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Chaves EJF, Coêlho DF, Cruz CHB, Moreira EG, Simões JCM, Nascimento-Filho MJ, Lins RD. Structure-based computational design of antibody mimetics: challenges and perspectives. FEBS Open Bio 2024. [PMID: 38925955 DOI: 10.1002/2211-5463.13855] [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: 03/03/2024] [Revised: 05/17/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024] Open
Abstract
The design of antibody mimetics holds great promise for revolutionizing therapeutic interventions by offering alternatives to conventional antibody therapies. Structure-based computational approaches have emerged as indispensable tools in the rational design of those molecules, enabling the precise manipulation of their structural and functional properties. This review covers the main classes of designed antigen-binding motifs, as well as alternative strategies to develop tailored ones. We discuss the intricacies of different computational protein-protein interaction design strategies, showcased by selected successful cases in the literature. Subsequently, we explore the latest advancements in the computational techniques including the integration of machine and deep learning methodologies into the design framework, which has led to an augmented design pipeline. Finally, we verse onto the current challenges that stand in the way between high-throughput computer design of antibody mimetics and experimental realization, offering a forward-looking perspective into the field and the promises it holds to biotechnology.
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Affiliation(s)
- Elton J F Chaves
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Brazil
| | - Danilo F Coêlho
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, Brazil
| | - Carlos H B Cruz
- Institute of Structural and Molecular Biology, University College London, UK
| | | | - Júlio C M Simões
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Brazil
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, Brazil
| | - Manassés J Nascimento-Filho
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Brazil
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, Brazil
| | - Roberto D Lins
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Brazil
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, Brazil
- Fiocruz Genomics Network, Brazil
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2
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Gelová Z, Ingles-Prieto A, Bohstedt T, Frommelt F, Chi G, Chang YN, Garcia J, Wolf G, Azzollini L, Tremolada S, Scacioc A, Hansen JS, Serrano I, Droce A, Bernal JC, Burgess-Brown NA, Carpenter EP, Dürr KL, Kristensen P, Geertsma ER, Štefanić S, Scarabottolo L, Wiedmer T, Puetter V, Sauer DB, Superti-Furga G. Protein Binder Toolbox for Studies of Solute Carrier Transporters. J Mol Biol 2024; 436:168665. [PMID: 38878854 DOI: 10.1016/j.jmb.2024.168665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 07/01/2024]
Abstract
Transporters of the solute carrier superfamily (SLCs) are responsible for the transmembrane traffic of the majority of chemical substances in cells and tissues and are therefore of fundamental biological importance. As is often the case with membrane proteins that can be heavily glycosylated, a lack of reliable high-affinity binders hinders their functional analysis. Purifying and reconstituting transmembrane proteins in their lipidic environments remains challenging and standard approaches to generate binders for multi-transmembrane proteins, such as SLCs, channels or G protein-coupled receptors (GPCRs) are lacking. While generating protein binders to 27 SLCs, we produced full length protein or cell lines as input material for binder generation by selected binder generation platforms. As a result, we obtained 525 binders for 22 SLCs. We validated the binders with a cell-based validation workflow using immunofluorescent and immunoprecipitation methods to process all obtained binders. Finally, we demonstrated the potential applications of the binders that passed our validation pipeline in structural, biochemical, and biological applications using the exemplary protein SLC12A6, an ion transporter relevant in human disease. With this work, we were able to generate easily renewable and highly specific binders against SLCs, which will greatly facilitate the study of this neglected protein family. We hope that the process will serve as blueprint for the generation of binders against the entire superfamily of SLC transporters.
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Affiliation(s)
- Zuzana Gelová
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tina Bohstedt
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Fabian Frommelt
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Julio Garcia
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gernot Wolf
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | | | - Andreea Scacioc
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jesper S Hansen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Iciar Serrano
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Aida Droce
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Nicola A Burgess-Brown
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elisabeth P Carpenter
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Katharina L Dürr
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Eric R Geertsma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Saša Štefanić
- Nanobody Service Facility, University of Zurich, AgroVet-Strickhof, Eschikon, Switzerland
| | | | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - David B Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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3
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Dinh-Fricke AV, Hantschel O. Improving the pharmacokinetics, biodistribution and plasma stability of monobodies. Front Pharmacol 2024; 15:fphar.2024.1393112. [PMID: 38617793 PMCID: PMC7615827 DOI: 10.3389/fphar.2024.1393112] [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: 02/28/2024] [Accepted: 03/21/2024] [Indexed: 04/16/2024] Open
Abstract
Cancer is a leading cause of death worldwide. Several targeted anticancer drugs entered clinical practice and improved survival of cancer patients with selected tumor types, but therapy resistance and metastatic disease remains a challenge. A major class of targeted anticancer drugs are therapeutic antibodies, but their use is limited to extracellular targets. Hence, alternative binding scaffolds have been investigated for intracellular use and better tumor tissue penetration. Among those, monobodies are small synthetic protein binders that were engineered to bind with high affinity and selectivity to central intracellular oncoproteins and inhibit their signaling. Despite their use as basic research tools, the potential of monobodies as protein therapeutics remains to be explored. In particular, the pharmacological properties of monobodies, including plasma stability, toxicity and pharmacokinetics have not been investigated. Here, we show that monobodies have high plasma stability, are well-tolerated in mice, but have a short half-life in vivo due to rapid renal clearance. Therefore, we engineered monobody fusions with an albumin-binding domain (ABD), which showed enhanced pharmacological properties without affecting their target binding: We found that ABD-monobody fusions display increased stability in mouse plasma. Most importantly, ABD-monobodies have a dramatically prolonged in vivo half-life and are not rapidly excreted by renal clearance, remaining in the blood significantly longer, while not accumulating in specific internal organs. Our results demonstrate the promise and versatility of monobodies to be developed into future therapeutics for cancer treatment. We anticipate that monobodies may be able to extend the spectrum of intracellular targets, resulting in a significant benefit to patient outcome.
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Affiliation(s)
| | - Oliver Hantschel
- Institute of Physiological Chemistry, Philipps-University of Marburg, Marburg, Germany
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4
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Amesaka H, Hara M, Sakai Y, Shintani A, Sue K, Yamanaka T, Tanaka S, Furukawa Y. Engineering a monobody specific to monomeric Cu/Zn-superoxide dismutase associated with amyotrophic lateral sclerosis. Protein Sci 2024; 33:e4961. [PMID: 38511674 PMCID: PMC10955725 DOI: 10.1002/pro.4961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/22/2024]
Abstract
Misfolding of mutant Cu/Zn-superoxide dismutase (SOD1) has been implicated in familial form of amyotrophic lateral sclerosis (ALS). A natively folded SOD1 forms a tight homodimer, and the dimer dissociation has been proposed to trigger the oligomerization/aggregation of SOD1. Besides increasing demand for probes allowing the detection of monomerized forms of SOD1 in various applications, the development of probes has been limited to conventional antibodies. Here, we have developed Mb(S4) monobody, a small synthetic binding protein based on the fibronectin type III scaffold, that recognizes a monomeric but not dimeric form of SOD1 by performing combinatorial library selections using phage and yeast-surface display methods. Although Mb(S4) was characterized by its excellent selectivity to the monomeric conformation of SOD1, the monomeric SOD1/Mb(S4) complex was not so stable (apparent Kd ~ μM) as to be detected in conventional pull-down experiments. Instead, the complex of Mb(S4) with monomeric but not dimeric SOD1 was successfully trapped by proximity-enabled chemical crosslinking even when reacted in the cell lysates. We thus anticipate that Mb(S4) binding followed by chemical crosslinking would be a useful strategy for in vitro and also ex vivo detection of the monomeric SOD1 proteins.
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Affiliation(s)
- Hiroshi Amesaka
- Department of Biomolecular ChemistryKyoto Prefectural UniversityKyotoJapan
| | - Mizuho Hara
- Department of Biomolecular ChemistryKyoto Prefectural UniversityKyotoJapan
| | - Yuki Sakai
- Department of Biomolecular ChemistryKyoto Prefectural UniversityKyotoJapan
| | | | - Kaori Sue
- Department of ChemistryKeio UniversityYokohamaJapan
| | - Tomoyuki Yamanaka
- Department of Neuroscience of DiseaseBrain Research Institute, Niigata UniversityNiigataJapan
| | - Shun‐ichi Tanaka
- Department of Biomolecular ChemistryKyoto Prefectural UniversityKyotoJapan
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5
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Pandey RK, Mehrotra S. Engineering high affinity antigen-binders: Beyond conventional antibodies. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 140:37-57. [PMID: 38762275 DOI: 10.1016/bs.apcsb.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
For decades, antibodies have remained the archetypal binding proteins that can be rapidly produced with high affinity and specificity against virtually any target. A conventional antibody is still considered the prototype of a binding molecule. It is therefore not surprising that antibodies are routinely used in basic scientific and biomedical research, analytical workflows, molecular diagnostics etc. and represent the fastest growing sector in the field of biotechnology. However, several limitations associated with conventional antibodies, including stringent requirement of animal immunizations, mammalian cells for expression, issues on stability and aggregation, bulkier size and the overall time and cost of production has propelled evolution of concepts along alternative antigen binders. Rapidly evolving protein engineering approaches and high throughput screening platforms have further complemented the development of myriads of classes of non-conventional protein binders including antibody derived as well as non-antibody based molecular scaffolds. These non-canonical binders are finding use across disciplines of which diagnostics and therapeutics are the most noteworthy.
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Affiliation(s)
- Rajeev Kumar Pandey
- Research and Development-Protein Biology, Thermo Fisher Scientific, Bangalore, India
| | - Sanjana Mehrotra
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India.
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6
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Campbell E, Luxton T, Kohl D, Goodchild SA, Walti C, Jeuken LJC. Chimeric Protein Switch Biosensors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:1-35. [PMID: 38273207 DOI: 10.1007/10_2023_241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Rapid detection of protein and small-molecule analytes is a valuable technique across multiple disciplines, but most in vitro testing of biological or environmental samples requires long, laborious processes and trained personnel in laboratory settings, leading to long wait times for results and high expenses. Fusion of recognition with reporter elements has been introduced to detection methods such as enzyme-linked immunoassays (ELISA), with enzyme-conjugated secondary antibodies removing one of the many incubation and wash steps. Chimeric protein switch biosensors go further and provide a platform for homogenous mix-and-read assays where long wash and incubation steps are eradicated from the process. Chimeric protein switch biosensors consist of an enzyme switch (the reporter) coupled to a recognition element, where binding of the analyte results in switching the activity of the reporter enzyme on or off. Several chimeric protein switch biosensors have successfully been developed for analytes ranging from small molecule drugs to large protein biomarkers. There are two main formats of chimeric protein switch biosensor developed, one-component and multi-component, and these formats exhibit unique advantages and disadvantages. Genetically fusing a recognition protein to the enzyme switch has many advantages in the production and performance of the biosensor. A range of immune and synthetic binding proteins have been developed as alternatives to antibodies, including antibody mimetics or antibody fragments. These are mainly small, easily manipulated proteins and can be genetically fused to a reporter for recombinant expression or manipulated to allow chemical fusion. Here, aspects of chimeric protein switch biosensors will be reviewed with a comparison of different classes of recognition elements and switching mechanisms.
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Affiliation(s)
- Emma Campbell
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Timothy Luxton
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Declan Kohl
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | | | - Christoph Walti
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK
| | - Lars J C Jeuken
- School of Biomedical Sciences, University of Leeds, Leeds, UK.
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
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7
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Whaby M, Nair RS, O'Bryan JP. Probing RAS Function Using Monobody and NanoBiT Technologies. Methods Mol Biol 2024; 2797:211-225. [PMID: 38570462 DOI: 10.1007/978-1-0716-3822-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Missense mutations in the RAS family of oncogenes (HRAS, KRAS, and NRAS) are present in approximately 20% of human cancers, making RAS a valuable therapeutic target (Prior et al., Cancer Res 80:2969-2974, 2020). Although decades of research efforts to develop therapeutic inhibitors of RAS were unsuccessful, there has been success in recent years with the entrance of FDA-approved KRASG12C-specific inhibitors to the clinic (Skoulidis et al., N Engl J Med 384:2371-2381, 2021; Jänne et al., N Engl J Med 387:120-131, 2022). Additionally, KRASG12D-specific inhibitors are presently undergoing clinical trials (Wang et al., J Med Chem 65:3123-3133, 2022). The advent of these allele specific inhibitors has disproved the previous notion that RAS is undruggable. Despite these advancements in RAS-targeted therapeutics, several RAS mutants that frequently arise in cancers remain without tractable drugs. Thus, it is critical to further understand the function and biology of RAS in cells and to develop tools to identify novel therapeutic vulnerabilities for development of anti-RAS therapeutics. To do this, we have exploited the use of monobody (Mb) technology to develop specific protein-based inhibitors of selected RAS isoforms and mutants (Spencer-Smith et al., Nat Chem Biol 13:62-68, 2017; Khan et al., Cell Rep 38:110322, 2022; Wallon et al., Proc Natl Acad Sci USA 119:e2204481119, 2022; Khan et al., Small GTPases 13:114-127, 2021; Khan et al., Oncogene 38:2984-2993, 2019). Herein, we describe our combined use of Mbs and NanoLuc Binary Technology (NanoBiT) to analyze RAS protein-protein interactions and to screen for RAS-binding small molecules in live-cell, high-throughput assays.
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Affiliation(s)
- Michael Whaby
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Rakesh Sathish Nair
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
- Ralph H. Johnson VA Medical Center, Charleston, SC, USA
| | - John P O'Bryan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA.
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA.
- Ralph H. Johnson VA Medical Center, Charleston, SC, USA.
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8
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Iwamoto N, Sato Y, Manabe A, Inuki S, Ohno H, Nonaka M, Oishi S. Design and Synthesis of Monobody Variants with Low Immunogenicity. ACS Med Chem Lett 2023; 14:1596-1601. [PMID: 37974939 PMCID: PMC10641909 DOI: 10.1021/acsmedchemlett.3c00342] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/27/2023] [Indexed: 11/19/2023] Open
Abstract
Mirror-image proteins (d-proteins) are promising scaffolds for drug discovery because of their high proteolytic stability and low immunogenic properties. Facile and reproducible processes for the preparation of functional d-proteins are required for their application in therapeutic biologics. In this study, we designed and synthesized a novel monobody variant with two cysteine substitutions that facilitate the synthetic process via sequential native chemical ligations and improve protein stability by disulfide bond formation. The synthetic anti-GFP monobody in this model study exhibited good binding affinity to the target enhanced green fluorescent protein. In vivo administration of the synthetic anti-GFP monobody (l-monobody) to mice induced antidrug antibody (ADA) production, whereas no ADA production was observed following immunization with the mirror-image anti-GFP monobody (d-monobody). These results suggest that the synthetic d-monobody is a non-antibody protein scaffold with low immunogenic properties.
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Affiliation(s)
- Naoya Iwamoto
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yukino Sato
- Laboratory
of Medicinal Chemistry, Kyoto Pharmaceutical
University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Asako Manabe
- Graduate
School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shinsuke Inuki
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroaki Ohno
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Motohiro Nonaka
- Graduate
School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shinya Oishi
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
- Laboratory
of Medicinal Chemistry, Kyoto Pharmaceutical
University, Yamashina-ku, Kyoto 607-8412, Japan
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9
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De Groot AS, Khan S, Mattei AE, Lelias S, Martin WD. Does human homology reduce the potential immunogenicity of non-antibody scaffolds? Front Immunol 2023; 14:1215939. [PMID: 38022550 PMCID: PMC10664710 DOI: 10.3389/fimmu.2023.1215939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Biologics developers are moving beyond antibodies for delivery of a wide range of therapeutic interventions. These non-antibody modalities are often based on 'natural' protein scaffolds that are modified to deliver bioactive sequences. Both human-derived and non-human-sourced scaffold proteins have been developed. New types of "non-antibody" scaffolds are still being discovered, as they offer attractive alternatives to monoclonals due to their smaller size, improved stability, and ease of synthesis. They are believed to have low immunogenic potential. However, while several human-sourced protein scaffolds have not been immunogenic in clinical studies, this may not predict their overall performance in other therapeutic applications. A preliminary evaluation of their potential for immunogenicity is warranted. Immunogenicity risk potential has been clearly linked to the presence of T "helper" epitopes in the sequence of biologic therapeutics. In addition, tolerogenic epitopes are present in some human proteins and may decrease their immunogenic potential. While the detailed sequences of many non-antibody scaffold therapeutic candidates remain unpublished, their backbone sequences are available for review and analysis. We assessed 12 example non-antibody scaffold backbone sequences using our epitope-mapping tools (EpiMatrix) for this perspective. Based on EpiMatrix scoring, their HLA DRB1-restricted T cell epitope content appears to be lower than the average protein, and sequences that may act as tolerogenic epitopes are present in selected human-derived scaffolds. Assessing the potential immunogenicity of scaffold proteins regarding self and non-self T cell epitopes may be of use for drug developers and clinicians, as these exciting new non-antibody molecules begin to emerge from the preclinical pipeline into clinical use.
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Affiliation(s)
- Anne S. De Groot
- EpiVax, Providence, RI, United States
- University of Georgia, Center for Vaccines and Immunology, Athens, GA, United States
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Buonocore M, Grimaldi M, Santoro A, Covelli V, Marino C, Napolitano E, Novi S, Tecce MF, Ciaglia E, Montella F, Lopardo V, Perugini V, Santin M, D’Ursi AM. Exploiting the Features of Short Peptides to Recognize Specific Cell Surface Markers. Int J Mol Sci 2023; 24:15610. [PMID: 37958593 PMCID: PMC10650159 DOI: 10.3390/ijms242115610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Antibodies are the macromolecules of choice to ensure specific recognition of biomarkers in biological assays. However, they present a range of shortfalls including a relatively high production cost and limited tissue penetration. Peptides are relatively small molecules able to reproduce sequences of highly specific paratopes and, although they have less biospecificity than antibodies, they offer advantages like ease of synthesis, modifications of their amino acid sequences and tagging with fluorophores and other molecules required for detection. This work presents a strategy to design peptide sequences able to recognize the CD44 hyaluronic acid receptor present in the plasmalemma of a range of cells including human bone marrow stromal mesenchymal cells. The protocol of identification of the optimal amino acid sequence was based on the combination of rational design and in silico methodologies. This protocol led to the identification of two peptide sequences which were synthesized and tested on human bone marrow mesenchymal stromal cells (hBM-MSCs) for their ability to ensure specific binding to the CD44 receptor. Of the two peptides, one binds CD44 with sensitivity and selectivity, thus proving its potential to be used as a suitable alternative to this antibody in conventional immunostaining. In the context of regenerative medicine, the availability of this peptide could be harnessed to functionalize tissue engineering scaffolds to anchor stem cells as well as to be integrated into systems such as cell sorters to efficiently isolate MSCs from biological samples including various cell subpopulations. The data here reported can represent a model for developing peptide sequences able to recognize hBM-MSCs and other types of cells and for their integration in a range of biomedical applications.
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Affiliation(s)
- Michela Buonocore
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- Department of Chemical Sciences, University of Naples Federico II, 80138 Naples, Italy
| | - Manuela Grimaldi
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
| | - Angelo Santoro
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- Scuola di Specializzazione in Farmacia Ospedaliera, University of Salerno, 84084 Fisciano, Italy
| | - Verdiana Covelli
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, 80138 Naples, Italy
| | - Carmen Marino
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- PhD Program in Drug Discovery and Development, Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy
| | - Enza Napolitano
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- PhD Program in Drug Discovery and Development, Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy
| | - Sara Novi
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- PhD Program in Drug Discovery and Development, Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy
| | - Mario Felice Tecce
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
| | - Elena Ciaglia
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (E.C.); (F.M.); (V.L.)
| | - Francesco Montella
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (E.C.); (F.M.); (V.L.)
| | - Valentina Lopardo
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (E.C.); (F.M.); (V.L.)
| | - Valeria Perugini
- Centre for Regenerative Medicine and Devices, School of Applied Sciences, University of Brighton, Brighton BN2 4AT, UK; (V.P.); (M.S.)
| | - Matteo Santin
- Centre for Regenerative Medicine and Devices, School of Applied Sciences, University of Brighton, Brighton BN2 4AT, UK; (V.P.); (M.S.)
| | - Anna Maria D’Ursi
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
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11
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David TI, Pestov NB, Korneenko TV, Barlev NA. Non-Immunoglobulin Synthetic Binding Proteins for Oncology. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1232-1247. [PMID: 37770391 DOI: 10.1134/s0006297923090043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 09/30/2023]
Abstract
Extensive application of technologies like phage display in screening peptide and protein combinatorial libraries has not only facilitated creation of new recombinant antibodies but has also significantly enriched repertoire of the protein binders that have polypeptide scaffolds without homology to immunoglobulins. These innovative synthetic binding protein (SBP) platforms have grown in number and now encompass monobodies/adnectins, DARPins, lipocalins/anticalins, and a variety of miniproteins such as affibodies and knottins, among others. They serve as versatile modules for developing complex affinity tools that hold promise in both diagnostic and therapeutic settings. An optimal scaffold typically has low molecular weight, minimal immunogenicity, and demonstrates resistance against various challenging conditions, including proteolysis - making it potentially suitable for peroral administration. Retaining functionality under reducing intracellular milieu is also advantageous. However, paramount to its functionality is the scaffold's ability to tolerate mutations across numerous positions, allowing for the formation of a sufficiently large target binding region. This is achieved through the library construction, screening, and subsequent expression in an appropriate system. Scaffolds that exhibit high thermodynamic stability are especially coveted by the developers of new SBPs. These are steadily making their way into clinical settings, notably as antagonists of oncoproteins in signaling pathways. This review surveys the diverse landscape of SBPs, placing particular emphasis on the inhibitors targeting the oncoprotein KRAS, and highlights groundbreaking opportunities for SBPs in oncology.
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Affiliation(s)
- Temitope I David
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
- Laboratory of Molecular Oncology, Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nikolay B Pestov
- Institute of Biomedical Chemistry, Moscow, 119121, Russia.
- Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, Moscow, 108819, Russia
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Tatyana V Korneenko
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Nikolai A Barlev
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
- Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, Moscow, 108819, Russia
- Institute of Cytology Russian Academy of Sciences, St.-Petersburg, 194064, Russia
- School of Medicine, Nazarbayev University, Astana, 010000, Kazakhstan
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12
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Rathje OH, Perryman L, Payne RJ, Hamprecht DW. PROTACs Targeting MLKL Protect Cells from Necroptosis. J Med Chem 2023; 66:11216-11236. [PMID: 37535857 DOI: 10.1021/acs.jmedchem.3c00665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Mixed Lineage Kinase domain-Like pseudokinase (MLKL) is implicated in a broad range of diseases due to its role as the ultimate effector of necroptosis and has therefore emerged as an attractive drug target. Here, we describe the development of PROteolysis TArgeting Chimeras (PROTACs) as a novel approach to knock down MLKL through chemical means. A series of candidate degraders were synthesized from a high-affinity pyrazole carboxamide-based MLKL ligand leading to the identification of a PROTAC molecule that effectively degraded MLKL and completely abrogated cell death in a TSZ model of necroptosis. By leveraging the innate ability of these PROTACs to degrade MLKL in a dose-dependent manner, the quantitative relationship between MLKL levels and necroptosis was interrogated. This work demonstrates the feasibility of targeting MLKL using a PROTAC approach and provides a powerful tool to further our understanding of the role of MLKL within the necroptotic pathway.
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Affiliation(s)
- Oliver H Rathje
- Pharmaxis Ltd., 20 Rodborough Road, Frenchs Forest, NSW 2086, Australia
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Lara Perryman
- Pharmaxis Ltd., 20 Rodborough Road, Frenchs Forest, NSW 2086, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
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13
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Zhang Y, Sultonova RD, You SH, Choi Y, Kim SY, Lee WS, Seong J, Min JJ, Hong Y. The anticancer effect of PASylated calreticulin-targeting L-ASNase in solid tumor bearing mice with immunogenic cell death-inducing chemotherapy. Biochem Pharmacol 2023; 210:115473. [PMID: 36863616 DOI: 10.1016/j.bcp.2023.115473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/03/2023] [Accepted: 02/24/2023] [Indexed: 03/04/2023]
Abstract
L-Asparaginase (L-ASNase), a bacterial enzyme that degrades asparagine, has been commonly used in combination with several chemical drugs to treat malignant hematopoietic cancers such as acute lymphoblastic leukemia (ALL). In contrast, the enzyme was known to inhibit the growth of solid tumor cells in vitro, but not to be effective in vivo. We previously reported that two novel monobodies (CRT3 and CRT4) bound specifically with calreticulin (CRT) exposed on tumor cells and tissues during immunogenic cell death (ICD). Here, we engineered L-ASNases conjugated with monobodies at the N-termini and PAS200 tags at the C-termini (CRT3LP and CRT4LP). These proteins were expected to possess four monobody and PAS200 tag moieties, which did not disrupt the L-ASNase conformation. These proteins were expressed 3.8-fold more highly in E. coli than those without PASylation. The purified proteins were highly soluble, with much greater apparent molecular weights than expected ones. Their affinity (Kd) against CRT was about 2 nM, 4-fold higher than that of monobodies. Their enzyme activity (∼6.5 IU/nmol) was similar to that of L-ASNase (∼7.2 IU/nmol), and their thermal stability was significantly increased at 55 °C. Their half-life times were > 9 h in mouse sera, about 5-fold longer than that of L-ASNase (∼1.8 h). Moreover, CRT3LP and CRT4LP bound specifically with CRT exposed on tumor cells in vitro, and additively suppressed the tumor growth in CT-26 and MC-38 tumor-bearing mice treated with ICD-inducing drugs (doxorubicin and mitoxantrone) but not with a non-ICD-inducing drug (gemcitabine). All data indicated that PASylated CRT-targeted L-ASNases enhanced the anticancer efficacy of ICD-inducing chemotherapy. Taken together, L-ASNase would be a potential anticancer drug for treating solid tumors.
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Affiliation(s)
- Ying Zhang
- Institute for Molecular Imaging and Theranostics, Department of Nuclear Medicine, Chonnam National University Medical School and Hwasun Hospital, Hwasun, Republic of Korea
| | - Rukhsora D Sultonova
- Institute for Molecular Imaging and Theranostics, Department of Nuclear Medicine, Chonnam National University Medical School and Hwasun Hospital, Hwasun, Republic of Korea
| | - Sung-Hwan You
- Institute for Molecular Imaging and Theranostics, Department of Nuclear Medicine, Chonnam National University Medical School and Hwasun Hospital, Hwasun, Republic of Korea
| | - Yoonjoo Choi
- Combinatorial Tumor Immunotherapy MRC, Chonnam National University Medical School, Hwasun, Republic of Korea
| | - So-Young Kim
- Institute for Molecular Imaging and Theranostics, Department of Nuclear Medicine, Chonnam National University Medical School and Hwasun Hospital, Hwasun, Republic of Korea
| | - Wan-Sik Lee
- Department of Internal Medicine, Chonnam National University Medical School, Hwasun, Republic of Korea
| | - Jihyoun Seong
- Institute for Molecular Imaging and Theranostics, Department of Nuclear Medicine, Chonnam National University Medical School and Hwasun Hospital, Hwasun, Republic of Korea; Department of Microbiology, Chonnam National University Medical School, Hwasun, Republic of Korea
| | - Jung-Joon Min
- Institute for Molecular Imaging and Theranostics, Department of Nuclear Medicine, Chonnam National University Medical School and Hwasun Hospital, Hwasun, Republic of Korea.
| | - Yeongjin Hong
- Institute for Molecular Imaging and Theranostics, Department of Nuclear Medicine, Chonnam National University Medical School and Hwasun Hospital, Hwasun, Republic of Korea; Department of Microbiology, Chonnam National University Medical School, Hwasun, Republic of Korea.
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14
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Ahmad M, Ha JH, Mayse LA, Presti MF, Wolfe AJ, Moody KJ, Loh SN, Movileanu L. A generalizable nanopore sensor for highly specific protein detection at single-molecule precision. Nat Commun 2023; 14:1374. [PMID: 36941245 PMCID: PMC10027671 DOI: 10.1038/s41467-023-36944-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/23/2023] [Indexed: 03/23/2023] Open
Abstract
Protein detection has wide-ranging implications in molecular diagnostics. Substantial progress has been made in protein analytics using nanopores and the resistive-pulse technique. Yet, a long-standing challenge is implementing specific interfaces for detecting proteins without the steric hindrance of the pore interior. Here, we formulate a class of sensing elements made of a programmable antibody-mimetic binder fused to a monomeric protein nanopore. This way, such a modular design significantly expands the utility of nanopore sensors to numerous proteins while preserving their architecture, specificity, and sensitivity. We prove the power of this approach by developing and validating nanopore sensors for protein analytes that drastically vary in size, charge, and structural complexity. These analytes produce unique electrical signatures that depend on their identity and quantity and the binder-analyte assembly at the nanopore tip. The outcomes of this work could impact biomedical diagnostics by providing a fundamental basis for biomarker detection in biofluids.
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Affiliation(s)
- Mohammad Ahmad
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York-Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Lauren A Mayse
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY, 13244, USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology, State University of New York-Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Aaron J Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
- Ichor Life Sciences, Inc., 2561 US Route 11, LaFayette, NY, 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699, USA
- Department of Chemistry, College of Environmental Science and Forestry, State University of New York, 1 Forestry Drive, Syracuse, NY, 13210, USA
| | - Kelsey J Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
- Ichor Life Sciences, Inc., 2561 US Route 11, LaFayette, NY, 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699, USA
- Department of Chemistry, College of Environmental Science and Forestry, State University of New York, 1 Forestry Drive, Syracuse, NY, 13210, USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, State University of New York-Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA.
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY, 13244, USA.
- The BioInspired Institute, Syracuse University, Syracuse, NY, 13244, USA.
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15
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Intracellular Antibodies for Drug Discovery and as Drugs of the Future. Antibodies (Basel) 2023; 12:antib12010024. [PMID: 36975371 PMCID: PMC10044824 DOI: 10.3390/antib12010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
The application of antibodies in cells was first shown in the early 1990s, and subsequently, the field of intracellular antibodies has expanded to encompass antibody fragments and their use in target validation and as engineered molecules that can be fused to moieties (referred to as warheads) to replace the Fc effector region of a whole immunoglobulin to elicit intracellular responses, such as cell death pathways or protein degradation. These various forms of intracellular antibodies have largely been used as research tools to investigate function within cells by perturbing protein activity. New applications of such molecules are on the horizon, namely their use as drugs per se and as templates for small-molecule drug discovery. The former is a potential new pharmacology that could harness the power and flexibility of molecular biology to generate new classes of drugs (herein referred to as macrodrugs when used in the context of disease control). Delivery of engineered intracellular antibodies, and other antigen-binding macromolecules formats, into cells to produce a therapeutic effect could be applied to any therapeutic area where regulation, degradation or other kinds of manipulation of target proteins can produce a therapeutic effect. Further, employing single-domain antibody fragments as competitors in small-molecule screening has been shown to enable identification of drug hits from diverse chemical libraries. Compounds selected in this way can mimic the effects of the intracellular antibodies that have been used for target validation. The capability of intracellular antibodies to discriminate between closely related proteins lends a new dimension to drug screening and drug development.
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16
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Sha F, Kurosawa K, Glasser E, Ketavarapu G, Albazzaz S, Koide A, Koide S. Monobody Inhibitor Selective to the Phosphatase Domain of SHP2 and its Use as a Probe for Quantifying SHP2 Allosteric Regulation. J Mol Biol 2023; 435:168010. [PMID: 36806475 PMCID: PMC10079645 DOI: 10.1016/j.jmb.2023.168010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 02/04/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023]
Abstract
SHP2 is a phosphatase/adaptor protein that plays an important role in various signaling pathways. Its mutations are associated with cancers and developmental diseases. SHP2 contains a protein tyrosine phosphatase (PTP) and two SH2 domains. Selective inhibition of these domains has been challenging due to the multitude of homologous proteins in the proteome. Here, we developed a monobody, synthetic binding protein, that bound to and inhibited the SHP2 PTP domain. It was selective to SHP2 PTP over close homologs. A crystal structure of the monobody-PTP complex revealed that the monobody bound both highly conserved residues in the active site and less conserved residues in the periphery, rationalizing its high selectivity. Its epitope overlapped with the interface between the PTP and N-terminal SH2 domains that is formed in auto-inhibited SHP2. By using the monobody as a probe for the accessibility of the PTP active site, we developed a simple, nonenzymatic assay for the allosteric regulation of SHP2. The assay showed that, in the absence of an activating phospho-Tyr ligand, wild-type SHP2 and the "PTP-dead" C459E mutant were predominantly in the closed state in which the PTP active site is inaccessible, whereas the E76K and C459S mutants were in the open, active state. It also revealed that previously developed monobodies to the SH2 domains, ligands lacking a phospho-Tyr, weakly favored the open state. These results provide corroboration for a conformational equilibrium underlying allosteric regulation of SHP2, provide powerful tools for characterizing and controlling SHP2 functions, and inform drug discovery against SHP2.
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Affiliation(s)
- Fern Sha
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, United States
| | - Kohei Kurosawa
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, United States; Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, United States
| | - Eliezra Glasser
- Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, United States
| | - Gayatri Ketavarapu
- Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, United States
| | - Samara Albazzaz
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, United States
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, United States; Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, United States; Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, United States
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, United States; Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, United States; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, United States.
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17
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Xu W, Cong Z, Duan Q, Wang Q, Su S, Wang R, Lu L, Xue J, Jiang S. A Protein-Based, Long-Acting HIV-1 Fusion Inhibitor with an Improved Pharmacokinetic Profile. Pharmaceuticals (Basel) 2022; 15:ph15040424. [PMID: 35455421 PMCID: PMC9025429 DOI: 10.3390/ph15040424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/24/2022] [Accepted: 03/29/2022] [Indexed: 02/01/2023] Open
Abstract
Recently, a series of highly effective peptide- or protein-based HIV fusion inhibitors have been identified. However, due to their short half-life, their clinical application is limited. Therefore, the development of long-acting HIV fusion inhibitors is urgently needed. Here, we designed and constructed a protein-based, long-acting HIV fusion inhibitor, termed FLT (FN3-L35-T1144), consisting of a monobody, FN3, which contains an albumin-binding domain (ABD), a 35-mer linker (L35), and a peptide-based HIV fusion inhibitor, T1144. We found that FLT bound, via its FN3 component, with human serum albumin (HSA) in a reversible manner, thus maintaining the high efficiency of T1144 against infection by both HIV-1 IIIB (X4) and Bal (R5) strains with IC50 of 11.6 nM and 15.3 nM, respectively, and remarkably prolonging the half-life of T1144 (~27 h in SD rats). This approach affords protein-based HIV fusion inhibitors with much longer half-life compared to enfuvirtide, a peptide-based HIV fusion inhibitor approved for use in clinics. Therefore, FLT is a promising candidate as a new protein-based anti-HIV drug with an improved pharmacokinetic profile.
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Affiliation(s)
- Wei Xu
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (W.X.); (Q.D.); (Q.W.); (S.S.)
| | - Zhe Cong
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China;
| | - Qianyu Duan
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (W.X.); (Q.D.); (Q.W.); (S.S.)
| | - Qian Wang
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (W.X.); (Q.D.); (Q.W.); (S.S.)
| | - Shan Su
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (W.X.); (Q.D.); (Q.W.); (S.S.)
| | - Rui Wang
- Beijing Prosperous Biopharm Company, Beijing 100021, China;
| | - Lu Lu
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (W.X.); (Q.D.); (Q.W.); (S.S.)
- Correspondence: (L.L.); (J.X.); (S.J.)
| | - Jing Xue
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China;
- Correspondence: (L.L.); (J.X.); (S.J.)
| | - Shibo Jiang
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (W.X.); (Q.D.); (Q.W.); (S.S.)
- Correspondence: (L.L.); (J.X.); (S.J.)
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18
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Jin S, Sun Y, Liang X, Gu X, Ning J, Xu Y, Chen S, Pan L. Emerging new therapeutic antibody derivatives for cancer treatment. Signal Transduct Target Ther 2022; 7:39. [PMID: 35132063 PMCID: PMC8821599 DOI: 10.1038/s41392-021-00868-x] [Citation(s) in RCA: 152] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 12/18/2022] Open
Abstract
Monoclonal antibodies constitute a promising class of targeted anticancer agents that enhance natural immune system functions to suppress cancer cell activity and eliminate cancer cells. The successful application of IgG monoclonal antibodies has inspired the development of various types of therapeutic antibodies, such as antibody fragments, bispecific antibodies, and antibody derivatives (e.g., antibody–drug conjugates and immunocytokines). The miniaturization and multifunctionalization of antibodies are flexible and viable strategies for diagnosing or treating malignant tumors in a complex tumor environment. In this review, we summarize antibodies of various molecular types, antibody applications in cancer therapy, and details of clinical study advances. We also discuss the rationale and mechanism of action of various antibody formats, including antibody–drug conjugates, antibody–oligonucleotide conjugates, bispecific/multispecific antibodies, immunocytokines, antibody fragments, and scaffold proteins. With advances in modern biotechnology, well-designed novel antibodies are finally paving the way for successful treatments of various cancers, including precise tumor immunotherapy, in the clinic.
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Affiliation(s)
- Shijie Jin
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Yanping Sun
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Xiao Liang
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Xinyu Gu
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Jiangtao Ning
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Yingchun Xu
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Shuqing Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China. .,Department of Precision Medicine on Tumor Therapeutics, ZJU-Hangzhou Global Scientific and Technological Innovation Center, 311200, Hangzhou, China.
| | - Liqiang Pan
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China. .,The First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China. .,Key Laboratory of Pancreatic Disease of Zhejiang Province, 310003, Hangzhou, China.
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19
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Schmidt N, Abendroth F, Vázquez O, Hantschel O. Synthesis of the l- and d-SH2 domain of the leukaemia oncogene Bcr-Abl. RSC Chem Biol 2022; 3:1008-1012. [PMID: 35975004 PMCID: PMC9347351 DOI: 10.1039/d2cb00108j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/01/2022] [Indexed: 11/29/2022] Open
Abstract
The d- and l-versions of the Bcr-Abl SH2 domain (12.7 kDa) were synthesized. Key optimizations included pseudoproline incorporation, N-terminal hydrophilic tail addition and mild N-acetoxy succinimide acetylation. Their folding and activity are as for the recombinant protein. Our results will enable engineering of mirror-image monobody antagonists of the central oncoprotein Bcr-Abl. The d- and l-versions of the Bcr-Abl SH2 domain (12.7 kDa) were synthesized successfully and show similar folding as compared to a recombinantly expressed version.![]()
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Affiliation(s)
- Nina Schmidt
- Institute of Physiological Chemistry, University of Marburg, 35032, Marburg, Germany
| | - Frank Abendroth
- Faculty of Chemistry, University of Marburg, 35032, Marburg, Germany
| | - Olalla Vázquez
- Faculty of Chemistry, University of Marburg, 35032, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, 35032, Marburg, Germany
| | - Oliver Hantschel
- Institute of Physiological Chemistry, University of Marburg, 35032, Marburg, Germany
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20
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Trainor K, Doyle CM, Metcalfe-Roach A, Steckner J, Lipovšek D, Malakian H, Langley D, Krystek SR, Meiering EM. Design for Solubility May Reveal Induction of Amide Hydrogen/Deuterium Exchange by Protein Self-Association. J Mol Biol 2021; 434:167398. [PMID: 34902431 DOI: 10.1016/j.jmb.2021.167398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 10/19/2022]
Abstract
Structural heterogeneity often constrains the characterization of aggregating proteins to indirect or low-resolution methods, obscuring mechanistic details of association. Here, we report progress in understanding the aggregation of Adnectins, engineered binding proteins with an immunoglobulin-like fold. We rationally design Adnectin solubility and measure amide hydrogen/deuterium exchange (HDX) under conditions that permit transient protein self-association. Protein-protein binding commonly slows rates of HDX; in contrast, we find that Adnectin association may induce faster HDX for certain amides, particularly in the C-terminal β-strand. In aggregation-prone proteins, we identify a pattern of very different rates of amide HDX for residues linked by reciprocal hydrogen bonds in the native structure. These results may be explained by local loss of native structure and formation of an inter-protein interface. Amide HDX induced by self-association, detected here by deliberate modulation of propensity for such interactions, may be a general phenomenon with the potential to expose mechanisms of aggregation by diverse proteins.
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Affiliation(s)
- Kyle Trainor
- Department of Chemistry, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Colleen M Doyle
- Department of Chemistry, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada.
| | - Avril Metcalfe-Roach
- Department of Chemistry, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada.
| | - Julia Steckner
- Department of Chemistry, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Daša Lipovšek
- Bristol Myers Squibb, Cambridge, MA 02140, United States.
| | | | - David Langley
- Bristol Myers Squibb, Cambridge, MA 02140, United States
| | | | - Elizabeth M Meiering
- Department of Chemistry, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada.
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21
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Akkapeddi P, Teng KW, Koide S. Monobodies as tool biologics for accelerating target validation and druggable site discovery. RSC Med Chem 2021; 12:1839-1853. [PMID: 34820623 PMCID: PMC8597423 DOI: 10.1039/d1md00188d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022] Open
Abstract
Despite increased investment and technological advancement, new drug approvals have not proportionally increased. Low drug approval rates, particularly for new targets, are linked to insufficient target validation at early stages. Thus, there remains a strong need for effective target validation techniques. Here, we review the use of synthetic binding proteins as tools for drug target validation, with focus on the monobody platform among several advanced synthetic binding protein platforms. Monobodies with high affinity and high selectivity can be rapidly developed against challenging targets, such as KRAS mutants, using protein engineering technologies. They have strong tendency to bind to functional sites and thus serve as drug-like molecules, and they can serve as targeting ligands for constructing bio-PROTACs. Genetically encoded monobodies are effective "tool biologics" for validating intracellular targets. They promote crystallization and help reveal the atomic structures of the monobody-target interface, which can inform drug design. Using case studies, we illustrate the potential of the monobody technology in accelerating target validation and small-molecule drug discovery.
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Affiliation(s)
- Padma Akkapeddi
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
| | - Kai Wen Teng
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine New York NY USA
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22
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Ito T, Nishi H, Kameda T, Yoshida M, Fukazawa R, Kawada S, Nakazawa H, Umetsu M. Combination Informatic and Experimental Approach for Selecting Scaffold Proteins for Development as Antibody Mimetics. CHEM LETT 2021. [DOI: 10.1246/cl.210443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tomoyuki Ito
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Hafumi Nishi
- Department of Applied Information Sciences, Graduate School of Information Science, Tohoku University, 6-3-09 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
- Faculty of Core Research, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Mayu Yoshida
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Reito Fukazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Sakiya Kawada
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
- Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan
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23
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Wang X, Li F, Qiu W, Xu B, Li Y, Lian X, Yu H, Zhang Z, Wang J, Li Z, Xue W, Zhu F. SYNBIP: synthetic binding proteins for research, diagnosis and therapy. Nucleic Acids Res 2021; 50:D560-D570. [PMID: 34664670 PMCID: PMC8728148 DOI: 10.1093/nar/gkab926] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/13/2021] [Accepted: 10/14/2021] [Indexed: 12/11/2022] Open
Abstract
The success of protein engineering and design has extensively expanded the protein space, which presents a promising strategy for creating next-generation proteins of diverse functions. Among these proteins, the synthetic binding proteins (SBPs) are smaller, more stable, less immunogenic, and better of tissue penetration than others, which make the SBP-related data attracting extensive interest from worldwide scientists. However, no database has been developed to systematically provide the valuable information of SBPs yet. In this study, a database named ‘Synthetic Binding Proteins for Research, Diagnosis, and Therapy (SYNBIP)’ was thus introduced. This database is unique in (a) comprehensively describing thousands of SBPs from the perspectives of scaffolds, biophysical & functional properties, etc.; (b) panoramically illustrating the binding targets & the broad application of each SBP and (c) enabling a similarity search against the sequences of all SBPs and their binding targets. Since SBP is a human-made protein that has not been found in nature, the discovery of novel SBPs relied heavily on experimental protein engineering and could be greatly facilitated by in-silico studies (such as AI and computational modeling). Thus, the data provided in SYNBIP could lay a solid foundation for the future development of novel SBPs. The SYNBIP is accessible without login requirement at both official (https://idrblab.org/synbip/) and mirror (http://synbip.idrblab.net/) sites.
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Affiliation(s)
- Xiaona Wang
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Wenqi Qiu
- Department of Surgery, HKU-SZH & Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Binbin Xu
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yanlin Li
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Xichen Lian
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hongyan Yu
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Zhao Zhang
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Zhaorong Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China.,College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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24
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Ahmadi MKB, Mohammadi SA, Makvandi M, Mamouei M, Rahmati M, Dehghani H, Wood DW. Recent Advances in the Scaffold Engineering of Protein Binders. Curr Pharm Biotechnol 2021; 22:878-891. [PMID: 32838715 DOI: 10.2174/1389201021999200824101035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 11/22/2022]
Abstract
In recent years, extensive attention has been given to the generation of new classes of ligand- specific binding proteins to supplement monoclonal antibodies. A combination of protein engineering and display technologies has been used to manipulate non-human antibodies for humanization and stabilization purposes or even the generation of new binding proteins. Engineered protein scaffolds can now be directed against therapeutic targets to treat cancer and immunological disorders. Although very few of these scaffolds have successfully passed clinical trials, their remarkable properties such as robust folding, high solubility, and small size motivate their employment as a tool for biology and applied science studies. Here, we have focused on the generation of new non-Ig binding proteins and single domain antibody manipulation, with a glimpse of their applications.
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Affiliation(s)
- Mohammad K B Ahmadi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyed A Mohammadi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Manoochehr Makvandi
- Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Morteza Mamouei
- Department of Animal Science, Ramin Agricultural and Natural Resources University, Ahvaz, Iran
| | - Mohammad Rahmati
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hesam Dehghani
- Stem Cells Regenerative Research Group, Ressearch Institute of Biotechnology, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
| | - David W Wood
- Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 W. Woodruff Ave., Columbus, OH 43210, United States
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25
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Tuning SAS-6 architecture with monobodies impairs distinct steps of centriole assembly. Nat Commun 2021; 12:3805. [PMID: 34155202 PMCID: PMC8217511 DOI: 10.1038/s41467-021-23897-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/17/2021] [Indexed: 02/05/2023] Open
Abstract
Centrioles are evolutionarily conserved multi-protein organelles essential for forming cilia and centrosomes. Centriole biogenesis begins with self-assembly of SAS-6 proteins into 9-fold symmetrical ring polymers, which then stack into a cartwheel that scaffolds organelle formation. The importance of this architecture has been difficult to decipher notably because of the lack of precise tools to modulate the underlying assembly reaction. Here, we developed monobodies against Chlamydomonas reinhardtii SAS-6, characterizing three in detail with X-ray crystallography, atomic force microscopy and cryo-electron microscopy. This revealed distinct monobody-target interaction modes, as well as specific consequences on ring assembly and stacking. Of particular interest, monobody MBCRS6-15 induces a conformational change in CrSAS-6, resulting in the formation of a helix instead of a ring. Furthermore, we show that this alteration impairs centriole biogenesis in human cells. Overall, our findings identify monobodies as powerful molecular levers to alter the architecture of multi-protein complexes and tune centriole assembly.
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26
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Zhang Y, Thangam R, You SH, Sultonova RD, Venu A, Min JJ, Hong Y. Engineering Calreticulin-Targeting Monobodies to Detect Immunogenic Cell Death in Cancer Chemotherapy. Cancers (Basel) 2021; 13:2801. [PMID: 34199835 PMCID: PMC8200062 DOI: 10.3390/cancers13112801] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 12/26/2022] Open
Abstract
Surface-exposed calreticulin (ecto-CRT) plays a crucial role in the phagocytic removal of apoptotic cells during immunotherapy. Ecto-CRT is an immunogenic signal induced in response to treatment with chemotherapeutic agents such as doxorubicin (DOX) and mitoxantrone (MTX), and two peptides (KLGFFKR (Integrin-α) and GQPMYGQPMY (CRT binding peptide 1, Hep-I)) are known to specifically bind CRT. To engineer CRT-specific monobodies as agents to detect immunogenic cell death (ICD), we fused these peptide sequences at the binding loops (BC and FG) of human fibronectin domain III (FN3). CRT-specific monobodies were purified from E. coli by affinity chromatography. Using these monobodies, ecto-CRT was evaluated in vitro, in cultured cancer cell lines (CT-26, MC-38, HeLa, and MDA-MB-231), or in mice after anticancer drug treatment. Monobodies with both peptide sequences (CRT3 and CRT4) showed higher binding to ecto-CRT than those with a single peptide sequence. The binding affinity of the Rluc8 fusion protein-engineered monobodies (CRT3-Rluc8 and CRT4-Rluc8) to CRT was about 8 nM, and the half-life in serum and tumor tissue was about 12 h. By flow cytometry and confocal immunofluorescence of cancer cell lines, and by in vivo optical bioluminescence imaging of tumor-bearing mice, CRT3-Rluc8 and CRT4-Rluc8 bound specifically to ecto-CRT and effectively detected pre-apoptotic cells after treatment with ICD-inducing agents (DOX and MTX) but not a non-ICD-inducing agent (gemcitabine). Using CRT-specific monobodies, it is possible to detect ecto-CRT induction in cancer cells in response to drug exposure. This technique may be used to predict the therapeutic efficiency of chemo- and immuno-therapeutics early during anticancer treatment.
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Affiliation(s)
- Ying Zhang
- Department of Nuclear Medicine, Institute for Molecular Imaging and Theranostics, Hwasun Hospital, Chonnam National University Medical School, Hwasun 58128, Korea; (Y.Z.); (R.T.); (S.-H.Y.); (R.D.S.); (A.V.)
| | - Ramar Thangam
- Department of Nuclear Medicine, Institute for Molecular Imaging and Theranostics, Hwasun Hospital, Chonnam National University Medical School, Hwasun 58128, Korea; (Y.Z.); (R.T.); (S.-H.Y.); (R.D.S.); (A.V.)
- Department of Materials Science & Engineering, Korea University, Seoul 02841, Korea
| | - Sung-Hwan You
- Department of Nuclear Medicine, Institute for Molecular Imaging and Theranostics, Hwasun Hospital, Chonnam National University Medical School, Hwasun 58128, Korea; (Y.Z.); (R.T.); (S.-H.Y.); (R.D.S.); (A.V.)
| | - Rukhsora D. Sultonova
- Department of Nuclear Medicine, Institute for Molecular Imaging and Theranostics, Hwasun Hospital, Chonnam National University Medical School, Hwasun 58128, Korea; (Y.Z.); (R.T.); (S.-H.Y.); (R.D.S.); (A.V.)
| | - Akhil Venu
- Department of Nuclear Medicine, Institute for Molecular Imaging and Theranostics, Hwasun Hospital, Chonnam National University Medical School, Hwasun 58128, Korea; (Y.Z.); (R.T.); (S.-H.Y.); (R.D.S.); (A.V.)
| | - Jung-Joon Min
- Department of Nuclear Medicine, Institute for Molecular Imaging and Theranostics, Hwasun Hospital, Chonnam National University Medical School, Hwasun 58128, Korea; (Y.Z.); (R.T.); (S.-H.Y.); (R.D.S.); (A.V.)
- Department of Microbiology, Chonnam National University Medical School, Hwasun 58128, Korea
| | - Yeongjin Hong
- Department of Nuclear Medicine, Institute for Molecular Imaging and Theranostics, Hwasun Hospital, Chonnam National University Medical School, Hwasun 58128, Korea; (Y.Z.); (R.T.); (S.-H.Y.); (R.D.S.); (A.V.)
- Department of Microbiology, Chonnam National University Medical School, Hwasun 58128, Korea
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27
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Garnish SE, Meng Y, Koide A, Sandow JJ, Denbaum E, Jacobsen AV, Yeung W, Samson AL, Horne CR, Fitzgibbon C, Young SN, Smith PPC, Webb AI, Petrie EJ, Hildebrand JM, Kannan N, Czabotar PE, Koide S, Murphy JM. Conformational interconversion of MLKL and disengagement from RIPK3 precede cell death by necroptosis. Nat Commun 2021; 12:2211. [PMID: 33850121 PMCID: PMC8044208 DOI: 10.1038/s41467-021-22400-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Phosphorylation of the MLKL pseudokinase by the RIPK3 kinase leads to MLKL oligomerization, translocation to, and permeabilization of, the plasma membrane to induce necroptotic cell death. The precise choreography of MLKL activation remains incompletely understood. Here, we report Monobodies, synthetic binding proteins, that bind the pseudokinase domain of MLKL within human cells and their crystal structures in complex with the human MLKL pseudokinase domain. While Monobody-32 constitutively binds the MLKL hinge region, Monobody-27 binds MLKL via an epitope that overlaps the RIPK3 binding site and is only exposed after phosphorylated MLKL disengages from RIPK3 following necroptotic stimulation. The crystal structures identified two distinct conformations of the MLKL pseudokinase domain, supporting the idea that a conformational transition accompanies MLKL disengagement from RIPK3. These studies provide further evidence that MLKL undergoes a large conformational change upon activation, and identify MLKL disengagement from RIPK3 as a key regulatory step in the necroptosis pathway.
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Affiliation(s)
- Sarah E Garnish
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Yanxiang Meng
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Akiko Koide
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Jarrod J Sandow
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Eric Denbaum
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Annette V Jacobsen
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Andre L Samson
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Cheree Fitzgibbon
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Samuel N Young
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Phoebe P C Smith
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Andrew I Webb
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Emma J Petrie
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Joanne M Hildebrand
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA.
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
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28
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Tanaka T, Thomas J, Van Montfort R, Miller A, Rabbitts T. Pan RAS-binding compounds selected from a chemical library by inhibiting interaction between RAS and a reduced affinity intracellular antibody. Sci Rep 2021; 11:1712. [PMID: 33462327 PMCID: PMC7814043 DOI: 10.1038/s41598-021-81262-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/28/2020] [Indexed: 02/07/2023] Open
Abstract
Intracellular antibodies are valuable tools for target validation studies for clinical situations such as cancer. Recently we have shown that antibodies can be used for drug discovery in screening for chemical compounds surrogates by showing that compounds could be developed to the so-called undruggable RAS protein family. This method, called Antibody-derived compound (Abd) technology, employed intracellular antibodies binding to RAS in a competitive surface plasmon resonance chemical library screen. Success with this method requires a high affinity interaction between the antibody and the target. We now show that reduction in the affinity (dematuration) of the anti-active RAS antibody facilitates the screening of a chemical library using an in vitro AlphaScreen method. This identified active RAS specific-binding Abd compounds that inhibit the RAS-antibody interaction. One compound is shown to be a pan-RAS binder to KRAS,
HRAS and NRAS-GTP proteins with a Kd of average 37 mM, offering the possibility of a new chemical series that interacts with RAS in the switch region where the intracellular antibody binds. This simple approach shows the druggability of RAS and is generally applicable to antibody-derived chemical library screening by affording flexibility through simple antibody affinity variation. This approach can be applied to find Abd compounds as surrogates of antibody-combining sites for novel drug development in a range of human diseases.
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Affiliation(s)
- Tomoyuki Tanaka
- Leeds Institute of Medical Research, St James Hospital, Brenner Building, Beckett St., Leeds, LS9 7TF, UK.,Sanofi K.K. Tokyo Opera City Tower, Shinjuku-ku, Tokyo, 163-1488, Japan
| | - Jemima Thomas
- Institute of Cancer Research, Division of Cancer Therapeutics, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Rob Van Montfort
- Institute of Cancer Research, Division of Cancer Therapeutics, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Ami Miller
- Institute of Cancer Research, Division of Cancer Therapeutics, 15 Cotswold Road, Sutton, London, SM2 5NG, UK.,, 114 Innovation Dr, Milton Park, Abingdon, OX14 4RZ, UK
| | - Terry Rabbitts
- Leeds Institute of Medical Research, St James Hospital, Brenner Building, Beckett St., Leeds, LS9 7TF, UK. .,Institute of Cancer Research, Division of Cancer Therapeutics, 15 Cotswold Road, Sutton, London, SM2 5NG, UK.
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29
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Kermani AA. A guide to membrane protein X‐ray crystallography. FEBS J 2020; 288:5788-5804. [DOI: 10.1111/febs.15676] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/17/2020] [Accepted: 12/14/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Ali A. Kermani
- Department of Molecular, Cellular, and Developmental Biology University of Michigan Ann Arbor MI USA
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30
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La Sala G, Michiels C, Kükenshöner T, Brandstoetter T, Maurer B, Koide A, Lau K, Pojer F, Koide S, Sexl V, Dumoutier L, Hantschel O. Selective inhibition of STAT3 signaling using monobodies targeting the coiled-coil and N-terminal domains. Nat Commun 2020; 11:4115. [PMID: 32807795 PMCID: PMC7431413 DOI: 10.1038/s41467-020-17920-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 07/27/2020] [Indexed: 12/23/2022] Open
Abstract
The transcription factor STAT3 is frequently activated in human solid and hematological malignancies and remains a challenging therapeutic target with no approved drugs to date. Here, we develop synthetic antibody mimetics, termed monobodies, to interfere with STAT3 signaling. These monobodies are highly selective for STAT3 and bind with nanomolar affinity to the N-terminal and coiled-coil domains. Interactome analysis detects no significant binding to other STATs or additional off-target proteins, confirming their exquisite specificity. Intracellular expression of monobodies fused to VHL, an E3 ubiquitin ligase substrate receptor, results in degradation of endogenous STAT3. The crystal structure of STAT3 in complex with monobody MS3-6 reveals bending of the coiled-coil domain, resulting in diminished DNA binding and nuclear translocation. MS3-6 expression strongly inhibits STAT3-dependent transcriptional activation and disrupts STAT3 interaction with the IL-22 receptor. Therefore, our study establishes innovative tools to interfere with STAT3 signaling by different molecular mechanisms. STAT3 is an attractive therapeutic target but its homology with other STAT proteins complicates the development of selective inhibitors. Here, the authors develop monobodies with high affinity and selectivity for STAT3 and show that they can interfere with cellular STAT3 activity.
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Affiliation(s)
- Grégory La Sala
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Camille Michiels
- Experimental Medicine Unit, De Duve Institute, Université catholique de Louvain, 1200, Brussels, Belgium
| | - Tim Kükenshöner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Tania Brandstoetter
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | - Barbara Maurer
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | - Akiko Koide
- Department of Medicine, New York University School of Medicine, 522 1st Avenue, New York, 10016, NY, USA.,Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, 522 1st Avenue, New York, 10016, NY, USA
| | - Kelvin Lau
- Protein Crystallography Core Facility, School of Life Sciences, École polytechnique fédérale de Lausanne, Station 19, 1015, Lausanne, Switzerland
| | - Florence Pojer
- Protein Crystallography Core Facility, School of Life Sciences, École polytechnique fédérale de Lausanne, Station 19, 1015, Lausanne, Switzerland
| | - Shohei Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, 522 1st Avenue, New York, 10016, NY, USA.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 1st Avenue, New York, 10016, NY, USA
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | - Laure Dumoutier
- Experimental Medicine Unit, De Duve Institute, Université catholique de Louvain, 1200, Brussels, Belgium
| | - Oliver Hantschel
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland. .,Faculty of Medicine, Institute of Physiological Chemistry, Philipps-University of Marburg, Karl-von-Frisch-Straße 1, 35032, Marburg, Germany.
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Carrasco-López C, Zhao EM, Gil AA, Alam N, Toettcher JE, Avalos JL. Development of light-responsive protein binding in the monobody non-immunoglobulin scaffold. Nat Commun 2020; 11:4045. [PMID: 32792484 PMCID: PMC7427095 DOI: 10.1038/s41467-020-17837-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 07/13/2020] [Indexed: 12/24/2022] Open
Abstract
Monobodies are synthetic non-immunoglobulin customizable protein binders invaluable to basic and applied research, and of considerable potential as future therapeutics and diagnostic tools. The ability to reversibly control their binding activity to their targets on demand would significantly expand their applications in biotechnology, medicine, and research. Here we present, as proof-of-principle, the development of a light-controlled monobody (OptoMB) that works in vitro and in cells and whose affinity for its SH2-domain target exhibits a 330-fold shift in binding affinity upon illumination. We demonstrate that our αSH2-OptoMB can be used to purify SH2-tagged proteins directly from crude E. coli extract, achieving 99.8% purity and over 40% yield in a single purification step. By virtue of their ability to be designed to bind any protein of interest, OptoMBs have the potential to find new powerful applications as light-switchable binders of untagged proteins with the temporal and spatial precision afforded by light.
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Affiliation(s)
- César Carrasco-López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Evan M Zhao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Agnieszka A Gil
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Nathan Alam
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA.
- Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, USA.
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Steyaert J, Yeates TO. Editorial overview: Engineered proteins as tools in structural biology. Curr Opin Struct Biol 2020; 60:v-vi. [DOI: 10.1016/j.sbi.2020.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Yimchuen W, Kadonosono T, Ota Y, Sato S, Kitazawa M, Shiozawa T, Kuchimaru T, Taki M, Ito Y, Nakamura H, Kizaka-Kondoh S. Strategic design to create HER2-targeting proteins with target-binding peptides immobilized on a fibronectin type III domain scaffold. RSC Adv 2020; 10:15154-15162. [PMID: 35495466 PMCID: PMC9052545 DOI: 10.1039/d0ra00427h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/05/2020] [Indexed: 11/21/2022] Open
Abstract
Tumor-binding peptides such as human epidermal growth factor receptor 2 (HER2)-binding peptides are attractive therapeutic and diagnostic options for cancer. However, the HER2-binding peptides (HBPs) developed thus far are susceptible to proteolysis and lose their affinity to HER2 in vivo. In this report, a method to create a HER2-binding fluctuation-regulated affinity protein (HBP-FLAP) consisting of a fibronectin type III domain (FN3) scaffold with a structurally immobilized HBP is presented. HBPs were selected by phage-library screening and grafted onto FN3 to create FN3-HBPs, and the HBP-FLAP with the highest affinity (HBP sequence: YCAHNM) was identified after affinity maturation of the grafted HBP. HBP-FLAP containing the YCAHNM peptide showed increased proteolysis-resistance, binding to HER2 with a dissociation constant (KD) of 58 nM in ELISA and 287 nM in biolayer interferometry and specifically detects HER2-expressing cancer cells. In addition, HBP-FLAP clearly delineated HER2-expressing tumors with a half-life of 6 h after intravenous injection into tumor-bearing mice. FN3-based FLAP is an excellent platform for developing target-binding small proteins for clinical applications. A HER2-binding protein, HBP-FLAP, developed by peptide immobilization specifically binds to HER2 and has improved resistance to proteases.![]()
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Affiliation(s)
- Wanaporn Yimchuen
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Tetsuya Kadonosono
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Yumi Ota
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Shinichi Sato
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Maika Kitazawa
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Tadashi Shiozawa
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Takahiro Kuchimaru
- Center for Molecular Medicine
- Jichi Medical University
- Shimotsuke 329-0498
- Japan
| | - Masumi Taki
- Graduate School of Informatics and Engineering
- The University of Electro-Communications
- Tokyo 182-8585
- Japan
| | - Yuji Ito
- Graduate School of Science and Engineering
- Kagoshima University
- Kagoshima 890-0065
- Japan
| | - Hiroyuki Nakamura
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Shinae Kizaka-Kondoh
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
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