1
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Bolding JE, Nielsen AL, Jensen I, Hansen TN, Ryberg LA, Jameson ST, Harris P, Peters GHJ, Denu JM, Rogers JM, Olsen CA. Substrates and Cyclic Peptide Inhibitors of the Oligonucleotide-Activated Sirtuin 7. Angew Chem Int Ed Engl 2023; 62:e202314597. [PMID: 37873919 DOI: 10.1002/anie.202314597] [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: 09/29/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023]
Abstract
The sirtuins are NAD+ -dependent lysine deacylases, comprising seven isoforms (SIRT1-7) in humans, which are involved in the regulation of a plethora of biological processes, including gene expression and metabolism. The sirtuins share a common hydrolytic mechanism but display preferences for different ϵ-N-acyllysine substrates. SIRT7 deacetylates targets in nuclei and nucleoli but remains one of the lesser studied of the seven isoforms, in part due to a lack of chemical tools to specifically probe SIRT7 activity. Here we expressed SIRT7 and, using small-angle X-ray scattering, reveal SIRT7 to be a monomeric enzyme with a low degree of globular flexibility in solution. We developed a fluorogenic assay for investigation of the substrate preferences of SIRT7 and to evaluate compounds that modulate its activity. We report several mechanism-based SIRT7 inhibitors as well as de novo cyclic peptide inhibitors selected from mRNA-display library screening that exhibit selectivity for SIRT7 over other sirtuin isoforms, stabilize SIRT7 in cells, and cause an increase in the acetylation of H3 K18.
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Affiliation(s)
- Julie E Bolding
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Alexander L Nielsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
- Current address: Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Iben Jensen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - 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
| | - Line A Ryberg
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Current address: Department of Immunology and Microbiology, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Samuel T Jameson
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Pernille Harris
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Current address: Department of Chemistry, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Joseph M Rogers
- 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
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2
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Liu M, Morewood R, Yoshisada R, Pascha MN, Hopstaken AJP, Tarcoveanu E, Poole DA, de Haan CAM, Nitsche C, Jongkees SAK. Selective thiazoline peptide cyclisation compatible with mRNA display and efficient synthesis. Chem Sci 2023; 14:10561-10569. [PMID: 37799990 PMCID: PMC10548512 DOI: 10.1039/d3sc03117a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/06/2023] [Indexed: 10/07/2023] Open
Abstract
Peptide display technologies are a powerful method for discovery of new bioactive sequences, but linear sequences are often very unstable in a biological setting. Macrocyclisation of such peptides is beneficial for target affinity, selectivity, stability, and cell permeability. However, macrocyclisation of a linear hit is unreliable and requires extensive structural knowledge. Genetically encoding macrocyclisation during the discovery process is a better approach, and so there is a need for diverse cyclisation options that can be deployed in the context of peptide display techniques such as mRNA display. In this work we show that meta-cyanopyridylalanine (mCNP) can be ribosomally incorporated into peptides, forming a macrocycle in a spontaneous and selective reaction with an N-terminal cysteine generated from bypassing the initiation codon in translation. This reactive amino acid can also be easily incorporated into peptides during standard Fmoc solid phase peptide synthesis, which can otherwise be a bottleneck in transferring from peptide discovery to peptide testing and application. We demonstrate the potential of this new method by discovery of macrocyclic peptides targeting influenza haemagglutinin, and molecular dynamics simulation indicates the mCNP cross-link stabilises a beta sheet structure in a representative of the most abundant cluster of active hits. Cyclisation by mCNP is also shown to be compatible with thioether macrocyclisation at a second cysteine to form bicycles of different architectures, provided that cysteine placement reinforces selectivity, with this bicyclisation happening spontaneously and in a controlled manner during peptide translation. Our new approach generates macrocycles with a more rigid cross-link and with better control of regiochemistry when additional cysteines are present, opening these up for further exploitation in chemical modification of in vitro translated peptides, and so is a valuable addition to the peptide discovery toolbox.
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Affiliation(s)
- Minglong Liu
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Richard Morewood
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
| | - Ryoji Yoshisada
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - 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
| | - Antonius J P Hopstaken
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Eliza Tarcoveanu
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
| | - David A Poole
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam 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
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
| | - Seino A K Jongkees
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
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3
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Coleman OD, Macdonald J, Thomson B, Ward JA, Stubbs CJ, McAllister TE, Clark S, Amin S, Cao Y, Abboud MI, Zhang Y, Sanganee H, Huber KVM, Claridge TDW, Kawamura A. Cyclic peptides target the aromatic cage of a PHD-finger reader domain to modulate epigenetic protein function. Chem Sci 2023; 14:7136-7146. [PMID: 37416723 PMCID: PMC10321576 DOI: 10.1039/d2sc05944d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/15/2023] [Indexed: 07/08/2023] Open
Abstract
Plant homeodomain fingers (PHD-fingers) are a family of reader domains that can recruit epigenetic proteins to specific histone modification sites. Many PHD-fingers recognise methylated lysines on histone tails and play crucial roles in transcriptional regulation, with their dysregulation linked to various human diseases. Despite their biological importance, chemical inhibitors for targeting PHD-fingers are very limited. Here we report a potent and selective de novo cyclic peptide inhibitor (OC9) targeting the Nε-trimethyllysine-binding PHD-fingers of the KDM7 histone demethylases, developed using mRNA display. OC9 disrupts PHD-finger interaction with histone H3K4me3 by engaging the Nε-methyllysine-binding aromatic cage through a valine, revealing a new non-lysine recognition motif for the PHD-fingers that does not require cation-π interaction. PHD-finger inhibition by OC9 impacted JmjC-domain mediated demethylase activity at H3K9me2, leading to inhibition of KDM7B (PHF8) but stimulation of KDM7A (KIAA1718), representing a new approach for selective allosteric modulation of demethylase activity. Chemoproteomic analysis showed selective engagement of OC9 with KDM7s in T cell lymphoblastic lymphoma SUP T1 cells. Our results highlight the utility of mRNA-display derived cyclic peptides for targeting challenging epigenetic reader proteins to probe their biology, and the broader potential of this approach for targeting protein-protein interactions.
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Affiliation(s)
- Oliver D Coleman
- School of Natural and Environmental Sciences - Chemistry, Newcastle University Newcastle NE1 7RU UK
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford Roosevelt Drive Old Road Campus Oxford OX3 7BN UK
| | - Jessica Macdonald
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Ben Thomson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Jennifer A Ward
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Old Road Campus Oxford OX3 7FZ UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford Oxford OX3 7FZ UK
| | - Christopher J Stubbs
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Cambridge CB4 0WG UK
| | - Tom E McAllister
- School of Natural and Environmental Sciences - Chemistry, Newcastle University Newcastle NE1 7RU UK
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford Roosevelt Drive Old Road Campus Oxford OX3 7BN UK
| | - Shane Clark
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Siddique Amin
- School of Natural and Environmental Sciences - Chemistry, Newcastle University Newcastle NE1 7RU UK
| | - Yimang Cao
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Martine I Abboud
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Yijia Zhang
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Hitesh Sanganee
- Emerging Innovations Unit, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - Kilian V M Huber
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Old Road Campus Oxford OX3 7FZ UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford Oxford OX3 7FZ UK
| | - Tim D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Akane Kawamura
- School of Natural and Environmental Sciences - Chemistry, Newcastle University Newcastle NE1 7RU UK
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford Roosevelt Drive Old Road Campus Oxford OX3 7BN UK
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4
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Franco HEO, Le AV, Chang NY, Hartman MCT. p-Chloropropynyl Phenylalanine, a Versatile Non-Canonical Amino Acid for Co-Translational Peptide Macrocyclization and Side Chain Diversification. Chembiochem 2023; 24:e202300020. [PMID: 37156744 PMCID: PMC11165969 DOI: 10.1002/cbic.202300020] [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: 01/11/2023] [Revised: 04/07/2023] [Indexed: 05/10/2023]
Abstract
Macrocyclization has proven to be a beneficial strategy to improve upon some of the disadvantages of peptides as therapeutics. Nevertheless, many peptide cyclization strategies are not compatible with in vitro display technologies like mRNA display. Here we describe the novel amino acid p-chloropropynyl phenylalanine (pCPF). pCPF is a substrate for a mutant phenylalanyl-tRNA synthetase and its introduction into peptides via in vitro translation leads to spontaneous peptide macrocyclization in the presence of peptides containing cysteine. Macrocyclization occurs efficiently with a wide variety of ring sizes. Moreover, pCPF can be reacted with thiols after charging onto tRNA, enabling the testing of diverse ncAAs in translation. The versatility of pCPF should facilitate downstream studies of translation and enable the creation of novel macrocyclic peptide libraries.
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Affiliation(s)
- H. Estheban Osorio Franco
- Chemistry, Virginia Commonwealth University, 1001 W Main St, Richmond, 23284, VA
- Massey Cancer Center, Virginia Commonwealth University
| | - Anthony V. Le
- Chemistry, Virginia Commonwealth University, 1001 W Main St, Richmond, 23284, VA
- Massey Cancer Center, Virginia Commonwealth University
| | - Nathan Y. Chang
- Chemistry, Virginia Commonwealth University, 1001 W Main St, Richmond, 23284, VA
- Massey Cancer Center, Virginia Commonwealth University
| | - Matthew C. T. Hartman
- Chemistry, Virginia Commonwealth University, 1001 W Main St, Richmond, 23284, VA
- Massey Cancer Center, Virginia Commonwealth University
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5
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Liu M, Yoshisada R, Amedi A, Hopstaken AJP, Pascha MN, de Haan CAM, Geerke DP, Poole DA, Jongkees SAK. An Efficient, Site-Selective and Spontaneous Peptide Macrocyclisation During in vitro Translation. Chemistry 2023; 29:e202203923. [PMID: 36529683 DOI: 10.1002/chem.202203923] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]
Abstract
Macrocyclisation provides a means of stabilising the conformation of peptides, often resulting in improved stability, selectivity, affinity, and cell permeability. In this work, a new approach to peptide macrocyclisation is reported, using a cyanobenzothiazole-containing amino acid that can be incorporated into peptides by both in vitro translation and solid phase peptide synthesis, meaning it should be applicable to peptide discovery by mRNA display. This cyclisation proceeds rapidly, with minimal by-products, is selective over other amino acids including non N-terminal cysteines, and is compatible with further peptide elaboration exploiting such an additional cysteine in bicyclisation and derivatisation reactions. Molecular dynamics simulations show that the new cyclisation group is likely to influence the peptide conformation as compared to previous thioether-based approaches, through rigidity and intramolecular aromatic interactions, illustrating their complementarity.
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Affiliation(s)
- Minglong Liu
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - Ryoji Yoshisada
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - Avand Amedi
- Department Chemical Biology and Drug Discovery and Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, 3584 CG, the Netherlands
| | - Antonius J P Hopstaken
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - Mirte N Pascha
- Section Virology Division of Infectious Diseases and Immunology Department of Biomolecular Health Sciences Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL, the Netherlands
| | - Cornelis A M de Haan
- Section Virology Division of Infectious Diseases and Immunology Department of Biomolecular Health Sciences Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL, the Netherlands
| | - Daan P Geerke
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - David A Poole
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - Seino A K Jongkees
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands.,Department Chemical Biology and Drug Discovery and Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, 3584 CG, the Netherlands
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6
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Kuroda T, Huang Y, Nishio S, Goto Y, Suga H. Post-translational backbone-acyl shift yields natural product-like peptides bearing hydroxyhydrocarbon units. Nat Chem 2022; 14:1413-1420. [PMID: 36329180 DOI: 10.1038/s41557-022-01065-1] [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: 09/09/2021] [Accepted: 08/09/2022] [Indexed: 11/06/2022]
Abstract
Hydroxyhydrocarbon (Hhc) moieties in the backbone of peptidic natural products can exert a substantial influence on the bioactivities of the products, making Hhc units an attractive class of building blocks for de novo peptides. However, despite advances in in vitro genetic code reprogramming, the ribosomal incorporation of Hhc units remains challenging. Here we report a method for in vitro ribosomal synthesis of natural-product-like peptides bearing Hhc units. A series of azide/hydroxy acids were designed as chemical precursors of Hhc units and incorporated into the nascent peptide chain by means of genetic code reprogramming. Post-translational reduction of the azide induced an O-to-N acyl shift to rearrange the peptide backbone. This method allows for one-pot ribosomal synthesis of designer macrocycles bearing various β-, γ- and δ-type Hhc units. We also report the synthesis of a statine-containing peptidomimetic inhibitor of β-secretase 1 as a showcase example.
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Affiliation(s)
- Tomohiro Kuroda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Yichao Huang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Soichiro Nishio
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan.
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7
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Wakabayashi R, Kawai M, Katoh T, Suga H. In Vitro Selection of Macrocyclic α/β 3-Peptides against Human EGFR. J Am Chem Soc 2022; 144:18504-18510. [PMID: 36173923 PMCID: PMC9563295 DOI: 10.1021/jacs.2c07624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Indexed: 11/30/2022]
Abstract
Here, we report ribosomal construction of thioether-macrocyclic α/β3-peptide libraries in which β-homoglycine, β-homoalanine, β-homophenylglycine, and β-homoglutamine are introduced by genetic code reprogramming. The libraries were applied to the RaPID (Random nonstandard Peptides Integrated Discovery) selection against human EGFR to obtain PPI (protein-protein interaction) inhibitors. The resulting peptides contained up to five β3-amino acid (β3AA) residues and exhibited outstanding binding affinity, PPI inhibitory activity, and proteolytic stability, which were attributed to the β3AAs included in the peptides. This showcase work has demonstrated that the use of such β3AAs enhances the drug-like properties of peptides, providing a unique platform for the discovery of de novo macrocycles against a protein of interest.
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Affiliation(s)
- Risa Wakabayashi
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Marina Kawai
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- 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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8
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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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9
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Goto Y, Suga H. The RaPID Platform for the Discovery of Pseudo-Natural Macrocyclic Peptides. Acc Chem Res 2021; 54:3604-3617. [PMID: 34505781 DOI: 10.1021/acs.accounts.1c00391] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Although macrocyclic peptides bearing exotic building blocks have proven their utility as pharmaceuticals, the sources of macrocyclic peptide drugs have been largely limited to mimetics of native peptides or natural product peptides. However, the recent emergence of technologies for discovering de novo bioactive peptides has led to their reconceptualization as a promising therapeutic modality. For the construction and screening of libraries of such macrocyclic peptides, our group has devised a platform to conduct affinity-based selection of massive libraries (>1012 unique sequences) of in vitro expressed macrocyclic peptides, which is referred to as the random nonstandard peptides integrated discovery (RaPID) system. The RaPID system integrates genetic code reprogramming using the FIT (flexible in vitro translation) system, which is largely facilitated by flexizymes (flexible tRNA-aminoacylating ribozymes), with mRNA display technology.We have demonstrated that the RaPID system enables rapid discovery of various de novo pseudo-natural peptide ligands for protein targets of interest. Many examples discussed in this Account prove that thioether-closed macrocyclic peptides (teMPs) obtained by the RaPID system generally exhibit remarkably high affinity and specificity, thereby potently inhibiting or activating a specific function(s) of the target. Moreover, such teMPs are used for a wide range of biochemical applications, for example, as crystallization chaperones for intractable transmembrane proteins and for in vivo recognition of specific cell types. Furthermore, recent studies demonstrate that some teMPs exhibit pharmacological activities in animal models and that even intracellular proteins can be inhibited by teMPs, illustrating the potential of this class of peptides as drug leads.Besides the ring-closing thioether linkage in the teMPs, genetic code reprogramming by the FIT system allows for incorporation of a variety of other exotic building blocks. For instance, diverse nonproteinogenic amino acids, hydroxy acids (ester linkage), amino carbothioic acid (thioamide linkage), and abiotic foldamer units have been successfully incorporated into ribosomally synthesized peptides. Despite such enormous successes in the conventional FIT system, multiple or consecutive incorporation of highly exotic amino acids, such as d- and β-amino acids, is yet challenging, and particularly the synthesis of peptides bearing non-carbonyl backbone structures remains a demanding task. To upgrade the RaPID system to the next generation, we have engaged in intensive manipulation of the FIT system to expand the structural diversity of peptides accessible by our in vitro biosynthesis strategy. Semilogical engineering of tRNA body sequences led to a new suppressor tRNA (tRNAPro1E2) capable of effectively recruiting translation factors, particularly EF-Tu and EF-P. The use of tRNAPro1E2 in the FIT system allows for not only single but also consecutive and multiple elongation of exotic amino acids, such as d-, β-, and γ-amino acids as well as aminobenzoic acids. Moreover, the integration of the FIT system with various chemical or enzymatic posttranslational modifications enables us to expand the range of accessible backbone structures to non-carbonyl moieties prominent in natural products and peptidomimetics. In such systems, FIT-expressed peptides undergo multistep backbone conversions in a one-pot manner to yield designer peptides composed of modified backbones such as azolines, azoles, and ring-closing pyridines. Our current research endeavors focus on applying such in vitro biosynthesis systems for the discovery of bioactive de novo pseudo-natural products.
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Affiliation(s)
- Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
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10
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Imanishi S, Katoh T, Yin Y, Yamada M, Kawai M, Suga H. In Vitro Selection of Macrocyclic d/l-Hybrid Peptides against Human EGFR. J Am Chem Soc 2021; 143:5680-5684. [PMID: 33822597 DOI: 10.1021/jacs.1c02593] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
d/l-Hybrid peptides are an attractive class of molecular modality because they are able to exhibit high proteolytic stability and unique structural diversity which cannot be accessed by those consisting of only proteinogenic l-amino acids. Despite such an expectation, it has not been possible to devise de novo d/l-hybrid peptides capable of disrupting the function of a protein target(s) due to the lack of an effective method that reliably constructs a highly diverse library and screens active species. Here we report for the first time construction of a library consisting of 1012 members of macrocyclic d/l-hybrid peptides containing five kinds of d-amino acids and performance of the RaPID selection against human EGFR as a showcase to uncover PPI (protein-protein interaction) inhibitors.
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Affiliation(s)
- Sayaka Imanishi
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yizhen Yin
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mituhiro Yamada
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Marina Kawai
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- 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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11
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Small and Simple, yet Sturdy: Conformationally Constrained Peptides with Remarkable Properties. Int J Mol Sci 2021; 22:ijms22041611. [PMID: 33562633 PMCID: PMC7915549 DOI: 10.3390/ijms22041611] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/20/2022] Open
Abstract
The sheer size and vast chemical space (i.e., diverse repertoire and spatial distribution of functional groups) underlie peptides’ ability to engage in specific interactions with targets of various structures. However, the inherent flexibility of the peptide chain negatively affects binding affinity and metabolic stability, thereby severely limiting the use of peptides as medicines. Imposing conformational constraints to the peptide chain offers to solve these problems but typically requires laborious structure optimization. Alternatively, libraries of constrained peptides with randomized modules can be screened for specific functions. Here, we present the properties of conformationally constrained peptides and review rigidification chemistries/strategies, as well as synthetic and enzymatic methods of producing macrocyclic peptides. Furthermore, we discuss the in vitro molecular evolution methods for the development of constrained peptides with pre-defined functions. Finally, we briefly present applications of selected constrained peptides to illustrate their exceptional properties as drug candidates, molecular recognition probes, and minimalist catalysts.
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12
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Dotter H, Boll M, Eder M, Eder AC. Library and post-translational modifications of peptide-based display systems. Biotechnol Adv 2021; 47:107699. [PMID: 33513435 DOI: 10.1016/j.biotechadv.2021.107699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 01/04/2021] [Accepted: 01/14/2021] [Indexed: 12/27/2022]
Abstract
Innovative biotechnological methods empower the successful identification of new drug candidates. Phage, ribosome and mRNA display represent high throughput screenings, allowing fast and efficient progress in the field of targeted drug discovery. The identification range comprises low molecular weight peptides up to whole antibodies. However, a major challenge poses the stability and affinity in particular of peptides. Chemical modifications e.g. the introduction of unnatural amino acids or cyclization, have been proven to be essential tools to overcome these limitations. This review article particularly focuses on available methods for the targeted chemical modification of peptides and peptide libraries in selected display approaches.
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Affiliation(s)
- Hanna Dotter
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Melanie Boll
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Matthias Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Ann-Christin Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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13
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Iskandar SE, Haberman VA, Bowers AA. Expanding the Chemical Diversity of Genetically Encoded Libraries. ACS COMBINATORIAL SCIENCE 2020; 22:712-733. [PMID: 33167616 PMCID: PMC8284915 DOI: 10.1021/acscombsci.0c00179] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The power of ribosomes has increasingly been harnessed for the synthesis and selection of molecular libraries. Technologies, such as phage display, yeast display, and mRNA display, effectively couple genotype to phenotype for the molecular evolution of high affinity epitopes for many therapeutic targets. Genetic code expansion is central to the success of these technologies, allowing researchers to surpass the intrinsic capabilities of the ribosome and access new, genetically encoded materials for these selections. Here, we review techniques for the chemical expansion of genetically encoded libraries, their abilities and limits, and opportunities for further development. Importantly, we also discuss methods and metrics used to assess the efficiency of modification and library diversity with these new techniques.
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Affiliation(s)
- Sabrina E Iskandar
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Victoria A Haberman
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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14
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Liu M, Thijssen V, Jongkees SAK. Suppression of Formylation Provides an Alternative Approach to Vacant Codon Creation in Bacterial In Vitro Translation. Angew Chem Int Ed Engl 2020; 59:21870-21874. [PMID: 32840944 PMCID: PMC7756408 DOI: 10.1002/anie.202003779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/04/2020] [Indexed: 11/22/2022]
Abstract
Genetic code reprogramming is a powerful approach to controlled protein modification. A remaining challenge, however, is the generation of vacant codons. We targeted the initiation machinery of E. coli, showing that restriction of the formyl donor or inhibition of the formyl transferase during in vitro translation is sufficient to prevent formylation of the acylated initiating tRNA and thereby create a vacant initiation codon that can be reprogrammed by exogenously charged tRNA. Our approach conveniently generates peptides and proteins tagged N‐terminally with non‐canonical functional groups at up to 99 % reprogramming efficiency, in combination with decoding the AUG elongation codons either with native methionine or with further reprogramming with azide‐ and alkyne‐containing cognates. We further show macrocyclization and intermolecular modifications with these click handles, thus emphasizing the applicability of our method to current challenges in peptide and protein chemistry.
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Affiliation(s)
- Minglong Liu
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| | - Vito Thijssen
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| | - Seino A K Jongkees
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
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15
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Liu M, Thijssen V, Jongkees SAK. Suppression of Formylation Provides an Alternative Approach to Vacant Codon Creation in Bacterial In Vitro Translation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Minglong Liu
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3584CG Utrecht The Netherlands
| | - Vito Thijssen
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3584CG Utrecht The Netherlands
| | - Seino A. K. Jongkees
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3584CG Utrecht The Netherlands
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16
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Okuma R, Kuwahara T, Yoshikane T, Watanabe M, Dranchak P, Inglese J, Shuto S, Goto Y, Suga H. A Macrocyclic Peptide Library with a Structurally Constrained Cyclopropane-containing Building Block Leads to Thiol-independent Inhibitors of Phosphoglycerate Mutase. Chem Asian J 2020; 15:2631-2636. [PMID: 32633882 DOI: 10.1002/asia.202000700] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/04/2020] [Indexed: 01/20/2023]
Abstract
Here we report the construction of an mRNA-encoded library of thioether-closed macrocyclic peptides by using an N-chloroacetyl-cyclopropane-containing exotic initiator whose structure is more constrained than the ordinary N-chloroacetyl-α-amino acid initiators. The use of such an initiator has led to a macrocycle library with significantly suppressed population of lariat-shaped species compared with the conventional libraries. We previously used a conventional library and identified a small lariat thioether-macrocycle with a tail peptide with a C-terminal free Cys whose sidechain plays an essential role in potent inhibitory activity against a parasitic model enzyme, phosphoglycerate mutase. On the other hand, the cyclopropane-containing macrocycle library has yielded a larger thioether-macrocycle lacking a free Cys residue, which exhibits potent inhibitory activity to the same enzyme with a different mode of action. This result indicates that such a cyclopropane-containing macrocycle library would allow us to access mechanistically distinct macrocycles.
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Affiliation(s)
- Rika Okuma
- Department of Chemistry Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Tomoki Kuwahara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Takafumi Yoshikane
- Department of Chemistry Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Mizuki Watanabe
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Patricia Dranchak
- Division of Preclinical Innovation National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - James Inglese
- Division of Preclinical Innovation National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Yuki Goto
- Department of Chemistry Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
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17
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Abstract
Approximately 75% of all disease-relevant human proteins, including those involved in intracellular protein-protein interactions (PPIs), are undruggable with the current drug modalities (i.e., small molecules and biologics). Macrocyclic peptides provide a potential solution to these undruggable targets because their larger sizes (relative to conventional small molecules) endow them the capability of binding to flat PPI interfaces with antibody-like affinity and specificity. Powerful combinatorial library technologies have been developed to routinely identify cyclic peptides as potent, specific inhibitors against proteins including PPI targets. However, with the exception of a very small set of sequences, the vast majority of cyclic peptides are impermeable to the cell membrane, preventing their application against intracellular targets. This Review examines common structural features that render most cyclic peptides membrane impermeable, as well as the unique features that allow the minority of sequences to enter the cell interior by passive diffusion, endocytosis/endosomal escape, or other mechanisms. We also present the current state of knowledge about the molecular mechanisms of cell penetration, the various strategies for designing cell-permeable, biologically active cyclic peptides against intracellular targets, and the assay methods available to quantify their cell-permeability.
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Affiliation(s)
- Patrick G. Dougherty
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
| | - Ashweta Sahni
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
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18
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Cui Z, Wu Y, Mureev S, Alexandrov K. Oligonucleotide-mediated tRNA sequestration enables one-pot sense codon reassignment in vitro. Nucleic Acids Res 2019; 46:6387-6400. [PMID: 29846683 PMCID: PMC6158751 DOI: 10.1093/nar/gky365] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 04/26/2018] [Indexed: 12/17/2022] Open
Abstract
Sense codon reassignment to unnatural amino acids (uAAs) represents a powerful approach for introducing novel properties into polypeptides. The main obstacle to this approach is competition between the native isoacceptor tRNA(s) and orthogonal tRNA(s) for the reassigned codon. While several chromatographic and enzymatic procedures for selective deactivation of tRNA isoacceptors in cell-free translation systems exist, they are complex and not scalable. We designed a set of tRNA antisense oligonucleotides composed of either deoxy-, ribo- or 2′-O-methyl ribonucleotides and tested their ability to efficiently complex tRNAs of choice. Methylated oligonucleotides targeting sequence between the anticodon and variable loop of tRNASerGCU displayed subnanomolar binding affinity with slow dissociation kinetics. Such oligonucleotides efficiently and selectively sequestered native tRNASerGCU directly in translation-competent Escherichia coli S30 lysate, thereby, abrogating its translational activity and liberating the AGU/AGC codons. Expression of eGFP protein from the template harboring a single reassignable AGU codon in tRNASerGCU-depleted E. coli lysate allowed its homogeneous modification with n-propargyl-l-lysine or p-azido-l-phenylalanine. The strategy developed here is generic, as demonstrated by sequestration of tRNAArgCCU isoacceptor in E. coli translation system. Furthermore, this method is likely to be species-independent and was successfully applied to the eukaryotic Leishmania tarentolae in vitro translation system. This approach represents a new direction in genetic code reassignment with numerous practical applications.
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Affiliation(s)
- Zhenling Cui
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Yue Wu
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Sergey Mureev
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Kirill Alexandrov
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia.,Australian Institute for Bioengeneering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
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19
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Yin Y, Fei Q, Liu W, Li Z, Suga H, Wu C. Chemical and Ribosomal Synthesis of Topologically Controlled Bicyclic and Tricyclic Peptide Scaffolds Primed by Selenoether Formation. Angew Chem Int Ed Engl 2019; 58:4880-4885. [PMID: 30762292 DOI: 10.1002/anie.201813827] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/11/2019] [Indexed: 12/31/2022]
Abstract
Bicyclic and tricyclic peptides have emerged as promising candidates for the development of protein binders and new therapeutics. However, convenient and efficient strategies that can generate topologically controlled bicyclic and tricyclic peptide scaffolds from fully-unprotected peptides are still much in demand, particularly for those amenable to the design of biosynthetic libraries. In this work, we report a reliable chemical and ribosomal synthesis of topologically controlled bicyclic and tricyclic peptide scaffolds. Our strategy involves the combination of selenoether cyclization followed by disulfide or thioether cyclization, yielding desirable bicyclic and tricyclic peptides. This work thus lays the foundation for developing peptide libraries with controlled topology of multicyclic scaffolds for in vitro display techniques.
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Affiliation(s)
- Yizhen Yin
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Qianran Fei
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surface, Xiamen University, Xiamen, 361005, P. R. China
| | - Weidong Liu
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surface, Xiamen University, Xiamen, 361005, P. R. China
| | - Zhuoru Li
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surface, Xiamen University, Xiamen, 361005, P. R. China
| | - Hiroaki Suga
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Chuanliu Wu
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surface, Xiamen University, Xiamen, 361005, P. R. China
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20
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Yin Y, Fei Q, Liu W, Li Z, Suga H, Wu C. Chemical and Ribosomal Synthesis of Topologically Controlled Bicyclic and Tricyclic Peptide Scaffolds Primed by Selenoether Formation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yizhen Yin
- Department of ChemistrySchool of ScienceThe University of Tokyo 7-3-1 Hongo Bunkyo Tokyo 113-0033 Japan
| | - Qianran Fei
- Department of ChemistryCollege of Chemistry and Chemical EngineeringThe MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid SurfaceXiamen University Xiamen 361005 P. R. China
| | - Weidong Liu
- Department of ChemistryCollege of Chemistry and Chemical EngineeringThe MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid SurfaceXiamen University Xiamen 361005 P. R. China
| | - Zhuoru Li
- Department of ChemistryCollege of Chemistry and Chemical EngineeringThe MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid SurfaceXiamen University Xiamen 361005 P. R. China
| | - Hiroaki Suga
- Department of ChemistrySchool of ScienceThe University of Tokyo 7-3-1 Hongo Bunkyo Tokyo 113-0033 Japan
| | - Chuanliu Wu
- Department of ChemistryCollege of Chemistry and Chemical EngineeringThe MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid SurfaceXiamen University Xiamen 361005 P. R. China
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21
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Tsiamantas C, Otero-Ramirez ME, Suga H. Discovery of Functional Macrocyclic Peptides by Means of the RaPID System. Methods Mol Biol 2019; 2001:299-315. [PMID: 31134577 DOI: 10.1007/978-1-4939-9504-2_14] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Flexizymes, highly flexible tRNA aminoacylation ribozymes, have enabled charging of virtually any amino acid (including non-proteogenic ones) onto tRNA molecules. Coupling to a custom-made in vitro translation system, namely the flexible in vitro translation (FIT) system, has unveiled the remarkable tolerance of the ribosome toward molecules, remote from what nature has selected to carry out its elaborate functions. Among the very diverse molecules and chemistries that have been ribosomally incorporated, a plethora of entities capable of mediating intramolecular cyclization have revolutionized the design and discovery of macrocyclic peptides. These macrocyclization reactions (which can be spontaneous, chemical, or enzymatic) have all served as tools for the discovery of peptides with natural-like structures and properties. Coupling of the FIT system and mRNA display techniques, known as the random non-standard peptide integrated discovery (RaPID) system, has in turn allowed for the simultaneous screening of trillions of macrocyclic peptides against challenging biological targets. The macrocyclization methodologies are chosen depending on the structural and functional characteristics of the desired molecule. Thus, they can emanate from the peptide's N-terminus or its side chains, attributing flexibility or rigidity, or even result in the installation of fluorescent probes.
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Affiliation(s)
- Christos Tsiamantas
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Manuel E Otero-Ramirez
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan.
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22
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Huang Y, Wiedmann MM, Suga H. RNA Display Methods for the Discovery of Bioactive Macrocycles. Chem Rev 2018; 119:10360-10391. [PMID: 30395448 DOI: 10.1021/acs.chemrev.8b00430] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The past two decades have witnessed the emergence of macrocycles, including macrocyclic peptides, as a promising yet underexploited class of de novo drug candidates. Both rational/computational design and in vitro display systems have contributed tremendously to the development of cyclic peptide binders of either traditional targets such as cell-surface receptors and enzymes or challenging targets such as protein-protein interaction surfaces. mRNA display, a key platform technology for the discovery of cyclic peptide ligands, has become one of the leading strategies that can generate natural-product-like macrocyclic peptide binders with antibody-like affinities. On the basis of the original cell-free transcription/translation system, mRNA display is highly evolvable to realize its full potential by applying genetic reprogramming and chemical/enzymatic modifications. In addition, mRNA display also allows the follow-up hit-to-lead development using high-throughput focused affinity maturation. Finally, mRNA-displayed peptides can be readily engineered to create chemical conjugates based on known small molecules or biologics. This review covers the birth and growth of mRNA display and discusses the above features of mRNA display with success stories and future perspectives and is up to date as of August 2018.
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Affiliation(s)
- Yichao Huang
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Mareike Margarete Wiedmann
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Hiroaki Suga
- 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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23
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Abstract
With the increasing utilization of high-throughput screening for lead identification in drug discovery, the need for easily constructed and diverse libraries which cover significant chemical space is greater than ever. Cyclic peptides address this need; they combine the advantageous properties of peptides (ease of production, high diversity, high potential specificity) with increased resistance to proteolysis and often increased biological activity (due to conformational locking). There are a number of techniques for the generation and screening of cyclic peptide libraries. As drug discovery moves toward tackling challenging targets, such as protein-protein interactions, cyclic peptide libraries are expected to continue producing hits where small molecule libraries may be stymied. However, it is important to design robust systems for the generation and screening of these large libraries, and to be able to make sense of structure-activity relationships in these highly variable scaffolds. There are a plethora of possible modifications that can be made to cyclic peptides, which is both a weakness and a strength of these scaffolds; high variability will allow more precise tuning of leads to targets, but exploring the whole range of modifications may become an overwhelming challenge.
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24
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Passioura T, Suga H. A RaPID way to discover nonstandard macrocyclic peptide modulators of drug targets. Chem Commun (Camb) 2018; 53:1931-1940. [PMID: 28091672 DOI: 10.1039/c6cc06951g] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Studies of the fundamental nature of RNA catalysis and the potential mechanism of a shift from the "RNA world" to proteinaceous life lead us to identify a set of ribozymes (flexizymes) capable of promiscuous tRNA acylation. Whilst theoretically and mechanistically interesting in their own right, flexizymes have turned out to have immense practical value for the simple synthesis of tRNAs acylated with unusual amino acids, which in turn can be used for the ribosomal synthesis of peptides containing non-canonical residues. Using this technique, it is possible to synthesise peptides containing a range of structural features (macrocyclic backbones, backbone N-methylation, d-stereochemistry, etc.) commonly observed in natural product secondary metabolites, a chemical class that has historically been a rich source of drug-like molecules. Moreover, when combined with biochemical display screening technologies, this synthetic approach can be used to generate (and screen for target affinity) extremely diverse (in excess of 1012 compound) chemical libraries, making it an extraordinary tool for drug discovery. The current review charts the history of flexizyme technology and its use for non-canonical peptide synthesis and screening.
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Affiliation(s)
- Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan. and Japan Science and Technology Agency (JST), Core Research for Evolutionary Science and Technology (CREST), Saitama 332-0012, Japan
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25
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Goto Y, Suga H. ArtificialIn VitroBiosynthesis Systems for the Development of Pseudo-Natural Products. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20170379] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
- JST-PRESTO, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
- JST-CREST, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
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26
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Suga H. Max-Bergmann award lecture:A RaPID way to discover bioactive nonstandard peptides assisted by the flexizyme and FIT systems. J Pept Sci 2018; 24. [DOI: 10.1002/psc.3055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 10/10/2017] [Accepted: 10/11/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Hiroaki Suga
- Department of Chemistry, Graduate School of Science; Tokyo; The University of Tokyo; Japan
- JST-CREST; 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
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27
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Yoshisada R, van Gijzel L, Jongkees SAK. Towards Tuneable Retaining Glycosidase-Inhibiting Peptides by Mimicry of a Plant Flavonol Warhead. Chembiochem 2017; 18:2333-2339. [PMID: 28984404 DOI: 10.1002/cbic.201700457] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Indexed: 11/06/2022]
Abstract
Retaining glycosidases are an important class of enzymes involved in glycan degradation. To study better the role of specific enzymes in deglycosylation processes, and thereby the importance of particular glycosylation patterns, a set of potent inhibitors, each specific to a particular glycosidase, would be an invaluable toolkit. Towards this goal, we detail here a more in-depth study of a prototypical macrocyclic peptide inhibitor of the model retaining glycosidase human pancreatic α-amylase (HPA). Notably, incorporation of l-DOPA into this peptide affords an inhibitor of HPA with potency that is tenfold higher (Ki =480 pm) than that of the previously found consensus sequence. This represents a first successful step in converting a recently discovered natural-product-derived motif, already specific for the catalytic side-chain arrangement conserved in the active sites of retaining glycosidases, into a tuneable retaining glycosidase inhibition warhead.
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Affiliation(s)
- Ryoji Yoshisada
- Department of Chemical Biology and Drug Discovery, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, Utrecht, 3584CG, The Netherlands
| | - Lieke van Gijzel
- Department of Chemical Biology and Drug Discovery, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, Utrecht, 3584CG, The Netherlands
| | - Seino A K Jongkees
- Department of Chemical Biology and Drug Discovery, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, Utrecht, 3584CG, The Netherlands
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28
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Macrocycles as protein-protein interaction inhibitors. Biochem J 2017; 474:1109-1125. [PMID: 28298556 DOI: 10.1042/bcj20160619] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/12/2017] [Accepted: 01/18/2017] [Indexed: 12/13/2022]
Abstract
Macrocyclic compounds such as cyclic peptides have emerged as a new and exciting class of drug candidates for inhibition of intracellular protein-protein interactions, which are challenging targets for conventional drug modalities (i.e. small molecules and proteins). Over the past decade, several complementary technologies have been developed to synthesize macrocycle libraries and screen them for binding to therapeutically relevant targets. Two different approaches have also been explored to increase the membrane permeability of cyclic peptides. In this review, we discuss these methods and their applications in the discovery of macrocyclic compounds against protein-protein interactions.
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29
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Rapid Discovery of Potent and Selective Glycosidase-Inhibiting De Novo Peptides. Cell Chem Biol 2017; 24:381-390. [PMID: 28262556 DOI: 10.1016/j.chembiol.2017.02.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 01/14/2017] [Accepted: 01/31/2017] [Indexed: 12/20/2022]
Abstract
Human pancreatic α-amylase (HPA) is responsible for degrading starch to malto-oligosaccharides, thence to glucose, and is therefore an attractive therapeutic target for the treatment of diabetes and obesity. Here we report the discovery of a unique lariat nonapeptide, by means of the RaPID (Random non-standard Peptides Integrated Discovery) system, composed of five amino acids in a head-to-side-chain thioether macrocycle and a further four amino acids in a 310 helical C terminus. This is a potent inhibitor of HPA (Ki = 7 nM) yet exhibits selectivity for the target over other glycosidases tested. Structural studies show that this nonapeptide forms a compact tertiary structure, and illustrate that a general inhibitory motif involving two phenolic groups is often accessed for tight binding of inhibitors to HPA. Furthermore, the work reported here demonstrates the potential of this methodology for the discovery of de novo peptide inhibitors against other glycosidases.
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30
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Triana V, Derda R. Tandem Wittig/Diels–Alder diversification of genetically encoded peptide libraries. Org Biomol Chem 2017; 15:7869-7877. [DOI: 10.1039/c7ob01635b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In this paper, we developed a tandem of two carbon–carbon bond-forming reactions to chemically diversify libraries of peptides displayed on a bacteriophage.
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Affiliation(s)
- Vivian Triana
- Department of Chemistry
- University of Alberta
- Edmonton
- Canada
| | - Ratmir Derda
- Department of Chemistry
- University of Alberta
- Edmonton
- Canada
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31
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Jongkees SAK, Umemoto S, Suga H. Linker-free incorporation of carbohydrates into in vitro displayed macrocyclic peptides. Chem Sci 2016; 8:1474-1481. [PMID: 28572907 PMCID: PMC5452274 DOI: 10.1039/c6sc04381j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 10/18/2016] [Indexed: 12/13/2022] Open
Abstract
We report a strategy for efficient post-translational modification of a library of ribosomally-translated peptides by activation and elimination of cysteine to dehydroalanine then conjugate addition of a range of exogenous thiols, with an emphasis on carbohydrates.
We report a strategy for efficient post-translational modification of a library of ribosomally-translated peptides by activation and elimination of cysteine to dehydroalanine then conjugate addition of a range of exogenous thiols, with an emphasis on carbohydrates. These reactions are selective for cysteine, and do not interfere with amplification of the nucleic acid component of an mRNA-displayed peptide. Furthermore, these reactions are shown to be compatible with two different macrocyclisation chemistries, and when applied to a peptide containing an N-terminal cysteine give a ketone that can be functionalised in an orthogonal manner. This new strategy can overcome a limitation of ribosomal translation, providing a means to incorporate untranslatable groups such as carbohydrates in amino acid side chains, and will allow for the ribosomal generation of glycopeptides, requiring only the introduction of a free thiol in the molecule to be incorporated. In combination with in vitro selection techniques, this strategy is envisaged to allow the discovery of biologically-active glycopeptides with a near-natural, but hydrolytically stable, thioglycosidic bond.
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Affiliation(s)
- S A K Jongkees
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan .
| | - S Umemoto
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan .
| | - H Suga
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan . .,JST CREST , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan
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32
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Maini R, Umemoto S, Suga H. Ribosome-mediated synthesis of natural product-like peptides via cell-free translation. Curr Opin Chem Biol 2016; 34:44-52. [DOI: 10.1016/j.cbpa.2016.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/06/2016] [Indexed: 11/29/2022]
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33
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A Fluorescent Imaging Probe Based on a Macrocyclic Scaffold That Binds to Cellular EpCAM. J Mol Evol 2015; 81:210-7. [PMID: 26553371 DOI: 10.1007/s00239-015-9710-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/24/2015] [Indexed: 12/17/2022]
Abstract
Here, we report a fluorescent probe based on a macrocyclic peptide scaffold that specifically stains EpCAM-expressing MCF7 cells. The 14-mer macrocyclic peptide binding to the extracellular domain of EpCAM with a dissociation constant in the low nM range (1.7 nM) was discovered using the random non-standard peptide-integrated discovery system. Notably, this probe containing a fluorescence tag is less than 3000 Da in total and able to visualize nearly every live cell under high cell-density conditions, which was not achieved by the conventional mAb staining method. This suggests that the molecular probe based on the compact macrocyclic scaffold has great potentials as an imaging tool for the EpCAM biomarker as well as a delivery vehicle for drug conjugates.
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34
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Bartoloni M, Jin X, Marcaida MJ, Banha J, Dibonaventura I, Bongoni S, Bartho K, Gräbner O, Sefkow M, Darbre T, Reymond JL. Bridged bicyclic peptides as potential drug scaffolds: synthesis, structure, protein binding and stability. Chem Sci 2015; 6:5473-5490. [PMID: 29861888 PMCID: PMC5949603 DOI: 10.1039/c5sc01699a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/12/2015] [Indexed: 12/28/2022] Open
Abstract
Double cyclization of short linear peptides obtained by solid phase peptide synthesis was used to prepare bridged bicyclic peptides (BBPs) corresponding to the topology of bridged bicyclic alkanes such as norbornane. Diastereomeric norbornapeptides were investigated by 1H-NMR, X-ray crystallography and CD spectroscopy and found to represent rigid globular scaffolds stabilized by intramolecular backbone hydrogen bonds with scaffold geometries determined by the chirality of amino acid residues and sharing structural features of β-turns and α-helices. Proteome profiling by capture compound mass spectrometry (CCMS) led to the discovery of the norbornapeptide 27c binding selectively to calmodulin as an example of a BBP protein binder. This and other BBPs showed high stability towards proteolytic degradation in serum.
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Affiliation(s)
- Marco Bartoloni
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
| | - Xian Jin
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
| | - Maria José Marcaida
- School of Life Sciences , Ecole Polytechnique de Lausanne , 1015 Lausanne , Switzerland
| | - João Banha
- caprotec bioanalytics GmbH , Berlin , Germany
| | - Ivan Dibonaventura
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
| | - Swathi Bongoni
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
| | | | | | | | - Tamis Darbre
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
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35
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Bionda N, Fasan R. Ribosomal Synthesis of Natural-Product-Like Bicyclic Peptides in Escherichia coli. Chembiochem 2015; 16:2011-6. [PMID: 26179106 DOI: 10.1002/cbic.201500179] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Indexed: 12/28/2022]
Abstract
Methods to access natural-product-like macrocyclic peptides can disclose new opportunities for the exploration of this important structural class for chemical biology and drug discovery applications. Here, the scope and mechanism of a novel strategy for directing the biosynthesis of thioether-bridged bicyclic peptides in bacterial cells was investigated. This method entails split intein-catalyzed head-to-tail cyclization of a ribosomally produced precursor peptide, combined with inter-side-chain crosslinking through a genetically encoded cysteine-reactive amino acid. This strategy could be successfully applied to achieve formation of structurally diverse bicyclic peptides with high efficiency and selectivity in Escherichia coli. Insights into the sequence of reactions underlying the peptide bicyclization process were gained from time-course experiments. Finally, the potential utility of this methodology toward the discovery of macrocyclic peptides with enhanced functional properties was demonstrated through the isolation of a bicyclic peptide with sub-micromolar affinity for streptavidin.
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Affiliation(s)
- Nina Bionda
- Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY, 14627, USA
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY, 14627, USA.
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36
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Bashiruddin NK, Nagano M, Suga H. Synthesis of fused tricyclic peptides using a reprogrammed translation system and chemical modification. Bioorg Chem 2015; 61:45-50. [PMID: 26117092 DOI: 10.1016/j.bioorg.2015.06.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 06/12/2015] [Accepted: 06/13/2015] [Indexed: 10/23/2022]
Abstract
Here we report a unique method of ribosomally synthesizing fused tricyclic peptides. Flexizyme-assisted in vitro translation of a linear peptide with the N-terminal chloroacetyl group and four downstream cysteines followed by the addition of 1,3,5-tris(bromomethyl)benzene results in selective production of the fused tricyclic peptide. This technology can be used for the ribosomal synthesis of fused tricyclic peptide libraries for the in vitro selection of bioactive peptides with tricyclic topology.
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Affiliation(s)
- Nasir Kato Bashiruddin
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masanobu Nagano
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- 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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37
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Construction and screening of vast libraries of natural product-like macrocyclic peptides using in vitro display technologies. Curr Opin Chem Biol 2015; 24:131-8. [DOI: 10.1016/j.cbpa.2014.11.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 11/07/2014] [Accepted: 11/14/2014] [Indexed: 11/20/2022]
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38
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Smith JM, Hill NC, Krasniak PJ, Fasan R. Synthesis of bicyclic organo-peptide hybrids via oxime/intein-mediated macrocyclization followed by disulfide bond formation. Org Biomol Chem 2014; 12:1135-42. [PMID: 24395107 DOI: 10.1039/c3ob42222d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A new strategy is described to generate bicyclic peptides that incorporate non-peptidic backbone elements starting from recombinant polypeptide precursors. These compounds are produced via a one-pot, two-step sequence, in which peptide macrocyclization by means of a bifunctional oxyamine/1,3-amino-thiol synthetic precursor is followed by intramolecular disulfide formation between the synthetic precursor-borne thiol and a cysteine embedded in the peptide sequence. This approach was found to be compatible with the cysteine residue occupying different positions within 8mer and 10mer target peptide sequences and across different synthetic precursor scaffolds, thereby enabling the formation of a variety of diverse bicyclic scaffolds.
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Affiliation(s)
- Jessica M Smith
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA.
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39
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Bionda N, Cryan AL, Fasan R. Bioinspired strategy for the ribosomal synthesis of thioether-bridged macrocyclic peptides in bacteria. ACS Chem Biol 2014; 9:2008-13. [PMID: 25079213 PMCID: PMC4168796 DOI: 10.1021/cb500311k] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
![]()
Inspired
by the biosynthetic logic of lanthipeptide natural products,
a new methodology was developed to direct the ribosomal synthesis
of macrocyclic peptides constrained by an intramolecular thioether
bond. As a first step, a robust and versatile strategy was implemented
to enable the cyclization of ribosomally derived peptide sequences
via a chemoselective reaction between a genetically encoded cysteine
and a cysteine-reactive unnatural amino acid (O-(2-bromoethyl)-tyrosine).
Combination of this approach with intein-catalyzed protein splicing
furnished an efficient route to achieve the spontaneous, post-translational
formation of structurally diverse macrocyclic peptides in bacterial
cells. The present peptide cyclization strategy was also found to
be amenable to integration with split intein-mediated circular ligation,
resulting in the intracellular synthesis of conformationally constrained
peptides featuring a bicyclic architecture.
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Affiliation(s)
- Nina Bionda
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Abby L. Cryan
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
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40
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Protein cocrystallization molecules originating from in vitro selected macrocyclic peptides. Curr Opin Struct Biol 2014; 26:24-31. [PMID: 24681557 DOI: 10.1016/j.sbi.2014.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 02/15/2014] [Accepted: 03/01/2014] [Indexed: 12/22/2022]
Abstract
Transmembrane proteins are intractable crystallization targets due to their low solubility and their substantial hydrophobic outer surfaces must be enclosed within a partial micelle composed of detergents to avoid aggregation. Unfortunately, encapsulation within a partial micelle diminishes specific protein-to-protein contacts needed for crystal lattice formation. In addition, the high conformational flexibility of certain transmembrane proteins reduces sample homogeneity causing difficulty in crystallization. Cocrystallization ligands, based on either antibody scaffolds or other proteinaceous non-antibody scaffolds, have greatly facilitated the crystallization of transmembrane proteins. Recently, in vitro selected macrocyclic peptide ligands have been shown to facilitate protein crystallization as well. In this review, we discuss selection strategies used for the discovery of macrocyclic peptide ligands and the three-dimensional crystal structure of the transporter PfMATE in complex with in vitro selected macrocyclic peptides.
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41
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Hipolito CJ, Tanaka Y, Katoh T, Nureki O, Suga H. A macrocyclic peptide that serves as a cocrystallization ligand and inhibits the function of a MATE family transporter. Molecules 2013; 18:10514-30. [PMID: 23999725 PMCID: PMC6270235 DOI: 10.3390/molecules180910514] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 08/24/2013] [Accepted: 08/27/2013] [Indexed: 11/29/2022] Open
Abstract
The random non-standard peptide integrated discovery (RaPID) system has proven to be a powerful approach to discover de novo natural product-like macrocyclic peptides that inhibit protein functions. We have recently reported three macrocyclic peptides that bind to Pyrococcus furiosus multidrug and toxic compound extrusion (PfMATE) transporter and inhibit the transport function. Moreover, these macrocyclic peptides were successfully employed as cocrystallization ligands of selenomethionine-labeled PfMATE. In this report, we disclose the details of the RaPID selection strategy that led to the identification of these three macrocyclic peptides as well as a fourth macrocyclic peptide, MaD8, which is exclusively discussed in this article. MaD8 was found to bind within the cleft of PfMATE’s extracellular side and blocked the path of organic small molecules being extruded. The results of an ethidium bromide efflux assay confirmed the efflux inhibitory activity of MaD8, whose behavior was similar to that of previously reported MaD5.
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Affiliation(s)
- Christopher J. Hipolito
- Department of Chemistry, Graduate School of Science, the University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan; E-Mails: (C.J.H.); (T.K.)
| | - Yoshiki Tanaka
- Department of Biophysics and Biochemistry, Graduate School of Science, the University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, the University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan; E-Mails: (C.J.H.); (T.K.)
| | - Osamu Nureki
- Department of Biophysics and Biochemistry, Graduate School of Science, the University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Authors to whom correspondence should be addressed; E-Mails: (O.N.); (H.S.); Tel./Fax: +81-3-5841-8372 (H.S)
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, the University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan; E-Mails: (C.J.H.); (T.K.)
- Authors to whom correspondence should be addressed; E-Mails: (O.N.); (H.S.); Tel./Fax: +81-3-5841-8372 (H.S)
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42
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Frost JR, Smith JM, Fasan R. Design, synthesis, and diversification of ribosomally derived peptide macrocycles. Curr Opin Struct Biol 2013; 23:571-80. [PMID: 23856642 DOI: 10.1016/j.sbi.2013.06.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/19/2013] [Accepted: 06/20/2013] [Indexed: 10/26/2022]
Abstract
Ring topologies are widespread structural motifs among biologically active peptides found in nature. The recurrence of this motif is linked to the inherent advantages resulting from backbone cyclization, which include increased resistance against proteolytic degradation, improved cell permeability, and tighter and more specific interaction with the respective biomolecular target. Inspired by these natural product topologies, a number of groups have recently focused on developing methodologies that hinge upon the chemical elaboration of ribosomally derived polypeptides toward the synthesis and diversification of macrocyclic peptide structures. In this review, we highlight recent advances in this emerging new area and discuss the opportunities created by these methods toward the discovery of new functional entities.
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Affiliation(s)
- John R Frost
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
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43
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Ito K, Passioura T, Suga H. Technologies for the synthesis of mRNA-encoding libraries and discovery of bioactive natural product-inspired non-traditional macrocyclic peptides. Molecules 2013; 18:3502-28. [PMID: 23507778 PMCID: PMC6270345 DOI: 10.3390/molecules18033502] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 02/04/2013] [Accepted: 02/25/2013] [Indexed: 01/04/2023] Open
Abstract
In this review, we discuss emerging technologies for drug discovery, which yields novel molecular scaffolds based on natural product-inspired non-traditional peptides expressed using the translation machinery. Unlike natural products, these technologies allow for constructing mRNA-encoding libraries of macrocyclic peptides containing non-canonical sidechains and N-methyl-modified backbones. The complexity of sequence space in such libraries reaches as high as a trillion (>1012), affording initial hits of high affinity ligands against protein targets. Although this article comprehensively covers several related technologies, we discuss in greater detail the technical development and advantages of the Random non-standard Peptide Integration Discovery (RaPID) system, including the recent identification of inhibitors against various therapeutic targets.
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Affiliation(s)
| | | | - Hiroaki Suga
- Author to whom correspondence should be addressed; E-Mail: ; Tel./Fax: +81-3-5841-8372
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44
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Genetically encoded libraries of nonstandard peptides. J Nucleic Acids 2012; 2012:713510. [PMID: 23097693 PMCID: PMC3477784 DOI: 10.1155/2012/713510] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/12/2012] [Indexed: 11/17/2022] Open
Abstract
The presence of a nonproteinogenic moiety in a nonstandard peptide often improves the biological properties of the peptide. Non-standard peptide libraries are therefore used to obtain valuable molecules for biological, therapeutic, and diagnostic applications. Highly diverse non-standard peptide libraries can be generated by chemically or enzymatically modifying standard peptide libraries synthesized by the ribosomal machinery, using posttranslational modifications. Alternatively, strategies for encoding non-proteinogenic amino acids into the genetic code have been developed for the direct ribosomal synthesis of non-standard peptide libraries. In the strategies for genetic code expansion, non-proteinogenic amino acids are assigned to the nonsense codons or 4-base codons in order to add these amino acids to the universal genetic code. In contrast, in the strategies for genetic code reprogramming, some proteinogenic amino acids are erased from the genetic code and non-proteinogenic amino acids are reassigned to the blank codons. Here, we discuss the generation of genetically encoded non-standard peptide libraries using these strategies and also review recent applications of these libraries to the selection of functional non-standard peptides.
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