1
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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024; 124:8130-8232. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
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Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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2
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Suarez AFL, Nguyen TQN, Chang L, Tooh YW, Yong RHS, Leow LC, Koh IYF, Chen H, Koh JWH, Selvanayagam A, Lim V, Tan YE, Agatha I, Winnerdy FR, Morinaka BI. Functional and Promiscuity Studies of Three-Residue Cyclophane Forming Enzymes Show Nonnative C-C Cross-Linked Products and Leader-Dependent Cyclization. ACS Chem Biol 2024; 19:774-783. [PMID: 38417140 DOI: 10.1021/acschembio.3c00795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Enzymes catalyzing peptide macrocyclization are important biochemical tools in drug discovery. The three-residue cyclophane-forming enzymes (3-CyFEs) are an emerging family of post-translational modifying enzymes that catalyze the formation of three-residue peptide cyclophanes. In this report, we introduce three additional 3-CyFEs, including ChlB, WnsB, and FnnB, that catalyze cyclophane formation on Tyr, Trp, and Phe, respectively. To understand the promiscuity of these enzymes and those previously reported (MscB, HaaB, and YxdB), we tested single amino acid substitutions at the three-residue motif of modification (Ω1X2X3, Ω1 = aromatic). Collectively, we observe that substrate promiscuity is observed at the Ω1 and X2 positions, but a greater specificity is observed for the X3 residue. Two nonnative cyclophane products were characterized showing a Phe-C3 to Arg-Cβ and His-C2 to Pro-Cβ cross-links, respectively. We also tested the leader dependence of selected 3-CyFEs and show that a predicted helix region is important for cyclophane formation. These results demonstrate the biocatalytic potential of these maturases and allow rational design of substrates to obtain a diverse array of genetically encoded 3-residue cyclophanes.
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Affiliation(s)
| | - Thi Quynh Ngoc Nguyen
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Litao Chang
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Yi Wei Tooh
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Rubin How Sheng Yong
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Li Chuan Leow
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Ivan Yu Fan Koh
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Huiyi Chen
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Jeffery Wei Heng Koh
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | | | - Vernon Lim
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Yi En Tan
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Irene Agatha
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Fernaldo R Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Brandon I Morinaka
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
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3
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Wang S, Wu K, Tang YJ, Deng H. Dehydroamino acid residues in bioactive natural products. Nat Prod Rep 2024; 41:273-297. [PMID: 37942836 PMCID: PMC10880069 DOI: 10.1039/d3np00041a] [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: 09/08/2023] [Indexed: 11/10/2023]
Abstract
Covering: 2000 to up to 2023α,β-Dehydroamino acids (dhAAs) are unsaturated nonproteinogenic amino acids found in a wide array of naturally occurring peptidyl metabolites, predominantly those from bacteria. Other organisms, such as fungi, higher plants and marine invertebrates, have also been found to produce dhAA-containing peptides. The α,β-unsaturation in dhAAs has profound effects on the properties of these molecules. They display significant synthetic flexibility, readily undergoing reactions such as Michael additions, transition-metal-catalysed cross-couplings, and cycloadditions. These residues in peptides/proteins also exhibit great potential in bioorthogonal applications using click chemistry. Peptides containing contiguous dhAA residues have been extensively investigated in the field of foldamers, self-assembling supermolecules that mimic biomacromolecules such as proteins to fold into well-defined conformations. dhAA residues in these peptidyl materials tend to form a 2.05-helix. As a result, stretches of dhAA residues arrange in an extended conformation. In particular, peptidyl foldamers containing β-enamino acid units display interesting conformational, electronic, and supramolecular aggregation properties that can be modulated by light-dependent E-Z isomerization. Among approximately 40 dhAAs found in the natural product inventory, dehydroalanine (Dha) and dehydrobutyrine (Dhb) are the most abundant. Dha is the simplest dehydro-α-amino acid, or α-dhAA, without any geometrical isomers, while its re-arranged isomer, 3-aminoacrylic acid (Aaa or ΔβAla), is the simplest dehydro-β-amino acid, or β-enamino acid, and displays E/Z isomerism. Dhb is the simplest α-dhAA that exhibits E/Z isomerism. The Z-isomer of Dhb (Z-Dhb) is sterically favourable and is present in the majority of naturally occurring peptides containing Dhb residues. Dha and Z-Dhb motifs are commonly found in ribosomally synthesized and post-translationally modified peptides (RiPPs). In the last decade, the formation of Dha and Dhb motifs in RiPPs has been extensively investigated, which will be briefly discussed in this review. The formation of other dhAA residues in natural products (NPs) is, however, less understood. In this review, we will discuss recent advances in the biosynthesis of peptidyl NPs containing unusual dhAA residues and cryptic dhAA residues. The proposed biosynthetic pathways of these natural products will also be discussed.
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Affiliation(s)
- Shan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Kewen Wu
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK.
| | - Ya-Jie Tang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK.
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4
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Tong Z, Xie X, Ge H, Jiao R, Wang T, Wang X, Zhuang W, Hu G, Tan R. Disulfide bridge-targeted metabolome mining unravels an antiparkinsonian peptide. Acta Pharm Sin B 2024; 14:881-892. [PMID: 38322339 PMCID: PMC10840396 DOI: 10.1016/j.apsb.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/06/2023] [Accepted: 09/13/2023] [Indexed: 02/08/2024] Open
Abstract
Peptides are a particular molecule class with inherent attributes of some small-molecule drugs and macromolecular biologics, thereby inspiring continuous searches for peptides with therapeutic and/or agrochemical potentials. However, the success rate is decreasing, presumably because many interesting but less-abundant peptides are so scarce or labile that they are likely 'overlooked' during the characterization effort. Here, we present the biochemical characterization and druggability improvement of an unprecedented minor fungal RiPP (ribosomally synthesized and post-translationally modified peptide), named acalitide, by taking the relevant advantages of metabolomics approach and disulfide-bridged substructure which is more frequently imprinted in the marketed peptide drug molecules. Acalitide is biosynthetically unique in the macrotricyclization via two disulfide bridges and a protease (AcaB)-catalyzed lactamization of AcaA, an unprecedented precursor peptide. Such a biosynthetic logic was successfully re-edited for its sample supply renewal to facilitate the identification of the in vitro and in vivo antiparkinsonian efficacy of acalitide which was further confirmed safe and rendered brain-targetable by the liposome encapsulation strategy. Taken together, the work updates the mining strategy and biosynthetic complexity of RiPPs to unravel an antiparkinsonian drug candidate valuable for combating Parkinson's disease that is globally prevailing in an alarming manner.
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Affiliation(s)
- Zhiwu Tong
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xiahong Xie
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Huiming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ruihua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Tingting Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xincun Wang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenying Zhuang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Gang Hu
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Renxiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
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5
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Jones MA, Butler ND, Anderson SR, Wirt SA, Govil I, Lyu X, Fang Y, Kunjapur AM. Discovery of L-threonine transaldolases for enhanced biosynthesis of beta-hydroxylated amino acids. Commun Biol 2023; 6:929. [PMID: 37696954 PMCID: PMC10495429 DOI: 10.1038/s42003-023-05293-0] [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: 03/24/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023] Open
Abstract
Beta-hydroxy non-standard amino acids (β-OH-nsAAs) have utility as small molecule drugs, precursors for beta-lactone antibiotics, and building blocks for polypeptides. While the L-threonine transaldolase (TTA), ObiH, is a promising enzyme for β-OH-nsAA biosynthesis, little is known about other natural TTA sequences. We ascertained the specificity of the TTA enzyme class more comprehensively by characterizing 12 candidate TTA gene products across a wide range (20-80%) of sequence identities. We found that addition of a solubility tag substantially enhanced the soluble protein expression level within this difficult-to-express enzyme family. Using an optimized coupled enzyme assay, we identified six TTAs, including one with less than 30% sequence identity to ObiH that exhibits broader substrate scope, two-fold higher L-Threonine (L-Thr) affinity, and five-fold faster initial reaction rates under conditions tested. We harnessed these TTAs for first-time bioproduction of β-OH-nsAAs with handles for bio-orthogonal conjugation from supplemented precursors during aerobic fermentation of engineered Escherichia coli, where we observed that higher affinity of the TTA for L-Thr increased titer. Overall, our work reveals an unexpectedly high level of sequence diversity and broad substrate specificity in an enzyme family whose members play key roles in the biosynthesis of therapeutic natural products that could benefit from chemical diversification.
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Affiliation(s)
- Michaela A Jones
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Neil D Butler
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Shelby R Anderson
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Sean A Wirt
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Ishika Govil
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Xinyi Lyu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Yinzhi Fang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Aditya M Kunjapur
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA.
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6
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Ozaki T. Structural diversification of fungal natural products by oxidative enzymes. Biosci Biotechnol Biochem 2023; 87:809-818. [PMID: 37197900 DOI: 10.1093/bbb/zbad062] [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: 03/14/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
Ascomycota and basidiomycota fungi are prolific producers of biologically active natural products. Fungal natural products exhibit remarkable structural diversity and complexity, which are generated by the enzymes involved in their biosynthesis. After the formation of core skeletons, oxidative enzymes play a critical role in converting them into mature natural products. Besides simple oxidations, more complex transformations, such as multiple oxidations by single enzymes, oxidative cyclization, and skeletal rearrangement, are often observed. Those oxidative enzymes are of significant interest for the identification of new enzyme chemistry and have the potential to be biocatalysts for the synthesis of complex molecules. This review presents selected examples of unique oxidative transformations that have been found in the biosynthesis of fungal natural products. The development of strategies for refactoring the fungal biosynthetic pathways with an efficient genome-editing method is also introduced.
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Affiliation(s)
- Taro Ozaki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba-ku, Sendai, Japan
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7
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Li X, Ma S, Zhang Q. Chemical Synthesis and Biosynthesis of Darobactin. Tetrahedron Lett 2023. [DOI: 10.1016/j.tetlet.2023.154337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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8
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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: 5] [Impact Index Per Article: 5.0] [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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9
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Umemura M, Tamano K. How to improve the production of peptidyl compounds in filamentous fungi. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:1085624. [PMID: 37746201 PMCID: PMC10512285 DOI: 10.3389/ffunb.2022.1085624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/02/2022] [Indexed: 09/26/2023]
Abstract
Peptidyl compounds produced by filamentous fungi, which are nonribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs), are rich sources of bioactive compounds with a wide variety of structures. Some of these peptidyl compounds are useful as pharmaceuticals and pesticides. However, for industrial use, their low production often becomes an obstacle, and various approaches have been challenged to overcome this weakness. In this article, we summarize the successful attempts to increase the production of NRPs and RiPPs in filamentous fungi and present our perspectives on how to improve it further.
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Affiliation(s)
- Maiko Umemura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Koichi Tamano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
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10
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Zhao Y, Marschall E, Treisman M, McKay A, Padva L, Crüsemann M, Nelson DR, Steer DL, Schittenhelm RB, Tailhades J, Cryle MJ. Cytochrome P450 Blt Enables Versatile Peptide Cyclisation to Generate Histidine- and Tyrosine-Containing Crosslinked Tripeptide Building Blocks. Angew Chem Int Ed Engl 2022; 61:e202204957. [PMID: 35851739 PMCID: PMC9542247 DOI: 10.1002/anie.202204957] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Indexed: 12/05/2022]
Abstract
We report our investigation of the utility of peptide crosslinking cytochrome P450 enzymes from biarylitide biosynthesis to generate a range of cyclic tripeptides from simple synthons. The crosslinked tripeptides produced by this P450 include both tyrosine-histidine (A-N-B) and tyrosine-tryptophan (A-O-B) crosslinked tripeptides, the latter a rare example of a phenolic crosslink to an indole moiety. Tripeptides are easily isolated following proteolytic removal of the leader peptide and can incorporate a wide range of amino acids in the residue inside the crosslinked tripeptide. Given the utility of peptide crosslinks in important natural products and the synthetic challenge that these can represent, P450 enzymes have the potential to play roles as important tools in the generation of high-value cyclic tripeptides for incorporation in synthesis, which can be yet further diversified using selective chemical techniques through specific handles contained within these tripeptides.
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Affiliation(s)
- Yongwei Zhao
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - Edward Marschall
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - Maxine Treisman
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - Alasdair McKay
- Department of ChemistryMonash UniversityClaytonVIC 3800Australia
| | - Leo Padva
- Institute of Pharmaceutical BiologyUniversity of Bonn53115BonnGermany
| | - Max Crüsemann
- Institute of Pharmaceutical BiologyUniversity of Bonn53115BonnGermany
| | - David R. Nelson
- Department of Microbiology, Immunology and BiochemistryUniversity of TennesseeMemphisTN 38163USA
| | - David L. Steer
- Monash Proteomics and Metabolomics FacilityMonash UniversityClaytonVIC 3800Australia
| | - Ralf B. Schittenhelm
- Monash Proteomics and Metabolomics FacilityMonash UniversityClaytonVIC 3800Australia
| | - Julien Tailhades
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - Max J. Cryle
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
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11
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Zhao Y, Marschall E, Treisman M, McKay A, Padva L, Crüsemann M, Nelson DR, Steer DL, Schittenhelm RB, Tailhades J, Cryle MJ. Cytochrome P450Blt Enables Versatile Peptide Cyclisation to Generate Histidine and Tyrosine Containing Crosslinked Tripeptide Building Blocks. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | | | | | - Leo Padva
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Institute of Pharmaceutical Biology GERMANY
| | - Max Crüsemann
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Pharmaceutical Biology GERMANY
| | - David R Nelson
- University of Tennessee College of Medicine: The University of Tennessee Health Science Center College of Medicine Microbiology UNITED STATES
| | - David L Steer
- Monash University Biochemistry and Molecular Biology AUSTRALIA
| | | | | | - Max J. Cryle
- Monash University Department of Biochemistry and Molecular Biology 15 Innovation WalkMonash University 3800 Melbourne AUSTRALIA
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12
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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: 27] [Impact Index Per Article: 13.5] [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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13
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Hill RA, Sutherland A. Hot off the press. Nat Prod Rep 2022. [PMID: 35133387 DOI: 10.1039/d2np90004a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as anisotanol A from Anisodus tanguticus.
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Affiliation(s)
- Robert A Hill
- School of Chemistry, Glasgow University, Glasgow, G12 8QQ, UK.
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