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Christinaki AC, Myridakis AI, Kouvelis VN. Genomic insights into the evolution and adaptation of secondary metabolite gene clusters in fungicolous species Cladobotryum mycophilum ATHUM6906. G3 (BETHESDA, MD.) 2024; 14:jkae006. [PMID: 38214578 PMCID: PMC10989895 DOI: 10.1093/g3journal/jkae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/01/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024]
Abstract
Mycophilic or fungicolous fungi can be found wherever fungi exist since they are able to colonize other fungi, which occupy a diverse range of habitats. Some fungicolous species cause important diseases on Basidiomycetes, and thus, they are the main reason for the destruction of mushroom cultivations. Nonetheless, despite their ecological significance, their genomic data remain limited. Cladobotryum mycophilum is one of the most aggressive species of the genus, destroying the economically important Agaricus bisporus cultivations. The 40.7 Mb whole genome of the Greek isolate ATHUM6906 is assembled in 16 fragments, including the mitochondrial genome and 2 small circular mitochondrial plasmids, in this study. This genome includes a comprehensive set of 12,282 protein coding, 56 rRNA, and 273 tRNA genes. Transposable elements, CAZymes, and pathogenicity related genes were also examined. The genome of C. mycophilum contained a diverse arsenal of genes involved in secondary metabolism, forming 106 biosynthetic gene clusters, which renders this genome as one of the most BGC abundant among fungicolous species. Comparative analyses were performed for genomes of species of the family Hypocreaceae. Some BGCs identified in C. mycophilum genome exhibited similarities to clusters found in the family Hypocreaceae, suggesting vertical heritage. In contrast, certain BGCs showed a scattered distribution among Hypocreaceae species or were solely found in Cladobotryum genomes. This work provides evidence of extensive BGC losses, horizontal gene transfer events, and formation of novel BGCs during evolution, potentially driven by neutral or even positive selection pressures. These events may increase Cladobotryum fitness under various environmental conditions and potentially during host-fungus interaction.
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Affiliation(s)
- Anastasia C Christinaki
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Antonis I Myridakis
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Vassili N Kouvelis
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Athens 15771, Greece
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Jiang X, Gao L, Li Z, Shen Y, Lin ZH. Development and Challenges of Cyclic Peptides for Immunomodulation. Curr Protein Pept Sci 2024; 25:353-375. [PMID: 37990433 DOI: 10.2174/0113892037272528231030074158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 11/23/2023]
Abstract
Cyclic peptides are polypeptide chains formed by cyclic sequences of amide bonds between protein-derived or non-protein-derived amino acids. Compared to linear peptides, cyclic peptides offer several unique advantages, such as increased stability, stronger affinity, improved selectivity, and reduced toxicity. Cyclic peptide has been proved to have a promising application prospect in the medical field. In addition, this paper mainly describes that cyclic peptides play an important role in anti-cancer, anti-inflammatory, anti-virus, treatment of multiple sclerosis and membranous nephropathy through immunomodulation. In order to know more useful information about cyclic peptides in clinical research and drug application, this paper also summarizes cyclic peptides currently in the clinical trial stage and cyclic peptide drugs approved for marketing in the recent five years. Cyclic peptides have many advantages and great potential in treating various diseases, but there are still many challenges to be solved in the development process of cyclic peptides.
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Affiliation(s)
- Xianqiong Jiang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, 405400 Chongqing, China
| | - Li Gao
- School of Pharmacy and Bioengineering, Chongqing University of Technology, 405400 Chongqing, China
| | - Zhilong Li
- School of Pharmacy and Bioengineering, Chongqing University of Technology, 405400 Chongqing, China
| | - Yan Shen
- School of Pharmacy and Bioengineering, Chongqing University of Technology, 405400 Chongqing, China
- Chongqing Key Laboratory of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China
- Chongqing Key Laboratory of Target Based Drug Screening and Activity Evaluation, Chongqing University of Technology, Chongqing 400054, China
| | - Zhi-Hua Lin
- School of Pharmacy and Bioengineering, Chongqing University of Technology, 405400 Chongqing, China
- Chongqing College of Traditional Chinese Medicine, 402760
- Chongqing Key Laboratory of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China
- Chongqing Key Laboratory of Target Based Drug Screening and Activity Evaluation, Chongqing University of Technology, Chongqing 400054, China
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Lu S, Zhang Z, Sharma AR, Nakajima-Shimada J, Harunari E, Oku N, Trianto A, Igarashi Y. Bulbiferamide, an Antitrypanosomal Hexapeptide Cyclized via an N-Acylindole Linkage from a Marine Obligate Microbulbifer. JOURNAL OF NATURAL PRODUCTS 2023; 86:1081-1086. [PMID: 36843290 DOI: 10.1021/acs.jnatprod.2c01083] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
UV absorption spectroscopy-guided fractionation of the culture extract of a marine obligate bacterium of the genus Microbulbifer yielded a novel cyclic hexapeptide, bulbiferamide (1). NMR spectroscopic and mass spectrometric analyses revealed the structure of 1 to be a cyclic tetrapeptide appending a ureido-bridged two amino acid unit. Notably, Trp is a junction residue, forming on one hand a very rare N-aminoacylated indole linkage for cyclization and on the other hand connecting the ureido-containing tail structure, which is an unprecedented way of configuring peptides. The component amino acids were determined to be l by the advanced Marfey's method. Compound 1 displayed growth inhibitory activity against Trypanosoma cruzi epimastigotes with an IC50 value of 4.1 μM, comparable to the currently approved drug benznidazole, while it was not cytotoxic to P388 murine leukemia cells at 100 μM.
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Affiliation(s)
- Shiyang Lu
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Zhiwei Zhang
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Amit Raj Sharma
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Junko Nakajima-Shimada
- Department of Molecular and Cellular Parasitology, Gunma University Graduate School of Health Sciences, 3-39-22 Showa-machi, Maebashi, Gunma 371-8514, Japan
| | - Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Naoya Oku
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Agus Trianto
- Department of Marine Science, Faculty of Fisheries and Marine Science, Diponegoro University, Tembalang Campus, St. Prof. Soedarto SH, Semarang, 50275 Central Java, Indonesia
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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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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Synthetic studies for destruxins and biological evaluation for osteoclast-like multinucleated cells: a review. J Antibiot (Tokyo) 2022; 75:420-431. [PMID: 35821085 DOI: 10.1038/s41429-022-00540-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 11/09/2022]
Abstract
Synthesis of various destruxin analogs was accomplished using Shiina's macrolactonization as a key reaction. Combinatorial synthesis of cyclization precursors using solid-phase peptide synthesis and macrolactonization in solution were successful. In the synthesis of destruxin E and its analogs, the hydroxyacid-proline (HA1-Pro2) dipeptide with an acetonide-protected diol moiety was synthesized in an asymmetric manner, and the protected diol was converted to an epoxide after macrocyclization. Destruxin E was synthesized on a gram scale using solution-phase synthesis. The structure-activity relationships of destruxins were elucidated through biological evaluation of synthetic destruxins A, B, and E and their analogs for morphological changes in osteoclast-like multinucleated cells.
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Donalle GC, Martorell MM, Siless GE, Ruberto L, Cabrera GM. Cyclic heptapeptides with metal binding properties isolated from the fungus Cadophora malorum from Antarctic soil. NATURAL PRODUCTS AND BIOPROSPECTING 2022; 12:26. [PMID: 35831516 PMCID: PMC9279517 DOI: 10.1007/s13659-022-00348-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
The Antarctic fungus Cadophora malorum produces previously undescribed cyclic heptapeptides (cadophorin A and B) containing an anthranilic acid residue. The planar structure of these peptides was determined by high-resolution mass spectrometry combined with extensive 1D and 2D NMR spectroscopy. The absolute configuration of the amino acids was determined by Marfey's method, with HPLC analysis of FDVA (Nα-(2,4-dinitro-5-fluorphenyl)-L-valinamide) derivatives making use of a PFP column. Remarkably, cadophorin 2 possesses both the uncommon D-Ile and D-allo-Ile in its structure. The peptides have metal binding properties as shown by LCMS with post column addition of metal salt solutions. These results were supported by DFT calculations.
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Affiliation(s)
- Guidmar C Donalle
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Unidad de Microanálisis y Métodos Físicos Aplicados a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Martha Martorell
- Instituto Antártico Argentino, Instituto Nanobiotec, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gastón E Siless
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Unidad de Microanálisis y Métodos Físicos Aplicados a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Lucas Ruberto
- Instituto Antártico Argentino, Instituto Nanobiotec, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - Gabriela M Cabrera
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Unidad de Microanálisis y Métodos Físicos Aplicados a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina.
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Liao J, Jia X, Wu F, Huang J, Shen G, You H, Chen FE. Rapid mild macrocyclization of depsipeptides under continuous flow: total syntheses of five cyclodepsipeptides. Org Chem Front 2022. [DOI: 10.1039/d2qo01577c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A systematic investigation of the flow macrocyclization approaches for five destruxin analogues natural products at three different cyclization point has been reported.
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Affiliation(s)
- Jingyuan Liao
- School of science, Harbin Institute of Technology (Shenzhen), Guangdong, China
| | - Xuelei Jia
- School of science, Harbin Institute of Technology (Shenzhen), Guangdong, China
- Shenzhen Zhonghe Headway Bio-Sci & Tech Co., Ltd, Guangdong, China
| | - Fusong Wu
- School of science, Harbin Institute of Technology (Shenzhen), Guangdong, China
| | - Junrong Huang
- School of science, Harbin Institute of Technology (Shenzhen), Guangdong, China
| | - Guifu Shen
- Shenzhen Zhonghe Headway Bio-Sci & Tech Co., Ltd, Guangdong, China
| | - Hengzhi You
- School of science, Harbin Institute of Technology (Shenzhen), Guangdong, China
- Green Pharmaceutical Engineering Research Center, Harbin Institute of Technology (Shenzhen), Guangdong, China
| | - Fen-Er Chen
- School of science, Harbin Institute of Technology (Shenzhen), Guangdong, China
- Green Pharmaceutical Engineering Research Center, Harbin Institute of Technology (Shenzhen), Guangdong, China
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, China
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Zhang Z, Zhou T, Xing T, Ishizaki T, Okuda T, Oku N, Igarashi Y. Pithohirolide, an antimicrobial tetradepsipeptide from a fungus Pithomyces chartarum. J Antibiot (Tokyo) 2021; 74:458-463. [PMID: 33963290 DOI: 10.1038/s41429-021-00423-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 11/09/2022]
Abstract
Pithohirolide (1), a new depsipeptide, was isolated from an ascomycetous fungus Pithomyces chartarum TAMA 581. The planar structure of 1 was elucidated on the basis of NMR and MS analyses and the absolute configuration was determined by the advanced Marfey's analysis, chiral-phase HPLC analysis, and synthesis of degradation product. Compound 1 possesses a cyclic structure comprising (S)-2-hydroxy-3-phenylpropanoic acid, (S)-3-hydroxy-3-phenylpropanoic acid, (S)-2-hydroxyisovaleric acid, and N-methyl-L-alanine, connected via three ester and one amide linkages. Compound 1 exhibited antimicrobial activity against Staphylococcus aureus and Saccharomyces cerevisiae at MIC 3.1 μg ml-1.
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Affiliation(s)
- Zhiwei Zhang
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama, Japan
| | - Tao Zhou
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama, Japan
| | - Tian Xing
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama, Japan
| | | | - Toru Okuda
- HyphaGenesis, Inc., Machida, Tokyo, Japan
| | - Naoya Oku
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama, Japan.
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