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Chekan JR, Mydy LS, Pasquale MA, Kersten RD. Plant peptides - redefining an area of ribosomally synthesized and post-translationally modified peptides. Nat Prod Rep 2024; 41:1020-1059. [PMID: 38411572 PMCID: PMC11253845 DOI: 10.1039/d3np00042g] [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] [Received: 09/19/2023] [Indexed: 02/28/2024]
Abstract
Covering 1965 to February 2024Plants are prolific peptide chemists and are known to make thousands of different peptidic molecules. These peptides vary dramatically in their size, chemistry, and bioactivity. Despite their differences, all plant peptides to date are biosynthesized as ribosomally synthesized and post-translationally modified peptides (RiPPs). Decades of research in plant RiPP biosynthesis have extended the definition and scope of RiPPs from microbial sources, establishing paradigms and discovering new families of biosynthetic enzymes. The discovery and elucidation of plant peptide pathways is challenging due to repurposing and evolution of housekeeping genes as both precursor peptides and biosynthetic enzymes and due to the low rates of gene clustering in plants. In this review, we highlight the chemistry, biosynthesis, and function of the known RiPP classes from plants and recommend a nomenclature for the recent addition of BURP-domain-derived RiPPs termed burpitides. Burpitides are an emerging family of cyclic plant RiPPs characterized by macrocyclic crosslinks between tyrosine or tryptophan side chains and other amino acid side chains or their peptide backbone that are formed by copper-dependent BURP-domain-containing proteins termed burpitide cyclases. Finally, we review the discovery of plant RiPPs through bioactivity-guided, structure-guided, and gene-guided approaches.
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Affiliation(s)
- Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Lisa S Mydy
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Michael A Pasquale
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Roland D Kersten
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
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2
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Smith BP, Truax NJ, Pollatos AS, Meanwell M, Bedekar P, Garrido-Castro AF, Baran PS. Total Synthesis of Dragocins A-C through Electrochemical Cyclization. Angew Chem Int Ed Engl 2024; 63:e202401107. [PMID: 38358802 DOI: 10.1002/anie.202401107] [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: 01/16/2024] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/16/2024]
Abstract
The first total synthesis of dragocins A-C, remarkable natural products containing an unusual C4' oxidized ribose architecture bridged by a polyhydroxylated pyrrolidine, is presented through a route featuring a number of uncommon maneuvers. Several generations towards the target molecules are presented, including the spectacular failure of a key C-H oxidation on a late-stage intermediate. The final route features rapid, stereocontrolled access to a densely functionalized pyrrolidine and an unprecedented diastereoselective oxidative electrochemical cyclization to forge the hallmark 9-membered ring. Preliminary studies suggest this electrochemical oxidation protocol is generally useful.
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Affiliation(s)
- Brendyn P Smith
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Nathanyal J Truax
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Alexandros S Pollatos
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael Meanwell
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB T6G 2N4, Canada
| | - Pranali Bedekar
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Alberto F Garrido-Castro
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, HCI, 8093, Zürich, Switzerland
| | - Phil S Baran
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
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3
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Zhang K, Carmo C, Deiana L, Grape ES, Inge AK, Córdova A. Sugar-Assisted Kinetic Resolutions in Metal/Chiral Amine Co-Catalyzed α-Allylations and [4+2] Cycloadditions: Highly Enantioselective Synthesis of Sugar and Chromane Derivatives. Chemistry 2023; 29:e202301725. [PMID: 37402648 DOI: 10.1002/chem.202301725] [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: 05/31/2023] [Revised: 07/04/2023] [Accepted: 07/04/2023] [Indexed: 07/06/2023]
Abstract
Functionalized triose-, furanose and chromane-derivatives were synthesized by the titled reactions. The sugar-assisted kinetic resolution/C-C bond-forming cascade processes generate a functionalized sugar derivative with a quaternary stereocenter in a highly enantioselective fashion (up to >99 % ee) by using a simple combination of metal and chiral amine co-catalysts. Notably, the interplay between the chiral sugar substrate and the chiral amino acid derivative allowed for the construction of a functionalized sugar product with high enantioselectivity (up to 99 %) also when using a combination of racemic amine catalyst (0 % ee) and metal catalyst.
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Affiliation(s)
- Kaiheng Zhang
- Department of Natural Sciences, Mid Sweden University, Holmgatan 10, 85179, Sundsvall, Sweden
| | - Chrislaura Carmo
- Department of Natural Sciences, Mid Sweden University, Holmgatan 10, 85179, Sundsvall, Sweden
| | - Luca Deiana
- Department of Natural Sciences, Mid Sweden University, Holmgatan 10, 85179, Sundsvall, Sweden
| | - Erik Svensson Grape
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, 10 691, Stockholm, Sweden
| | - A Ken Inge
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, 10 691, Stockholm, Sweden
| | - Armando Córdova
- Department of Natural Sciences, Mid Sweden University, Holmgatan 10, 85179, Sundsvall, Sweden
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4
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Ozaki T, Minami A, Oikawa H. Recent advances in the biosynthesis of ribosomally synthesized and posttranslationally modified peptides of fungal origin. J Antibiot (Tokyo) 2023; 76:3-13. [PMID: 36424516 DOI: 10.1038/s41429-022-00576-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/25/2022]
Abstract
Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are growing class of natural products with potent biological activities. Although the core scaffolds of RiPPs are composed of proteinogenic amino acids, remarkable structural diversity is generated through posttranslational modifications (PTMs) of precursor peptides. In addition, ribosomal origin of biosynthetic precursors enables supply of its analogs through genetic approach such as site-directed mutagenesis on corresponding genes. As PTM enzymes often exhibit substrate tolerance, RiPP biosynthetic machineries are considered as efficient tools for generation of unique peptide derivatives. RiPP pathways are distributed among all domains of life and those derived from bacteria and plants have been known for decades. In contrast, fungal RiPPs (F-RiPPs) have fewer examples. Amatoxins and omphalotins are F-RiPPs produced by Basidiomycota fungi. In the biosynthesis of these compounds, macrocyclization by prolyl oligopeptidase homologs and N-methylations of back bone amides have been characterized, respectively. Ustiloxins and related compounds are another group of F-RiPPs with characteristic macrocyclic ethers. UstYa family proteins, which are fungi-specific putative oxidases, have been identified as common proteins involved in PTMs of these compounds. Despite a limited number of characterized examples, recent progress in sequencing of fungal genomes indicated that a number of RiPP pathways are hidden in fungal resources, making F-RiPPs as attractive target for genome mining studies while more detailed understandings of key biosynthetic enzymes are still necessary. This review seeks to describe recent advances on the F-RiPP biosynthesis with slight emphasis on the function of UstYa family proteins.
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Affiliation(s)
- Taro Ozaki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Atsushi Minami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan. .,Innovation Center of Marine Biotechnology and Pharmaceuticals, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, Guangdong, China.
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Munawar S, Zahoor AF, Ali S, Javed S, Irfan M, Irfan A, Kotwica-Mojzych K, Mojzych M. Mitsunobu Reaction: A Powerful Tool for the Synthesis of Natural Products: A Review. Molecules 2022; 27:6953. [PMID: 36296545 PMCID: PMC9609662 DOI: 10.3390/molecules27206953] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 08/13/2023] Open
Abstract
The Mitsunobu reaction plays a vital part in organic chemistry due to its wide synthetic applications. It is considered as a significant reaction for the interconversion of one functional group (alcohol) to another (ester) in the presence of oxidizing agents (azodicarboxylates) and reducing agents (phosphines). It is a renowned stereoselective reaction which inverts the stereochemical configuration of end products. One of the most important applications of the Mitsunobu reaction is its role in the synthesis of natural products. This review article will focus on the contribution of the Mitsunobu reaction towards the total synthesis of natural products, highlighting their biological potential during recent years.
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Affiliation(s)
- Saba Munawar
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Ameer Fawad Zahoor
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Shafaqat Ali
- College of Agriculture and Environmental Sciences, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Sadia Javed
- Department of Biochemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Irfan
- Department of Pharmaceutics, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Ali Irfan
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Katarzyna Kotwica-Mojzych
- Laboratory of Experimental Cytology, Medical University of Lublin, Radziwiłłowska 11, 20-080 Lublin, Poland
| | - Mariusz Mojzych
- Department of Chemistry, Siedlce University of Natural Sciences and Humanities, 3-go Maja 54, 08-110 Siedlce, Poland
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6
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Sugiyama R, Suarez AFL, Morishita Y, Nguyen TQN, Tooh YW, Roslan MNHB, Lo Choy J, Su Q, Goh WY, Gunawan GA, Wong FT, Morinaka BI. The Biosynthetic Landscape of Triceptides Reveals Radical SAM Enzymes That Catalyze Cyclophane Formation on Tyr- and His-Containing Motifs. J Am Chem Soc 2022; 144:11580-11593. [PMID: 35729768 DOI: 10.1021/jacs.2c00521] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Peptide-derived cyclophanes inhabit a unique niche in the chemical space of macrocyclic peptides with several examples of pharmaceutical importance. Although both synthetic and biocatalytic methods are available for constructing these macrocycles, versatile (bio)catalysts able to incorporate a variety of amino acids that compose the macrocycle would be useful for the creation of diverse peptide cyclophanes. In this report, we synergized the use of bioinformatic tools to map the biosynthetic landscape of radical SAM enzymes (3-CyFEs) that catalyze three-residue cyclophane formation in the biosynthesis of a new family of RiPP natural products, the triceptides. This analysis revealed 3940 (3113 unique) putative precursor sequences predicted to be modified by 3-CyFEs. Several uncharacterized maturase systems were identified that encode unique precursor types. Functional studies were carried out in vivo in Escherichia coli to identify modified precursors containing His and Tyr residues. NMR analysis of the products revealed that Tyr and His can also be incorporated into cyclophane macrocycles by 3-CyFEs. Collectively, all aromatic amino acids can be incorporated by 3-CyFEs, and the cyclophane formation strictly occurs via a C(sp2)-C(sp3) cross-link between the (hetero)aromatic ring to Cβ. In addition to 3-CyFEs, we functionally validated an Fe(II)/α-ketoglutarate-dependent hydroxylase, resulting in β-hydroxylated residues within the cyclophane rings. This study reveals the potential breadth of triceptide precursors and a systematic approach for studying these enzymes to broaden the diversity of peptide macrocycles.
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Affiliation(s)
- Ryosuke Sugiyama
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | | | - Yohei Morishita
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Thi Quynh Ngoc Nguyen
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Yi Wei Tooh
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | | | - Justin Lo Choy
- Department of Pharmacology and Toxicology, University of Toronto, Toronto M5S 1A8, Canada
| | - Qi Su
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Wei Yang Goh
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Gregory Adrian Gunawan
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore.,Molecular Engineering Lab, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.,Organic & Biomolecular Chemistry, Institute of Sustainability for Chemicals, Energy and Environment, A*STAR, Singapore 138665, Singapore
| | - Fong Tian Wong
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.,Singapore Institute of Food and Biotechnology Innovation, A*STAR, Singapore 138673, Singapore
| | - Brandon I Morinaka
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
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7
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Chigumba DN, Mydy LS, de Waal F, Li W, Shafiq K, Wotring JW, Mohamed OG, Mladenovic T, Tripathi A, Sexton JZ, Kautsar S, Medema MH, Kersten RD. Discovery and biosynthesis of cyclic plant peptides via autocatalytic cyclases. Nat Chem Biol 2022; 18:18-28. [PMID: 34811516 DOI: 10.1038/s41589-021-00892-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/02/2021] [Indexed: 12/28/2022]
Abstract
Many bioactive plant cyclic peptides form side-chain-derived macrocycles. Lyciumins, cyclic plant peptides with tryptophan macrocyclizations, are ribosomal peptides (RiPPs) originating from repetitive core peptide motifs in precursor peptides with plant-specific BURP (BNM2, USP, RD22 and PG1beta) domains, but the biosynthetic mechanism for their formation has remained unknown. Here, we characterize precursor-peptide BURP domains as copper-dependent autocatalytic peptide cyclases and use a combination of tandem mass spectrometry-based metabolomics and plant genomics to systematically discover five BURP-domain-derived plant RiPP classes, with mono- and bicyclic structures formed via tryptophans and tyrosines, from botanical collections. As BURP-domain cyclases are scaffold-generating enzymes in plant specialized metabolism that are physically connected to their substrates in the same polypeptide, we introduce a bioinformatic method to mine plant genomes for precursor-peptide-encoding genes by detection of repetitive substrate domains and known core peptide features. Our study sets the stage for chemical, biosynthetic and biological exploration of plant RiPP natural products from BURP-domain cyclases.
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Affiliation(s)
- Desnor N Chigumba
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Lisa S Mydy
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Floris de Waal
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
| | - Wenjie Li
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Khadija Shafiq
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Jesse W Wotring
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Osama G Mohamed
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.,Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Tim Mladenovic
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Ashootosh Tripathi
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.,Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan Z Sexton
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.,Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Satria Kautsar
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands.
| | - Roland D Kersten
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
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8
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Shabani S, Wu Y, Ryan HG, Hutton CA. Progress and perspectives on directing group-assisted palladium-catalysed C-H functionalisation of amino acids and peptides. Chem Soc Rev 2021; 50:9278-9343. [PMID: 34254063 DOI: 10.1039/d0cs01441a] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Peptide modifications can unlock a variety of compounds with structural diversity and abundant biological activity. In nature, peptide modifications, such as functionalisation at the side-chain position of amino acids, are performed using post-translational modification enzymes or incorporation of unnatural amino acids. However, accessing these modifications remains a challenge for organic chemists. During the past decades, selective C-H activation/functionalisation has attracted considerable attention in synthetic organic chemistry as a pathway to peptide modification. Various directing group strategies have been discovered that assist selective C-H activation. In particular, bidentate directing groups that enable tuneable and reversible coordination are now recognised as one of the most efficient methods for the site-selective C-H activation and functionalisation of numerous families of organic compounds. Synthetic peptide chemists have harnessed bidentate directing group strategies for selective functionalisation of the β- and γ-positions of amino acids. This method has been expanded and recognised as an effective device for the late stage macrocyclisation and total synthesis of complex peptide natural products. In this review, we discuss various β-, γ-, and δ-C(sp3)-H bond functionalisation reactions of amino acids for the formation of C-X bonds with the aid of directing groups and their application in late-stage macrocyclisation and the total synthesis of complex peptide natural products.
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Affiliation(s)
- Sadegh Shabani
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, 3010, Australia.
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