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Ide M, Tabata N, Yonemura Y, Murai K, Wang Y, Ishida A, Honda M, Kaneko S, Ito S, Yanagawa H. Hepatitis B virus evades the immune system by suppressing the NF-κB signaling pathway with DENND2A. Microbiol Spectr 2024; 12:e0378523. [PMID: 38240571 PMCID: PMC10913737 DOI: 10.1128/spectrum.03785-23] [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: 10/26/2023] [Accepted: 12/08/2023] [Indexed: 03/06/2024] Open
Abstract
Overcoming hepatitis B virus (HBV) is a challenging problem because HBV deceives the host immune system. We have found that DENN domain-containing 2A (DENND2A) was essential for HBV maintenance, although its role remains unclear. In this study, we elucidate its function by screening a novel DENND2A-binding peptide, DENP4-3S. DENP4-3S exhibits homology to SAM and SH3 domain-containing protein 1 (SASH1), a scaffold protein involved in Toll-like receptor signaling that promotes proinflammatory cytokine production. We confirmed that DENND2A interacts with SASH1 specifically. Overexpression and knockdown experiments showed that overexpression of DENND2A suppressed the transcriptional activity of NF-κB, and the knockdown of DENND2A promoted it and the production of cytokines and interferons. Here, we constructed a fusion protein (10M-DEN3SN) consisting of an anti-asialoglycoprotein receptor antibody and DENP4-3S to deliver the peptide to hepatocytes specifically. 10M-DEN3SN inhibited the interaction between DENND2A and SASH1, and rescued SASH1 trapped by DENND2A, leading to the upregulation of NF-κB and its downstream signaling. In addition, 10M-DEN3SN suppressed HBV proliferation in PXB chimeric mice. These results with the DENND2A-binding peptide delivered into hepatocytes suggested the involvement of DENND2A, SASH, and NF-κB signaling pathway in the HBV infection and onset of hepatitis. In conclusion, this study indicates that HBV utilizes DENND2A and SASH1 to evade the immune system.IMPORTANCEHepatitis B virus (HBV) is a serious liver infection with no established cure, causing an abnormal host immune response. Here, we identified a novel peptide that interacts with DENN domain-containing 2A (DENND2A), a host factor essential for HBV maintenance. The resulting peptide showed sequence homology, revealing an interaction between DENND2A and the immune system regulator SASH1. This study suggests that DENND2A contributes to HBV infection by suppressing the cellular immune system by inhibiting SASH1. The DENND2A-binding peptide, incorporated into our hepatocyte-specific peptide delivery system, inhibited the DENND2A-SASH1 interaction and promoted the production of cytokines and interferons in cultured hepatocytes. As a consequence, the peptide suppressed HBV proliferation in humanized mice. We report new insights into the role of DENND2A and SASH1 in HBV maintenance and highlight the importance of the immune system.
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Affiliation(s)
- Mayuko Ide
- Research Department, Purotech Bio Inc, Yokohama, Kanagawa, Japan
| | - Noriko Tabata
- Research Department, Purotech Bio Inc, Yokohama, Kanagawa, Japan
| | - Yuko Yonemura
- Research Department, Purotech Bio Inc, Yokohama, Kanagawa, Japan
| | - Kazuhisa Murai
- Department of Clinical Laboratory Medicine, Kanazawa University Graduate School of Health Medicine, Kanazawa, Ishikawa, Japan
| | - Ying Wang
- Department of Clinical Laboratory Medicine, Kanazawa University Graduate School of Health Medicine, Kanazawa, Ishikawa, Japan
| | - Atsuya Ishida
- Department of Clinical Laboratory Medicine, Kanazawa University Graduate School of Health Medicine, Kanazawa, Ishikawa, Japan
| | - Masao Honda
- Department of Clinical Laboratory Medicine, Kanazawa University Graduate School of Health Medicine, Kanazawa, Ishikawa, Japan
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Ishikawa, Japan
| | - Shuichi Kaneko
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Ishikawa, Japan
| | - Satoru Ito
- Research Department, Purotech Bio Inc, Yokohama, Kanagawa, Japan
| | - Hiroshi Yanagawa
- Research Department, Purotech Bio Inc, Yokohama, Kanagawa, Japan
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2
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Choi SH, Hwang HS, Han S, Eom H, Choi JS, Han S, Lee D, Lee SY, Koo H, Kwon HJ, Lim YB. Inhibition of protein-protein interactions using biodegradable depsipeptide nanoassemblies. J Control Release 2024; 366:104-113. [PMID: 38128883 DOI: 10.1016/j.jconrel.2023.12.028] [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: 09/28/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Although peptides notoriously have poor intrinsic pharmacokinetic properties, it is well-known that nanostructures with excellent pharmacokinetic properties can be designed. Noticing that peptide inhibitors are generally nonpolar, here, we consolidate the peptide inhibitor targeting intracellular protein-protein interactions (PPIs) as an integral part of biodegradable self-assembled depsipeptide nanostructures (SdPNs). Because the peptide inhibitor has the dual role of PPI inhibition and self-assembly in this design, problems associated with the poor pharmacokinetics of peptides and encapsulation/entrapment processes can be overcome. Optimized SdPNs displayed better tumor targeting and PPI inhibition properties than the comparable small molecule inhibitor in vivo. Kinetics of PPI inhibition for SdPNs were gradual and controllable in contrast to the rapid inhibition kinetics of the small molecule. Because SdPN is modular, any appropriate peptide inhibitor can be incorporated into the platform without concern for the poor pharmacokinetic properties of the peptide.
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Affiliation(s)
- Se-Hwan Choi
- Department of Materials Science and Engineering, Yonsei University, Seoul, Republic of Korea
| | - Hyun-Seok Hwang
- Department of Materials Science and Engineering, Yonsei University, Seoul, Republic of Korea
| | - Seongryeong Han
- Department of Medical Life Sciences, Department of Biomedicine & Health Sciences, Catholic Photomedicine Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hohyeon Eom
- Chemical Genomics Leader Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jun Shik Choi
- Department of Materials Science and Engineering, Yonsei University, Seoul, Republic of Korea; Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Sanghun Han
- Department of Materials Science and Engineering, Yonsei University, Seoul, Republic of Korea
| | - Donghyun Lee
- Department of Medical Life Sciences, Department of Biomedicine & Health Sciences, Catholic Photomedicine Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Soo Yeon Lee
- Chemical Genomics Leader Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Heebeom Koo
- Department of Medical Life Sciences, Department of Biomedicine & Health Sciences, Catholic Photomedicine Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Ho Jeong Kwon
- Chemical Genomics Leader Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea.
| | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University, Seoul, Republic of Korea.
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3
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Brango-Vanegas J, Leite ML, de Oliveira KBS, da Cunha NB, Franco OL. From exploring cancer and virus targets to discovering active peptides through mRNA display. Pharmacol Ther 2023; 252:108559. [PMID: 37952905 DOI: 10.1016/j.pharmthera.2023.108559] [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: 08/09/2023] [Revised: 10/26/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
During carcinogenesis, neoplastic cells accumulate mutations in genes important for cellular homeostasis, producing defective proteins. Viral infections occur when viral capsid proteins bind to the host cell receptor, allowing the virus to enter the cells. In both cases, proteins play important roles in cancer development and viral infection, so these targets can be exploited to develop alternative treatments. mRNA display technology is a very powerful tool for the development of peptides capable of acting on specific targets in neoplastic cells or on viral capsid proteins. mRNA display technology allows the selection and evolution of peptides with desired functional properties from libraries of many nucleic acid variants. Among other advantages of this technology, the use of flexizymes allows the production of peptides with unnatural amino acid residues, which can enhance the activity of these molecules. From target immobilization, peptides with greater specificity for the targets of interest are generated during the selection rounds. Herein, we will explore the use of mRNA display technology for the development of active peptides after successive rounds of selection, using proteins present in neoplastic cells and viral particles as targets.
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Affiliation(s)
- José Brango-Vanegas
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Michel Lopes Leite
- Departamento de Biologia Molecular, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Kamila Botelho Sampaio de Oliveira
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Nicolau Brito da Cunha
- Universidade de Brasília, Faculdade de Agronomia e Medicina Veterinária, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Octávio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.
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4
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Su W, Wang Y, Zou S, Zhao Y, Li Y, Zhang C, Guo X, Li S. Construction of Peptide Library in Mammalian Cells by dsDNA-Based Strategy. ACS OMEGA 2023; 8:1037-1046. [PMID: 36643544 PMCID: PMC9835800 DOI: 10.1021/acsomega.2c06402] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/19/2022] [Indexed: 06/16/2023]
Abstract
While different display technologies, represented by phage display, have been widely used in drug discovery, they still can hardly achieve function-based peptide screening, which in most cases is performed in mammalian cells. And most attempts to screen functional peptides with mammalian platforms utilized plasmids to store coding information. Our previous work established double-stranded DNAs (dsDNAs) as innovative biological parts to implement AND-gate genetic circuits in mammalian cells. In the current study, we employ dsDNAs with terminal NNK degenerate codons to implement AND-gate genetic circuits and generate peptide libraries in mammalian cells. This dsDNA-based AND-gate (DBAG) peptide library construction strategy is easy to perform, requiring only PCR reaction and cell transfection. High-throughput sequencing (HTS) and single-cell sequencing results revealed both peptide length and amino acid sequence diversity of DBAG peptide libraries. Moreover, as a feasibility test of this strategy, we identified an MDM2-interacting peptide by applying the DBAG peptide library to a mammalian cell-based two-hybrid system. Our work establishes dsDNAs with terminal degenerate codons as biological parts to build peptide libraries in mammalian cells, which may have great application potential in the future.
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Affiliation(s)
- Weijun Su
- School
of Medicine, Nankai University, Tianjin 300071, China
| | - Yi Wang
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & Hospital, National Clinical Research
Center for Cancer; Key Laboratory of Cancer Prevention and Therapy,
Tianjin, Tianjin’s Clinical Research
Center for Cancer, Tianjin 300060, China
| | - Siqi Zou
- School
of Medicine, Nankai University, Tianjin 300071, China
| | - Yanjie Zhao
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & Hospital, National Clinical Research
Center for Cancer; Key Laboratory of Cancer Prevention and Therapy,
Tianjin, Tianjin’s Clinical Research
Center for Cancer, Tianjin 300060, China
| | - Yifan Li
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & Hospital, National Clinical Research
Center for Cancer; Key Laboratory of Cancer Prevention and Therapy,
Tianjin, Tianjin’s Clinical Research
Center for Cancer, Tianjin 300060, China
| | - Chunze Zhang
- Department
of Colorectal Surgery, Tianjin Union Medical
Center, Tianjin 300121, China
| | - Xiaojing Guo
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & Hospital, National Clinical Research
Center for Cancer; Key Laboratory of Cancer Prevention and Therapy,
Tianjin, Tianjin’s Clinical Research
Center for Cancer, Tianjin 300060, China
| | - Shuai Li
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & Hospital, National Clinical Research
Center for Cancer; Key Laboratory of Cancer Prevention and Therapy,
Tianjin, Tianjin’s Clinical Research
Center for Cancer, Tianjin 300060, China
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5
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Ide M, Tabata N, Yonemura Y, Shirasaki T, Murai K, Wang Y, Ishida A, Okada H, Honda M, Kaneko S, Doi N, Ito S, Yanagawa H. Guanine nucleotide exchange factor DOCK11-binding peptide fused with a single chain antibody inhibits Hepatitis B Virus infection and replication. J Biol Chem 2022; 298:102097. [PMID: 35660020 PMCID: PMC9241042 DOI: 10.1016/j.jbc.2022.102097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 12/26/2022] Open
Abstract
Hepatitis B virus (HBV) infection is a major global health problem with no established cure. Dedicator of cytokinesis 11 (DOCK11), known as a guanine nucleotide exchange factor (GEF) for Cdc42, is reported to be essential for the maintenance of HBV. However, potential therapeutic strategies targeting DOCK11 have not yet been explored. We have previously developed an in vitro virus method as a more efficient tool for the analysis of proteomics and evolutionary protein engineering. In this study, using the in vitro virus method, we screened and identified a novel antiasialoglycoprotein receptor (ASGR) antibody, ASGR3-10M, and a DOCK11-binding peptide, DCS8-42A, for potential use in HBV infection. We further constructed a fusion protein (10M-D42AN) consisting of ASGR3-10M, DCS8-42A, a fusogenic peptide, and a nuclear localization signal to deliver the peptide inside hepatocytes. We show using immunofluorescence staining that 10M-D42AN was endocytosed into early endosomes and released into the cytoplasm and nucleus. Since DCS8-42A shares homology with activated cdc42-associated kinase 1 (Ack1), which promotes EGFR endocytosis required for HBV infection, we also found that 10M-D42AN inhibited endocytosis of EGFR and Ack1. Furthermore, we show 10M-D42AN suppressed the function of DOCK11 in the host DNA repair system required for covalently closed circular DNA synthesis and suppressed HBV proliferation in mice. In conclusion, this study realizes a novel hepatocyte-specific drug delivery system using an anti-ASGR antibody, a fusogenic peptide, and DOCK11-binding peptide to provide a novel treatment for HBV.
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Affiliation(s)
- Mayuko Ide
- Research Department, Purotech Bio Inc, Yokohama, Kanagawa, 230-0045, Japan
| | - Noriko Tabata
- Research Department, Purotech Bio Inc, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuko Yonemura
- Research Department, Purotech Bio Inc, Yokohama, Kanagawa, 230-0045, Japan
| | - Takayoshi Shirasaki
- Department of Clinical Laboratory Medicine, Kanazawa University Graduate School of Health Medicine, Kanazawa, Ishikawa, 920-0942, Japan
| | - Kazuhisa Murai
- Department of Clinical Laboratory Medicine, Kanazawa University Graduate School of Health Medicine, Kanazawa, Ishikawa, 920-0942, Japan
| | - Ying Wang
- Department of Clinical Laboratory Medicine, Kanazawa University Graduate School of Health Medicine, Kanazawa, Ishikawa, 920-0942, Japan
| | - Atsuya Ishida
- Department of Clinical Laboratory Medicine, Kanazawa University Graduate School of Health Medicine, Kanazawa, Ishikawa, 920-0942, Japan
| | - Hikari Okada
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Ishikawa, 920-8641, Japan
| | - Masao Honda
- Department of Clinical Laboratory Medicine, Kanazawa University Graduate School of Health Medicine, Kanazawa, Ishikawa, 920-0942, Japan; Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Ishikawa, 920-8641, Japan
| | - Shuichi Kaneko
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Ishikawa, 920-8641, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, 223-8522, Japan
| | - Satoru Ito
- Research Department, Purotech Bio Inc, Yokohama, Kanagawa, 230-0045, Japan
| | - Hiroshi Yanagawa
- Research Department, Purotech Bio Inc, Yokohama, Kanagawa, 230-0045, Japan.
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6
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Ganier L, Betzi S, Derviaux C, Roche P, Dessaux C, Muller C, Hoffer L, Morelli X, Borg JP. Discovery of Small-Molecule Inhibitors of the PTK7/β-Catenin Interaction Targeting the Wnt Signaling Pathway in Colorectal Cancer. ACS Chem Biol 2022; 17:1061-1072. [PMID: 35483008 DOI: 10.1021/acschembio.1c00826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC), the second cause of death due to cancer worldwide, is a major public health issue. The discovery of new therapeutic targets is thus essential. Pseudokinase PTK7 intervenes in the regulation of the Wnt/β-catenin pathway signaling, in part, through a kinase domain-dependent interaction with the β-catenin protein. PTK7 is overexpressed in CRC, an event associated with metastatic development and reduced survival of nonmetastatic patients. In addition, numerous alterations have been identified in CRC inducing constitutive activation of the Wnt/β-catenin pathway signaling through β-catenin accumulation. Thus, targeting the PTK7/β-catenin interaction could be of interest for future drug development. We have developed a NanoBRET screening assay recapitulating the interaction between PTK7 and β-catenin to identify compounds able to disrupt this protein-protein interaction. A high-throughput screening allowed us to identify small-molecule inhibitors targeting the Wnt pathway signaling and inducing antiproliferative and antitumor effects in vitro in CRC cells harboring β-catenin or adenomatous polyposis coli (APC) mutations. Thus, inhibition of the PTK7/β-catenin interaction could represent a new therapeutic strategy to inhibit cell growth dependent on the Wnt signaling pathway. Moreover, despite a lack of enzymatic activity of its tyrosine kinase domain, targeting the PTK7 kinase domain-dependent functions appears to be of interest for further therapeutic development.
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Affiliation(s)
- Laetitia Ganier
- Aix Marseille Univ., CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue “Cell Polarity, Cell Signaling and Cancer”, 27 Blvd Lei Roure CS30059, 13273 Marseille Cedex 9, France
- Aix Marseille Univ., CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Team “Integrative Structural and Chemical Biology”, 27 Blvd Lei Roure CS30059, 13273 Marseille Cedex 9, France
| | - Stephane Betzi
- Aix Marseille Univ., CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Team “Integrative Structural and Chemical Biology”, 27 Blvd Lei Roure CS30059, 13273 Marseille Cedex 9, France
- Aix Marseille Univ., CNRS, INSERM, Institut Paoli-Calmettes, CRCM, “HiTS/IPCdd─High Throughput Screening Platform”, 27 Blvd Lei Roure CS30059, 13273 Marseille Cedex 9, France
| | - Carine Derviaux
- Aix Marseille Univ., CNRS, INSERM, Institut Paoli-Calmettes, CRCM, “HiTS/IPCdd─High Throughput Screening Platform”, 27 Blvd Lei Roure CS30059, 13273 Marseille Cedex 9, France
| | - Philippe Roche
- Aix Marseille Univ., CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Team “Integrative Structural and Chemical Biology”, 27 Blvd Lei Roure CS30059, 13273 Marseille Cedex 9, France
- Aix Marseille Univ., CNRS, INSERM, Institut Paoli-Calmettes, CRCM, “HiTS/IPCdd─High Throughput Screening Platform”, 27 Blvd Lei Roure CS30059, 13273 Marseille Cedex 9, France
| | - Charlotte Dessaux
- Aix Marseille Univ., CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue “Cell Polarity, Cell Signaling and Cancer”, 27 Blvd Lei Roure CS30059, 13273 Marseille Cedex 9, France
| | - Christophe Muller
- Aix Marseille Univ., CNRS, INSERM, Institut Paoli-Calmettes, CRCM, “HiTS/IPCdd─High Throughput Screening Platform”, 27 Blvd Lei Roure CS30059, 13273 Marseille Cedex 9, France
| | - Laurent Hoffer
- Aix Marseille Univ., CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Team “Integrative Structural and Chemical Biology”, 27 Blvd Lei Roure CS30059, 13273 Marseille Cedex 9, France
| | - Xavier Morelli
- Aix Marseille Univ., CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Team “Integrative Structural and Chemical Biology”, 27 Blvd Lei Roure CS30059, 13273 Marseille Cedex 9, France
- Aix Marseille Univ., CNRS, INSERM, Institut Paoli-Calmettes, CRCM, “HiTS/IPCdd─High Throughput Screening Platform”, 27 Blvd Lei Roure CS30059, 13273 Marseille Cedex 9, France
| | - Jean-Paul Borg
- Aix Marseille Univ., CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue “Cell Polarity, Cell Signaling and Cancer”, 27 Blvd Lei Roure CS30059, 13273 Marseille Cedex 9, France
- Institut Universitaire de France, 17 Rue de France, 69100 Villeurbanne, France
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7
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Kamalinia G, Grindel BJ, Takahashi TT, Millward SW, Roberts RW. Directing evolution of novel ligands by mRNA display. Chem Soc Rev 2021; 50:9055-9103. [PMID: 34165126 PMCID: PMC8725378 DOI: 10.1039/d1cs00160d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
mRNA display is a powerful biological display platform for the directed evolution of proteins and peptides. mRNA display libraries covalently link the displayed peptide or protein (phenotype) with the encoding genetic information (genotype) through the biochemical activity of the small molecule puromycin. Selection for peptide/protein function is followed by amplification of the linked genetic material and generation of a library enriched in functional sequences. Iterative selection cycles are then performed until the desired level of function is achieved, at which time the identity of candidate peptides can be obtained by sequencing the genetic material. The purpose of this review is to discuss the development of mRNA display technology since its inception in 1997 and to comprehensively review its use in the selection of novel peptides and proteins. We begin with an overview of the biochemical mechanism of mRNA display and its variants with a particular focus on its advantages and disadvantages relative to other biological display technologies. We then discuss the importance of scaffold choice in mRNA display selections and review the results of selection experiments with biological (e.g., fibronectin) and linear peptide library architectures. We then explore recent progress in the development of "drug-like" peptides by mRNA display through the post-translational covalent macrocyclization and incorporation of non-proteogenic functionalities. We conclude with an examination of enabling technologies that increase the speed of selection experiments, enhance the information obtained in post-selection sequence analysis, and facilitate high-throughput characterization of lead compounds. We hope to provide the reader with a comprehensive view of current state and future trajectory of mRNA display and its broad utility as a peptide and protein design tool.
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Affiliation(s)
- Golnaz Kamalinia
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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8
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Dowarha D, Chou RH, Yu C. S100A1 blocks the interaction between p53 and mdm2 and decreases cell proliferation activity. PLoS One 2020; 15:e0234152. [PMID: 32497081 PMCID: PMC7272100 DOI: 10.1371/journal.pone.0234152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/19/2020] [Indexed: 01/10/2023] Open
Abstract
About 50% of human cancers across the globe arise due to a mutation in the p53 gene which gives rise to its functional inactive form, and in the rest of the cancer the efficacy of active p53 (wild-type) is hindered by MDM2-mediated degradation. Breakdown of the p53-MDM2 association may constitute an effective strategy to stimulate or reinstate the activity of wild type p53, thereby reviving the p53 tumor suppressor capability. S100A1 has been revealed to associate with the N-terminal domain of MDM2 and p53 protein. We utilized NMR spectroscopy to study the interface amongst the S100A1 and N-terminal domain of MDM2. Additionally, the S100A1-MDM2 complex generated through the HADDOCK program was then superimposed with the p53 (peptide) -MDM2 complex reported earlier. The overlay indicated that a segment of S100A1 could block the interaction of p53 (peptide) -MDM2 complex significantly. To further justify our assumption, we performed HSQC-NMR titration for the S100A1 and p53 N-terminal domain (p53-TAD). The data obtained indicated that the S100A1 segment comprising nearly 17 residues have some common residues that interact with both MDM2 and p53-TAD. Further, we synthesized the 17-residue peptide derived from the S100A1 protein and attached it to the cell-penetrating HIV-TAT peptide. The HSQC-NMR competitive binding experiment revealed that Peptide 1 could successfully interfere with the p53-MDM2 interaction. Furthermore, functional effects of the peptide was validated in cancer cells. The results showed that Peptide 1 effectively inhibited cell proliferation, and increased the protein levels of p53 and its downstream p21 in MCF-7 cells. Treatment of Peptide 1 resulted in cell cycle arrest at G2/M phase, and also induced apoptotic cell death at higher concentration. Taken together, the results suggest that disruption of the interaction of p53 and MDM2 by Peptide 1 could activate normal p53 functions, leading to cell cycle arrest and apoptotic cell death in cancer cells. We proposed here that S100A1 could influence the p53-MDM2 interaction credibly and possibly reactivates the wild type p53 pathway.
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Affiliation(s)
- Deepu Dowarha
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Ruey-Hwang Chou
- Graduate Institute of Biomedical Sciences and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
- Department of Biotechnology, Asia University, Wufeng, Taichung, Taiwan
- * E-mail: (CY); (RHC)
| | - Chin Yu
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
- * E-mail: (CY); (RHC)
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9
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Accurate and rapid calculation of hydration free energy and its physical implication for biomolecular functions. Biophys Rev 2020; 12:469-480. [PMID: 32180122 DOI: 10.1007/s12551-020-00686-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2020] [Indexed: 01/19/2023] Open
Abstract
Here we review a new method for calculating a hydration free energy (HFE) of a solute and discuss its physical implication for biomolecular functions in aqueous environments. The solute hydration is decomposed into processes 1 and 2. A cavity matching the geometric characteristics of the solute at the atomic level is created in process 1. Solute-water van der Waals and electrostatic interaction potentials are incorporated in process 2. The angle-dependent integral equation theory combined with our morphometric approach is applied to process 1, and the three-dimensional reference interaction site model theory is employed for process 2. Molecular models are adopted for water. The new method is characterized by the following. Solutes with various sizes including proteins can be treated in the same manner. It is almost as accurate as the molecular dynamics simulation despite its far smaller computational burden. It enables us to handle a solute possessing a significantly large total charge without difficulty. The HFE can be decomposed into a variety of physically insightful, energetic, and entropic components. It is best suited to the elucidation of mechanisms of protein folding, pressure and cold denaturation of a protein, and different types of molecular recognition.
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10
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Yamada T, Hayashi T, Hikiri S, Kobayashi N, Yanagawa H, Ikeguchi M, Katahira M, Nagata T, Kinoshita M. How Does the Recently Discovered Peptide MIP Exhibit Much Higher Binding Affinity than an Anticancer Protein p53 for an Oncoprotein MDM2? J Chem Inf Model 2019; 59:3533-3544. [PMID: 31282659 DOI: 10.1021/acs.jcim.9b00226] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An oncoprotein MDM2 binds to the extreme N-terminal peptide region of a tumor suppressor protein p53 (p53NTD) and inhibits its anticancer activity. We recently discovered a peptide named MIP which exhibits much higher binding affinity for MDM2 than p53NTD. Experiments showed that the binding free energy (BFE) of MDM2-MIP is lower than that of MDM2-p53NTD by approximately -4 kcal/mol. Here, we develop a theoretical method which is successful in reproducing this quantitative difference and elucidating its physical origins. It enables us to decompose the BFE into a variety of energetic and entropic components, evaluate their relative magnitudes, and identify the physical factors driving or opposing the binding. It should be applicable also to the assessment of differences among ligands in the binding affinity for a particular receptor, which is a central issue in modern chemistry. In the MDM2 case, the higher affinity of MIP is ascribed to a larger gain of translational, configurational entropy of water upon binding. This result is useful to the design of a peptide possessing even higher affinity for MDM2 as a reliable drug against a cancer.
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Affiliation(s)
- Tatsuya Yamada
- Institute of Advanced Energy, Kyoto University , Uji , Kyoto 611-0011 , Japan
| | - Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University , Uji , Kyoto 611-0011 , Japan
| | - Simon Hikiri
- Institute of Advanced Energy, Kyoto University , Uji , Kyoto 611-0011 , Japan.,Graduate School of Science , Chiba University , 1-33 Yayoi-cho , Inage , Chiba 263-8522 , Japan
| | - Naohiro Kobayashi
- Institute for Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Hiroshi Yanagawa
- Y-Lab. of IDAC Theranostics, Inc. , 1-1-48 Suehiro-cho , Tsurumi, Yokohama 230-0045 , Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science , Yokohama City University , 1-7-29, Suehiro-cho , Tsurumi-ku, Yokohama 230-0045 , Japan.,RIKEN Medical Sciences Innovation Hub Program , 1-7-22 Suehiro-cho , Tsurumi-ku, Yokohama 230-0045 , Japan
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University , Uji , Kyoto 611-0011 , Japan
| | - Takashi Nagata
- Institute of Advanced Energy, Kyoto University , Uji , Kyoto 611-0011 , Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University , Uji , Kyoto 611-0011 , Japan
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11
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Engineering Optogenetic Control of Endogenous p53 Protein Levels. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9102095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The transcription factor p53 is a stress sensor that turns specific sets of genes on to allow the cell to respond to the stress depending on its severity and type. p53 is classified as tumor suppressor because its function is to maintain genome integrity promoting cell cycle arrest, apoptosis, or senescence to avoid proliferation of cells with damaged DNA. While in many human cancers the p53 gene is itself mutated, there are some in which the dysfunction of the p53 pathway is caused by the overexpression of negative regulators of p53, such as Mdm2, that keep it at low levels at all times. Here we develop an optogenetic approach to control endogenous p53 levels with blue light. Specifically, we control the nuclear localization of the Mmd2-binding PMI peptide using the light-inducible export system LEXY. In the dark, the PMI-LEXY fusion is nuclear and binds to Mdm2, consenting to p53 to accumulate and transcribe the target gene p21. Blue light exposure leads to the export of the PMI-LEXY fusion into the cytosol, thereby Mdm2 is able to degrade p53 as in the absence of the peptide. This approach may be useful to study the effect of localized p53 activation within a tissue or organ.
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12
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Peptidomimetics: A Synthetic Tool for Inhibiting Protein–Protein Interactions in Cancer. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09831-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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13
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Miyafusa T, Hirota K, Honda S. Generation of ubiquitin-based binder with an inserted active peptide. Biochem Biophys Res Commun 2018; 503:3162-3166. [PMID: 30146256 DOI: 10.1016/j.bbrc.2018.08.110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 08/16/2018] [Indexed: 12/19/2022]
Abstract
The grafting of active peptides onto structurally stable scaffold proteins is effective for the generation of functional proteins. In this study, we aimed to develop a grafting method using ubiquitin as a scaffold protein. Ubiquitin is a small protein consisting of 76 amino acid residues that is highly stable against heat and pH stress, which are desirable characteristics for a scaffold protein. Moreover, its structure is maintained even if it is split or additional residues are inserted. Therefore, we assumed that grafting of an active peptide into ubiquitin would result in a functional protein. As a proof of concept, we developed the ubiquitin-based binder (UbB), into which the p53 (17-28) peptide was inserted between Ile36 and Pro37. The p53 (17-28) peptide, utilized as a model active peptide in this work, is known to bind to mouse double minute 2 homolog (Mdm2). Size exclusion chromatography and circular dichroism indicated that UbB maintained a similar structure to that of ubiquitin. The affinity for Mdm2 measured by surface plasmon resonance was 292 times greater than that of the p53 (17-28) peptide. These observations indicate that ubiquitin is a robust scaffold for peptide grafting. We hope that this study will aid further development of ubiquitin-based protein engineering.
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Affiliation(s)
- Takamitsu Miyafusa
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Kiyonori Hirota
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Shinya Honda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
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14
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Yadahalli S, Li J, Lane DP, Gosavi S, Verma CS. Characterizing the conformational landscape of MDM2-binding p53 peptides using Molecular Dynamics simulations. Sci Rep 2017; 7:15600. [PMID: 29142290 PMCID: PMC5688104 DOI: 10.1038/s41598-017-15930-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/03/2017] [Indexed: 11/09/2022] Open
Abstract
The conformational landscapes of p53 peptide variants and phage derived peptide (12/1) variants, all known to bind to MDM2, are studied using hamiltonian replica exchange molecular dynamics simulations. Complementing earlier observations, the current study suggests that the p53 peptides largely follow the ‘conformational selection’ paradigm in their recognition of and complexation by MDM2 while the 12/1 peptides likely undergo some element of conformational selection but are mostly driven by ‘binding induced folding’. This hypothesis is further supported by pulling simulations that pull the peptides away from their bound states with MDM2. This data extends the earlier mechanisms proposed to rationalize the entropically driven binding of the p53 set and the enthalpically driven binding of the 12/1 set. Using our hypothesis, we suggest mutations to the 12/1 peptide that increase its helicity in simulations and may, in turn, shift the binding towards conformational selection. In summary, understanding the conformational landscapes of the MDM2-binding peptides may suggest new peptide designs with bespoke binding mechanisms.
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Affiliation(s)
- Shilpa Yadahalli
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, 560065, India.,Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore.,Manipal University, Madhav Nagar, Manipal, 576104, India.,p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore, 138648, Singapore
| | - Jianguo Li
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore.,Singapore Eye Research Institute, 11 Third Hospital Avenue, #06-00, Singapore, 168751, Singapore
| | - David P Lane
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore, 138648, Singapore
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, 560065, India
| | - Chandra S Verma
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore. .,Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 11758, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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15
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Teveroni E, Lucà R, Pellegrino M, Ciolli G, Pontecorvi A, Moretti F. Peptides and peptidomimetics in the p53/MDM2/MDM4 circuitry - a patent review. Expert Opin Ther Pat 2016; 26:1417-1429. [DOI: 10.1080/13543776.2017.1233179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Emanuela Teveroni
- Institute of Cell Biology and Neurobiology, CNR, Roma, Italy
- Institute of Medical Pathology, Catholic University of Roma, Roma, Italy
| | - Rossella Lucà
- Institute of Cell Biology and Neurobiology, CNR, Roma, Italy
| | | | - Germana Ciolli
- Institute of Cell Biology and Neurobiology, CNR, Roma, Italy
- Institute of Medical Pathology, Catholic University of Roma, Roma, Italy
| | - Alfredo Pontecorvi
- Institute of Medical Pathology, Catholic University of Roma, Roma, Italy
| | - Fabiola Moretti
- Institute of Cell Biology and Neurobiology, CNR, Roma, Italy
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16
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ElSawy KM, Lane DP, Verma CS, Caves LSD. Recognition Dynamics of p53 and MDM2: Implications for Peptide Design. J Phys Chem B 2016; 120:320-8. [PMID: 26701330 DOI: 10.1021/acs.jpcb.5b11162] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Peptides that inhibit MDM2 and attenuate MDM2-p53 interactions, thus activating p53, are currently being pursued as anticancer drug leads for tumors harboring wild type p53. The thermodynamic determinants of peptide-MDM2 interactions have been extensively studied. However, a detailed understanding of the dynamics that underlie these interactions is largely missing. In this study, we explore the kinetics of the binding of a set of peptides using Brownian dynamics simulations. We systematically investigate the effect of peptide C-terminal substitutions (Ser, Ala, Asn, Pro) of a Q16ETFSDLWKLLP27 p53-based peptide and a M1PRFMDYWEGLN12 12/1 phage-derived peptide on their interaction dynamics with MDM2. The substitutions modulate peptide residence times around the MDM2 protein. In particular, the highest affinity peptide, Q16ETFSDLWKLLS27, has the longest residence time (t ∼ 25 μs) around MDM2, suggesting its potentially important contribution to binding affinity. The binding of the p53-based peptides appears to be kinetically driven while that of the phage-derived series appears to be thermodynamically driven. The phage-derived peptides were found to adopt distinctly different modes of interaction with the MDM2 protein compared to their p53-based counterparts. The p53-based peptides approach the N-terminal region of the MDM2 protein with the peptide C-terminal end oriented toward the protein, while the M1PRFMDYWEGLN12-based peptides adopt the reverse orientation. To probe the determinants of this switch in orientation, a designed mutant of the phage-derived peptide, R3E (M1PEFMDYWEGLN12), was simulated and found to adopt the orientation adopted by the p53-based peptides and also to result in almost a 5-fold increase in the peptide residence time (∼120 μs) relative to the p53-based peptides. On this basis, we suggest that the R3E mutant phage-derived peptide has a higher affinity for MDM2 than the p53-based peptides and would therefore, competitively inhibit MDM2-p53. The study, therefore, provides a novel computational framework for kinetics-based lead optimization for anticancer drug development strategies.
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Affiliation(s)
- Karim M ElSawy
- York Centre for Complex Systems Analysis (YCCSA), University of York , York, YO10 5GE, United Kingdom.,Department of Chemistry, College of Science, Qassim University , Buraydah 52571, Saudi Arabia
| | - David P Lane
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore , 138648
| | - Chandra S Verma
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research) , 30 Biopolis Street, #07-01 Matrix , Singapore , 138671.,Department of Biological Sciences, National University of Singapore , 14 Science Drive 4 , Singapore 117543.,School of Biological Sciences, Nanyang Technological University , 50 Nanyang Drive , Singapore 637551
| | - Leo S D Caves
- York Centre for Complex Systems Analysis (YCCSA), University of York , York, YO10 5GE, United Kingdom.,Department of Biology, University of York , York YO10 5DD, United Kingdom
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17
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. Angew Chem Int Ed Engl 2015; 54:8896-927. [PMID: 26119925 PMCID: PMC4557054 DOI: 10.1002/anie.201412070] [Citation(s) in RCA: 496] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are involved at all levels of cellular organization, thus making the development of PPI inhibitors extremely valuable. The identification of selective inhibitors is challenging because of the shallow and extended nature of PPI interfaces. Inhibitors can be obtained by mimicking peptide binding epitopes in their bioactive conformation. For this purpose, several strategies have been evolved to enable a projection of side chain functionalities in analogy to peptide secondary structures, thereby yielding molecules that are generally referred to as peptidomimetics. Herein, we introduce a new classification of peptidomimetics (classes A-D) that enables a clear assignment of available approaches. Based on this classification, the Review summarizes strategies that have been applied for the structure-based design of PPI inhibitors through stabilizing or mimicking turns, β-sheets, and helices.
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Affiliation(s)
- Marta Pelay-Gimeno
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Adrian Glas
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Oliver Koch
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
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18
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Strukturbasierte Entwicklung von Protein-Protein-Interaktionsinhibitoren: Stabilisierung und Nachahmung von Peptidliganden. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412070] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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19
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Yang L, Cui Y, Shen J, Lin F, Wang X, Long M, Wei J, Zhang H. Antitumor activity of SA12, a novel peptide, on SKBr-3 breast cancer cells via the mitochondrial apoptosis pathway. Drug Des Devel Ther 2015; 9:1319-30. [PMID: 25767377 PMCID: PMC4354433 DOI: 10.2147/dddt.s75780] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Breast cancer is considered to be the most common malignancy in women. Treatment of breast cancer has been focused on molecular targeted therapy, and anticancer peptides are considered to be some of the most promising candidate drugs. In the current study, we used mRNA-peptide display technology to screen antibreast cancer peptides and identified a novel peptide, SA12, which showed significant activity in the inhibition of proliferation and induction of apoptosis in SKBr-3 breast cancer cells. The mechanism by which SA12 peptide triggers apoptosis was further investigated using a pull-down assay, reverse transcription-polymerase chain reaction, and Western blotting analysis. The results demonstrated that this peptide could interact with tumor-associated proteins MECP2 and CDC20B, which further induced apoptosis of tumor cells via the mitochondrial pathway involving the Bcl-2 family and related caspases. We propose that the novel SA12 peptide has the potential to provide a new strategy for the development of targeted therapy in breast cancer.
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Affiliation(s)
- Longfei Yang
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Ying Cui
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Jianjun Shen
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Fang Lin
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Xi Wang
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Min Long
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Junxia Wei
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Huizhong Zhang
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
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20
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Structural basis for inhibition of the MDM2:p53 interaction by an optimized MDM2-binding peptide selected with mRNA display. PLoS One 2014; 9:e109163. [PMID: 25275651 PMCID: PMC4183577 DOI: 10.1371/journal.pone.0109163] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 08/29/2014] [Indexed: 12/21/2022] Open
Abstract
The oncoprotein MDM2 binds to tumor suppressor protein p53 and inhibits its anticancer activity, which leads to promotion of tumor cell growth and tumor survival. Abrogation of the p53:MDM2 interaction reportedly results in reactivation of the p53 pathway and inhibition of tumor cell proliferation. We recently performed rigorous selection of MDM2-binding peptides by means of mRNA display and identified an optimal 12-mer peptide (PRFWEYWLRLME), named MDM2 Inhibitory Peptide (MIP), which shows higher affinity for MDM2 (and also its homolog, MDMX) and higher tumor cell proliferation suppression activity than known peptides. Here we determined the NMR solution structure of a MIP-MDM2 fusion protein to elucidate the structural basis of the tight binding of MIP to MDM2. A region spanning from Phe3 to Met11 of MIP forms a single α-helix, which is longer than those of the other MDM2-binding peptides. MIP shares a conserved Phe3-Trp7-Leu10 triad, whose side chains are oriented towards and fit into the hydrophobic pockets of MDM2. Additionally, hydrophobic surface patches that surround the hydrophobic pockets of MDM2 are covered by solvent-exposed MIP residues, Trp4, Tyr6, and Met11. Their hydrophobic interactions extend the interface of the two molecules and contribute to the strong binding. The potential MDM2 inhibition activity observed for MIP turned out to originate from its enlarged binding interface. The structural information obtained in the present study provides a road map for the rational design of strong inhibitors of MDM2:p53 binding.
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21
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Yanagawa H. Exploration of the Origin and Evolution of Globular Proteins by mRNA Display. Biochemistry 2013; 52:3841-51. [DOI: 10.1021/bi301704x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Hiroshi Yanagawa
- Department of Biosciences and Informatics,
Faculty
of Sciences and Technology, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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22
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Shiheido H, Naito Y, Kimura H, Genma H, Takashima H, Tokunaga M, Ono T, Hirano T, Du W, Yamada T, Doi N, Iijima S, Hattori Y, Yanagawa H. An anilinoquinazoline derivative inhibits tumor growth through interaction with hCAP-G2, a subunit of condensin II. PLoS One 2012; 7:e44889. [PMID: 23028663 PMCID: PMC3441599 DOI: 10.1371/journal.pone.0044889] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 08/15/2012] [Indexed: 11/18/2022] Open
Abstract
We screened 46 novel anilinoquinazoline derivatives for activity to inhibit proliferation of a panel of human cancer cell lines. Among them, Q15 showed potent in vitro growth-inhibitory activity towards cancer cell lines derived from colorectal cancer, lung cancer and multiple myeloma. It also showed antitumor activity towards multiple myeloma KMS34 tumor xenografts in lcr/scid mice in vivo. Unlike the known anilinoquinazoline derivative gefitinib, Q15 did not inhibit cytokine-mediated intracellular tyrosine phosphorylation. Using our mRNA display technology, we identified hCAP-G2, a subunit of condensin II complex, which is regarded as a key player in mitotic chromosome condensation, as a Q15 binding partner. Immunofluorescence study indicated that Q15 compromises normal segregation of chromosomes, and therefore might induce apoptosis. Thus, our results indicate that hCAP-G2 is a novel therapeutic target for development of drugs active against currently intractable neoplasms.
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Affiliation(s)
- Hirokazu Shiheido
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
| | - Yuhei Naito
- Clinical Physiology and Therapeutics, Faculty of Pharmacy, Keio University, Minato-ku, Tokyo, Japan
| | - Hironobu Kimura
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
| | - Hiroaki Genma
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
| | - Hideaki Takashima
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
| | - Mayuko Tokunaga
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
| | - Takao Ono
- Chromosome Dynamics Laboratory, RIKEN Advanced Science Institute, Wako, Saitama, Japan
| | - Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN Advanced Science Institute, Wako, Saitama, Japan
| | - Wenlin Du
- Department of Pathology, School of Medicine, Keio University, Shinjuku-ku, Tokyo, Japan
| | - Taketo Yamada
- Department of Pathology, School of Medicine, Keio University, Shinjuku-ku, Tokyo, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
| | - Shiro Iijima
- Clinical Physiology and Therapeutics, Faculty of Pharmacy, Keio University, Minato-ku, Tokyo, Japan
| | - Yutaka Hattori
- Clinical Physiology and Therapeutics, Faculty of Pharmacy, Keio University, Minato-ku, Tokyo, Japan
| | - Hiroshi Yanagawa
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
- * E-mail:
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23
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Recent work in the development and application of protein–peptide docking. Future Med Chem 2012; 4:1619-44. [DOI: 10.4155/fmc.12.99] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Interest in the development of novel peptide-based drugs is growing. There is, thus, a pressing need for the development of effective methods to enable novel peptide-based drug discovery. A cogent case can be made for the development and application of computational or in silico methods to assist with peptide discovery. In particular, there is a need for the development of effective protein–peptide docking methods. Here, recent work in the area of protein–peptide docking method development is reviewed and several drug-discovery projects that benefited from protein–peptide docking are discussed. In the present review, special attention is given to the search and scoring problems, the use of peptide docking to enable hit identification, and the use of peptide docking to help rationalize experimental results, and generate and test structure-based hypotheses. Finally, some recommendations are made for improving the future development and application of protein–peptide docking.
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