1
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Pascha M, Thijssen V, Egido JE, Linthorst MW, van Lanen JH, van Dongen DAA, Hopstaken AJP, van Kuppeveld FJM, Snijder J, de Haan CAM, Jongkees SAK. Inhibition of H1 and H5 Influenza A Virus Entry by Diverse Macrocyclic Peptides Targeting the Hemagglutinin Stem Region. ACS Chem Biol 2022; 17:2425-2436. [PMID: 35926224 PMCID: PMC9486808 DOI: 10.1021/acschembio.2c00040] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Influenza A viruses pose a serious pandemic risk, while generation of efficient vaccines against seasonal variants remains challenging. There is thus a pressing need for new treatment options. We report here a set of macrocyclic peptides that inhibit influenza A virus infection at low nanomolar concentrations by binding to hemagglutinin, selected using ultrahigh-throughput screening of a diverse peptide library. The peptides are active against both H1 and H5 variants, with no detectable cytotoxicity. Despite the high sequence diversity across hits, all tested peptides were found to bind to the same region in the hemagglutinin stem by HDX-MS epitope mapping. A mutation in this region identified in an escape variant confirmed the binding site. This stands in contrast to the immunodominance of the head region for antibody binding and suggests that macrocyclic peptides from in vitro display may be well suited for finding new druggable sites not revealed by antibodies. Functional analysis indicates that these peptides stabilize the prefusion conformation of the protein and thereby prevent virus-cell fusion. High-throughput screening of macrocyclic peptides is thus shown here to be a powerful method for the discovery of novel broadly acting viral fusion inhibitors with therapeutic potential.
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Affiliation(s)
- Mirte
N. Pascha
- Section
Virology, Division Infectious Diseases and Immunology, Department
of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584
CL Utrecht, The Netherlands
| | - Vito Thijssen
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Julia E. Egido
- Section
Virology, Division Infectious Diseases and Immunology, Department
of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584
CL Utrecht, The Netherlands,Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Mirte W. Linthorst
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jipke H. van Lanen
- Section
Virology, Division Infectious Diseases and Immunology, Department
of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584
CL Utrecht, The Netherlands
| | - David A. A. van Dongen
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Antonius J. P. Hopstaken
- Department
of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for
Molecular and Life Sciences, VU Amsterdam, de Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Frank J. M. van Kuppeveld
- Section
Virology, Division Infectious Diseases and Immunology, Department
of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584
CL Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Cornelis A. M. de Haan
- Section
Virology, Division Infectious Diseases and Immunology, Department
of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584
CL Utrecht, The Netherlands,
| | - Seino A. K. Jongkees
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands,Department
of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for
Molecular and Life Sciences, VU Amsterdam, de Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands,
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2
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McAllister TE, Coleman OD, Roper G, Kawamura A. Structural diversity in
de novo
cyclic peptide ligands from genetically encoded library technologies. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24204] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tom E. McAllister
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Oliver D. Coleman
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Grace Roper
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
- Chemistry Research Laboratory, Department of Chemistry University of Oxford Oxford UK
| | - Akane Kawamura
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
- Chemistry Research Laboratory, Department of Chemistry University of Oxford Oxford UK
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3
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Rogers JM. Peptide Folding and Binding Probed by Systematic Non-canonical Mutagenesis. Front Mol Biosci 2020; 7:100. [PMID: 32671094 PMCID: PMC7326784 DOI: 10.3389/fmolb.2020.00100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/04/2020] [Indexed: 12/20/2022] Open
Abstract
Many proteins and peptides fold upon binding another protein. Mutagenesis has proved an essential tool in the study of these multi-step molecular recognition processes. By comparing the biophysical behavior of carefully selected mutants, the concert of interactions and conformational changes that occur during folding and binding can be separated and assessed. Recently, this mutagenesis approach has been radically expanded by deep mutational scanning methods, which allow for many thousands of mutations to be examined in parallel. Furthermore, these high-throughput mutagenesis methods have been expanded to include mutations to non-canonical amino acids, returning peptide structure-activity relationships with unprecedented depth and detail. These developments are timely, as the insights they provide can guide the optimization of de novo cyclic peptides, a promising new modality for chemical probes and therapeutic agents.
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Affiliation(s)
- Joseph M Rogers
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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4
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Chao L, Jongkees S. High-Throughput Approaches in Carbohydrate-Active Enzymology: Glycosidase and Glycosyl Transferase Inhibitors, Evolution, and Discovery. Angew Chem Int Ed Engl 2019; 58:12750-12760. [PMID: 30913359 PMCID: PMC6771893 DOI: 10.1002/anie.201900055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/05/2019] [Indexed: 01/13/2023]
Abstract
Carbohydrates are attached and removed in living systems through the action of carbohydrate-active enzymes such as glycosyl transferases and glycoside hydrolases. The molecules resulting from these enzymes have many important roles in organisms, such as cellular communication, structural support, and energy metabolism. In general, each carbohydrate transformation requires a separate catalyst, and so these enzyme families are extremely diverse. To make this diversity manageable, high-throughput approaches look at many enzymes at once. Similarly, high-throughput approaches can be a powerful way of finding inhibitors that can be used to tune the reactivity of these enzymes, either in an industrial, a laboratory, or a medicinal setting. In this review, we provide an overview of how these enzymes and inhibitors can be sought using techniques such as high-throughput natural product and combinatorial library screening, phage and mRNA display of (glyco)peptides, fluorescence-activated cell sorting, and metagenomics.
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Affiliation(s)
- Lemeng Chao
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUniversiteitsweg 993581AGUtrechtThe Netherlands
| | - Seino Jongkees
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUniversiteitsweg 993581AGUtrechtThe Netherlands
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5
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Goldbach L, Vermeulen BJA, Caner S, Liu M, Tysoe C, van Gijzel L, Yoshisada R, Trellet M, van Ingen H, Brayer GD, Bonvin AMJJ, Jongkees SAK. Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase. ACS Chem Biol 2019; 14:1751-1759. [PMID: 31241898 PMCID: PMC6700688 DOI: 10.1021/acschembio.9b00290] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/26/2019] [Indexed: 12/14/2022]
Abstract
De novo macrocyclic peptides, derived using selection technologies such as phage and mRNA display, present unique and unexpected solutions to challenging biological problems. This is due in part to their unusual folds, which are able to present side chains in ways not available to canonical structures such as α-helices and β-sheets. Despite much recent interest in these molecules, their folding and binding behavior remains poorly characterized. In this work, we present cocrystallization, docking, and solution NMR structures of three de novo macrocyclic peptides that all bind as competitive inhibitors with single-digit nanomolar Ki to the active site of human pancreatic α-amylase. We show that a short stably folded motif in one of these is nucleated by internal hydrophobic interactions in an otherwise dynamic conformation in solution. Comparison of the solution structures with a target-bound structure from docking indicates that stabilization of the bound conformation is provided through interactions with the target protein after binding. These three structures also reveal a surprising functional convergence to present a motif of a single arginine sandwiched between two aromatic residues in the interactions of the peptide with the key catalytic residues of the enzyme, despite little to no other structural homology. Our results suggest that intramolecular hydrophobic interactions are important for priming binding of small macrocyclic peptides to their target and that high rigidity is not necessary for high affinity.
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Affiliation(s)
- Leander Goldbach
- NMR
Spectroscopy Research Group and Computational Structural Biology, Bijvoet Center for Biomolecular Research, Science
Faculty, Utrecht University, 3512 Utrecht, The Netherlands
| | - Bram J. A. Vermeulen
- NMR
Spectroscopy Research Group and Computational Structural Biology, Bijvoet Center for Biomolecular Research, Science
Faculty, Utrecht University, 3512 Utrecht, The Netherlands
| | - Sami Caner
- Department of Biochemistry and Molecular Biology, Centre for High-Throughput
Biology, and Department of
Chemistry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Minglong Liu
- Department
of Chemical Biology and Drug Discovery, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Christina Tysoe
- Department of Biochemistry and Molecular Biology, Centre for High-Throughput
Biology, and Department of
Chemistry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Lieke van Gijzel
- Department
of Chemical Biology and Drug Discovery, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Ryoji Yoshisada
- Department
of Chemical Biology and Drug Discovery, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Mikael Trellet
- NMR
Spectroscopy Research Group and Computational Structural Biology, Bijvoet Center for Biomolecular Research, Science
Faculty, Utrecht University, 3512 Utrecht, The Netherlands
| | - Hugo van Ingen
- NMR
Spectroscopy Research Group and Computational Structural Biology, Bijvoet Center for Biomolecular Research, Science
Faculty, Utrecht University, 3512 Utrecht, The Netherlands
| | - Gary D. Brayer
- Department of Biochemistry and Molecular Biology, Centre for High-Throughput
Biology, and Department of
Chemistry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Alexandre M. J. J. Bonvin
- NMR
Spectroscopy Research Group and Computational Structural Biology, Bijvoet Center for Biomolecular Research, Science
Faculty, Utrecht University, 3512 Utrecht, The Netherlands
| | - Seino A. K. Jongkees
- Department
of Chemical Biology and Drug Discovery, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
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6
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Chao L, Jongkees S. High‐Throughput Approaches in Carbohydrate‐Active Enzymology: Glycosidase and Glycosyl Transferase Inhibitors, Evolution, and Discovery. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Lemeng Chao
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3581AG Utrecht The Netherlands
| | - Seino Jongkees
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3581AG Utrecht The Netherlands
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