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Zhao YJ, Li L, Zhang YH, Yang YY, Li LF, Yang K, Liu YF, Cao F. ( ±)-Dibrevianamides Q1 and Q2, the key precursors of asperginulin A from a marine-derived fungus. Appl Microbiol Biotechnol 2023; 107:6459-6467. [PMID: 37658880 DOI: 10.1007/s00253-023-12739-2] [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: 05/10/2023] [Revised: 07/23/2023] [Accepted: 08/21/2023] [Indexed: 09/05/2023]
Abstract
Two pairs of new dimeric diketopiperazine alkaloids, ( ±)-dibrevianamides Q1 and Q2 (( ±)-1 and ( ±)-2), together with seven previously reported analogues (( ±)-3, 4-6, and ( ±)-7) were obtained from a marine-derived fungus Aspergillus sp. The structures of ( ±)-1 and ( ±)-2 were clarified using comprehensive spectroscopic analyses, the calculated ECD, and DP4 + probability methods. Speculated from the biogenesis, ( ±)-dibrevianamides Q1 and Q2 (( ±)-1 and ( ±)-2) might be the key precursor of [2 + 2] diketopiperazine dimers (( ±)-3). Compounds ( +)-1 and ( -)-2 displayed anti-H1N1 virus activity with IC50 values of 12.6 and 19.5 μM. Compound ( +)-1 showed significant activity against Mycobacterium tuberculosis (MIC, 10.2 μg/mL). KEY POINTS: • Two pairs of new dimeric diketopiperazine alkaloids were obtained from the marine-derived fungus Aspergillus sp. • The structures of the new compounds were clarified using comprehensive spectroscopic analyses, the calculated ECD, and DP4 + probability methods. • ( ±)-Dibrevianamides Q1 and Q2 were speculated to be the key precursor of [2 + 2] diketopiperazine dimers ( ±)-asperginulin A.
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Affiliation(s)
- Ying-Jie Zhao
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, 071002, China
| | - Lei Li
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, 071002, China
| | - Ya-Hui Zhang
- College of Life Sciences, Key Laboratory of Medicinal Chemistry and Molecular Diagnostics of Education Ministry of China, Hebei University, Baoding, 071002, China
| | - Yun-Yi Yang
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, 071002, China
| | - Long-Fei Li
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, 071002, China
| | - Kan Yang
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, 071002, China
| | - Yun-Feng Liu
- College of Life Sciences, Key Laboratory of Medicinal Chemistry and Molecular Diagnostics of Education Ministry of China, Hebei University, Baoding, 071002, China.
| | - Fei Cao
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, 071002, China.
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Liu J, Yang Y, Harken L, Li SM. Elucidation of the Streptoazine Biosynthetic Pathway in Streptomyces aurantiacus Reveals the Presence of a Promiscuous Prenyltransferase/Cyclase. JOURNAL OF NATURAL PRODUCTS 2021; 84:3100-3109. [PMID: 34846144 DOI: 10.1021/acs.jnatprod.1c00844] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Heterologous expression of a three-gene cluster from Streptomyces aurantiacus coding for a cyclodipeptide synthase, a prenyltransferase, and a methyltransferase led to the elucidation of the biosynthetic steps of streptoazine C (2). In vivo biotransformation experiments proved the high flexibility of the prenyltransferase SasB toward tryptophan-containing cyclodipeptides for regular C-3-prenylation. Furthermore, their corresponding dehydrogenated derivatives prepared by using cyclodipeptide oxidases were also used for prenylation. This study provides an enzyme with high substrate promiscuity from a less explored group of prenyltransferases for potential use to generate prenylated derivatives.
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Affiliation(s)
- Jing Liu
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch Straße 4, 35037 Marburg, Germany
| | - Yiling Yang
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch Straße 4, 35037 Marburg, Germany
| | - Lauritz Harken
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch Straße 4, 35037 Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch Straße 4, 35037 Marburg, Germany
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3
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Bojarska J, Mieczkowski A, Ziora ZM, Skwarczynski M, Toth I, Shalash AO, Parang K, El-Mowafi SA, Mohammed EHM, Elnagdy S, AlKhazindar M, Wolf WM. Cyclic Dipeptides: The Biological and Structural Landscape with Special Focus on the Anti-Cancer Proline-Based Scaffold. Biomolecules 2021; 11:1515. [PMID: 34680148 PMCID: PMC8533947 DOI: 10.3390/biom11101515] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Cyclic dipeptides, also know as diketopiperazines (DKP), the simplest cyclic forms of peptides widespread in nature, are unsurpassed in their structural and bio-functional diversity. DKPs, especially those containing proline, due to their unique features such as, inter alia, extra-rigid conformation, high resistance to enzyme degradation, increased cell permeability, and expandable ability to bind a diverse of targets with better affinity, have emerged in the last years as biologically pre-validated platforms for the drug discovery. Recent advances have revealed their enormous potential in the development of next-generation theranostics, smart delivery systems, and biomaterials. Here, we present an updated review on the biological and structural profile of these appealing biomolecules, with a particular emphasis on those with anticancer properties, since cancers are the main cause of death all over the world. Additionally, we provide a consideration on supramolecular structuring and synthons, based on the proline-based DKP privileged scaffold, for inspiration in the design of compound libraries in search of ideal ligands, innovative self-assembled nanomaterials, and bio-functional architectures.
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Affiliation(s)
- Joanna Bojarska
- Faculty of Chemistry, Institute of General & Inorganic Chemistry, Technical University of Lodz, 90-924 Lodz, Poland;
| | - Adam Mieczkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland;
| | - Zyta M. Ziora
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (Z.M.Z.); (I.T.)
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
| | - Istvan Toth
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (Z.M.Z.); (I.T.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Ahmed O. Shalash
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Shaima A. El-Mowafi
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Eman H. M. Mohammed
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Sherif Elnagdy
- Botany Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (S.E.); (M.A.)
| | - Maha AlKhazindar
- Botany Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (S.E.); (M.A.)
| | - Wojciech M. Wolf
- Faculty of Chemistry, Institute of General & Inorganic Chemistry, Technical University of Lodz, 90-924 Lodz, Poland;
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Harken L, Li SM. Modifications of diketopiperazines assembled by cyclodipeptide synthases with cytochrome P 450 enzymes. Appl Microbiol Biotechnol 2021; 105:2277-2285. [PMID: 33625545 PMCID: PMC7954767 DOI: 10.1007/s00253-021-11178-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 12/22/2022]
Abstract
2,5-Diketopiperazines are the smallest cyclic peptides comprising two amino acids connected via two peptide bonds. They can be biosynthesized in nature by two different enzyme families, either by nonribosomal peptide synthetases or by cyclodipeptide synthases. Due to the stable scaffold of the diketopiperazine ring, they can serve as precursors for further modifications by different tailoring enzymes, such as methyltransferases, prenyltransferases, oxidoreductases like cyclodipeptide oxidases, 2-oxoglutarate-dependent monooxygenases and cytochrome P450 enzymes, leading to the formation of intriguing secondary metabolites. Among them, cyclodipeptide synthase-associated P450s attracted recently significant attention, since they are able to catalyse a broader variety of astonishing reactions than just oxidation by insertion of an oxygen. The P450-catalysed reactions include hydroxylation at a tertiary carbon, aromatisation of the diketopiperazine ring, intramolecular and intermolecular carbon-carbon and carbon-nitrogen bond formation of cyclodipeptides and nucleobase transfer reactions. Elucidation of the crystal structures of three P450s as cyclodipeptide dimerases provides a structural basis for understanding the reaction mechanism and generating new enzymes by protein engineering. This review summarises recent publications on cyclodipeptide modifications by P450s.Key Points• Intriguing reactions catalysed by cyclodipeptide synthase-associated cytochrome P450s• Homo- and heterodimerisation of diketopiperazines• Coupling of guanine and hypoxanthine with diketopiperazines.
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Affiliation(s)
- Lauritz Harken
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Str. 4, 35037, Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Str. 4, 35037, Marburg, Germany.
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Le Chevalier F, Correia I, Matheron L, Babin M, Moutiez M, Canu N, Gondry M, Lequin O, Belin P. In vivo characterization of the activities of novel cyclodipeptide oxidases: new tools for increasing chemical diversity of bioproduced 2,5-diketopiperazines in Escherichia coli. Microb Cell Fact 2020; 19:178. [PMID: 32894164 PMCID: PMC7487605 DOI: 10.1186/s12934-020-01432-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 08/27/2020] [Indexed: 11/23/2022] Open
Abstract
Background Cyclodipeptide oxidases (CDOs) are enzymes involved in the biosynthesis of 2,5-diketopiperazines, a class of naturally occurring compounds with a large range of pharmaceutical activities. CDOs belong to cyclodipeptide synthase (CDPS)-dependent pathways, in which they play an early role in the chemical diversification of cyclodipeptides by introducing Cα-Cβ dehydrogenations. Although the activities of more than 100 CDPSs have been determined, the activities of only a few CDOs have been characterized. Furthermore, the assessment of the CDO activities on chemically-synthesized cyclodipeptides has shown these enzymes to be relatively promiscuous, making them interesting tools for cyclodipeptide chemical diversification. The purpose of this study is to provide the first completely microbial toolkit for the efficient bioproduction of a variety of dehydrogenated 2,5-diketopiperazines. Results We mined genomes for CDOs encoded in biosynthetic gene clusters of CDPS-dependent pathways and selected several for characterization. We co-expressed each with their associated CDPS in the pathway using Escherichia coli as a chassis and showed that the cyclodipeptides and the dehydrogenated derivatives were produced in the culture supernatants. We determined the biological activities of the six novel CDOs by solving the chemical structures of the biologically produced dehydrogenated cyclodipeptides. Then, we assessed the six novel CDOs plus two previously characterized CDOs in combinatorial engineering experiments in E. coli. We co-expressed each of the eight CDOs with each of 18 CDPSs selected for the diversity of cyclodipeptides they synthesize. We detected more than 50 dehydrogenated cyclodipeptides and determined the best CDPS/CDO combinations to optimize the production of 23. Conclusions Our study establishes the usefulness of CDPS and CDO for the bioproduction of dehydrogenated cyclodipeptides. It constitutes the first step toward the bioproduction of more complex and diverse 2,5-diketopiperazines.
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Affiliation(s)
- Fabien Le Chevalier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Isabelle Correia
- Laboratoire des Biomolécules (LBM), Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, 75005, Paris, France
| | - Lucrèce Matheron
- Sorbonne Université, Institut de Biologie Paris Seine (IBPS), FRE3631, 75005, Paris, France
| | - Morgan Babin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Mireille Moutiez
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Nicolas Canu
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Muriel Gondry
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Olivier Lequin
- Laboratoire des Biomolécules (LBM), Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, 75005, Paris, France
| | - Pascal Belin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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Strategy for the Biosynthesis of Short Oligopeptides: Green and Sustainable Chemistry. Biomolecules 2019; 9:biom9110733. [PMID: 31766233 PMCID: PMC6920838 DOI: 10.3390/biom9110733] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 02/07/2023] Open
Abstract
Short oligopeptides are some of the most promising and functionally important amide bond-containing components, with widespread applications. Biosynthesis of these oligopeptides may potentially become the ultimate strategy because it has better cost efficiency and environmental-friendliness than conventional solid phase peptide synthesis and chemo-enzymatic synthesis. To successfully apply this strategy for the biosynthesis of structurally diverse amide bond-containing components, the identification and selection of specific biocatalysts is extremely important. Given that perspective, this review focuses on the current knowledge about the typical enzymes that might be potentially used for the synthesis of short oligopeptides. Moreover, novel enzymatic methods of producing desired peptides via metabolic engineering are highlighted. It is believed that this review will be helpful for technological innovation in the production of desired peptides.
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