1
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Imai M, Colas K, Suga H. Protein Grafting Techniques: From Peptide Epitopes to Lasso-Grafted Neobiologics. Chempluschem 2024:e202400152. [PMID: 38693599 DOI: 10.1002/cplu.202400152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/03/2024]
Abstract
Protein engineering techniques have vastly expanded their domain of impact, notably following the success of antibodies. Likewise, smaller peptide therapeutics have carved an increasingly significant niche for themselves in the pharmaceutical landscape. The concept of grafting such peptides onto larger protein scaffolds, thus harvesting the advantages of both, has given rise to a variety of protein engineering strategies that are reviewed herein. We also describe our own "Lasso-Grafting" approach, which combines traditional grafting concepts with mRNA display to streamline the production of multiple grafted drug candidates for virtually any target.
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Affiliation(s)
- Mikio Imai
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kilian Colas
- 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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2
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Cioffi VB, de Castro-Amarante MF, Lulla A, Andreata-Santos R, Cruz MC, Moreno ACR, de Oliveira Silva M, de Miranda Peres B, de Freitas Junior LHG, Moraes CB, Durigon EL, Gordon NC, Hyvönen M, de Souza Ferreira LC, Balan A. SARS-CoV-2 Spike protein peptides displayed in the Pyrococcus furiosus RAD system preserve epitopes antigenicity, immunogenicity, and virus-neutralizing activity of antibodies. Sci Rep 2023; 13:16821. [PMID: 37798298 PMCID: PMC10556064 DOI: 10.1038/s41598-023-43720-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023] Open
Abstract
Amongst the potential contribution of protein or peptide-display systems to study epitopes with relevant immunological features, the RAD display system stands out as a highly stable scaffold protein that allows the presentation of constrained target peptides. Here, we employed the RAD display system to present peptides derived from the SARS-CoV-2 Spike (S) protein as a tool to detect specific serum antibodies and to generate polyclonal antibodies capable of inhibiting SARS-CoV-2 infectivity in vitro. 44 linear S-derived peptides were genetically fused with the RAD scaffold (RAD-SCoV-epitopes) and screened for antigenicity with sera collected from COVID-19-infected patients. In a second step, selected RAD-SCoV-epitopes were used to immunize mice and generate antibodies. Phenotypic screening showed that some of these antibodies were able to recognize replicating viral particles in VERO CCL-81 and most notably seven of the RAD-SCoV-epitopes were able to induce antibodies that inhibited viral infection. Our findings highlight the RAD display system as an useful platform for the immunological characterization of peptides and a potentially valuable strategy for the design of antigens for peptide-based vaccines, for epitope-specific antibody mapping, and for the development of antibodies for diagnostic and therapeutic purposes.
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Affiliation(s)
- Victor Bolsanelli Cioffi
- Laboratory of Applied Structural Biology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Maria Fernanda de Castro-Amarante
- Laboratory of Vaccine Development, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Aleksei Lulla
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Robert Andreata-Santos
- Laboratory of Vaccine Development, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Mario Costa Cruz
- Core Facilities to Support Research (CEFAP), Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, São Paulo, 173005508-000, Brazil
| | - Ana Carolina Ramos Moreno
- Laboratory of Vaccine Development, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
- Vaccine Development Laboratory, Butantan Institute, Av. Vital Brasil, 1500, São Paulo, SP, 05503-900, Brazil
| | - Mariângela de Oliveira Silva
- Phenotypic Screening Platform, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Bianca de Miranda Peres
- Phenotypic Screening Platform, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Lucio Holanda Gondim de Freitas Junior
- Phenotypic Screening Platform, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Carolina Borsoi Moraes
- Phenotypic Screening Platform, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Edison Luiz Durigon
- Laboratory of Clinical and Molecular Virology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
- Institut Pasteur de São Paulo, Av. Prof. Lucio Martins Rodrigues, 370, São Paulo, 05508-020, Brazil
| | - Nicola Coker Gordon
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Luís Carlos de Souza Ferreira
- Laboratory of Vaccine Development, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
- Institut Pasteur de São Paulo, Av. Prof. Lucio Martins Rodrigues, 370, São Paulo, 05508-020, Brazil
| | - Andrea Balan
- Laboratory of Applied Structural Biology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil.
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3
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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.
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Affiliation(s)
- Golnaz Kamalinia
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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4
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Chee SMQ, Wongsantichon J, Yi LS, Sana B, Frosi Y, Robinson RC, Ghadessy FJ. Functional display of bioactive peptides on the vGFP scaffold. Sci Rep 2021; 11:10127. [PMID: 33980885 PMCID: PMC8115314 DOI: 10.1038/s41598-021-89421-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/27/2021] [Indexed: 11/24/2022] Open
Abstract
Grafting bioactive peptides into recipient protein scaffolds can often increase their activities by conferring enhanced stability and cellular longevity. Here, we describe use of vGFP as a novel scaffold to display peptides. vGFP comprises GFP fused to a bound high affinity Enhancer nanobody that potentiates its fluorescence. We show that peptides inserted into the linker region between GFP and the Enhancer are correctly displayed for on-target interaction, both in vitro and in live cells by pull-down, measurement of target inhibition and imaging analyses. This is further confirmed by structural studies highlighting the optimal display of a vGFP-displayed peptide bound to Mdm2, the key negative regulator of p53 that is often overexpressed in cancer. We also demonstrate a potential biosensing application of the vGFP scaffold by showing target-dependent modulation of intrinsic fluorescence. vGFP is relatively thermostable, well-expressed and inherently fluorescent. These properties make it a useful scaffold to add to the existing tool box for displaying peptides that can disrupt clinically relevant protein–protein interactions.
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Affiliation(s)
- Sharon Min Qi Chee
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Jantana Wongsantichon
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Lau Sze Yi
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Barindra Sana
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Yuri Frosi
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand.,Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Farid J Ghadessy
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore.
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5
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Mihara E, Watanabe S, Bashiruddin NK, Nakamura N, Matoba K, Sano Y, Maini R, Yin Y, Sakai K, Arimori T, Matsumoto K, Suga H, Takagi J. Lasso-grafting of macrocyclic peptide pharmacophores yields multi-functional proteins. Nat Commun 2021; 12:1543. [PMID: 33750839 PMCID: PMC7943567 DOI: 10.1038/s41467-021-21875-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/17/2021] [Indexed: 12/27/2022] Open
Abstract
Protein engineering has great potential for devising multifunctional recombinant proteins to serve as next-generation protein therapeutics, but it often requires drastic modifications of the parental protein scaffolds e.g., additional domains at the N/C-terminus or replacement of a domain by another. A discovery platform system, called RaPID (Random non-standard Peptides Integrated Discovery) system, has enabled rapid discovery of small de novo macrocyclic peptides that bind a target protein with high binding specificity and affinity. Capitalizing on the optimized binding properties of the RaPID-derived peptides, here we show that RaPID-derived pharmacophore sequences can be readily implanted into surface-exposed loops on recombinant proteins and maintain both the parental peptide binding function(s) and the host protein function. We refer to this protein engineering method as lasso-grafting and demonstrate that it can endow specific binding capacity toward various receptors into a diverse set of scaffolds that includes IgG, serum albumin, and even capsid proteins of adeno-associated virus, enabling us to rapidly formulate and produce bi-, tri-, and even tetra-specific binder molecules.
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Affiliation(s)
- Emiko Mihara
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Satoshi Watanabe
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Nasir K Bashiruddin
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nozomi Nakamura
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kyoko Matoba
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Yumi Sano
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Rumit Maini
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yizhen Yin
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Katsuya Sakai
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
- WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Takao Arimori
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kunio Matsumoto
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
- WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan.
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6
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Madden SK, Itzhaki LS. Exploring the binding of rationally engineered tandem-repeat proteins to E3 ubiquitin ligase Keap1. Protein Eng Des Sel 2021; 34:gzab027. [PMID: 34882773 PMCID: PMC8660007 DOI: 10.1093/protein/gzab027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/06/2021] [Accepted: 10/04/2021] [Indexed: 11/12/2022] Open
Abstract
The process of displaying functional peptides by 'grafting' them onto loops of a stable protein scaffold can be used to impart binding affinity for a target, but it can be difficult to predict the affinity of the grafted peptide and the effect of grafting on scaffold stability. In this study, we show that a series of peptides that bind to the E3 ubiquitin ligase Keap1 can be grafted into the inter-repeat loop of a consensus-designed tetratricopeptide repeat (CTPR) protein resulting in proteins with high stability. We found that these CTPR-grafted peptides had similar affinities to their free peptide counterparts and achieved a low nanomolar range. This result is likely due to a good structural match between the inter-repeat loop of the CTPR and the Keap1-binding peptide. The grafting process led to the discovery of a new Keap1-binding peptide, Ac-LDPETGELL-NH2, with low nanomolar affinity for Keap1, highlighting the potential of the repeat-protein class for application in peptide display.
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Affiliation(s)
- Sarah K Madden
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
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7
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Diamante A, Chaturbedy PK, Rowling PJE, Kumita JR, Eapen RS, McLaughlin SH, de la Roche M, Perez-Riba A, Itzhaki LS. Engineering mono- and multi-valent inhibitors on a modular scaffold. Chem Sci 2021; 12:880-895. [PMID: 33623657 PMCID: PMC7885266 DOI: 10.1039/d0sc03175e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
Here we exploit the simple, ultra-stable, modular architecture of consensus-designed tetratricopeptide repeat proteins (CTPRs) to create a platform capable of displaying both single as well as multiple functions and with diverse programmable geometrical arrangements by grafting non-helical short linear binding motifs (SLiMs) onto the loops between adjacent repeats. As proof of concept, we built synthetic CTPRs to bind and inhibit the human tankyrase proteins (hTNKS), which play a key role in Wnt signaling and are upregulated in cancer. A series of mono-valent and multi-valent hTNKS binders was assembled. To fully exploit the modular scaffold and to further diversify the multi-valent geometry, we engineered the binding modules with two different formats, one monomeric and the other trimeric. We show that the designed proteins are stable, correctly folded and capable of binding to and inhibiting the cellular activity of hTNKS leading to downregulation of the Wnt pathway. Multivalency in both the CTPR protein arrays and the hTNKS target results in the formation of large macromolecular assemblies, which can be visualized both in vitro and in the cell. When delivered into the cell by nanoparticle encapsulation, the multivalent CTPR proteins displayed exceptional activity. They are able to inhibit Wnt signaling where small molecule inhibitors have failed to date. Our results point to the tremendous potential of the CTPR platform to exploit a range of SLiMs and assemble synthetic binding molecules with built-in multivalent capabilities and precise, pre-programmed geometries.
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Affiliation(s)
- Aurora Diamante
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Piyush K Chaturbedy
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Pamela J E Rowling
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Janet R Kumita
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Rohan S Eapen
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Stephen H McLaughlin
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge Biomedical Campus , Cambridge , CB2 0QH , UK
| | - Marc de la Roche
- Department of Biochemistry , University of Cambridge , Tennis Court Road , Cambridge CB2 1GA , UK
| | - Albert Perez-Riba
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Laura S Itzhaki
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
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8
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Raybould MIJ, Rees AR, Deane CM. Current strategies for detecting functional convergence across B-cell receptor repertoires. MAbs 2021; 13:1996732. [PMID: 34781829 PMCID: PMC8604390 DOI: 10.1080/19420862.2021.1996732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
Convergence across B-cell receptor (BCR) and antibody repertoires has become instrumental in prioritizing candidates in recent rapid therapeutic antibody discovery campaigns. It has also increased our understanding of the immune system, providing evidence for the preferential selection of BCRs to particular (immunodominant) epitopes post vaccination/infection. These important implications for both drug discovery and immunology mean that it is essential to consider the optimal way to combine experimental and computational technology when probing BCR repertoires for convergence signatures. Here, we discuss the theoretical basis for observing BCR repertoire functional convergence and explore factors of study design that can impact functional signal. We also review the computational arsenal available to detect antibodies with similar functional properties, highlighting opportunities enabled by recent clustering algorithms that exploit structural similarities between BCRs. Finally, we suggest future areas of development that should increase the power of BCR repertoire functional clustering.
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Affiliation(s)
- Matthew I. J. Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
| | | | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
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9
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Iegre J, Brear P, Baker DJ, Tan YS, Atkinson EL, Sore HF, O' Donovan DH, Verma CS, Hyvönen M, Spring DR. Efficient development of stable and highly functionalised peptides targeting the CK2α/CK2β protein-protein interaction. Chem Sci 2019; 10:5056-5063. [PMID: 31183056 PMCID: PMC6530537 DOI: 10.1039/c9sc00798a] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/11/2019] [Indexed: 12/15/2022] Open
Abstract
The discovery of new Protein-Protein Interaction (PPI) modulators is currently limited by the difficulties associated with the design and synthesis of selective small molecule inhibitors. Peptides are a potential solution for disrupting PPIs; however, they typically suffer from poor stability in vivo and limited tissue penetration hampering their wide spread use as new chemical biology tools and potential therapeutics. In this work, a combination of CuAAC chemistry, molecular modelling, X-ray crystallography, and biological validation allowed us to develop highly functionalised peptide PPI inhibitors of the protein CK2. The lead peptide, CAM7117, prevents the formation of the holoenzyme assembly in vitro, slows down proliferation, induces apoptosis in cancer cells and is stable in human serum. CAM7117 could aid the development of novel CK2 inhibitors acting at the interface and help to fully understand the intracellular pathways involving CK2. Importantly, the approach adopted herein could be applied to many PPI targets and has the potential to ease the study of PPIs by efficiently providing access to functionalised peptides.
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Affiliation(s)
- Jessica Iegre
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW , Cambridge , UK .
| | - Paul Brear
- Department of Biochemistry , University of Cambridge , Tennis Court Road , CB2 1GA , Cambridge , UK .
| | - David J Baker
- Discovery Sciences , IMED Biotech Unit , AstraZeneca , Cambridge , UK
| | - Yaw Sing Tan
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671
| | - Eleanor L Atkinson
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW , Cambridge , UK .
| | - Hannah F Sore
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW , Cambridge , UK .
| | | | - Chandra S Verma
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671
- Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
| | - Marko Hyvönen
- Department of Biochemistry , University of Cambridge , Tennis Court Road , CB2 1GA , Cambridge , UK .
| | - David R Spring
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW , Cambridge , UK .
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10
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Madden SK, Perez‐Riba A, Itzhaki LS. Exploring new strategies for grafting binding peptides onto protein loops using a consensus-designed tetratricopeptide repeat scaffold. Protein Sci 2019; 28:738-745. [PMID: 30746804 PMCID: PMC6423998 DOI: 10.1002/pro.3586] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 12/27/2022]
Abstract
Peptide display approaches, in which peptide epitopes of known binding activities are grafted onto stable protein scaffolds, have been developed to constrain the peptide in its bioactive conformation and to enhance its stability. However, peptide grafting can be a lengthy process requiring extensive computational modeling and/or optimisation by directed evolution techniques. In this study, we show that ultra-stable consensus-designed tetratricopeptide repeat (CTPR) proteins are amenable to the grafting of peptides that bind the Kelch-like ECH-associated protein 1 (Keap1) onto the loop between adjacent repeats. We explore simple strategies to optimize the grafting process and show that modest improvements in Keap1-binding affinity can be obtained by changing the composition of the linker sequence flanking either side of the binding peptide.
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Affiliation(s)
- Sarah K. Madden
- Department of PharmacologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Albert Perez‐Riba
- Department of PharmacologyUniversity of CambridgeCambridgeUnited Kingdom
- Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoCanada
| | - Laura S. Itzhaki
- Department of PharmacologyUniversity of CambridgeCambridgeUnited Kingdom
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