1
|
Byerly-Duke J, Donovan A, O'Brien EA, Sharma KK, Ibrahim R, Stanley LM, VanVeller B. Complementary Strategies for Installation of Thioimidates into Peptide Backbones. J Org Chem 2024. [PMID: 39364858 DOI: 10.1021/acs.joc.4c01386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2024]
Abstract
Thioimidates are a precursor and synthetic branch point to access either thioamide or amidine isosteres of the native amide (peptide bond). Previous syntheses of thioimidate-containing peptides were prone to side reactivity and required slow, cumbersome steps that were difficult to monitor. We describe a more efficient approach to directly couple thioimidates onto the growing peptide chain. This work also outlines optimal conditions for thioimidate formation on solid support and identifies potential off-target sites for alkylation that impact the choice of protecting group.
Collapse
Affiliation(s)
- Jacob Byerly-Duke
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Aaron Donovan
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Emily A O'Brien
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Krishna K Sharma
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Rida Ibrahim
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Levi M Stanley
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| |
Collapse
|
2
|
Paquette AR, Brazeau-Henrie JT, Boddy CN. Thioesterases as tools for chemoenzymatic synthesis of macrolactones. Chem Commun (Camb) 2024; 60:3379-3388. [PMID: 38456624 DOI: 10.1039/d4cc00401a] [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: 03/09/2024]
Abstract
Macrocycles are a key functional group that can impart unique properties into molecules. Their synthesis has led to the development of many outstanding chemical methodologies and yet still remains challenging. Thioesterase (TE) domains are frequently responsible for macrocyclization in natural product biosynthesis and provide unique strengths for the enzymatic synthesis of macrocycles. In this feature article, we describe our work to characterize the substrate selectivity of TEs and to use these enzymes as biocatalysts. Our efforts have shown that the linear thioester activated substrates are loaded on TEs with limited substrate selectivity to generate acyl-enzyme intermediates. We show that cyclization of the acyl-enzyme intermediates can be highly selective, with competing hydrolysis of the acyl-enzyme intermediates. The mechanisms controlling TE-mediated macrocyclization versus hydrolysis are a significant unsolved problem in TE biochemistry. The potential of TEs as biocatalysts was demonstrated by using them in the chemoenzymatic total synthesis of macrocyclic depsipeptide natural products. This article highlights the strengths and potential of TEs as biocatalysts as well as their limitations, opening exciting research opportunities including TE engineering to optimize these powerful biocatalysts.
Collapse
Affiliation(s)
- André R Paquette
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada K1N 6N5.
| | - Jordan T Brazeau-Henrie
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada K1N 6N5.
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada K1N 6N5.
| |
Collapse
|
3
|
Byerly-Duke J, VanVeller B. Thioimidate Solutions to Thioamide Problems during Thionopeptide Deprotection. Org Lett 2024; 26:1452-1457. [PMID: 38341867 PMCID: PMC11031844 DOI: 10.1021/acs.orglett.4c00035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024]
Abstract
Thioamides have structural and chemical similarity to peptide bonds, offering valuable insights when probing peptide backbone interactions, but are prone to side reactions during solid-phase peptide synthesis (SPPS). Thioimidates have been demonstrated to be effective protecting groups for thioamides during peptide elongation. We further demonstrate how thioimidates can assist thioamides through the most yield-crippling step of thionopeptide deprotection, allowing for the first isolation of an important benchmark α-helical peptide that had previously eluded synthesis and isolation.
Collapse
Affiliation(s)
- Jacob Byerly-Duke
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| |
Collapse
|
4
|
Hansen TN, Olsen CA. Contemporary Applications of Thioamides and Methods for Their Synthesis. Chemistry 2024; 30:e202303770. [PMID: 38088462 DOI: 10.1002/chem.202303770] [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: 11/13/2023] [Indexed: 12/23/2023]
Abstract
Thioamides are naturally occurring isosteres of amide bonds in which the chalcogen atom of the carbonyl is changed from oxygen to sulfur. This substitution gives rise to altered nucleophilicity and hydrogen bonding properties with importance for both chemical reactivity and non-covalent interactions. As such, thioamides have been introduced into biologically active compounds to achieve improved target affinity and/or stability towards hydrolytic enzymes but have also been applied as probes of protein and peptide folding and dynamics. Recently, a series of new methods have been developed for the synthesis of thioamides as well as their utilization in peptide chemistry. Further, novel strategies for the incorporation of thioamides into proteins have been developed, enabling both structural and functional studies to be performed. In this Review, we highlight the recent developments in the preparation of thioamides and their applications for peptide modification and study of protein function.
Collapse
Affiliation(s)
- Tobias N Hansen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| |
Collapse
|
5
|
Lepetit CA, Paquette AR, Brazeau-Henrie JT, Boddy CN. Total and chemoenzymatic synthesis of the lipodepsipeptide rhizomide A. Bioorg Med Chem Lett 2023; 96:129506. [PMID: 37820774 DOI: 10.1016/j.bmcl.2023.129506] [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: 07/31/2023] [Revised: 09/27/2023] [Accepted: 10/07/2023] [Indexed: 10/13/2023]
Abstract
Rhizomides are a family of depsipeptide macrolactones synthesized by a non-ribosomal peptide synthetase (NRPS) encoded in the genome of Paraburkholderia rhizoxinica str. HKI 454. In this study, the total and chemoenzymatic synthesis of the depsipeptide rhizomide A is described. Rhizomide A was generated through macrolactamization while thelinear C-terminal N-acetylcysteamine (SNAC) thioester substrate was synthesized through a C-terminal thioesterification strategy. It was shown that the rhizomide A thioesterase (RzmA-TE) is an active macrocyclization catalyst, allowing the chemoenzymatic synthesis of rhizomide A.This work further showcases the biocatalytic power of TEs in accessing complex macrocyclic natural products.
Collapse
Affiliation(s)
- Corinne A Lepetit
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada; Cergy Paris Université, 5 Mail Gay Lussac, 95000 Cergy, France
| | - André R Paquette
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Jordan T Brazeau-Henrie
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| |
Collapse
|
6
|
Paquette AR, Boddy CN. Macrocyclization strategies for the total synthesis of cyclic depsipeptides. Org Biomol Chem 2023; 21:8043-8053. [PMID: 37750186 DOI: 10.1039/d3ob01229h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Cyclic depsipeptides are an important class of peptide natural products that are defined by the presence of ester and amide bonds within the macrocycle. The structural diversity of depsipeptides has required the development of a broad range of synthetic strategies to access these biologically active compounds. Solid phase peptide synthesis (SPPS) strategies have been an invaluable tool in their synthesis. The key aspect of their synthesis is the macrocyclization strategy. Three main strategies are used, solution phase macrolactamization of acyclic ester containing peptide, on-resin macrolactamization of a sidechain-anchored peptide, and the solution phase macrolactonization of a linear peptide. Additionally, biocatalysts have been used to produce these compounds in a regio- and chemo-selective manner. Each compound offers unique challenges, requiring careful synthetic design to avoid undesirable side reactivity or unwanted epimerization during the esterification and macrocyclizing steps. This focused review analyzes these three strategies for cyclic depsipeptide natural product total synthesis with selected examples from the literature between 2001-2023.
Collapse
Affiliation(s)
- André R Paquette
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
| |
Collapse
|
7
|
Sharma K, Sharma KK, Sharma A, Jain R. Peptide-based drug discovery: Current status and recent advances. Drug Discov Today 2023; 28:103464. [PMID: 36481586 DOI: 10.1016/j.drudis.2022.103464] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
The progressive development of peptides from reaction vessels to life-saving drugs via rigorous preclinical and clinical assessments is fascinating. Peptide therapeutics have gained momentum with the evolution of techniques in peptide chemistry, such as microwave irradiation in solid- and solution-phase synthesis, ligation chemistry, recombinant synthesis, and amalgamation with synthetic tools, including metal catalysis. Diverse emerging technologies, such as DNA-encoded libraries (DELs) and display techniques, are changing the status quo in the discovery of peptide therapeutics. In this review, we analyzed US Food and Drug Administration (FDA)-approved peptide drugs and those in clinical trials, highlighting recent advances in peptide-based drug discovery.
Collapse
Affiliation(s)
- Komal Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Krishna K Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Anku Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India.
| |
Collapse
|
8
|
O’Brien EA, Sharma KK, Byerly-Duke J, Camacho LA, VanVeller B. A General Strategy to Install Amidine Functional Groups Along the Peptide Backbone. J Am Chem Soc 2022; 144:22397-22402. [PMID: 36469014 PMCID: PMC9886086 DOI: 10.1021/jacs.2c09085] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Amidines are a structural surrogate for peptide bonds, yet have received considerably little attention in peptides due to limitations in existing methods to access them. The synthetic strategy developed in this study represents the first robust and general procedure for the introduction of amidines into the peptide backbone. We exploit and further develop the utility and efficiency of thioimidate protecting groups as a means to side-step reactivity that ultimately renders existing methods unsuitable for the installation of amidines along the main-chain of peptides. This work is significant because it describes a generally applicable path to access unexplored peptide designs and architectures for new therapeutics made possible by the unique properties of amidines.
Collapse
|
9
|
Taresh AB, Hutton CA. Site Specific Preparation of N-Glycosylated Peptides: Thioamide-Directed Activation of Aspartate. Angew Chem Int Ed Engl 2022; 61:e202210367. [PMID: 36068172 PMCID: PMC9826000 DOI: 10.1002/anie.202210367] [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: 07/15/2022] [Indexed: 01/11/2023]
Abstract
A site-specific method for the preparation of N-glycosylated peptides is described. Incorporation of a peptide backbone thioamide linkage adjacent to an Asp residue facilitates a AgI -promoted, site-specific conversion to N-glycosylated Asn residues in peptides.
Collapse
Affiliation(s)
- Ameer B. Taresh
- School of Chemistry and Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneMelbourneVictoria 3010Australia
| | - Craig A. Hutton
- School of Chemistry and Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneMelbourneVictoria 3010Australia
| |
Collapse
|
10
|
Taresh AB, Hutton CA. Site Specific Preparation of N‐Glycosylated Peptides: Thioamide‐Directed Activation of Aspartate. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202210367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ameer B. Taresh
- University of Melbourne School of Chemistry School of Chemistry AUSTRALIA
| | - Craig Anthony Hutton
- University of Melbourne School of Chemistry 30 Flemington Rd. VIC 3095 Parkville AUSTRALIA
| |
Collapse
|
11
|
Brazeau-Henrie JT, Paquette AR, O'Rourke AQ, Darnowski MG, Boddy CN. Total and Chemoenzymatic Synthesis of Seongsanamide E. Org Lett 2022; 24:6369-6373. [PMID: 36006794 DOI: 10.1021/acs.orglett.2c02271] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The total and chemoenzymatic synthesis of the depsipeptide natural product seongsanamide E, 3, is described. The synthetic C-terminal N-acetylcysteamine thioester of linear natural product 1 was macrolactonized by the excised recombinant purified seongsanamide thioesterase (Sgd-TE) domain, generating 3. Sgd-TE also effects the ring opening of 3. Chemical synthesis provided 3 through a macrolactamization strategy. This work confirms the biosynthesis of 3 and demonstrates the power of Sgd-TE as a biocatalyst.
Collapse
Affiliation(s)
- Jordan T Brazeau-Henrie
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - André R Paquette
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Allison Q O'Rourke
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Michael G Darnowski
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| |
Collapse
|
12
|
Ibara M, Abe T, Sawada D. Chemo- and Site-Selective Replacement of N-Terminal Carbamates in Peptides. Org Lett 2022; 24:2131-2136. [PMID: 35285651 DOI: 10.1021/acs.orglett.2c00370] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In peptide synthesis, it is important to distinguish the terminal amino group and carry out the selective transformation of only the N-terminal protecting group. We describe herein a reaction for the chemo- and site-selective replacement of carbamates with various other carbamates only at the N-terminus of peptides. We demonstrate the scope of carbamates and peptides and the introduction of fluorine into a peptide. This strategy is applicable to the late stage of peptide synthesis.
Collapse
Affiliation(s)
- Miho Ibara
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 7008530, Japan
| | - Takumi Abe
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 7008530, Japan
| | - Daisuke Sawada
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 7008530, Japan
| |
Collapse
|
13
|
Nagano M, Huang Y, Obexer R, Suga H. Chemical peptide macrolactonization via intramolecular
S
‐to‐
S
‐to‐
O
acyl transfer. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Masanobu Nagano
- Graduate School of Science The University of Tokyo Bunkyo‐ku Tokyo Japan
| | - Yichao Huang
- Graduate School of Science The University of Tokyo Bunkyo‐ku Tokyo Japan
| | - Richard Obexer
- Graduate School of Science The University of Tokyo Bunkyo‐ku Tokyo Japan
| | - Hiroaki Suga
- Graduate School of Science The University of Tokyo Bunkyo‐ku Tokyo Japan
| |
Collapse
|
14
|
Taresh AB, Hutton CA. Backbone thioamide directed macrocyclisation: lactam stapling of peptides. Org Biomol Chem 2022; 20:1488-1492. [PMID: 35103273 DOI: 10.1039/d1ob02461b] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A novel method for lactam stapling of Asp/Lys-containing peptides has been developed that does not require coupling agents. A backbone thioamide is incorporated at the N-terminal side of the aspartate residue. Ag(I)-promoted activation of the thioamide in the vicinity of the Asp carboxylate generates a cyclic isoimide intermediate that is trapped by the Lys amine to generate the macrolactam. This method is suitable for generation of i,i+2, i,i+3, and i,i+4-spaced lactam-bridged peptides.
Collapse
Affiliation(s)
- Ameer B Taresh
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Craig A Hutton
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia.
| |
Collapse
|
15
|
Shabani S, Wu Y, Ryan HG, Hutton CA. Progress and perspectives on directing group-assisted palladium-catalysed C-H functionalisation of amino acids and peptides. Chem Soc Rev 2021; 50:9278-9343. [PMID: 34254063 DOI: 10.1039/d0cs01441a] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Peptide modifications can unlock a variety of compounds with structural diversity and abundant biological activity. In nature, peptide modifications, such as functionalisation at the side-chain position of amino acids, are performed using post-translational modification enzymes or incorporation of unnatural amino acids. However, accessing these modifications remains a challenge for organic chemists. During the past decades, selective C-H activation/functionalisation has attracted considerable attention in synthetic organic chemistry as a pathway to peptide modification. Various directing group strategies have been discovered that assist selective C-H activation. In particular, bidentate directing groups that enable tuneable and reversible coordination are now recognised as one of the most efficient methods for the site-selective C-H activation and functionalisation of numerous families of organic compounds. Synthetic peptide chemists have harnessed bidentate directing group strategies for selective functionalisation of the β- and γ-positions of amino acids. This method has been expanded and recognised as an effective device for the late stage macrocyclisation and total synthesis of complex peptide natural products. In this review, we discuss various β-, γ-, and δ-C(sp3)-H bond functionalisation reactions of amino acids for the formation of C-X bonds with the aid of directing groups and their application in late-stage macrocyclisation and the total synthesis of complex peptide natural products.
Collapse
Affiliation(s)
- Sadegh Shabani
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, 3010, Australia.
| | | | | | | |
Collapse
|