| | - Yuguo Du
- State Key Laboratory of Environmental Chemistry and Eco-toxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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41
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Dashti Y, Nakou IT, Mullins AJ, Webster G, Jian X, Mahenthiralingam E, Challis GL. Discovery and Biosynthesis of Bolagladins: Unusual Lipodepsipeptides from Burkholderia gladioli Clinical Isolates*. Angew Chem Int Ed Engl 2020; 59:21553-21561. [PMID: 32780452 PMCID: PMC7756342 DOI: 10.1002/anie.202009110] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Indexed: 01/01/2023]
Abstract
Two Burkholderia gladioli strains isolated from the lungs of cystic fibrosis patients were found to produce unusual lipodepsipeptides containing a unique citrate-derived fatty acid and a rare dehydro-β-alanine residue. The gene cluster responsible for their biosynthesis was identified by bioinformatics and insertional mutagenesis. In-frame deletions and enzyme activity assays were used to investigate the functions of several proteins encoded by the biosynthetic gene cluster, which was found in the genomes of about 45 % of B. gladioli isolates, suggesting that its metabolic products play an important role in the growth and/or survival of the species. The Chrome Azurol S assay indicated that these metabolites bind ferric iron, which suppresses their production when added to the growth medium. Moreover, a gene encoding a TonB-dependent ferric-siderophore receptor is adjacent to the biosynthetic genes, suggesting that these metabolites may function as siderophores in B. gladioli.
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Affiliation(s)
- Yousef Dashti
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Current address: The Centre for Bacterial Cell BiologyBiosciences InstituteMedical SchoolNewcastle UniversityNewcastle upon TyneNE2 4AXUK
| | - Ioanna T. Nakou
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
| | - Alex J. Mullins
- Microbiomes, Microbes and Informatics GroupOrganisms and Environment DivisionSchool of BiosciencesCardiff UniversityCardiffCF103 ATUK
| | - Gordon Webster
- Microbiomes, Microbes and Informatics GroupOrganisms and Environment DivisionSchool of BiosciencesCardiff UniversityCardiffCF103 ATUK
| | - Xinyun Jian
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Warwick Integrative Synthetic Biology CentreUniversity of WarwickCoventryCV4 7ALUK
| | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics GroupOrganisms and Environment DivisionSchool of BiosciencesCardiff UniversityCardiffCF103 ATUK
| | - Gregory L. Challis
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Warwick Integrative Synthetic Biology CentreUniversity of WarwickCoventryCV4 7ALUK
- Department of Biochemistry and Molecular Biology, ARC Centre of Excellence for Innovations in Peptide and Protein ScienceMonash UniversityClaytonVIC3800Australia
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42
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Dashti Y, Nakou IT, Mullins AJ, Webster G, Jian X, Mahenthiralingam E, Challis GL. Discovery and Biosynthesis of Bolagladins: Unusual Lipodepsipeptides from
Burkholderia gladioli
Clinical Isolates**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yousef Dashti
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Current address: The Centre for Bacterial Cell Biology Biosciences Institute Medical School Newcastle University Newcastle upon Tyne NE2 4AX UK
| | - Ioanna T. Nakou
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
| | - Alex J. Mullins
- Microbiomes, Microbes and Informatics Group Organisms and Environment Division School of Biosciences Cardiff University Cardiff CF103 AT UK
| | - Gordon Webster
- Microbiomes, Microbes and Informatics Group Organisms and Environment Division School of Biosciences Cardiff University Cardiff CF103 AT UK
| | - Xinyun Jian
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Warwick Integrative Synthetic Biology Centre University of Warwick Coventry CV4 7AL UK
| | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics Group Organisms and Environment Division School of Biosciences Cardiff University Cardiff CF103 AT UK
| | - Gregory L. Challis
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Warwick Integrative Synthetic Biology Centre University of Warwick Coventry CV4 7AL UK
- Department of Biochemistry and Molecular Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton VIC 3800 Australia
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43
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Thapa P, Katila N, Choi DY, Choi H, Nam JW. Suntamide A, a neuroprotective cyclic peptide from Cicadidae Periostracum. Bioorg Chem 2020; 106:104493. [PMID: 33268010 DOI: 10.1016/j.bioorg.2020.104493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/10/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022]
Abstract
Suntamide A (1), a new cyclic peptide, was isolated from Cicadidae Periostracum. The gross structure of 1 was elucidated by detailed analysis of HRMS and 1D/2D NMR spectra, and the absolute configuration was established by C3 Marfey's method. We extended our study to examine biological activity of 1, and found that 1 protected SH-SY5Y cells against rotenone-induced neurotoxicity. This effect of 1 seemed to be attributed to antioxidant induction and protection of mitochondria from rotenone-caused injury. Along with augmentation of the antioxidant system by 1, there was an evident activation of Nrf2, a transcription factor involved in the activation of the antioxidant system. These results indicate that 1 rescued the cells from rotenone-mediated neurotoxicity by enhancing antioxidant capacity via induction of Nrf2, suggesting that the compound could be used as a therapeutic intervention in neurodegenerative diseases such as Parkinson's disease.
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Affiliation(s)
- Punam Thapa
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbuk-do 38541, Republic of Korea
| | - Nikita Katila
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbuk-do 38541, Republic of Korea
| | - Dong-Young Choi
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbuk-do 38541, Republic of Korea.
| | - Hyukjae Choi
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbuk-do 38541, Republic of Korea; Research Institute of Cell Culture, Yeungnam University, Gyeongsangbuk-do 38531, Republic of Korea.
| | - Joo-Won Nam
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbuk-do 38541, Republic of Korea.
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44
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Lee J, Gamage CDB, Kim GJ, Hillman PF, Lee C, Lee EY, Choi H, Kim H, Nam SJ, Fenical W. Androsamide, a Cyclic Tetrapeptide from a Marine Nocardiopsis sp., Suppresses Motility of Colorectal Cancer Cells. JOURNAL OF NATURAL PRODUCTS 2020; 83:3166-3172. [PMID: 32985880 DOI: 10.1021/acs.jnatprod.0c00815] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A cyclic tetrapeptide, androsamide (1), was isolated from a marine actinomycete of the genus Nocardiopsis, strain CNT-189. The planar structure of 1 was assigned by the interpretation of 1D and 2D NMR spectroscopic data. The absolute configurations of constituent amino acids of 1 were determined by application of the Marfey's and advanced Marfey's methods. Androsamide (1) strongly suppressed the motility of Caco2 cells caused by epithelial-mesenchymal transition.
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Affiliation(s)
- Jihye Lee
- Laboratories of Marine New Drugs, REDONE Seoul, Seoul 08594, Korea
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Korea
| | - Chathurika D B Gamage
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam 57922, Korea
| | - Geum Jin Kim
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Korea
- Research Institute of Cell Culture, Yeungnam University, Yeungnam, Gyeongsangbukdo 38531, Republic of Korea
| | - Prima F Hillman
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Korea
| | - Chaeyoung Lee
- College of Pharmacy, Ewha Womans University, Seoul 03760, Korea
| | - Eun Young Lee
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Korea
| | - Hyukjae Choi
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Korea
- Research Institute of Cell Culture, Yeungnam University, Yeungnam, Gyeongsangbukdo 38531, Republic of Korea
| | - Hangun Kim
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam 57922, Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Korea
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, California 92093-0204, United States
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Hawaiian Bobtail Squid Symbionts Inhibit Marine Bacteria via Production of Specialized Metabolites, Including New Bromoalterochromides BAC-D/D'. mSphere 2020; 5:5/4/e00166-20. [PMID: 32611694 PMCID: PMC7333567 DOI: 10.1128/msphere.00166-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Animals that deposit eggs must protect their embryos from fouling and disease by microorganisms to ensure successful development. Although beneficial bacteria are hypothesized to contribute to egg defense in many organisms, the mechanisms of this protection are only recently being elucidated. Our previous studies of the Hawaiian bobtail squid focused on fungal inhibition by beneficial bacterial symbionts of a female reproductive gland and eggs. Herein, using genomic and chemical analyses, we demonstrate that symbiotic bacteria from this gland can also inhibit other marine bacteria in vitro. One bacterial strain in particular, Pseudoalteromonas sp. JC28, had broad-spectrum abilities to inhibit potential fouling bacteria, in part via production of novel bromoalterochromide metabolites, confirmed via genomic annotation of the associated biosynthetic gene cluster. Our results suggest that these bacterial metabolites may contribute to antimicrobial activity in this association and that such defensive symbioses are underutilized sources for discovering novel antimicrobial compounds. The Hawaiian bobtail squid, Euprymna scolopes, has a symbiotic bacterial consortium in the accessory nidamental gland (ANG), a female reproductive organ that protects eggs against fouling microorganisms. To test the antibacterial activity of ANG community members, 19 bacterial isolates were screened for their ability to inhibit Gram-negative and Gram-positive bacteria, of which two strains were inhibitory. These two antibacterial isolates, Leisingera sp. ANG59 and Pseudoalteromonas sp. JC28, were subjected to further genomic characterization. Genomic analysis of Leisingera sp. ANG59 revealed a biosynthetic gene cluster encoding the antimicrobial compound indigoidine. The genome of Pseudoalteromonas sp. JC28 had a 14-gene cluster with >95% amino acid identity to a known bromoalterochromide (BAC) cluster. Chemical analysis confirmed production of known BACs, BAC-A/A′ (compounds 1a/1b), as well as two new derivatives, BAC-D/D′ (compounds 2a/2b). Extensive nuclear magnetic resonance (NMR) analyses allowed complete structural elucidation of compounds 2a/2b, and the absolute stereochemistry was unambiguously determined using an optimized Marfey’s method. The BACs were then investigated for in vitro antibacterial, antifungal, and nitric oxide (NO) inhibitory activity. Compounds 1a/1b were active against the marine bacteria Bacillus algicola and Vibrio fischeri, while compounds 2a/2b were active only against B. algicola. Compounds 1a/1b inhibited NO production via lipopolysaccharide (LPS)-induced inflammation in RAW264.7 macrophage cells and also inhibited the pathogenic fungus Fusarium keratoplasticum, which, coupled with their antibacterial activity, suggests that these polyketide-nonribosomal peptides may be used for squid egg defense against potential pathogens and/or fouling microorganisms. These results indicate that BACs may provide Pseudoalteromonas sp. JC28 an ecological niche, facilitating competition against nonsymbiotic microorganisms in the host’s environment. IMPORTANCE Animals that deposit eggs must protect their embryos from fouling and disease by microorganisms to ensure successful development. Although beneficial bacteria are hypothesized to contribute to egg defense in many organisms, the mechanisms of this protection are only recently being elucidated. Our previous studies of the Hawaiian bobtail squid focused on fungal inhibition by beneficial bacterial symbionts of a female reproductive gland and eggs. Herein, using genomic and chemical analyses, we demonstrate that symbiotic bacteria from this gland can also inhibit other marine bacteria in vitro. One bacterial strain in particular, Pseudoalteromonas sp. JC28, had broad-spectrum abilities to inhibit potential fouling bacteria, in part via production of novel bromoalterochromide metabolites, confirmed via genomic annotation of the associated biosynthetic gene cluster. Our results suggest that these bacterial metabolites may contribute to antimicrobial activity in this association and that such defensive symbioses are underutilized sources for discovering novel antimicrobial compounds.
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Maenaka R, Tani S, Hikichi Y, Kai K. Actinomycins inhibit the production of the siderophore pyoverdines in the plant pathogen Pseudomonas cichorii SPC9018. Biosci Biotechnol Biochem 2020; 84:1975-1985. [PMID: 32594848 DOI: 10.1080/09168451.2020.1785839] [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] [Indexed: 01/24/2023]
Abstract
Pyoverdines, a group of peptide siderophores produced by Pseudomonas species, function not only in iron acquisition, but also in their virulence in hosts. Thus, chemical inhibition of pyoverdine production may be an effective strategy to control Pseudomonas virulence. In the plant pathogen Pseudomonas cichorii SPC9018 (SPC9018), pyoverdine production is required for virulence on eggplant. We screened microbial culture extracts in a pyoverdine-production inhibition assay of SPC9018 and found Streptomyces sp. RM-32 as a candidate-producer. We isolated two active compounds from RM-32 cultures, and elucidated their structures to be actinomycins X2 and D. Actinomycins X2 and D inhibited pyoverdine production by SPC9018 with IC50 values of 17.6 and 29.6 μM, respectively. Furthermore, pyoverdine production in other Pseudomonas bacteria, such as the mushroom pathogen P. tolaasii, was inhibited by the actinomycins. Therefore, these actinomycins may be useful as chemical tools to examine pyoverdine functions and as seed compounds for anti-Pseudomonas virulence agents.
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Affiliation(s)
- Risa Maenaka
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University , Osaka, Japan
| | - Shuji Tani
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University , Osaka, Japan
| | - Yasufumi Hikichi
- Laboratory of Plant Pathology and Biotechnology, Kochi University , Kochi, Japan
| | - Kenji Kai
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University , Osaka, Japan
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Zhang SY, Li JS, Zhang H, Qi H, Wang RJ, Wu CF, Zhang LQ, Chen AL, Wang JD, Hao ZK. Two new threonine-containing metabolites from fungus Curvularia inaequalis strain HS-FG-257. Nat Prod Res 2020; 36:482-487. [PMID: 32586138 DOI: 10.1080/14786419.2020.1784168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Two new threonine-containing metabolites, N-[4-hydroxy-3-prenyl-benzoyl]-L-threonine (1) and N-[2,2-dimethyl-2H-chromene-6-carbonyl]-L-threonine (2), were isolated from the fermentation broth of the soil fungus Curvularia inaequalis strain HS-FG-257. Their structures were elucidated through the interpretation of HR-ESIMS and extensive NMR spectroscopic data. Both compounds exhibited no cytotoxic activity against the test cell lines A549 and HCT-116.
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Affiliation(s)
- Shao-Yong Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou, China
| | - Jian-Song Li
- Institute of Applied Biotechnology, School of Medicine and Pharmaceutical Engineering, Taizhou Vocational and Technical College, Taizhou, China
| | - Hui Zhang
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd, Taizhou, China
| | - Huan Qi
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou, China
| | - Rui-Jun Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou, China
| | - Chou-Fei Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou, China
| | - Li-Qin Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou, China
| | - An-Liang Chen
- Provincial Joint Engineering Laboratory of Biopesticide Preparation, School of Forestry & Biotechnology, Zhejiang Agricultural and Forestry University, China
| | - Ji-Dong Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou, China
| | - Zhi-Kui Hao
- Institute of Applied Biotechnology, School of Medicine and Pharmaceutical Engineering, Taizhou Vocational and Technical College, Taizhou, China
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Zhou B, Shetye G, Yu Y, Santarsiero BD, Klein LL, Abad-Zapatero C, Wolf NM, Cheng J, Jin Y, Lee H, Suh JW, Lee H, Bisson J, McAlpine JB, Chen SN, Cho SH, Franzblau SG, Pauli GF. Antimycobacterial Rufomycin Analogues from Streptomyces atratus Strain MJM3502. JOURNAL OF NATURAL PRODUCTS 2020; 83:657-667. [PMID: 32031795 PMCID: PMC7384767 DOI: 10.1021/acs.jnatprod.9b01095] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This study represents a systematic chemical and biological study of the rufomycin (RUF) class of cyclic heptapeptides, which our anti-TB drug discovery efforts have identified as potentially promising anti-TB agents that newly target the caseinolytic protein C1, ClpC1. Eight new RUF analogues, rufomycins NBZ1-NBZ8 (1-8), as well as five known peptides (9-13) were isolated and characterized from the Streptomyces atratus strain MJM3502. Advanced Marfey's and X-ray crystallographic analysis led to the assignment of the absolute configuration of the RUFs. Several isolates exhibited potent activity against both pathogens M. tuberculosis H37Rv and M. abscessus, paired with favorable selectivity (selectivity index >60), which collectively underscores the promise of the rufomycins as potential anti-TB drug leads.
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Affiliation(s)
- Bin Zhou
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Gauri Shetye
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Yang Yu
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Bernard D. Santarsiero
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 900 S. Ashland Street, Chicago, Illinois 60612, United States
| | - Larry L. Klein
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Cele Abad-Zapatero
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 900 S. Ashland Street, Chicago, Illinois 60612, United States
| | - Nina M. Wolf
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Jinhua Cheng
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin-si, Gyeonggi-do, Republic of Korea
- Division of Bioscience and Bioinformatics, College of Natural Science, Myongji University, Cheoin-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Yingyu Jin
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Hanki Lee
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Joo-Won Suh
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Hyun Lee
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 900 S. Ashland Street, Chicago, Illinois 60612, United States
| | - Jonathan Bisson
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - James B. McAlpine
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Shao-Nong Chen
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Sang-Hyun Cho
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Scott G. Franzblau
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Guido F. Pauli
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
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Li Y, Liu L, Zhang G, He N, Guo W, Hong B, Xie Y. Potashchelins, a Suite of Lipid Siderophores Bearing Both L- threo and L- erythro Beta-Hydroxyaspartic Acids, Acquired From the Potash-Salt-Ore-Derived Extremophile Halomonas sp. MG34. Front Chem 2020; 8:197. [PMID: 32266214 PMCID: PMC7100376 DOI: 10.3389/fchem.2020.00197] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/03/2020] [Indexed: 12/12/2022] Open
Abstract
Four new lipid siderophores bearing both L-threo- and L-erythro-β-hydroxyaspartic acids, potashchelins A-D (1-4), were isolated from the potash-salt-ore-derived extremophile Halomonas sp. MG34. The planar structures of 1-4 were elucidated on the basis of extensive 1D and 2D NMR studies and MS/MS data. Potashchelins 1-4 contain a hydrophilic nonapeptide headgroup sequentially consisting of β-hydroxyaspartic acid, serine, glycine, serine, serine, β-hydroxyaspartic acid, threonine, serine, and cyclic N(δ)-hydroxy-ornithine, which is appended by one of a series of fatty acids ranging from dodecanoic acid to tetradecanoic acid. The absolute configurations of the amino acids of potashchelins 1-4 were determined by C3 and advanced Marfey's reaction, partial hydrolysis, and bioinformatics analysis, which revealed that potashchelins 1-4 bear both L-threo- and L-erythro-β-hydroxyaspartic acid. Phylogenetic analysis showed that the stand-alone β-hydroxylase, PtcA, and the fused domain with β-hydroxylase activity in PtcB are expected to be responsible for the formation of L-erythro and L-threo diastereomers, respectively. Additionally, utilizing a comparative genomics approach, we revealed an evolutionary mechanism for lipid siderophores in Halomonas involving horizontal transfer. Bioassays showed that potashchelin A and D had weak antibacterial activity against B. subtilis CPCC 100029 with an MIC value of 64 μg/mL.
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Affiliation(s)
- Yihong Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li Liu
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Gengxin Zhang
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, China Academy of Sciences, Beijing, China
| | - Ning He
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Wenqiang Guo
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bin Hong
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yunying Xie
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Khalil ZG, Salim AA, Capon RJ. Microbioreactor Techniques for the Production and Spectroscopic Characterization of Microbial Peptides. Methods Mol Biol 2020; 2103:303-322. [PMID: 31879935 DOI: 10.1007/978-1-0716-0227-0_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We have demonstrated that the simple and low-cost microbioreactor can speed up the bioprocessing techniques by using small amount of reagents and very few seed cultures to give results comparable with those obtained from the shake flask. The microbioreactor has the potential of replacing the normal conventional-scale process and offers a high-throughput efficient and analytical technique in addressing some of the challenges encountered in bioprocessing starting that includes bacterial growth and secondary metabolites production targeting the discovery of new antibacterial peptides. In our case studies, we proved that microbes were capable of growing in the microbioreactor and the production of microbial secondary metabolites (i.e., peptides) was detectable in HPLC-DAD-MS. We used QTOF-MS/MS to detect the production of peptides in the microbial culture. The purified peptides were characterized using 1D and 2D NMR, QTOF-MS/MS, and Marfey's analysis.
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Affiliation(s)
- Zeinab G Khalil
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Angela A Salim
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Robert J Capon
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.
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