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Li B, Parker J, Tong J, Kodadek T. Synthesis of Membrane-Permeable Macrocyclic Peptides via Imidazopyridinium Grafting. J Am Chem Soc 2024; 146:14633-14644. [PMID: 38752889 DOI: 10.1021/jacs.4c01920] [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: 05/30/2024]
Abstract
Macrocyclic peptides (MPs) are a class of compounds that have been shown to be particularly well suited for engaging difficult protein targets. However, their utility is limited by their generally poor cell permeability and bioavailability. Here, we report an efficient solid-phase synthesis of novel MPs by trapping a reversible intramolecular imine linkage with a 2-formyl- or 2-keto-pyridine to create an imidazopyridinium (IP+)-linked ring. This chemistry is useful for the creation of macrocycles of different sizes and geometries, including head-to-side and side-to-side chain configurations. Many of the IP+-linked MPs exhibit far better passive membrane permeability than expected for "beyond Rule of 5" molecules, in some cases exceeding that of much lower molecular weight, traditional drug molecules. We demonstrate that this chemistry is suitable for the creation of libraries of IP+-linked MPs and show that these libraries can be mined for protein ligands.
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Affiliation(s)
- Bo Li
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, Florida 33458, United States
| | - Joshua Parker
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, Florida 33458, United States
| | - Joel Tong
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, Florida 33458, United States
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2
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Liu Y, Lu X, Chen M, Wei Z, Peng G, Yang J, Tang C, Yu P. Advances in screening, synthesis, modification, and biomedical applications of peptides and peptide aptamers. Biofactors 2024; 50:33-57. [PMID: 37646383 DOI: 10.1002/biof.2001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
Peptides and peptide aptamers have emerged as promising molecules for a wide range of biomedical applications due to their unique properties and versatile functionalities. The screening strategies for identifying peptides and peptide aptamers with desired properties are discussed, including high-throughput screening, display screening technology, and in silico design approaches. The synthesis methods for the efficient production of peptides and peptide aptamers, such as solid-phase peptide synthesis and biosynthesis technology, are described, along with their advantages and limitations. Moreover, various modification techniques are explored to enhance the stability, specificity, and pharmacokinetic properties of peptides and peptide aptamers. This includes chemical modifications, enzymatic modifications, biomodifications, genetic engineering modifications, and physical modifications. Furthermore, the review highlights the diverse biomedical applications of peptides and peptide aptamers, including targeted drug delivery, diagnostics, and therapeutic. This review provides valuable insights into the advancements in screening, synthesis, modification, and biomedical applications of peptides and peptide aptamers. A comprehensive understanding of these aspects will aid researchers in the development of novel peptide-based therapeutics and diagnostic tools for various biomedical challenges.
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Affiliation(s)
- Yijie Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Xiaoling Lu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Meilun Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Zheng Wei
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Guangnan Peng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Jie Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Chunhua Tang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Peng Yu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
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3
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Synthesis and characterization of chemically fueled supramolecular materials driven by carbodiimide-based fuels. Nat Protoc 2021; 16:3901-3932. [PMID: 34194049 DOI: 10.1038/s41596-021-00563-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
Many supramolecular materials in biological systems are driven to a nonequilibrium state by the irreversible consumption of high-energy molecules such as ATP or GTP. As a result, they exhibit unique dynamic properties such as a tunable lifetime, adaptivity or the ability to self-heal. In contrast, synthetic counterparts that exist in or close to equilibrium are controlled by thermodynamic parameters and therefore lack these dynamic properties. To mimic biological materials more closely, synthetic self-assembling systems have been developed that are driven out of equilibrium by chemical reactions. This protocol describes the synthesis and characterization of such an assembly, which is driven by carbodiimide fuels. Depending on the amount of chemical fuel added to the material, its lifetime can be tuned. In the first step, the protocol details the synthesis and purification of the peptide-based precursors for the fuel-driven assemblies by solid-phase peptide synthesis. Then, we explain how to analyze the kinetic response of the precursors to a carbodiimide-based chemical fuel by HPLC and kinetic models. Finally, we detail how to study the emerging assembly's macro- and microscopic properties by time-lapse photography, UV-visible spectroscopy, shear rheology, confocal laser scanning microscopy and electron microscopy. The procedure is described using the example of a colloid-forming precursor Fmoc-E-OH and a fiber-forming precursor Fmoc-AAD-OH to emphasize the differences in characterization depending on the type of assembly. The characterization of a precursor's transient assembly can be done within 5 d. The synthesis and purification of a peptide precursor requires 2 d of work.
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Mothukuri GK, Kale SS, Stenbratt CL, Zorzi A, Vesin J, Bortoli Chapalay J, Deyle K, Turcatti G, Cendron L, Angelini A, Heinis C. Macrocycle synthesis strategy based on step-wise "adding and reacting" three components enables screening of large combinatorial libraries. Chem Sci 2020; 11:7858-7863. [PMID: 34094158 PMCID: PMC8163216 DOI: 10.1039/d0sc01944e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/25/2020] [Indexed: 02/04/2023] Open
Abstract
Macrocycles provide an attractive modality for drug development, but generating ligands for new targets is hampered by the limited availability of large macrocycle libraries. We have established a solution-phase macrocycle synthesis strategy in which three building blocks are coupled sequentially in efficient alkylation reactions that eliminate the need for product purification. We demonstrate the power of the approach by combinatorially reacting 15 bromoacetamide-activated tripeptides, 42 amines, and 6 bis-electrophile cyclization linkers to generate a 3780-compound library with minimal effort. Screening against thrombin yielded a potent and selective inhibitor (K i = 4.2 ± 0.8 nM) that efficiently blocked blood coagulation in human plasma. Structure-activity relationship and X-ray crystallography analysis revealed that two of the three building blocks acted synergistically and underscored the importance of combinatorial screening in macrocycle development. The three-component library synthesis approach is general and offers a promising avenue to generate macrocycle ligands to other targets.
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Affiliation(s)
- Ganesh K Mothukuri
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne Switzerland
| | - Sangram S Kale
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne Switzerland
| | - Carl L Stenbratt
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne Switzerland
| | - Alessandro Zorzi
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne Switzerland
| | - Jonathan Vesin
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne Switzerland
| | - Julien Bortoli Chapalay
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne Switzerland
| | - Kaycie Deyle
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne Switzerland
| | - Gerardo Turcatti
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne Switzerland
| | - Laura Cendron
- Department of Biology, University of Padova 35131 Padova Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice Via Torino 155, Venezia Mestre Venice 30172 Italy
- European Centre for Living Technology (ECLT), Ca' Bottacin Dorsoduro 3911, Calle Crosera Venice 30124 Italy
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne Switzerland
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Vasco AV, Méndez Y, Porzel A, Balbach J, Wessjohann LA, Rivera DG. A Multicomponent Stapling Approach to Exocyclic Functionalized Helical Peptides: Adding Lipids, Sugars, PEGs, Labels, and Handles to the Lactam Bridge. Bioconjug Chem 2018; 30:253-259. [DOI: 10.1021/acs.bioconjchem.8b00906] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Aldrin V. Vasco
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany
| | - Yanira Méndez
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany
- Center for Natural Products Research, Faculty of Chemistry, University of Havana, Zapata y G, Havana 10400, Cuba
| | - Andrea Porzel
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany
| | - Jochen Balbach
- Institute of Physics/Biophysics and Center for Structural and Dynamics of Proteins, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
| | - Ludger A. Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany
| | - Daniel G. Rivera
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany
- Center for Natural Products Research, Faculty of Chemistry, University of Havana, Zapata y G, Havana 10400, Cuba
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Angyal A, Demjén A, Wéber E, Kovács AK, Wölfling J, Puskás LG, Kanizsai I. Lewis Acid-Catalyzed Diastereoselective Synthesis of Multisubstituted N-Acylaziridine-2-carboxamides from 2H-Azirines via Joullié–Ugi Three-Component Reaction. J Org Chem 2018; 83:3570-3581. [DOI: 10.1021/acs.joc.7b03189] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Anikó Angyal
- AVIDIN Ltd., Alsó kikötő sor 11/D, Szeged H-6726, Hungary
- Department of Organic Chemistry, University of Szeged, Dóm tér 8, Szeged H-6720, Hungary
| | - András Demjén
- AVIDIN Ltd., Alsó kikötő sor 11/D, Szeged H-6726, Hungary
- Department of Organic Chemistry, University of Szeged, Dóm tér 8, Szeged H-6720, Hungary
| | - Edit Wéber
- SZTE-MTA Lendület Foldamer Research Group, Institute of Pharmaceutical Analysis, University of Szeged, Somogyi u. 4, Szeged H-6720, Hungary
| | - Anita K. Kovács
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, Szeged 6720, Hungary
| | - János Wölfling
- Department of Organic Chemistry, University of Szeged, Dóm tér 8, Szeged H-6720, Hungary
| | | | - Iván Kanizsai
- AVIDIN Ltd., Alsó kikötő sor 11/D, Szeged H-6726, Hungary
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Tangara S, Kanazawa A, Py S. The Baldwin Rearrangement: Synthesis of 2-Acylaziridines. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700920] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Salia Tangara
- Univ. Grenoble Alpes; DCM; CNRS; 38000 Grenoble France
| | | | - Sandrine Py
- Univ. Grenoble Alpes; DCM; CNRS; 38000 Grenoble France
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8
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Taskova M, Mantsiou A, Astakhova K. Synthetic Nucleic Acid Analogues in Gene Therapy: An Update for Peptide-Oligonucleotide Conjugates. Chembiochem 2017; 18:1671-1682. [PMID: 28614621 DOI: 10.1002/cbic.201700229] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Indexed: 12/29/2022]
Abstract
The main objective of this work is to provide an update on synthetic nucleic acid analogues and nanoassemblies as tools in gene therapy. In particular, the synthesis and properties of peptide-oligonucleotide conjugates (POCs), which have high potential in research and as therapeutics, are described in detail. The exploration of POCs has already led to fruitful results in the treatment of neurological diseases, lung disorders, cancer, leukemia, viral, and bacterial infections. However, delivery and in vivo stability are the major barriers to the clinical application of POCs and other analogues that still have to be overcome. This review summarizes recent achievements in the delivery and in vivo administration of synthetic nucleic acid analogues, focusing on POCs, and compares their efficiency.
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Affiliation(s)
- Maria Taskova
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Anna Mantsiou
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Kira Astakhova
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.,Technical University of Denmark, Department of Chemistry, Kemitorvet, 2800, Kongens Lyngby, Denmark
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