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Li X, Wang N, Liu Y, Li W, Bai X, Liu P, He CY. Backbone N-methylation of peptides: Advances in synthesis and applications in pharmaceutical drug development. Bioorg Chem 2023; 141:106892. [PMID: 37776681 DOI: 10.1016/j.bioorg.2023.106892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/16/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
Peptide-based drugs have garnered considerable attention in recent years owing to their increasingly crucial role in the treatment of diverse diseases. However, the limited pharmacokinetic properties of peptides have hindered their full potential. One prominent strategy for enhancing the druggability of peptides is N-methylation, which involves the addition of a methyl group to the nitrogen atom of the peptide backbone. This modification significantly improves the stability, bioavailability, receptor binding affinity and selectivity of peptide drug candidates. In this review, we provide a comprehensive overview of the advancements in synthetic methods for N-methylated peptide synthesis, as well as the associated limitations. Moreover, we explore the versatile effects of N-methylation on various aspects of peptide properties. Furthermore, we emphasize the efforts dedicated to N-methylated peptide pharmaceuticals that have successfully obtained marketing approval.
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Affiliation(s)
- Xuefei Li
- Key Laboratory of Basic Pharmacology of Ministry of Education, Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China; Central Research Institute, United-Imaging Healthcare Group Co., Ltd, Shanghai, China
| | - Ningchao Wang
- Central Research Institute, United-Imaging Healthcare Group Co., Ltd, Shanghai, China
| | - Yuhang Liu
- Central Research Institute, United-Imaging Healthcare Group Co., Ltd, Shanghai, China
| | - Weipiao Li
- Key Laboratory of Basic Pharmacology of Ministry of Education, Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Xinyu Bai
- Key Laboratory of Basic Pharmacology of Ministry of Education, Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Ping Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education, Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Chun-Yang He
- Key Laboratory of Basic Pharmacology of Ministry of Education, Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China.
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Matabaro E, Kaspar H, Dahlin P, Bader DLV, Murar CE, Staubli F, Field CM, Bode JW, Künzler M. Identification, heterologous production and bioactivity of lentinulin A and dendrothelin A, two natural variants of backbone N-methylated peptide macrocycle omphalotin A. Sci Rep 2021; 11:3541. [PMID: 33574430 PMCID: PMC7878506 DOI: 10.1038/s41598-021-83106-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/27/2021] [Indexed: 12/02/2022] Open
Abstract
Backbone N-methylation and macrocyclization improve the pharmacological properties of peptides by enhancing their proteolytic stability, membrane permeability and target selectivity. Borosins are backbone N-methylated peptide macrocycles derived from a precursor protein which contains a peptide α-N-methyltransferase domain autocatalytically modifying the core peptide located at its C-terminus. Founding members of borosins are the omphalotins from the mushroom Omphalotus olearius (omphalotins A-I) with nine out of 12 L-amino acids being backbone N-methylated. The omphalotin biosynthetic gene cluster codes for the precursor protein OphMA, the protease prolyloligopeptidase OphP and other proteins that are likely to be involved in other post-translational modifications of the peptide. Mining of available fungal genome sequences revealed the existence of highly homologous gene clusters in the basidiomycetes Lentinula edodes and Dendrothele bispora. The respective borosins, referred to as lentinulins and dendrothelins are naturally produced by L. edodes and D. bispora as shown by analysis of respective mycelial extracts. We produced all three homologous peptide natural products by coexpression of OphMA hybrid proteins and OphP in the yeast Pichia pastoris. The recombinant peptides differ in their nematotoxic activity against the plant pathogen Meloidogyne incognita. Our findings pave the way for the production of borosin peptide natural products and their potential application as novel biopharmaceuticals and biopesticides.
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Affiliation(s)
- Emmanuel Matabaro
- Department of Biology, Institute of Microbiology, ETH Zürich, Room HCI F409, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Hannelore Kaspar
- Department of Biology, Institute of Microbiology, ETH Zürich, Room HCI F409, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Paul Dahlin
- Agroscope, Phytopathology and Zoology in Fruit and Vegetable Production, Müller-Thurgau-Strasse 29, CH-8820, Wädenswil, Switzerland
| | - Daniel L V Bader
- Department of Chemistry and Applied Biosciences, Laboratorium Für Organische Chemie, ETH-Zürich, Vladimir-Prelog-Weg 3, CH-8093, Zürich, Switzerland
| | - Claudia E Murar
- Department of Chemistry and Applied Biosciences, Laboratorium Für Organische Chemie, ETH-Zürich, Vladimir-Prelog-Weg 3, CH-8093, Zürich, Switzerland
| | - Florian Staubli
- Department of Biology, Institute of Microbiology, ETH Zürich, Room HCI F409, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Christopher M Field
- Department of Biology, Institute of Microbiology, ETH Zürich, Room HCI F409, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Jeffrey W Bode
- Department of Chemistry and Applied Biosciences, Laboratorium Für Organische Chemie, ETH-Zürich, Vladimir-Prelog-Weg 3, CH-8093, Zürich, Switzerland.,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Markus Künzler
- Department of Biology, Institute of Microbiology, ETH Zürich, Room HCI F409, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland.
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Buckton LK, Rahimi MN, McAlpine SR. Cyclic Peptides as Drugs for Intracellular Targets: The Next Frontier in Peptide Therapeutic Development. Chemistry 2020; 27:1487-1513. [PMID: 32875673 DOI: 10.1002/chem.201905385] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 08/26/2020] [Indexed: 12/18/2022]
Abstract
Developing macrocyclic peptides that can reach intracellular targets is a significant challenge. This review discusses the most recent strategies used to develop cell permeable cyclic peptides that maintain binding to their biological target inside the cell. Macrocyclic peptides are unique from small molecules because traditional calculated physical properties are unsuccessful for predicting cell membrane permeability. Peptide synthesis and experimental membrane permeability is the only strategy that effectively differentiates between cell permeable and cell impermeable molecules. Discussed are chemical strategies, including backbone N-methylation and stereochemical changes, which have produced molecular scaffolds with improved cell permeability. However, these improvements often come at the expense of biological activity as chemical modifications alter the peptide conformation, frequently impacting the compound's ability to bind to the target. Highlighted is the most promising approach, which involves side-chain alterations that improve cell permeability without impact binding events.
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Affiliation(s)
- Laura K Buckton
- Department of Chemistry, University of New South Wales, Sydney, Gate 2 High Street, SEB 701, Kensington, NSW, 2052, Australia
| | - Marwa N Rahimi
- Department of Chemistry, University of New South Wales, Sydney, Gate 2 High Street, SEB 701, Kensington, NSW, 2052, Australia
| | - Shelli R McAlpine
- Department of Chemistry, University of New South Wales, Sydney, Gate 2 High Street, SEB 701, Kensington, NSW, 2052, Australia
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Farazi S, Chen F, Foster H, Boquiren R, McAlpine SR, Chapman R. Real time monitoring of peptide delivery in vitro using high payload pH responsive nanogels. Polym Chem 2020. [DOI: 10.1039/c9py01120j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A pH responsive pMAA nanogel that demonstrates high loading capacity and rapid intracellular delivery of hydrophilic peptides.
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Affiliation(s)
- Shegufta Farazi
- School of Chemistry
- UNSW Sydney
- Australia
- Centre for Advanced Macromolecular Design (CAMD)
- UNSW Sydney
| | - Fan Chen
- School of Chemistry
- UNSW Sydney
- Australia
- Centre for Advanced Macromolecular Design (CAMD)
- UNSW Sydney
| | - Henry Foster
- School of Chemistry
- UNSW Sydney
- Australia
- Centre for Advanced Macromolecular Design (CAMD)
- UNSW Sydney
| | | | | | - Robert Chapman
- School of Chemistry
- UNSW Sydney
- Australia
- Centre for Advanced Macromolecular Design (CAMD)
- UNSW Sydney
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Saavedra CJ, Carro C, Hernández D, Boto A. Conversion of “Customizable Units” into N-Alkyl Amino Acids and Generation of N-Alkyl Peptides. J Org Chem 2019; 84:8392-8410. [DOI: 10.1021/acs.joc.9b00114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Carlos J. Saavedra
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
- BIOSIGMA, Antonio Domı́nguez Alfonso 16, 38003-Sta. Cruz de Tenerife, Tenerife, Spain
| | - Carmen Carro
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
- BIOSIGMA, Antonio Domı́nguez Alfonso 16, 38003-Sta. Cruz de Tenerife, Tenerife, Spain
| | - Dácil Hernández
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
| | - Alicia Boto
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
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Huo Y, Buckton LK, Bennett JL, Smith EC, Byrne FL, Hoehn KL, Rahimi MN, McAlpine SR. Delivering bioactive cyclic peptides that target Hsp90 as prodrugs. J Enzyme Inhib Med Chem 2019; 34:728-739. [PMID: 30822267 PMCID: PMC6407599 DOI: 10.1080/14756366.2019.1580276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The most challenging issue facing peptide drug development is producing a molecule with optimal physical properties while maintaining target binding affinity. Masking peptides with protecting groups that can be removed inside the cell, produces a cell-permeable peptide, which theoretically can maintain its biological activity. Described are series of prodrugs masked using: (a) O-alkyl, (b) N-alkyl, and (c) acetyl groups, and their binding affinity for Hsp90. Alkyl moieties increased compound permeability, Papp, from 3.3 to 5.6, however alkyls could not be removed by liver microsomes or in-vivo and their presence decreased target binding affinity (IC50 of ≥10 µM). Thus, unlike small molecules, peptide masking groups cannot be predictably removed; their removal is related to the 3-D conformation. O-acetyl groups were cleaved but are labile, increasing challenges during synthesis. Utilising acetyl groups coupled with mono-methylated amines may decrease the polarity of a peptide, while maintaining binding affinity.
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Affiliation(s)
- Yuantao Huo
- a School of Chemistry, University of New South Wales , Sydney , Australia
| | - Laura K Buckton
- a School of Chemistry, University of New South Wales , Sydney , Australia
| | - Jack L Bennett
- a School of Chemistry, University of New South Wales , Sydney , Australia
| | - Eloise C Smith
- a School of Chemistry, University of New South Wales , Sydney , Australia
| | - Frances L Byrne
- b School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney , Australia
| | - Kyle L Hoehn
- b School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney , Australia
| | - Marwa N Rahimi
- a School of Chemistry, University of New South Wales , Sydney , Australia
| | - Shelli R McAlpine
- a School of Chemistry, University of New South Wales , Sydney , Australia
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