1
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Matsuda K, Ichihara R, Wakimoto T. FlkO, a penicillin-binding protein-type thioesterase in cyclofaulknamycin biosynthesis. Org Biomol Chem 2024; 22:6713-6717. [PMID: 39119636 DOI: 10.1039/d4ob00907j] [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: 08/10/2024]
Abstract
Penicillin-binding protein-type thioesterases (PBP-type TEs) catalyze head-to-tail macrolactamization in bacterial nonribosomal peptide biosynthesis. Here the scope of FlkO, a new PBP-type TE in cyclofaulknamycin biosynthesis, was thoroughly evaluated. The preference for small residues at the substrate C-terminus was consistent with the decreased volume of its putative substrate-binding pocket.
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Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0812, Japan.
| | - Rintaro Ichihara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0812, Japan.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0812, Japan.
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2
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Tanifuji R, Oguri H. Chemo-enzymatic total synthesis: current approaches toward the integration of chemical and enzymatic transformations. Beilstein J Org Chem 2024; 20:1693-1712. [PMID: 39076288 PMCID: PMC11285072 DOI: 10.3762/bjoc.20.151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 07/02/2024] [Indexed: 07/31/2024] Open
Abstract
A steadily increasing number of reports have been published on chemo-enzymatic synthesis methods that integrate biosynthetic enzymatic transformations with chemical conversions. This review focuses on the total synthesis of natural products and classifies the enzymatic reactions into three categories. The total synthesis of five natural products: cotylenol, trichodimerol, chalcomoracin, tylactone, and saframycin A, as well as their analogs, is outlined with an emphasis on comparing these chemo-enzymatic syntheses with the corresponding natural biosynthetic pathways.
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Affiliation(s)
- Ryo Tanifuji
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroki Oguri
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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3
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Lamartina CW, Chartier CA, Hirano JM, Shah NH, Rovis T. Crafting Unnatural Peptide Macrocycles via Rh(III)-Catalyzed Carboamidation. J Am Chem Soc 2024. [PMID: 39024122 DOI: 10.1021/jacs.4c05248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Contemporary developments in the field of peptide macrocyclization methodology are imperative for enabling the advance of drug design in medicinal chemistry. This report discloses a Rh(III)-catalyzed macrocyclization via carboamidation, reacting acryloyl-peptide-dioxazolone precursors and arylboronic acids to form complex cyclic peptides with concomitant incorporation of noncanonical α-amino acids. The diverse and modular technology allows for expedient access to a wide variety of cyclic peptides from 4 to 15 amino acids in size and features simultaneous formation of unnatural phenylalanine and tyrosine derivatives with up to >20:1 diastereoselectivity. The reaction showcases an expansive substrate scope with 45 examples and is compatible with the majority of standard protected amino acids used in Fmoc-solid phase peptide synthesis. The methodology is applied to the synthesis of multiple peptidomimetic macrocyclic analogs, including derivatives of cyclosomatostatin and gramicidin S.
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Affiliation(s)
| | - Cassandra A Chartier
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Jillian M Hirano
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Neel H Shah
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Tomislav Rovis
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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4
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Ding Y, Lambden E, Peate J, Picken LJ, Rees TW, Perez-Ortiz G, Newgas SA, Spicer LAR, Hicks T, Hess J, Ulmschneider MB, Müller MM, Barry SM. Rapid Peptide Cyclization Inspired by the Modular Logic of Nonribosomal Peptide Synthetases. J Am Chem Soc 2024; 146:16787-16801. [PMID: 38842580 PMCID: PMC11191687 DOI: 10.1021/jacs.4c04711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 06/07/2024]
Abstract
Nonribosomal cyclic peptides (NRcPs) are structurally complex natural products and a vital pool of therapeutics, particularly antibiotics. Their structural diversity arises from the ability of the multidomain enzyme assembly lines, nonribosomal peptide synthetases (NRPSs), to utilize bespoke nonproteinogenic amino acids, modify the linear peptide during elongation, and catalyze an array of cyclization modes, e.g., head to tail, side chain to tail. The study and drug development of NRcPs are often limited by a lack of easy synthetic access to NRcPs and their analogues, with selective macrolactamization being a major bottleneck. Herein, we report a generally applicable chemical macrocyclization method of unprecedented speed and selectivity. Inspired by biosynthetic cyclization, it combines the deprotected linear biosynthetic precursor peptide sequence with a highly reactive C-terminus to produce NRcPs and analogues in minutes. The method was applied to several NRcPs of varying sequences, ring sizes, and cyclization modes including rufomycin, colistin, and gramicidin S with comparable success. We thus demonstrate that the linear order of modules in NRPS enzymes that determines peptide sequence encodes the key structural information to produce peptides conformationally biased toward macrocyclization. To fully exploit this conformational bias synthetically, a highly reactive C-terminal acyl azide is also required, alongside carefully balanced pH and solvent conditions. This allows for consistent, facile cyclization of exceptional speed, selectivity, and atom efficiency. This exciting macrolactamization method represents a new enabling technology for the biosynthetic study of NRcPs and their development as therapeutics.
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Affiliation(s)
- Yaoyu Ding
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Edward Lambden
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Jessica Peate
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Lewis J. Picken
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Thomas W. Rees
- The
Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K.
| | - Gustavo Perez-Ortiz
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Sophie A. Newgas
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Lucy A. R. Spicer
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Thomas Hicks
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Jeannine Hess
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
- The
Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K.
| | - Martin B. Ulmschneider
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Manuel M. Müller
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Sarah M. Barry
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
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5
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Matsuda K, Wakimoto T. Penicillin-binding protein-type thioesterases: An emerging family of non-ribosomal peptide cyclases with biocatalytic potentials. Curr Opin Chem Biol 2024; 80:102465. [PMID: 38759287 DOI: 10.1016/j.cbpa.2024.102465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/19/2024]
Abstract
Macrocyclization of peptides reduces conformational flexibilities, potentially leading to improved drug-like properties, such as target specificities and metabolic stabilities. As chemical methodologies often allow side reactions like epimerization and oligomerization, keen attention has been directed toward enzymatic peptide cyclization using peptide cyclases from specialized metabolic pathways. Penicillin-binding protein-type thioesterases (PBP-type TEs) are a recently identified family of peptide cyclases involved in the biosynthesis of non-ribosomal peptides in actinobacteria. PBP-type TEs have undergone intensive investigation due to their outstanding potential as biocatalysts. This review summarizes the rapidly growing knowledge on PBP-type TEs, with special emphasis on their functions, scopes, and structures, and efforts towards their biocatalytic applications.
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Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.
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6
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Qiao S, Cheng Z, Li F. Chemoenzymatic synthesis of macrocyclic peptides and polyketides via thioesterase-catalyzed macrocyclization. Beilstein J Org Chem 2024; 20:721-733. [PMID: 38590533 PMCID: PMC10999997 DOI: 10.3762/bjoc.20.66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
Chemoenzymatic strategies that combine synthetic and enzymatic transformations offer efficient approaches to yield target molecules, which have been increasingly employed in the synthesis of bioactive natural products. In the biosynthesis of macrocyclic nonribosomal peptides, polyketides, and their hybrids, thioesterase (TE) domains play a significant role in late-stage macrocyclization. These domains can accept mimics of native substrates in vitro and exhibit potential for use in total synthesis. This review summarizes the recent advances of TE domains in the chemoenzymatic synthesis for these natural products that aim to address the common issues in classical synthetic approaches and increase synthetic efficiencies, which have the potential to facilitate further pharmaceutical research.
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Affiliation(s)
- Senze Qiao
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Zhongyu Cheng
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Fuzhuo Li
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China
- Key Laboratory of Smart Drug Delivery (Ministry of Education), State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, 201203, China
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7
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Kobayashi M, Onozawa N, Matsuda K, Wakimoto T. Chemoenzymatic tandem cyclization for the facile synthesis of bicyclic peptides. Commun Chem 2024; 7:67. [PMID: 38548970 PMCID: PMC10978974 DOI: 10.1038/s42004-024-01147-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/13/2024] [Indexed: 04/01/2024] Open
Abstract
Bicyclic peptides exhibit improved metabolic stabilities and target specificities when compared to their linear or mono-cyclic counterparts; however, efficient and straightforward synthesis remains challenging due to their intricate architectures. Here, we present a highly selective and operationally simple one-pot chemoenzymatic tandem cyclization approach to synthesize bicyclic peptides with small to medium ring sizes. Penicillin-binding protein-type thioesterases (PBP-type TEs) efficiently cyclized azide/alkyne-containing peptides in a head-to-tail manner. Successive copper (I)-catalyzed azide-alkyne cycloaddition generated bicyclic peptides in one-pot, thus omitting the purification of monocyclic intermediates. This chemoenzymatic strategy enabled the facile synthesis of bicyclic peptides bearing hexa-, octa-, and undecapeptidyl head-to-tail cyclic scaffolds.
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Affiliation(s)
- Masakazu Kobayashi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Naho Onozawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
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8
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Maw ZA, Haltli B, Guo JJ, Baldisseri DM, Cartmell C, Kerr RG. Discovery of Acyl-Surugamide A2 from Marine Streptomyces albidoflavus RKJM-0023-A New Cyclic Nonribosomal Peptide Containing an N-ε-acetyl-L-lysine Residue. Molecules 2024; 29:1482. [PMID: 38611762 PMCID: PMC11012974 DOI: 10.3390/molecules29071482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
We report the discovery of a novel cyclic nonribosomal peptide (NRP), acyl-surugamide A2, from a marine-derived Streptomyces albidoflavus RKJM-0023 (CP133227). The structure of acyl-surugamide A2 was elucidated using a combination of NMR spectroscopy, MS2 fragmentation analysis, and comparative analysis of the sur biosynthetic gene cluster. Acyl-surugamide A2 contains all eight core amino acids of surugamide A, with a modified N-ε-acetyl-L-lysine residue. Our study highlights the potential of marine Streptomyces strains to produce novel natural products with potential therapeutic applications. The structure of cyclic peptides can be solved using MS2 spectra and analysis of their biosynthetic gene clusters.
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Affiliation(s)
- Zacharie A. Maw
- Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada; (Z.A.M.)
| | - Bradley Haltli
- Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada; (Z.A.M.)
- Nautilus Biosciences, Croda Canada Limited, Charlottetown, PE C1A 4P3, Canada
| | - Jason J. Guo
- Department of Chemistry & Chemical Biology, Barnett Institute for Chemical and Biological Analysis, Northeastern University, Boston, MA 02115, USA
| | | | - Christopher Cartmell
- Department of Pharmacology, Comprehensive Center for Pain & Addiction, College of Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Russell G. Kerr
- Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada; (Z.A.M.)
- Nautilus Biosciences, Croda Canada Limited, Charlottetown, PE C1A 4P3, Canada
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
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9
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Du Z, Ma Y, Shen Y, Jiang X, Zhou Y, Shi T. Exploring the substrate stereoselectivity and catalytic mechanism of nonribosomal peptide macrocyclization in surugamides biosynthesis. iScience 2024; 27:108876. [PMID: 38313049 PMCID: PMC10835440 DOI: 10.1016/j.isci.2024.108876] [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: 10/02/2023] [Revised: 12/12/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024] Open
Abstract
SurE, the first reported penicillin-binding protein-like thioesterase (PBP-like TE), is known as a new off-loading cyclase, which catalyzes heterochiral coupling in nonribosomal peptides (NRPs). However, the structural rationale for substrate stereoselectivity and enzymatic mechanism remains mysterious. Here, computational models, integrating MD simulations and QM/MM methods, unveiled SurE's substrate recognition and catalytic process. An oxyanion hole stabilized the C-terminal D-residue during recognition. Residue R446 anchored the substrate for macrocyclization. A vital hydrogen-bonding network (Y154, K66, N156), verified by mutation results, was responsible for the recognition of N-terminal L-residue and involvement in catalytic process with a calculated 19.4 kcal/mol energy barrier. Four novel-designed peptide precursors were effectively cyclized into cyclopeptides by SurE based on computational analysis. Our results provide a comprehensive understanding of SurE's catalytic mechanism and guiding design of versatile PBP-like TEs for novel macrocyclic NRPs.
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Affiliation(s)
- Zeqian Du
- State Key Laboratory of Microbial Metabolism, Joint International Research, Laboratory of Metabolic and Developmental Sciences, School of Life Sciences, and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yinhao Ma
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Yaoyao Shen
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xuefeng Jiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Yongjun Zhou
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research, Laboratory of Metabolic and Developmental Sciences, School of Life Sciences, and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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10
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Budimir ZL, Patel RS, Eggly A, Evans CN, Rondon-Cordero HM, Adams JJ, Das C, Parkinson EI. Biocatalytic cyclization of small macrolactams by a penicillin-binding protein-type thioesterase. Nat Chem Biol 2024; 20:120-128. [PMID: 38062262 PMCID: PMC10999230 DOI: 10.1038/s41589-023-01495-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023]
Abstract
Macrocyclic peptides represent promising scaffolds for chemical tools and potential therapeutics. Synthetic methods for peptide macrocyclization are often hampered by C-terminal epimerization and oligomerization, leading to difficult scalability. While chemical strategies to circumvent this issue exist, they often require specific amino acids to be present in the peptide sequence. Herein, we report the characterization of Ulm16, a peptide cyclase belonging to the penicillin-binding protein-type class of thioesterases that catalyze head-to-tail macrolactamization of nonribosmal peptides. Ulm16 efficiently cyclizes various nonnative peptides ranging from 4 to 6 amino acids with catalytic efficiencies of up to 3 × 106 M-1 s-1. Unlike many previously described homologs, Ulm16 tolerates a variety of C- and N-terminal amino acids. The crystal structure of Ulm16, along with modeling of its substrates and site-directed mutagenesis, allows for rationalization of this wide substrate scope. Overall, Ulm16 represents a promising tool for the biocatalytic production of macrocyclic peptides.
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Affiliation(s)
| | - Rishi S Patel
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Alyssa Eggly
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Claudia N Evans
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | | | - Jessica J Adams
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Elizabeth I Parkinson
- Department of Chemistry, Purdue University, West Lafayette, IN, USA.
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
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11
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Su L, Deng H. Size matters. Nat Chem Biol 2024; 20:8-10. [PMID: 38114808 DOI: 10.1038/s41589-023-01503-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Affiliation(s)
- Li Su
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen, UK.
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12
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Kobayashi M, Fujita K, Matsuda K, Wakimoto T. Streamlined Chemoenzymatic Synthesis of Cyclic Peptides by Non-ribosomal Peptide Cyclases. J Am Chem Soc 2023; 145:3270-3275. [PMID: 36638272 DOI: 10.1021/jacs.2c11082] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Macrocyclization improves the pharmaceutical properties of peptides; however, regio- and chemoselective intramolecular cyclizations remain challenging. Here we developed a streamlined chemoenzymatic approach to synthesize cyclic peptides by exploiting non-ribosomal peptide (NRP) cyclases. Linear peptides linked to the resin through a C-terminal diol ester functionality are synthesized on a solid support, to circumvent the installation of leaving groups to the peptidic substrates in the liquid phase which often triggers undesirable epimerization. Cleavage of the resin-bound peptides yielded the diol esters with sufficient purity to be readily cyclized in a head-to-tail manner by SurE, a representative penicillin-binding protein-type thioesterase (PBP-type TE). Explorations of homologous wild-type enzymes as well as rational protein engineering have broadened the scope of the enzymatic macrolactamization. This method will potentially accelerate the exploitation of NRP cyclases as biocatalysts.
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Affiliation(s)
- Masakazu Kobayashi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo060-0812, Japan
| | - Kei Fujita
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo060-0812, Japan
| | - Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Kita 12, Nishi 6, Sapporo060-0812, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Kita 12, Nishi 6, Sapporo060-0812, Japan
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13
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Kuranaga T. Total syntheses of surugamides and thioamycolamides toward understanding their biosynthesis. J Nat Med 2023; 77:1-11. [PMID: 36348140 PMCID: PMC9810689 DOI: 10.1007/s11418-022-01662-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/23/2022] [Indexed: 11/09/2022]
Abstract
Peptidic natural products have received much attention as potential drug leads, and biosynthetic studies of peptidic natural products have contributed to the field of natural product chemistry over the past several decades. However, the key biosynthetic intermediates are generally not isolated from natural sources, and this can hamper a detailed analysis of biosynthesis. Furthermore, reported unusual structures, which are targets for biosynthetic studies, are sometimes the results of structural misassignments. Chemical synthesis techniques are imperative in solving these problems. This review focuses on the chemical syntheses of surugamides and thioamycolamides toward understanding their biosynthesis. These studies can provide the key biosynthetic intermediates that can reveal the biosynthetic pathways and/or true structures of these natural products.
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Affiliation(s)
- Takefumi Kuranaga
- Division of Bioinformatics and Chemical Genomics, Department of System Chemotherapy and Molecular Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan.
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14
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Kobayashi M, Fujita K, Matsuda K, Wakimoto T. Chemo-Enzymatic Synthesis of Non-ribosomal Macrolactams by a Penicillin-Binding Protein-Type Thioesterase. Methods Mol Biol 2023; 2670:127-144. [PMID: 37184702 DOI: 10.1007/978-1-0716-3214-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Penicillin-binding protein-type thioesterases (PBP-type TEs) are an emerging family of non-ribosomal peptide cyclases. PBP-type TEs exhibit distinct substrate scopes from the well-exploited ribosomal peptide cyclases and traditional non-ribosomal peptide cyclases. Their unique properties, as well as their stand-alone nature, highlight PBP-type TEs as valuable candidates for development as biocatalysts for peptide macrocyclization. Here in this chapter, we describe the scheme for the chemoenzymatic synthesis of non-ribosomal macrolactam by SurE, a representative member of PBP-type TEs.
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Affiliation(s)
| | - Kei Fujita
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan.
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15
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Fazal A, Wheeler J, Webb ME, Seipke RF. The N-terminal substrate specificity of the SurE peptide cyclase. Org Biomol Chem 2022; 20:7232-7235. [PMID: 36062889 PMCID: PMC9491159 DOI: 10.1039/d2ob01061e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SurE is a standalone peptide cyclase essential for the production of surugamide antibiotics. Although SurE catalyses the cyclisation of varied nonribosomal peptides in vivo, its substrate specificity is poorly understood. To address this issue, an on-resin SurE cyclisation assay was developed and in combination with SNAC thioesters and kinetic measurements was used to define the chemical space of the N-terminal substrate residue. The N-terminal substrate specificity of the SurE peptide cyclase was elucidated using a combination of on-resin biomemtic substrates and conventional SNAC thioesters.![]()
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Affiliation(s)
- Asif Fazal
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Jake Wheeler
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Michael E Webb
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Ryan F Seipke
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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16
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Hostetler MA, Smith C, Nelson S, Budimir Z, Modi R, Woolsey I, Frerk A, Baker B, Gantt J, Parkinson EI. Synthetic Natural Product Inspired Cyclic Peptides. ACS Chem Biol 2021; 16:2604-2611. [PMID: 34699170 PMCID: PMC8610019 DOI: 10.1021/acschembio.1c00641] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Natural products
are a bountiful source of bioactive molecules.
Unfortunately, discovery of novel bioactive natural products is challenging
due to cryptic biosynthetic gene clusters, low titers, and arduous
purifications. Herein, we describe SNaPP (Synthetic Natural Product
Inspired Cyclic Peptides), a method for identifying
NP-inspired bioactive peptides. SNaPP expedites bioactive molecule
discovery by combining bioinformatics predictions of nonribosomal
peptide synthetases with chemical synthesis of the predicted natural
products (pNPs). SNaPP utilizes a recently discovered cyclase, the
penicillin binding protein-like cyclase, as the lynchpin for the development
of a library of head-to-tail cyclic peptide pNPs. Analysis of 500
biosynthetic gene clusters allowed for identification of 131 novel
pNPs. Fifty-one diverse pNPs were synthesized using solid phase peptide
synthesis and solution-phase cyclization. Antibacterial testing revealed
14 pNPs with antibiotic activity, including activity against multidrug-resistant
Gram-negative bacteria. Overall, SNaPP demonstrates the power of combining
bioinformatics predictions with chemical synthesis to accelerate the
discovery of bioactive molecules.
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Affiliation(s)
- Matthew A. Hostetler
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chloe Smith
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Samantha Nelson
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zachary Budimir
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ramya Modi
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ian Woolsey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Autumn Frerk
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Braden Baker
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jessica Gantt
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Elizabeth I. Parkinson
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
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17
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Adrover-Castellano ML, Schmidt JJ, Sherman DH. Biosynthetic Cyclization Catalysts for the Assembly of Peptide and Polyketide Natural Products. ChemCatChem 2021; 13:2095-2116. [PMID: 34335987 PMCID: PMC8320681 DOI: 10.1002/cctc.202001886] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Indexed: 12/13/2022]
Abstract
Many biologically active natural products are synthesized by nonribosomal peptide synthetases (NRPSs), polyketide synthases (PKSs) and their hybrids. These megasynthetases contain modules possessing distinct catalytic domains that allow for substrate initiation, chain extension, processing and termination. At the end of a module, a terminal domain, usually a thioesterase (TE), is responsible for catalyzing the release of the NRPS or PKS as a linear or cyclized product. In this review, we address the general cyclization mechanism of the TE domain, including oligomerization and the fungal C-C bond forming Claisen-like cyclases (CLCs). Additionally, we include examples of cyclization catalysts acting within or at the end of a module. Furthermore, condensation-like (CT) domains, terminal reductase (R) domains, reductase-like domains that catalyze Dieckmann condensation (RD), thioesterase-like Dieckmann cyclases, trans-acting TEs from the penicillin binding protein (PBP) enzyme family, product template (PT) domains and others will also be reviewed. The studies summarized here highlight the remarkable diversity of NRPS and PKS cyclization catalysts for the production of biologically relevant, complex cyclic natural products and related compounds.
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Affiliation(s)
| | - Jennifer J Schmidt
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA)
| | - David H Sherman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA)
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18
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Liu C, Hashimoto J, Kudo K, Shin-Ya K, Kakeya H. An Atypical Arginine Dihydrolase Involved in the Biosynthesis of Cyclic Hexapeptide Longicatenamides. Chem Asian J 2021; 16:1382-1387. [PMID: 33886165 DOI: 10.1002/asia.202100181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/02/2021] [Indexed: 11/07/2022]
Abstract
The incorporation of non-proteinogenic amino acids (NPAAs) enriches the structural diversity of nonribosomal peptides. Recently, four NPAA-containing cyclic hexapeptides, longicatenamides A-D, were isolated using a combined-culture strategy. Based on in silico analysis, we discovered their putative biosynthetic gene cluster (lon) and proposed a possible biosynthetic mechanism. Surprisingly, the lon22 gene encodes an atypical arginine dihydrolase, which can also catalyze the hydrolysis of citrulline to ornithine. Phylogenetic analysis showed that Lon22-like proteins form a novel clade that is separated from other guanidine-modifying enzymes. After rational design, the catalytic efficiencies of a Lon22 Y80F mutant for arginine and citrulline substrates were 2.31- and 4.70-fold that of the wild-type (WT), respectively. In addition, characterization of the Lon20-A4 adenylation domain suggested that it can incorporate both ornithine and lysine into the final products.
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Affiliation(s)
- Chao Liu
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo-ku, Kyoto, 606-8501, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kei Kudo
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo-ku, Kyoto, 606-8501, Japan
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19
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Matsuda K, Fujita K, Wakimoto T. PenA, a penicillin-binding protein-type thioesterase specialized for small peptide cyclization. J Ind Microbiol Biotechnol 2021; 48:6169712. [PMID: 33713128 PMCID: PMC9113502 DOI: 10.1093/jimb/kuab023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/19/2021] [Indexed: 12/31/2022]
Abstract
Penicillin-binding protein-type thioesterases (PBP-type TEs) are a recently identified group of peptide cyclases that catalyze head-to-tail macrolactamization of nonribosomal peptides. PenA, a new member of this group, is involved in the biosyntheses of cyclic pentapeptides. In this study, we demonstrated the enzymatic activity of PenA in vitro, and analyzed its substrate scope with a series of synthetic substrates. A comparison of the reaction profiles between PenA and SurE, a representative PBP-type TE, showed that PenA is more specialized for small peptide cyclization. A computational model provided a possible structural rationale for the altered specificity for substrate chain lengths.
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Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Kei Fujita
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Kita 12, Nishi 6, Sapporo 060-0812, Japan
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20
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Bacterial-Like Nonribosomal Peptide Synthetases Produce Cyclopeptides in the Zygomycetous Fungus Mortierella alpina. Appl Environ Microbiol 2021; 87:AEM.02051-20. [PMID: 33158886 DOI: 10.1128/aem.02051-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/30/2020] [Indexed: 12/20/2022] Open
Abstract
Fungi are traditionally considered a reservoir of biologically active natural products. However, an active secondary metabolism has long not been attributed to early-diverging fungi such as Mortierella Here, we report on the biosynthesis of two series of cyclic pentapeptides, the malpicyclins and malpibaldins, as products of Mortierella alpina ATCC 32222. The molecular structures of malpicyclins were elucidated by high-resolution tandem mass spectrometry (HR-MS/MS), Marfey's method, and one-dimensional (1D) and 2D nuclear magnetic resonance (NMR) spectroscopy. In addition, malpibaldin biosynthesis was confirmed by HR-MS. Genome mining and comparative quantitative real-time PCR (qRT-PCR) expression analysis pointed at two pentamodular nonribosomal peptide synthetases (NRPSs), malpicyclin synthetase MpcA and malpibaldin synthetase MpbA, as candidate biosynthetic enzymes. Heterologous production of the respective adenylation domains and substrate specificity assays proved promiscuous substrate selection and confirmed their respective biosynthetic roles. In stark contrast to known fungal NRPSs, MpbA and MpcA contain bacterial-like dual epimerase/condensation domains allowing the racemization of enzyme-tethered l-amino acids and the subsequent incorporation of d-amino acids into the metabolites. Phylogenetic analyses of both NRPS genes indicated a bacterial origin and a horizontal gene transfer into the fungal genome. We report on the as-yet-unexplored nonribosomal peptide biosynthesis in basal fungi which highlights this paraphylum as a novel and underrated resource of natural products.IMPORTANCE Fungal natural compounds are industrially produced, with application in antibiotic treatment, cancer medications, and crop plant protection. Traditionally, higher fungi have been intensively investigated concerning their metabolic potential, but reidentification of already known compounds is frequently observed. Hence, alternative strategies to acquire novel bioactive molecules are required. We present the genus Mortierella as representative of the early-diverging fungi as an underestimated resource of natural products. Mortierella alpina produces two families of cyclopeptides, designated malpicyclins and malpibaldins, respectively, via two pentamodular nonribosomal peptide synthetases (NRPSs). These enzymes are much more closely related to bacterial than to other fungal NRPSs, suggesting a bacterial origin of these NRPS genes in Mortierella Both enzymes were biochemically characterized and are involved in as-yet-unknown biosynthetic pathways of natural products in basal fungi. Hence, this report establishes early-diverging fungi as prolific natural compound producers and sheds light on the origin of their biosynthetic capacity.
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21
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Pentaminomycins C-E: Cyclic Pentapeptides as Autophagy Inducers from a Mealworm Beetle Gut Bacterium. Microorganisms 2020; 8:microorganisms8091390. [PMID: 32927831 PMCID: PMC7565604 DOI: 10.3390/microorganisms8091390] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/08/2020] [Accepted: 09/08/2020] [Indexed: 01/04/2023] Open
Abstract
Pentaminomycins C–E (1–3) were isolated from the culture of the Streptomyces sp. GG23 strain from the guts of the mealworm beetle, Tenebrio molitor. The structures of the pentaminomycins were determined to be cyclic pentapeptides containing a modified amino acid, N5-hydroxyarginine, based on 1D and 2D NMR and mass spectroscopic analyses. The absolute configurations of the amino acid residues were assigned using Marfey’s method and bioinformatics analysis of their nonribosomal peptide biosynthetic gene cluster (BGC). Detailed analysis of the BGC enabled us to propose that the structural variations in 1–3 originate from the low specificity of the adenylation domain in the nonribosomal peptide synthetase (NRPS) module 1, and indicate that macrocyclization can be catalyzed noncanonically by penicillin binding protein (PBP)-type TE. Furthermore, pentaminomycins C and D (1 and 2) showed significant autophagy-inducing activities and were cytoprotective against oxidative stress in vitro.
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22
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The Desotamide Family of Antibiotics. Antibiotics (Basel) 2020; 9:antibiotics9080452. [PMID: 32727132 PMCID: PMC7459860 DOI: 10.3390/antibiotics9080452] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/14/2020] [Accepted: 07/25/2020] [Indexed: 12/22/2022] Open
Abstract
Microbial natural products underpin the majority of antimicrobial compounds in clinical use and the discovery of new effective antibacterial treatments is urgently required to combat growing antimicrobial resistance. Non-ribosomal peptides are a major class of natural products to which many notable antibiotics belong. Recently, a new family of non-ribosomal peptide antibiotics were discovered-the desotamide family. The desotamide family consists of desotamide, wollamide, surugamide, ulleungmycin and noursamycin/curacomycin, which are cyclic peptides ranging in size between six and ten amino acids in length. Their biosynthesis has attracted significant attention because their highly functionalised scaffolds are cyclised by a recently identified standalone cyclase. Here, we provide a concise review of the desotamide family of antibiotics with an emphasis on their biosynthesis.
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