1
|
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.
Collapse
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,
| |
Collapse
|
2
|
Liu W, de Veer SJ, Huang YH, Sengoku T, Okada C, Ogata K, Zdenek CN, Fry BG, Swedberg JE, Passioura T, Craik DJ, Suga H. An Ultrapotent and Selective Cyclic Peptide Inhibitor of Human β-Factor XIIa in a Cyclotide Scaffold. J Am Chem Soc 2021; 143:18481-18489. [PMID: 34723512 DOI: 10.1021/jacs.1c07574] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cyclotides are plant-derived peptides with complex structures shaped by their head-to-tail cyclic backbone and cystine knot core. These structural features underpin the native bioactivities of cyclotides, as well as their beneficial properties as pharmaceutical leads, including high proteolytic stability and cell permeability. However, their inherent structural complexity presents a challenge for cyclotide engineering, particularly for accessing libraries of sufficient chemical diversity to design potent and selective cyclotide variants. Here, we report a strategy using mRNA display enabling us to select potent cyclotide-based FXIIa inhibitors from a library comprising more than 1012 members based on the cyclotide scaffold of Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II). The most potent and selective inhibitor, cMCoFx1, has a pM inhibitory constant toward FXIIa with greater than three orders of magnitude selectivity over related serine proteases, realizing specific inhibition of the intrinsic coagulation pathway. The cocrystal structure of cMCoFx1 and FXIIa revealed interactions at several positions across the contact interface that conveyed high affinity binding, highlighting that such cyclotides are attractive cystine knot scaffolds for therapeutic development.
Collapse
Affiliation(s)
- Wenyu Liu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Simon J de Veer
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yen-Hua Huang
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Toru Sengoku
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - Chikako Okada
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - Christina N Zdenek
- Venom Evolution Lab, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Bryan G Fry
- Venom Evolution Lab, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia.,School of Life and Environmental Sciences, School of Chemistry and Sydney Analytical, The University of Sydney, Sydney, NSW 2006, Australia
| | - David J Craik
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia
| |
Collapse
|
3
|
Kamalinia G, Grindel BJ, Takahashi TT, Millward SW, Roberts RW. Directing evolution of novel ligands by mRNA display. Chem Soc Rev 2021; 50:9055-9103. [PMID: 34165126 PMCID: PMC8725378 DOI: 10.1039/d1cs00160d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
mRNA display is a powerful biological display platform for the directed evolution of proteins and peptides. mRNA display libraries covalently link the displayed peptide or protein (phenotype) with the encoding genetic information (genotype) through the biochemical activity of the small molecule puromycin. Selection for peptide/protein function is followed by amplification of the linked genetic material and generation of a library enriched in functional sequences. Iterative selection cycles are then performed until the desired level of function is achieved, at which time the identity of candidate peptides can be obtained by sequencing the genetic material. The purpose of this review is to discuss the development of mRNA display technology since its inception in 1997 and to comprehensively review its use in the selection of novel peptides and proteins. We begin with an overview of the biochemical mechanism of mRNA display and its variants with a particular focus on its advantages and disadvantages relative to other biological display technologies. We then discuss the importance of scaffold choice in mRNA display selections and review the results of selection experiments with biological (e.g., fibronectin) and linear peptide library architectures. We then explore recent progress in the development of "drug-like" peptides by mRNA display through the post-translational covalent macrocyclization and incorporation of non-proteogenic functionalities. We conclude with an examination of enabling technologies that increase the speed of selection experiments, enhance the information obtained in post-selection sequence analysis, and facilitate high-throughput characterization of lead compounds. We hope to provide the reader with a comprehensive view of current state and future trajectory of mRNA display and its broad utility as a peptide and protein design tool.
Collapse
Affiliation(s)
- Golnaz Kamalinia
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
| | | | | | | | | |
Collapse
|
4
|
Xie Q, Wiedmann MM, Zhao A, Pagan IR, Novick RP, Suga H, Muir TW. Discovery of quorum quenchers targeting the membrane-embedded sensor domain of the Staphylococcus aureus receptor histidine kinase, AgrC. Chem Commun (Camb) 2021; 56:11223-11226. [PMID: 32820778 DOI: 10.1039/d0cc04873a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We combined mRNA display technology with lipid-nanodisc based selections and identified high-affinity ligands targeting the integral membrane sensor domain of the histidine kinase AgrC as potent inhibitors of Staphylococcus aureus quorum sensing-modulated virulence. Our study highlights the potential of this integrated approach for identifying functional modulators of integral membrane proteins.
Collapse
Affiliation(s)
- Qian Xie
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
| | - Mareike M Wiedmann
- Department of Chemistry, University of Tokyo, Graduate School of Science, Tokyo, Japan.
| | - Aishan Zhao
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
| | - Ivelisse R Pagan
- Skirball Institute, Department of Microbiology, NYU Medical Center, New York, NY, USA
| | - Richard P Novick
- Skirball Institute, Department of Microbiology, NYU Medical Center, New York, NY, USA
| | - Hiroaki Suga
- Department of Chemistry, University of Tokyo, Graduate School of Science, Tokyo, Japan.
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
El‐Gammal O, El‐Brashy S, Abu El‐Reash G. Macrocyclic Cr
3+
, Mn
2+
and Fe
3+
complexes of a mimic SOD moiety: Design, structural aspects, DFT, XRD, optical properties and biological activity. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.5456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- O.A. El‐Gammal
- Faculty of Science, Chemistry DepartmentMansoura University Mansoura P.O: 35566; Box: 70 Egypt
| | - S.A. El‐Brashy
- Faculty of Science, Chemistry DepartmentMansoura University Mansoura P.O: 35566; Box: 70 Egypt
| | - G.M. Abu El‐Reash
- Faculty of Science, Chemistry DepartmentMansoura University Mansoura P.O: 35566; Box: 70 Egypt
| |
Collapse
|
7
|
Methods for generating and screening libraries of genetically encoded cyclic peptides in drug discovery. Nat Rev Chem 2020; 4:90-101. [PMID: 37128052 DOI: 10.1038/s41570-019-0159-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2019] [Indexed: 12/14/2022]
Abstract
Drug discovery has traditionally focused on using libraries of small molecules to identify therapeutic drugs, but new modalities, especially libraries of genetically encoded cyclic peptides, are increasingly used for this purpose. Several technologies now exist for the production of libraries of cyclic peptides, including phage display, mRNA display and split-intein circular ligation of peptides and proteins. These different approaches are each compatible with particular methods of screening libraries, such as functional or affinity-based screening, and screening in vitro or in cells. These techniques allow the rapid preparation of libraries of hundreds of millions of molecules without the need for chemical synthesis, and have therefore lowered the entry barrier to generating and screening for inhibitors of a given target. This ease of use combined with the inherent advantages of the cyclic-peptide scaffold has yielded inhibitors of targets that have proved difficult to drug with small molecules. Multiple reports demonstrate that cyclic peptides act as privileged scaffolds in drug discovery, particularly against 'undruggable' targets such as protein-protein interactions. Although substantial challenges remain in the clinical translation of hits from screens of cyclic-peptide libraries, progress continues to be made in this area, with an increasing number of cyclic peptides entering clinical trials. Here, we detail the various platforms for producing and screening libraries of genetically encoded cyclic peptides and discuss and evaluate the advantages and disadvantages of each approach when deployed for drug discovery.
Collapse
|
8
|
Kusakizako T, Miyauchi H, Ishitani R, Nureki O. Structural biology of the multidrug and toxic compound extrusion superfamily transporters. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183154. [PMID: 31866287 DOI: 10.1016/j.bbamem.2019.183154] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/05/2019] [Accepted: 12/08/2019] [Indexed: 12/27/2022]
Abstract
Xenobiotic and metabolite extrusion is an important process for the proper functions of cells and their compartments, including acidic organelles. MATE (multidrug and toxic compound extrusion) is a large family of secondary active transporters involved in the transport of various compounds across cellular and organellar membranes, and is present in the three domains of life. The major substrates of the bacterial MATE transporters are cationic compounds, including clinically important antibiotics, and thereby MATE transporters confer multi-drug resistance to pathogenic bacteria. The plant MATE transporters are important for the accumulation of various metabolites in organelles, including vacuoles. The human MATE transporters are expressed in the brush-border membrane of the kidney, and are involved in the clearance of cationic drugs from the body. During the past decade, progress in structural biology has clarified the transport mechanism of these MATE transporters in atomic detail. The present review summarizes the reported structures of MATE family transporters, along with their structure-guided functional analyses. This integrated view of the structures of MATE transporters provides novel insights into their transport mechanism.
Collapse
Affiliation(s)
- Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hirotake Miyauchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| |
Collapse
|
9
|
Generation of non-standard macrocyclic peptides specifically binding TSC-22 homologous gene-1. Biochem Biophys Res Commun 2019; 516:445-450. [PMID: 31227214 DOI: 10.1016/j.bbrc.2019.06.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 06/07/2019] [Indexed: 01/19/2023]
Abstract
Transforming growth factor-β 1 (TGFβ1)-stimulated clone 22 (TSC22) family includes proteins containing a leucine zipper domain and a TSC-box that are highly conserved during evolution. Currently, limited data are available on the function of this protein family, especially of TSC-22 homologous gene-1 (THG-1)/TSC22 domain family member 4 (TSC22D4). Similar to other family members, THG-1 functions depending on its interaction with the partner proteins and it is suggested to mediate a broad range of biological processes. THG-1-specific binding molecules will be instrumental for elucidating its functions. Therefore, the Random non-standard Peptide Integrated Discovery (RaPID) system was modified using commercially available materials and used for selecting macrocyclic peptides (MCPs) that bind to THG-1. Several MCPs were identified to bind THG-1. Fluorescein- and biotin-tagged MCPs were synthesized and employed as THG-1 detection probes. Notably, a fluorescein-tagged MCP specifically detected THG-1-expressing cells. Biotin-tagged MCPs can be successfully used for Enzyme-Linked Protein Sorbent Assay (ELISA) like assay of THG-1 protein and affinity-precipitation of purified THG-1 and endogenous THG-1 in esophageal squamous cell carcinoma cell lysates. The modified RaPID system rapidly and successfully identified THG-1-binding MCPs in vitro and the synthesized THG-1 binding MCPs are useful alternatives acting for antibodies.
Collapse
|
10
|
Ottl J, Leder L, Schaefer JV, Dumelin CE. Encoded Library Technologies as Integrated Lead Finding Platforms for Drug Discovery. Molecules 2019; 24:E1629. [PMID: 31027189 PMCID: PMC6514559 DOI: 10.3390/molecules24081629] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/17/2019] [Accepted: 04/21/2019] [Indexed: 01/22/2023] Open
Abstract
The scope of targets investigated in pharmaceutical research is continuously moving into uncharted territory. Consequently, finding suitable chemical matter with current compound collections is proving increasingly difficult. Encoded library technologies enable the rapid exploration of large chemical space for the identification of ligands for such targets. These binders facilitate drug discovery projects both as tools for target validation, structural elucidation and assay development as well as starting points for medicinal chemistry. Novartis internalized two complementing encoded library platforms to accelerate the initiation of its drug discovery programs. For the identification of low-molecular weight ligands, we apply DNA-encoded libraries. In addition, encoded peptide libraries are employed to identify cyclic peptides. This review discusses how we apply these two platforms in our research and why we consider it beneficial to run both pipelines in-house.
Collapse
Affiliation(s)
- Johannes Ottl
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | - Lukas Leder
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | - Jonas V Schaefer
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | | |
Collapse
|
11
|
Katoh T, Suga H. Engineering Translation Components Improve Incorporation of Exotic Amino Acids. Int J Mol Sci 2019; 20:ijms20030522. [PMID: 30691159 PMCID: PMC6386890 DOI: 10.3390/ijms20030522] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 12/19/2022] Open
Abstract
Methods of genetic code manipulation, such as nonsense codon suppression and genetic code reprogramming, have enabled the incorporation of various nonproteinogenic amino acids into the peptide nascent chain. However, the incorporation efficiency of such amino acids largely varies depending on their structural characteristics. For instance, l-α-amino acids with artificial, bulky side chains are poorer substrates for ribosomal incorporation into the nascent peptide chain, mainly owing to the lower affinity of their aminoacyl-tRNA toward elongation factor-thermo unstable (EF-Tu). Phosphorylated Ser and Tyr are also poorer substrates for the same reason; engineering EF-Tu has turned out to be effective in improving their incorporation efficiencies. On the other hand, exotic amino acids such as d-amino acids and β-amino acids are even poorer substrates owing to their low affinity to EF-Tu and poor compatibility to the ribosome active site. Moreover, their consecutive incorporation is extremely difficult. To solve these problems, the engineering of ribosomes and tRNAs has been executed, leading to successful but limited improvement of their incorporation efficiency. In this review, we comprehensively summarize recent attempts to engineer the translation systems, resulting in a significant improvement of the incorporation of exotic amino acids.
Collapse
Affiliation(s)
- 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.
| |
Collapse
|
12
|
Otero-Ramirez ME, Passioura T, Suga H. Structural Features and Binding Modes of Thioether-Cyclized Peptide Ligands. Biomedicines 2018; 6:biomedicines6040116. [PMID: 30551606 PMCID: PMC6316662 DOI: 10.3390/biomedicines6040116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 01/26/2023] Open
Abstract
Macrocyclic peptides are an emerging class of bioactive compounds for therapeutic use. In part, this is because they are capable of high potency and excellent target affinity and selectivity. Over the last decade, several biochemical techniques have been developed for the identification of bioactive macrocyclic peptides, allowing for the rapid isolation of high affinity ligands to a target of interest. A common feature of these techniques is a general reliance on thioether formation to effect macrocyclization. Increasingly, the compounds identified using these approaches have been subjected to x-ray crystallographic analysis bound to their respective targets, providing detailed structural information about their conformation and mechanism of target binding. The present review provides an overview of the target bound thioether-closed macrocyclic peptide structures that have been obtained to date.
Collapse
Affiliation(s)
- Manuel E Otero-Ramirez
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, 113-0033 Tokyo, Bunkyo-ku, Japan.
| | - Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, 113-0033 Tokyo, Bunkyo-ku, Japan.
| | - Hiroaki 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.
| |
Collapse
|
13
|
Structural Basis of H +-Dependent Conformational Change in a Bacterial MATE Transporter. Structure 2018; 27:293-301.e3. [PMID: 30449688 DOI: 10.1016/j.str.2018.10.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 08/07/2018] [Accepted: 10/10/2018] [Indexed: 12/28/2022]
Abstract
Multidrug and toxic compound extrusion (MATE) transporters efflux toxic compounds using a Na+ or H+ gradient across the membrane. Although the structures of MATE transporters have been reported, the cation-coupled substrate transport mechanism remains controversial. Here we report crystal structures of VcmN, a Vibrio cholerae MATE transporter driven by the H+ gradient. High-resolution structures in two distinct conformations associated with different pHs revealed that the rearrangement of the hydrogen-bonding network around the conserved Asp35 induces the bending of transmembrane helix 1, as in the case of the H+-coupled Pyrococcus furiosus MATE transporter. We also determined the crystal structure of the D35N mutant, which captured a unique conformation of TM1 facilitated by an altered hydrogen-bonding network. Based on the present results, we propose a common step in the transport cycle shared among prokaryotic H+-coupled MATE transporters.
Collapse
|
14
|
Cellular signaling and gene expression profiles evoked by a bivalent macrocyclic peptide that serves as an artificial MET receptor agonist. Sci Rep 2018; 8:16492. [PMID: 30405161 PMCID: PMC6220203 DOI: 10.1038/s41598-018-34835-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/26/2018] [Indexed: 11/11/2022] Open
Abstract
Non-native ligands for growth factor receptors that are generated by chemical synthesis are applicable to therapeutics. However, non-native ligands often regulate cellular signaling and biological responses in a different manner than native ligands. Generation of surrogate ligands comparable to native ligands is a challenging need. Here we investigated changes in signal transduction and gene expression evoked by a bivalent macrocyclic peptide (aMD5-PEG11) capable of high-affinity binding to the MET/hepatocyte growth factor (HGF) receptor. Binding of aMD5-PEG11 to the MET extracellular region was abolished by deletion of the IPT3−IPT4 domain, indicating the involvement of IPT3−IPT4 in the binding of aMD5-PEG11 to the MET receptor. aMD5-PEG11 induced dimerization and activation of the MET receptor and promoted cell migration that was comparable to induction of these activities by HGF. Signal activation profiles indicated that aMD5-PEG11 induced phosphorylation of intracellular signaling molecules, with a similar intensity and time dependency as HGF. In 3-D culture, aMD5-PEG11 as well as HGF induced epithelial tubulogenesis and up-regulated the same sets of functionally classified genes involved in multicellular organism development. Thus, a non-native surrogate ligand that consisted of a bivalent macrocyclic peptide can serve as an artificial MET receptor agonist that functionally substitutes for the native ligand, HGF.
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Sodium and proton coupling in the conformational cycle of a MATE antiporter from Vibrio cholerae. Proc Natl Acad Sci U S A 2018; 115:E6182-E6190. [PMID: 29915043 DOI: 10.1073/pnas.1802417115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Secondary active transporters belonging to the multidrug and toxic compound extrusion (MATE) family harness the potential energy of electrochemical ion gradients to export a broad spectrum of cytotoxic compounds, thus contributing to multidrug resistance. The current mechanistic understanding of ion-coupled substrate transport has been informed by a limited set of MATE transporter crystal structures from multiple organisms that capture a 12-transmembrane helix topology adopting similar outward-facing conformations. Although these structures mapped conserved residues important for function, the mechanistic role of these residues in shaping the conformational cycle has not been investigated. Here, we use double-electron electron resonance (DEER) spectroscopy to explore ligand-dependent conformational changes of NorM from Vibrio cholerae (NorM-Vc), a MATE transporter proposed to be coupled to both Na+ and H+ gradients. Distance measurements between spin labels on the periplasmic side of NorM-Vc identified unique structural intermediates induced by binding of Na+, H+, or the substrate doxorubicin. The Na+- and H+-dependent intermediates were associated with distinct conformations of TM1. Site-directed mutagenesis of conserved residues revealed that Na+- and H+-driven conformational changes are facilitated by a network of polar residues in the N-terminal domain cavity, whereas conserved carboxylates buried in the C-terminal domain are critical for stabilizing the drug-bound state. Interpreted in conjunction with doxorubicin binding of mutant NorM-Vc and cell toxicity assays, these results establish the role of ion-coupled conformational dynamics in the functional cycle and implicate H+ in the doxorubicin release mechanism.
Collapse
|
17
|
Passioura T, Watashi K, Fukano K, Shimura S, Saso W, Morishita R, Ogasawara Y, Tanaka Y, Mizokami M, Sureau C, Suga H, Wakita T. De Novo Macrocyclic Peptide Inhibitors of Hepatitis B Virus Cellular Entry. Cell Chem Biol 2018; 25:906-915.e5. [PMID: 29779957 DOI: 10.1016/j.chembiol.2018.04.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 02/01/2018] [Accepted: 04/11/2018] [Indexed: 12/19/2022]
Abstract
Hepatitis B virus (HBV) constitutes a significant public health burden, and currently available treatment options are not generally curative, necessitating the development of new therapeutics. Here we have applied random non-standard peptide integrated discovery (RaPID) screening to identify small macrocyclic peptide inhibitors of HBV entry that target the cell-surface receptor for HBV, sodium taurocholate cotransporting polypeptide (NTCP). In addition to their anti-HBV activity, these molecules also inhibit cellular entry by the related hepatitis D virus (HDV), and are active against diverse strains of HBV (including clinically relevant nucleos(t)ide analog-resistant and vaccine escaping strains). Importantly, these macrocyclic peptides, in contrast to other NTCP-binding HBV entry inhibitors, exhibited no inhibition of NTCP-mediated bile acid uptake, making them appealing candidates for therapeutic development.
Collapse
Affiliation(s)
- Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; Department of Applied Biological Sciences, Tokyo University of Science, Noda 278-8510, Japan; JST CREST, Saitama 332-0012, Japan
| | - Kento Fukano
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; Department of Analytical Biochemistry, Meiji Pharmaceutical University, Kiyose 204-8588, Japan
| | - Satomi Shimura
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Wakana Saso
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Ryo Morishita
- CellFree Sciences Co., Ltd., Matsuyama 790-8577, Japan
| | - Yuki Ogasawara
- Department of Analytical Biochemistry, Meiji Pharmaceutical University, Kiyose 204-8588, Japan
| | - Yasuhito Tanaka
- Department of Virology and Liver Unit, Nagoya City University, Graduate School of Medicinal Sciences, Nagoya 467-8601, Japan
| | - Masashi Mizokami
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Ichikawa 272-8516, Japan
| | - Camille Sureau
- Laboratoire de Virologie Moléculaire, Institut National de la Transfusion Sanguine, INSERM U1134, Paris 75015, France
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan; JST CREST, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan.
| |
Collapse
|
18
|
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: 120] [Impact Index Per Article: 20.0] [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.
Collapse
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
| |
Collapse
|
19
|
Kusakizako T, Tanaka Y, Hipolito CJ, Suga H, Nureki O. Crystallographic Analysis of MATE-Type Multidrug Exporter with Its Inhibitors. Methods Mol Biol 2018; 1700:37-57. [PMID: 29177824 DOI: 10.1007/978-1-4939-7454-2_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Multidrug exporters expressed in pathogens efflux substrate drugs such as antibiotics, and thus, the development of inhibitors against them has eagerly been anticipated. Furthermore, the crystal structures of multidrug exporters with their inhibitors provide novel insights into the inhibitory mechanism and the development of more specific and effective inhibitors. We previously reported the complex structures of the Multidrug And Toxic compound Extrusion (MATE)-type multidrug exporter with the macrocyclic peptides, which inhibit the efflux of substrates by the MATE-type multidrug exporter (Tanaka et al., Nature 496:247-251, 2013). In this chapter, we describe methodologies of the screening and synthesis of macrocyclic peptides as inhibitors, as well as the purification, crystallization, and structure determination of the complexes of the MATE-type multidrug exporter with its inhibitors.
Collapse
Affiliation(s)
- Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Yoshiki Tanaka
- Department of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Christopher J Hipolito
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
| |
Collapse
|
20
|
Taylor RD, Rey-Carrizo M, Passioura T, Suga H. Identification of nonstandard macrocyclic peptide ligands through display screening. DRUG DISCOVERY TODAY. TECHNOLOGIES 2017; 26:17-23. [PMID: 29249238 DOI: 10.1016/j.ddtec.2017.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/23/2017] [Indexed: 11/25/2022]
Abstract
Techniques facilitating the synthesis and screening of very high diversity nonstandard macrocyclic peptide libraries have led to such compounds receiving increasing attention as potential drug candidates. Specifically, approaches which allow the use of non-proteinogenic amino acids are proving to be particularly effective, since they expand the accessible chemical space of the starting library and thus allow the identification of compounds with structural similarity to known drugs. This review focuses on mRNA display screening platforms for drug discovery and their combined use with genetic code reprogramming to identify novel macrocyclic peptides with high affinities for disease-related targets of interest.
Collapse
Affiliation(s)
- Rhys Dylan Taylor
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Matias Rey-Carrizo
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toby Passioura
- 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.
| |
Collapse
|
21
|
Yu H, Dranchak P, Li Z, MacArthur R, Munson MS, Mehzabeen N, Baird NJ, Battalie KP, Ross D, Lovell S, Carlow CKS, Suga H, Inglese J. Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases. Nat Commun 2017; 8:14932. [PMID: 28368002 PMCID: PMC5382265 DOI: 10.1038/ncomms14932] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 02/13/2017] [Indexed: 11/22/2022] Open
Abstract
Glycolytic interconversion of phosphoglycerate isomers is catalysed in numerous pathogenic microorganisms by a cofactor-independent mutase (iPGM) structurally distinct from the mammalian cofactor-dependent (dPGM) isozyme. The iPGM active site dynamically assembles through substrate-triggered movement of phosphatase and transferase domains creating a solvent inaccessible cavity. Here we identify alternate ligand binding regions using nematode iPGM to select and enrich lariat-like ligands from an mRNA-display macrocyclic peptide library containing >1012 members. Functional analysis of the ligands, named ipglycermides, demonstrates sub-nanomolar inhibition of iPGM with complete selectivity over dPGM. The crystal structure of an iPGM macrocyclic peptide complex illuminated an allosteric, locked-open inhibition mechanism placing the cyclic peptide at the bi-domain interface. This binding mode aligns the pendant lariat cysteine thiolate for coordination with the iPGM transition metal ion cluster. The extended charged, hydrophilic binding surface interaction rationalizes the persistent challenges these enzymes have presented to small-molecule screening efforts highlighting the important roles of macrocyclic peptides in expanding chemical diversity for ligand discovery.
Collapse
Affiliation(s)
- Hao Yu
- Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Patricia Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA
| | - Zhiru Li
- Division of Genome Biology, New England Biolabs, Ipswich, Massachusetts 01938, USA
| | - Ryan MacArthur
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA
| | - Matthew S. Munson
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Nurjahan Mehzabeen
- Proton Structure Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, USA
| | - Nathan J. Baird
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kevin P. Battalie
- IMCA-CAT Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - David Ross
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Scott Lovell
- Proton Structure Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, USA
| | | | - Hiroaki Suga
- Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA
| |
Collapse
|
22
|
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.
Collapse
|
23
|
Allosteric Inhibition of a Semaphorin 4D Receptor Plexin B1 by a High-Affinity Macrocyclic Peptide. Cell Chem Biol 2016; 23:1341-1350. [DOI: 10.1016/j.chembiol.2016.09.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/08/2016] [Accepted: 10/10/2016] [Indexed: 02/04/2023]
|
24
|
Leenheer D, ten Dijke P, Hipolito CJ. A current perspective on applications of macrocyclic-peptide-based high-affinity ligands. Biopolymers 2016; 106:889-900. [PMID: 27352774 PMCID: PMC5132055 DOI: 10.1002/bip.22900] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 05/24/2016] [Accepted: 05/31/2016] [Indexed: 01/05/2023]
Abstract
Monoclonal antibodies can bind with high affinity and high selectivity to their targets. As a tool in therapeutics or diagnostics, however, their large size (∼150 kDa) reduces penetration into tissue and prevents passive cellular uptake. To overcome these and other problems, minimized protein scaffolds have been chosen or engineered, with care taken to not compromise binding affinity or specificity. An alternate approach is to begin with a minimal non-antibody scaffold and select functional ligands from a de novo library. We will discuss the structure, production, applications, strengths, and weaknesses of several classes of antibody-derived ligands, that is, antibodies, intrabodies, and nanobodies, and nonantibody-derived ligands, that is, monobodies, affibodies, and macrocyclic peptides. In particular, this review is focussed on macrocyclic peptides produced by the Random non-standard Peptides Integrated Discovery (RaPID) system that are small in size (typically ∼2 kDa), but are able to perform tasks typically handled by larger proteinaceous ligands.
Collapse
Affiliation(s)
- Daniël Leenheer
- Ph.D. Program in Human Biology, School of Integrative and Global MajorsUniversity of TsukubaTsukubaIbarakiJapan
| | - Peter ten Dijke
- Leiden University Medical Center, Department of Molecular Cell BiologyLeidenSouth HollandThe Netherlands
- Cancer Signaling, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of TsukubaTsukubaIbarakiJapan
| | - Christopher John Hipolito
- Cancer Signaling, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of TsukubaTsukubaIbarakiJapan
| |
Collapse
|
25
|
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]
|
26
|
Kusakizako T, Tanaka Y, Hipolito CJ, Kuroda T, Ishitani R, Suga H, Nureki O. LCP crystallization and X-ray diffraction analysis of VcmN, a MATE transporter from Vibrio cholerae. Acta Crystallogr F Struct Biol Commun 2016; 72:552-7. [PMID: 27380372 PMCID: PMC4933005 DOI: 10.1107/s2053230x16008931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 06/03/2016] [Indexed: 11/10/2022] Open
Abstract
Multidrug and toxic compound extrusion (MATE) transporters, one of the multidrug exporter families, efflux xenobiotics towards the extracellular side of the membrane. Since MATE transporters expressed in bacterial pathogens contribute to multidrug resistance, they are important therapeutic targets. Here, a MATE-transporter homologue from Vibrio cholerae, VcmN, was overexpressed in Escherichia coli, purified and crystallized in lipidic cubic phase (LCP). X-ray diffraction data were collected to 2.5 Å resolution from a single crystal obtained in a sandwich plate. The crystal belonged to space group P212121, with unit-cell parameters a = 52.3, b = 93.7, c = 100.2 Å. As a result of further LCP crystallization trials, crystals of larger size were obtained using sitting-drop plates. X-ray diffraction data were collected to 2.2 Å resolution from a single crystal obtained in a sitting-drop plate. The crystal belonged to space group P212121, with unit-cell parameters a = 61.9, b = 91.8, c = 100.9 Å. The present work provides valuable insights into the atomic resolution structure determination of membrane transporters.
Collapse
Affiliation(s)
- Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yoshiki Tanaka
- Department of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Christopher J. Hipolito
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
| | - Teruo Kuroda
- Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| |
Collapse
|
27
|
Jin X, Shao Y, Bai Q, Xue W, Liu H, Yao X. Insights into conformational regulation of PfMATE transporter from Pyrococcus furiosus induced by alternating protonation state of Asp41 residue: A molecular dynamics simulation study. Biochim Biophys Acta Gen Subj 2016; 1860:1173-80. [DOI: 10.1016/j.bbagen.2016.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 02/03/2016] [Accepted: 02/11/2016] [Indexed: 01/01/2023]
|
28
|
Hipolito CJ, Nishio K, Suga H. [In Vitro Selected Macrocyclic Peptides: Tools for Regulating the Conformational Freedom of Transmembrane Proteins]. YAKUGAKU ZASSHI 2016; 136:191-6. [PMID: 26831792 DOI: 10.1248/yakushi.15-00229-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Membrane proteins allow a cell to communicate with its environment by relaying a signal or transporting a molecule through the cell membrane. Elucidation of the three-dimensional structure of a membrane protein provides a greater understanding of its function and mechanisms. Ultimately, this knowledge will enlighten researchers on how these proteins can be regulated to elicit a desired cellular response, which could lead to novel therapeutic medicine. Unfortunately, the determination of the high-resolution crystal structures of transmembrane proteins remains a challenge due to their poor solubility and high conformational flexibility. Additives and cocrystallization ligands are being used to address these problems. In vitro selected macrocyclic peptides have recently been successfully employed as cocrystallization ligands. Although originally intended as inhibitors and drug lead molecules, in vitro selected macrocyclic peptides are now showing that their pharmacodynamic properties also allow them to serve as excellent cocrystallization ligands. Structures for macrocyclic peptide-bound transporters, the multidrug and toxic compound extrusion family transporter from Pyrococcus furiosus (PfMATE) and the ABC transporter subfamily B member 1 from Cyanidioschyzon meraloe (CmABCB1), have been elucidated using X-ray crystallography. The cocrystal structures reveal that the macrocyclic peptides improve crystallization by binding in a similar manner as a small molecule or a biologic. The PfMATE-binding macrocyclic peptides MaD3S and MaD5 bind to the surfaces buried in the center channel of the transporters. Although both transporters possess a center channel and substrate-binding pocket, the CmABCB1-binding macrocyclic peptide, aCAP, binds to the outer surface of the transporter in a similar manner to a biologic.
Collapse
|
29
|
Fujino T, Murakami H. In VitroSelection Combined with Ribosomal Translation Containing Non-proteinogenic Amino Acids. CHEM REC 2016; 16:365-77. [DOI: 10.1002/tcr.201500239] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Tomoshige Fujino
- Department of Chemical and Biological Engineering, School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hiroshi Murakami
- Department of Chemical and Biological Engineering, School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| |
Collapse
|
30
|
Mousa JJ, Bruner SD. Structural and mechanistic diversity of multidrug transporters. Nat Prod Rep 2016; 33:1255-1267. [DOI: 10.1039/c6np00006a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The review article surveys recent structural and mechanistic advances in the field of multi-drug and natural product transporters.
Collapse
|
31
|
Rogers JM, Suga H. Discovering functional, non-proteinogenic amino acid containing, peptides using genetic code reprogramming. Org Biomol Chem 2015; 13:9353-63. [PMID: 26280393 DOI: 10.1039/c5ob01336d] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The protein synthesis machinery of the cell, the ribosome and associated factors, is able to accurately follow the canonical genetic code, that which maps RNA sequence to protein sequence, to assemble functional proteins from the twenty or so proteinogenic amino acids. A number of innovative methods have arisen to take advantage of this accurate, and efficient, machinery to direct the assembly of non-proteinogenic amino acids. We review and compare these routes to 'reprogram the genetic code' including in vitro translation, engineered aminoacyl tRNA synthetases, and RNA 'flexizymes'. These studies show that the ribosome is highly tolerant of unnatural amino acids, with hundreds of unusual substrates of varying structure and chemistries being incorporated into protein chains. We also discuss how these methods have been coupled to selection techniques, such as phage display and mRNA display, opening up an exciting new avenue for the production of proteins and peptides with properties and functions beyond that which is possible using proteins composed entirely of the proteinogenic amino acids.
Collapse
Affiliation(s)
- J M Rogers
- Department of Chemistry, The University of Tokyo, Graduate School of Science, Tokyo, Japan.
| | | |
Collapse
|
32
|
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.
Collapse
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.
| |
Collapse
|
33
|
Selection-based discovery of macrocyclic peptides for the next generation therapeutics. Curr Opin Chem Biol 2015; 26:34-41. [DOI: 10.1016/j.cbpa.2015.01.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 01/23/2015] [Indexed: 12/27/2022]
|
34
|
Ito K, Sakai K, Suzuki Y, Ozawa N, Hatta T, Natsume T, Matsumoto K, Suga H. Artificial human Met agonists based on macrocycle scaffolds. Nat Commun 2015; 6:6373. [PMID: 25758345 PMCID: PMC4382702 DOI: 10.1038/ncomms7373] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 01/23/2015] [Indexed: 12/27/2022] Open
Abstract
Hepatocyte growth factor (HGF) receptor, also known as Met, is a member of the receptor tyrosine kinase family. The Met-HGF interaction regulates various signalling pathways involving downstream kinases, such as Akt and Erk. Met activation is implicated in wound healing of tissues via multiple biological responses triggered by the above-mentioned signalling cascade. Here we report the development of artificial Met-activating dimeric macrocycles. We identify Met-binding monomeric macrocyclic peptides by means of the RaPID (random non-standard peptide integrated discovery) system, and dimerize the respective monomers through rational design. These dimeric macrocycles specifically and strongly activate Met signalling pathways through receptor dimerization and induce various HGF-like cellular responses, such as branching morphogenesis, in human cells. This work suggests our approach for generating dimeric macrocycles as non-protein ligands for cell surface receptors can be useful for developing potential therapeutics with a broad range of potential applications.
Collapse
Affiliation(s)
- Kenichiro Ito
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Katsuya Sakai
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan
| | - Yoshinori Suzuki
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan
| | - Naoya Ozawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Tomohisa Hatta
- National Institute of Advanced Industrial Science and Technology, Biological Information Research Center, Tokyo 135-0064, Japan
| | - Tohru Natsume
- National Institute of Advanced Industrial Science and Technology, Biological Information Research Center, Tokyo 135-0064, Japan
| | - Kunio Matsumoto
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| |
Collapse
|
35
|
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]
|
36
|
Jongkees SAK, Hipolito CJ, Rogers JM, Suga H. Model foldamers: applications and structures of stable macrocyclic peptides identified using in vitro selection. NEW J CHEM 2015. [DOI: 10.1039/c4nj01633e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A survey of crystal- and solution-structure information for macrocyclic peptides, illustrating common folding patterns and target binding effects.
Collapse
Affiliation(s)
- Seino A. K. Jongkees
- Department of Chemistry
- Graduate School of Science
- University of Tokyo
- Tokyo 113-0033
- Japan
| | | | - Joseph M. Rogers
- Department of Chemistry
- Graduate School of Science
- University of Tokyo
- Tokyo 113-0033
- Japan
| | - Hiroaki Suga
- Department of Chemistry
- Graduate School of Science
- University of Tokyo
- Tokyo 113-0033
- Japan
| |
Collapse
|
37
|
Passioura T, Suga H. Reprogramming the genetic code in vitro. Trends Biochem Sci 2014; 39:400-8. [DOI: 10.1016/j.tibs.2014.07.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 07/16/2014] [Accepted: 07/16/2014] [Indexed: 02/07/2023]
|
38
|
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.
Collapse
|