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Matabaro E, Witte L, Gherlone F, Vogt E, Kaspar H, Künzler M. Promiscuity of Omphalotin A Biosynthetic Enzymes Allows de novo Production of Non-Natural Multiply Backbone N-Methylated Peptide Macrocycles in Yeast. Chembiochem 2024; 25:e202300626. [PMID: 38059521 DOI: 10.1002/cbic.202300626] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/08/2023]
Abstract
Multiple backbone N-methylation and macrocyclization improve the proteolytic stability and oral availability of therapeutic peptides. Chemical synthesis of such peptides is challenging, in particular for the generation of peptide libraries for screening purposes. Enzymatic backbone N-methylation and macrocyclization occur as part of both non-ribosomal and ribosomal peptide biosynthesis, exemplified by the fungal natural products cyclosporin A and omphalotin A, respectively. Omphalotin A, a 9fold backbone N-methylated dodecamer isolated from the agaricomycete Omphalotus olearius, can be produced in Pichia pastoris by coexpression of the ophMA and ophP genes coding for the peptide precursor protein harbouring an autocatalytic peptide α-N-methyltransferase domain, and a peptide macrocyclase, respectively. Since both OphMA and OphP were previously shown to be relatively promiscuous in terms of peptide substrates, we expressed mutant versions of ophMA, encoding OphMA variants with altered core peptide sequences, along with wildtype ophP and assessed the production of the respective peptide macrocycles by the platform by high-performance liquid chromatography, coupled with tandem mass spectrometry (HPLC-MS/MS). Our results demonstrate the successful production of fifteen non-natural omphalotin-derived macrocycles, containing polar, aromatic and charged residues, and, thus, suggest that the system may be used as biotechnological platform to generate libraries of non-natural multiply backbone N-methylated peptide macrocycles.
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Affiliation(s)
- Emmanuel Matabaro
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog Weg 4, HCI F423, 8093, Zürich, Switzerland
| | - Luca Witte
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog Weg 4, HCI F423, 8093, Zürich, Switzerland
| | - Fabio Gherlone
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog Weg 4, HCI F423, 8093, Zürich, Switzerland
| | - Eva Vogt
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog Weg 4, HCI F423, 8093, Zürich, Switzerland
| | - Hannelore Kaspar
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog Weg 4, HCI F423, 8093, Zürich, Switzerland
| | - Markus Künzler
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog Weg 4, HCI F423, 8093, Zürich, Switzerland
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Colombano A, Dalponte L, Dall'Angelo S, Clemente C, Idress M, Ghazal A, Houssen WE. Chemoenzymatic Late-Stage Modifications Enable Downstream Click-Mediated Fluorescent Tagging of Peptides. Angew Chem Int Ed Engl 2023; 62:e202215979. [PMID: 36815722 PMCID: PMC10946513 DOI: 10.1002/anie.202215979] [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: 10/30/2022] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 02/24/2023]
Abstract
Aromatic prenyltransferases from cyanobactin biosynthetic pathways catalyse the chemoselective and regioselective intramolecular transfer of prenyl/geranyl groups from isoprene donors to an electron-rich position in these macrocyclic and linear peptides. These enzymes often demonstrate relaxed substrate specificity and are considered useful biocatalysts for structural diversification of peptides. Herein, we assess the isoprene donor specificity of the N1-tryptophan prenyltransferase AcyF from the anacyclamide A8P pathway using a library of 22 synthetic alkyl pyrophosphate analogues, of which many display reactive groups that are amenable to additional functionalization. We further used AcyF to introduce a reactive moiety into a tryptophan-containing cyclic peptide and subsequently used click chemistry to fluorescently label the enzymatically modified peptide. This chemoenzymatic strategy allows late-stage modification of peptides and is useful for many applications.
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Affiliation(s)
- Alessandro Colombano
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
| | - Luca Dalponte
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
| | - Sergio Dall'Angelo
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
| | - Claudia Clemente
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
| | - Mohannad Idress
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
- Abzena, Babraham Research CampusCambridgeUK
| | - Ahmad Ghazal
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
| | - Wael E. Houssen
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
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Amazonian Guarana- and Açai-Conjugated Extracts Improve Scratched Fibroblast Healing and Eisenia fetida Surgical Tail Amputation by Modulating Oxidative Metabolism. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:3094362. [PMID: 35795860 PMCID: PMC9251138 DOI: 10.1155/2022/3094362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/09/2022] [Indexed: 11/26/2022]
Abstract
Background Previous studies have suggested that guarana (Paullinia cupana) and açai (Euterpe oleracea) have antioxidant, anti-inflammatory, and proliferative properties, indicating their potential therapeutic action in wound healing. We produced a conjugated guarana-açai (GA) extract and tested its healing action on earthworms (Eisenia fetida) subjected to tail amputation by surgical incision. Methods Extract from roasted guarana seeds and fresh açai seed berries was produced. The antioxidant and genoprotective capacity of GA extract was tested. The concentration with the most remarkable healing potential was used in subsequent tests. The last three posterior segments of the clitellate earthworm tail reared under standardized conditions were surgically amputated. Next, topical PBS or GA extract was applied to the surgical wound. The rate of cell migration and tissue regeneration at the local wound site was histologically evaluated after the procedure. Expression of the SOX4 gene that acts in epithelial-to-mesenchymal transition was determined by RT-qPCR. Results Sixteen bioactive molecules, including some previously described substances, were identified. All tested concentrations exhibited antioxidant and genoprotective effects. The GA extract accelerated the healing processes as observed through macroscopic and histological analyses and increased expression of SOX4. Conclusion The GA extract has a potential role in the healing of surgically induced wounds.
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Zhang CH, Shao XX, Wang XB, Shou LL, Liu YL, Xu ZG, Guo ZY. Development of a general bioluminescent activity assay for peptide ligases. FEBS J 2022; 289:5241-5258. [PMID: 35239242 DOI: 10.1111/febs.16416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/13/2022] [Accepted: 02/28/2022] [Indexed: 11/28/2022]
Abstract
In recent years, some peptide ligases have been identified, such as bacterial sortases and certain plant asparaginyl or prolyl endopeptidases. Peptide ligases have wide applications in protein labelling and cyclic peptide synthesis. To characterize various known peptide ligases or identify new ones, we propose a general bioluminescent activity assay via the genetic fusion of a recognition motif of peptide ligase(s) to the C-terminus of an inactive large NanoLuc fragment (LgBiT) and the chemical introduction of a nucleophilic motif preferred by the peptide ligase(s) to the N-terminus of the low-affinity SmBiT complementation tag. After the inactive ligation version LgBiT protein was ligated with the low-affinity ligation version SmBiT tag by the expected peptide ligase(s), its luciferase activity would be restored and could be quantified sensitively according to the measured bioluminescence. In the present study, we first validated the bioluminescent activity assay using bacterial sortase A and plant-derived butelase-1. Subsequently, we screened novel peptide ligases from crude extracts of selected plants using two LgBiT-SmBiT ligation pairs. Among 80 common higher plants, we identified that five of them likely express asparaginyl endopeptidase-type peptide ligase and four of them likely express prolyl endopeptidase-type peptide ligase, suggesting that peptide ligases are not so rare in higher plants and more of them await discovery. The present bioluminescent activity assay is ultrasensitive, convenient for use, and resistant to protease interference, and thus would have wide applications for characterizing known peptide ligases or screening new ones from various sources in future studies.
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Affiliation(s)
- Cong-Hui Zhang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiao-Xia Shao
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xin-Bo Wang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Li-Li Shou
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ya-Li Liu
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zeng-Guang Xu
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhan-Yun Guo
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
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Possible Functional Roles of Patellamides in the Ascidian-Prochloron Symbiosis. Mar Drugs 2022; 20:md20020119. [PMID: 35200648 PMCID: PMC8875616 DOI: 10.3390/md20020119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/27/2022] [Accepted: 01/27/2022] [Indexed: 02/04/2023] Open
Abstract
Patellamides are highly bioactive compounds found along with other cyanobactins in the symbiosis between didemnid ascidians and the enigmatic cyanobacterium Prochloron. The biosynthetic pathway of patellamide synthesis is well understood, the relevant operons have been identified in the Prochloron genome and genes involved in patellamide synthesis are among the most highly transcribed cyanobacterial genes in hospite. However, a more detailed study of the in vivo dynamics of patellamides and their function in the ascidian-Prochloron symbiosis is complicated by the fact that Prochloron remains uncultivated despite numerous attempts since its discovery in 1975. A major challenge is to account for the highly dynamic microenvironmental conditions experienced by Prochloron in hospite, where light-dark cycles drive rapid shifts between hyperoxia and anoxia as well as pH variations from pH ~6 to ~10. Recently, work on patellamide analogues has pointed out a range of different catalytic functions of patellamide that could prove essential for the ascidian-Prochloron symbiosis and could be modulated by the strong microenvironmental dynamics. Here, we review fundamental properties of patellamides and their occurrence and dynamics in vitro and in vivo. We discuss possible functions of patellamides in the ascidian-Prochloron symbiosis and identify important knowledge gaps and needs for further experimental studies.
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Rodríguez V. Insights into post-translational modification enzymes from RiPPs: A toolkit for applications in peptide synthesis. Biotechnol Adv 2022; 56:107908. [PMID: 35032597 DOI: 10.1016/j.biotechadv.2022.107908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 12/30/2021] [Accepted: 01/09/2022] [Indexed: 11/02/2022]
Abstract
The increasing length and complexity of peptide drug candidates foster the development of novel strategies for their manufacture, which should include sustainable and efficient technologies. In this context, including enzymatic catalysis in the production of peptide molecules has gained interest. Here, several enzymes from ribosomally synthesized and post-translationally modified peptides biosynthesis pathways are reviewed, with attention to their capacity to introduce stability-promoting structural features on peptides, providing an initial framework towards their use in therapeutic peptide production processes.
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Affiliation(s)
- Vida Rodríguez
- Faculty of Engineering, Science and Technology, Bernardo O'Higgins University, Viel 1497, Santiago, Chile.
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Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep 2021; 38:130-239. [PMID: 32935693 PMCID: PMC7864896 DOI: 10.1039/d0np00027b] [Citation(s) in RCA: 410] [Impact Index Per Article: 136.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
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Sarkar S, Gu W, Schmidt EW. Expanding the chemical space of synthetic cyclic peptides using a promiscuous macrocyclase from prenylagaramide biosynthesis. ACS Catal 2020; 10:7146-7153. [PMID: 33457065 PMCID: PMC7805243 DOI: 10.1021/acscatal.0c00623] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cyclic peptides are excellent drug candidates, placing macrocyclization reactions at the apex of drug development. PatG and related dual-action proteases from cyanobactin biosynthesis are responsible for cleaving off the C-terminal recognition sequence and macrocyclizing the substrate to provide cyclic peptides. This reaction has found use in the enzymatic synthesis of diverse macrocycles. However, these enzymes function best on substrates that terminate with the non-proteinogenic thiazole/thiazoline residue, complicating synthetic strategies. Here, we biochemically characterize a new class of PatG-like macrocyclases that natively use proline, obviating the necessity of additional chemical or biochemical steps. We experimentally define the biochemical steps involved in synthesizing the widespread prenylagaramide-like natural products, including macrocyclization and prenylation. Using saturation mutagenesis, we show that macrocyclase PagG and prenyltransferase PagF are highly promiscuous, producing a library of more than 100 cyclic peptides and their prenylated derivatives in vitro. By comparing our results to known cyanobactin macrocyclases, we catalog a series of enzymes from this family that should synthesize most small macrocycles. Collectively, these data reveal that, by selecting the right cyanobactin macrocyclase, a large array of enzymatically synthesized macrocycles are accessible.
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Affiliation(s)
- Snigdha Sarkar
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Wenjia Gu
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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10
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Franke B, Mylne JS, Rosengren KJ. Buried treasure: biosynthesis, structures and applications of cyclic peptides hidden in seed storage albumins. Nat Prod Rep 2019; 35:137-146. [PMID: 29379937 DOI: 10.1039/c7np00066a] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Covering: 1999 up to the end of 2017The small cyclic peptide SunFlower Trypsin Inhibitor-1 (SFTI-1) from sunflower seeds is the prototypic member of a novel family of natural products. The biosynthesis of these peptides is intriguing as their gene-encoded peptide backbone emerges from a precursor protein that also contains a seed storage albumin. The peptide sequence is cleaved out from the precursor and cyclised by the albumin-maturing enzymatic machinery. Three-dimensional solution NMR structures of a number of these peptides, and of the intact precursor protein preproalbumin with SFTI-1, have now been elucidated. Furthermore, the evolution of the family has been described and a detailed understanding of the biosynthetic steps, which are necessary to produce cyclic SFTI-1, is emerging. Macrocyclisation provides peptide stability and thus represents a key strategy in peptide drug development. Consequently the constrained structure of SFTI-1 has been explored as a template for protein engineering, for tuning selectivity towards clinically relevant proteases and for grafting in sequences with completely novel functions. Here we review the discovery of the SFTI-1 peptide family, their evolution, biosynthetic origin, and structural features, as well as highlight the potential applications of this unique class of natural products.
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Affiliation(s)
- B Franke
- The University of Queensland, Faculty of Medicine, School of Biomedical Sciences, Brisbane, QLD 4072, Australia.
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Abstract
Cyclic peptides are an emerging class of therapeutics that can modulate targets not amenable to traditional small molecule intervention (e.g., protein-protein interactions). However, N-to-C macrocyclization of peptides is a challenging and often a low yielding chemical transformation. Several macrocyclases from cyanobactin biosynthetic clusters have been used to catalyze this reaction.This chapter provides practical guidance to the processes of heterologous expression and purification of these enzymes as well as performing in vitro biochemical reactions. Finally, approaches to recover the final product from an enzymatic reaction mixture are also discussed.
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Affiliation(s)
- Wael E Houssen
- Marine Biodiscovery Centre, Chemistry Department, University of Aberdeen, Aberdeen, UK.,Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK.,Pharmacognosy Department, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
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12
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Gu W, Dong SH, Sarkar S, Nair SK, Schmidt EW. The Biochemistry and Structural Biology of Cyanobactin Pathways: Enabling Combinatorial Biosynthesis. Methods Enzymol 2018; 604:113-163. [PMID: 29779651 DOI: 10.1016/bs.mie.2018.03.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyanobactin biosynthetic enzymes have exceptional versatility in the synthesis of natural and unnatural products. Cyanobactins are ribosomally synthesized and posttranslationally modified peptides synthesized by multistep pathways involving a broad suite of enzymes, including heterocyclases/cyclodehydratases, macrocyclases, proteases, prenyltransferases, methyltransferases, and others. Here, we describe the enzymology and structural biology of cyanobactin biosynthetic enzymes, aiming at the twin goals of understanding biochemical mechanisms and biosynthetic plasticity. We highlight how this common suite of enzymes may be utilized to generate a large array or structurally and chemically diverse compounds.
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Affiliation(s)
- Wenjia Gu
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Shi-Hui Dong
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Snigdha Sarkar
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, United States.
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Morita M, Schmidt EW. Parallel lives of symbionts and hosts: chemical mutualism in marine animals. Nat Prod Rep 2018; 35:357-378. [PMID: 29441375 PMCID: PMC6025756 DOI: 10.1039/c7np00053g] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: up to 2018 Symbiotic microbes interact with animals, often by producing natural products (specialized metabolites; secondary metabolites) that exert a biological role. A major goal is to determine which microbes produce biologically important compounds, a deceptively challenging task that often rests on correlative results, rather than hypothesis testing. Here, we examine the challenges and successes from the perspective of marine animal-bacterial mutualisms. These animals have historically provided a useful model because of their technical accessibility. By comparing biological systems, we suggest a common framework for establishing chemical interactions between animals and microbes.
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Affiliation(s)
- Maho Morita
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA 84112.
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