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Cluet D, Vergier B, Levy NP, Dehau L, Thurman A, Amri I, Spichty M. Titration of apparent in-cellula affinities of protein-protein interactions. Chembiochem 2021; 23:e202100640. [PMID: 34932835 DOI: 10.1002/cbic.202100640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/21/2021] [Indexed: 11/07/2022]
Abstract
A genetic assay permits simultaneous quantification of two interacting proteins and their bound fraction at the single-cell level using flow cytometry. Apparent in-cellula affinities of protein-protein interactions can be extracted from the acquired data through a titration-like analysis. The applicability of this approach is demonstrated on a diverse set of interactions with proteins from different families and organisms and with in-vitro dissociation constants ranging from picomolar to micromolar.
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Affiliation(s)
- David Cluet
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Blandine Vergier
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Nicolas-Pierre Levy
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Lucie Dehau
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Alexandre Thurman
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Ikram Amri
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Martin Spichty
- Laboratoire d'Innovation Moléculaire et Applications, Université de Strasbourg -, Centre National de la Recherche Scientifique, Université de Haute-Alsace, 3 bis rue Alfred Werner, 68057, Mulhouse Cedex, France
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Zhong L, Zhu L, Cai ZW. Mass Spectrometry-based Proteomics and Glycoproteomics in COVID-19 Biomarkers Identification: A Mini-review. J Anal Test 2021; 5:298-313. [PMID: 34513131 PMCID: PMC8423835 DOI: 10.1007/s41664-021-00197-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/27/2021] [Indexed: 12/11/2022]
Abstract
The first corona-pandemic, coronavirus disease 2019 (COVID-19) caused a huge health crisis and incalculable damage worldwide. Knowledge of how to cure the disease is urgently needed. Emerging immune escaping mutants of the virus suggested that it may be potentially persistent in human society as a regular health threat as the flu virus. Therefore, it is imperative to identify appropriate biomarkers to indicate pathological and physiological states, and more importantly, clinic outcomes. Proteins are the performers of life functions, and their abundance and modification status can directly reflect the immune status. Protein glycosylation serves a great impact in modulating protein function. The use of both unmodified and glycosylated proteins as biomarkers has also been proved feasible in the studies of SARS, Zika virus, influenza, etc. In recent years, mass spectrometry-based glycoproteomics, as well as proteomics approaches, advanced significantly due to the evolution of mass spectrometry. We focus on the current development of the mass spectrometry-based strategy for COVID-19 biomarkers' investigation. Potential application of glycoproteomics approaches and challenges in biomarkers identification are also discussed.
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Affiliation(s)
- Li Zhong
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong SAR, China
| | - Lin Zhu
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong SAR, China
| | - Zong-Wei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong SAR, China
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Lei X, Ou Z, Yang Z, Zhong J, Zhu Y, Tian J, Wu J, Deng H, Lin X, Peng Y, Li B, He L, Tu Z, Chen W, Li Q, Liu N, Zhang H, Wang Z, Fang Z, Yamada T, Lv X, Tian T, Pan G, Wu F, Xiao L, Zhang L, Cai T, Wang X, Tannous BA, Li J, Kontos F, Ferrone S, Fan S. A Pan-Histone Deacetylase Inhibitor Enhances the Antitumor Activity of B7-H3-Specific CAR T Cells in Solid Tumors. Clin Cancer Res 2021; 27:3757-3771. [PMID: 33811153 DOI: 10.1158/1078-0432.ccr-20-2487] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/03/2020] [Accepted: 03/29/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE The limited efficacy of chimeric antigen receptor (CAR) T-cell therapies with solid malignancies prompted us to test whether epigenetic therapy could enhance the antitumor activity of B7-H3.CAR T cells with several solid cancer types. EXPERIMENTAL DESIGN We evaluated B7-H3 expression in many human solid cancer and normal tissue samples. The efficacy of the combinatorial therapy with B7-H3.CAR T cells and the deacetylase inhibitor SAHA with several solid cancer types and the potential underlying mechanisms were characterized with in vitro and ex vivo experiments. RESULTS B7-H3 is expressed in most of the human solid tumor samples tested, but exhibits a restricted expression in normal tissues. B7-H3.CAR T cells selectively killed B7-H3 expressing human cancer cell lines in vitro. A low dose of SAHA upregulated B7-H3 expression in several types of solid cancer cells at the transcriptional level and B7-H3.CAR expression on human transgenic T-cell membrane. In contrast, the expression of immunosuppressive molecules, such as CTLA-4 and TET2, by T cells was downregulated upon SAHA treatment. A low dose of SAHA significantly enhanced the antitumor activity of B7-H3.CAR T cells with solid cancers in vitro and ex vivo, including orthotopic patient-derived xenograft and metastatic models treated with autologous CAR T-cell infusions. CONCLUSIONS Our results show that our novel strategy which combines SAHA and B7-H3.CAR T cells enhances their therapeutic efficacy with solid cancers and justify its translation to a clinical setting.
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Affiliation(s)
- Xinyuan Lei
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China.,State University of New York at Stony Brook, Stony Brook, New York
| | - Zhanpeng Ou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Zhaohui Yang
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jianglong Zhong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Yanliang Zhu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Jing Tian
- Department of Ultrasound, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiannan Wu
- Department of Breast Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Heran Deng
- Department of Breast Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xinyu Lin
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yu Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Bowen Li
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lile He
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Zhiming Tu
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Weixiong Chen
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qunxing Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Niu Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Hanqing Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Zhangsong Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Zezhen Fang
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Teppei Yamada
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Xiaobin Lv
- Nanchang Key Laboratory of Cancer Pathogenesis and Translational Research, Center Laboratory, the Third Affiliated Hospital, Nanchang University, Nanchang, China
| | - Tian Tian
- Department of Neurobiology, Key Laboratory of Human Functional Genomics of Jiangsu, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Guokai Pan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Fan Wu
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Liping Xiao
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lizao Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Tingting Cai
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Xinhui Wang
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bakhos A Tannous
- Experimental Therapeutics and Molecular Imaging Lab, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jinsong Li
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Filippos Kontos
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Soldano Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Song Fan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China. .,Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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Cluet D, Amri I, Vergier B, Léault J, Audibert A, Grosjean C, Calabrési D, Spichty M. A Quantitative Tri-fluorescent Yeast Two-hybrid System: From Flow Cytometry to In cellula Affinities. Mol Cell Proteomics 2020; 19:701-715. [PMID: 32015065 PMCID: PMC7124468 DOI: 10.1074/mcp.tir119.001692] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 01/31/2020] [Indexed: 12/14/2022] Open
Abstract
We present a technological advancement for the estimation of the affinities of Protein-Protein Interactions (PPIs) in living cells. A novel set of vectors is introduced that enables a quantitative yeast two-hybrid system based on fluorescent fusion proteins. The vectors allow simultaneous quantification of the reaction partners (Bait and Prey) and the reporter at the single-cell level by flow cytometry. We validate the applicability of this system on a small but diverse set of PPIs (eleven protein families from six organisms) with different affinities; the dissociation constants range from 117 pm to 17 μm After only two hours of reaction, expression of the reporter can be detected even for the weakest PPI. Through a simple gating analysis, it is possible to select only cells with identical expression levels of the reaction partners. As a result of this standardization of expression levels, the mean reporter levels directly reflect the affinities of the studied PPIs. With a set of PPIs with known affinities, it is straightforward to construct an affinity ladder that permits rapid classification of PPIs with thus far unknown affinities. Conventional software can be used for this analysis. To permit automated analysis, we provide a graphical user interface for the Python-based FlowCytometryTools package.
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Affiliation(s)
- David Cluet
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Ikram Amri
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Blandine Vergier
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Jérémie Léault
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Astrid Audibert
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Clémence Grosjean
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Dylan Calabrési
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Martin Spichty
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France.
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Corda E, Du X, Shim SY, Klein AN, Siltberg-Liberles J, Gilch S. Interaction of Peptide Aptamers with Prion Protein Central Domain Promotes α-Cleavage of PrP C. Mol Neurobiol 2018; 55:7758-74. [PMID: 29460268 DOI: 10.1007/s12035-018-0944-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 01/31/2018] [Indexed: 11/03/2022]
Abstract
Prion diseases are infectious and fatal neurodegenerative diseases affecting humans and animals. Transmission is possible within and between species with zoonotic potential. Currently, no prophylaxis or treatment exists. Prions are composed of the misfolded isoform PrPSc of the cellular prion protein PrPC. Expression of PrPC is a prerequisite for prion infection, and conformational conversion of PrPC is induced upon its direct interaction with PrPSc. Inhibition of this interaction can abrogate prion propagation, and we have previously established peptide aptamers (PAs) binding to PrPC as new anti-prion compounds. Here, we mapped the interaction site of PA8 in PrP and modeled the complex in silico to design targeted mutations in PA8 which presumably enhance binding properties. Using these PA8 variants, we could improve PA-mediated inhibition of PrPSc replication and de novo infection of neuronal cells. Furthermore, we demonstrate that binding of PA8 and its variants increases PrPC α-cleavage and interferes with its internalization. This gives rise to high levels of the membrane-anchored PrP-C1 fragment, a transdominant negative inhibitor of prion replication. PA8 and its variants interact with PrPC at its central and most highly conserved domain, a region which is crucial for prion conversion and facilitates toxic signaling of Aβ oligomers characteristic for Alzheimer's disease. Our strategy allows for the first time to induce α-cleavage, which occurs within this central domain, independent of targeting the responsible protease. Therefore, interaction of PAs with PrPC and enhancement of α-cleavage represent mechanisms that can be beneficial for the treatment of prion and other neurodegenerative diseases.
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Zheng X, Xing XH, Zhang C. Targeted mutagenesis: A sniper-like diversity generator in microbial engineering. Synth Syst Biotechnol 2017; 2:75-86. [PMID: 29062964 PMCID: PMC5636951 DOI: 10.1016/j.synbio.2017.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 12/26/2022] Open
Abstract
Mutations, serving as the raw materials of evolution, have been extensively utilized to increase the chances of engineering molecules or microbes with tailor-made functions. Global and targeted mutagenesis are two main methods of obtaining various mutations, distinguished by the range of action they can cover. While the former one stresses the mining of novel genetic loci within the whole genomic background, targeted mutagenesis performs in a more straightforward manner, bringing evolutionary escape and error catastrophe under control. In this review, we classify the existing techniques of targeted mutagenesis into two categories in terms of whether the diversity is generated in vitro or in vivo, and briefly introduce the mechanisms and applications of them separately. The inherent connections and development trends of the two classes are also discussed to provide an insight into the next generation evolution research.
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Key Words
- 3′-LTR, 3’-long terminal repeat
- 5-FOA, 5-fluoro-orotic acid
- CRISPR/Cas9, clustered regularly interspaced short palindromic repeats and associated protein 9
- DNA Pol III, DNA polymerase III
- DNA PolI, DNA polymerase I
- DSB, double strand break
- Evolution
- FLASH, fast ligation-based automatable solid-phase high-throughput
- HDR, homology-directed repair
- HIV, human immunodeficiency virus
- ICE, in vivo continuous evolution
- LIC, ligation-independent cloning
- MAGE, multiplex automated genome engineering
- MMEJ, microhomology-mediated end-joining
- Mutations
- NHEJ, error-prone non-homologous end-joining
- ORF, open reading frame
- PAM, protospacer-adjacent motif
- RVD, repeat variable di-residue
- Synthetic biology
- TALE, transcription activator-like effector
- TALEN, transcription activator-like effector nuclease
- TP, terminal protein
- TP-DNAP, TP-DNA polymerase fusion
- TaGTEAM, targeting glycosylase to embedded arrays for mutagenesis
- Targeted mutagenesis
- YOGE, yeast oligo-mediated genome engineering
- ZF, zinc-finger protein
- ZFN, zinc-finger nuclease
- dCas9, catalytically dead Cas9
- dNTP, deoxy-ribonucleoside triphosphate
- dsDNA, double-stranded DNA
- error-prone PCR, error-prone polymerase chain reaction
- non-GMO, non-genetically modified organism
- pre-crRNA, pre-CRISPR RNA
- sctetR, single chain tetR
- sgRNA, single-guide RNA
- ssDNA, single-stranded DNA
- tracrRNA, trans-encoded RNA
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Affiliation(s)
- Xiang Zheng
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Institute of Biochemical Engineering, Department of Chemical Engineering, Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
| | - Xin-Hui Xing
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Institute of Biochemical Engineering, Department of Chemical Engineering, Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
| | - Chong Zhang
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Institute of Biochemical Engineering, Department of Chemical Engineering, Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
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Weckman NE, McRae C, Ko Ferrigno P, Seshia AA. Comparison of the specificity and affinity of surface immobilised Affimer binders using the quartz crystal microbalance. Analyst 2016; 141:6278-6286. [DOI: 10.1039/c6an01602b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study investigates the performance of surface bound Affimer proteins, comparing the affinity and specificity of different binders for closely related immunoglobulin molecules using the quartz crystal microbalance with dissipation monitoring (QCM-D).
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Affiliation(s)
| | | | | | - Ashwin A. Seshia
- Nanoscience Centre
- University of Cambridge
- Cambridge CB3 0FF
- UK
- Department of Engineering
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8
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Yeh JT, Binari R, Gocha T, Dasgupta R, Perrimon N. PAPTi: a peptide aptamer interference toolkit for perturbation of protein-protein interaction networks. Sci Rep 2013; 3:1156. [PMID: 23362456 DOI: 10.1038/srep01156] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 12/11/2012] [Indexed: 01/11/2023] Open
Abstract
Signaling proteins often form dynamic protein-protein interaction (PPI) complexes to achieve multi-functionality. Methods to abrogate a subset of PPI interfaces without depleting the full-length protein will be valuable for structure-function relationship annotations. Here, we describe the use of Peptide Aptamer Interference (PAPTi) approach for structure-function network studies. We identified peptide aptamers against Dishevelled (Dsh) and β-catenin (β-cat) to target the Wnt signaling pathway and demonstrate that these FN3-based MONOBODYs (FNDYs) can be used to perturb protein activities both in vitro and in vivo. Further, to investigate the crosstalk between the Wnt and Notch pathways, we isolated FNDYs against the Notch Ankyrin (ANK) region and demonstrate that perturbing the ANK domain of Notch increases the inhibitory activity of Notch towards Wnt signaling. Altogether, these studies demonstrate the power of the PAPTi approach to dissect specific PPI interactions within signaling networks.
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Abstract
This article focuses on drug targeting to specific cellular organelles for therapeutic purposes. Drugs can be delivered to all major organelles of the cell (cytosol, endosome/lysosome, nucleus, nucleolus, mitochondria, endoplasmic reticulum, Golgi apparatus, peroxisomes and proteasomes) where they exert specific effects in those particular subcellular compartments. Delivery can be achieved by chemical (e.g., polymeric) or biological (e.g., signal sequences) means. Unidirectional targeting to individual organelles has proven to be immensely successful for drug therapy. Newer technologies that accommodate multiple signals (e.g., protein switch and virus-like delivery systems) mimic nature and allow for a more sophisticated approach to drug delivery. Harnessing different methods of targeting multiple organelles in a cell will lead to better drug delivery and improvements in disease therapy.
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10
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Russo LC, Asega AF, Castro LM, Negraes PD, Cruz L, Gozzo FC, Ulrich H, Camargo ACM, Rioli V, Ferro ES. Natural intracellular peptides can modulate the interactions of mouse brain proteins and thimet oligopeptidase with 14-3-3ε and calmodulin. Proteomics 2012; 12:2641-55. [DOI: 10.1002/pmic.201200032] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 05/31/2012] [Accepted: 06/03/2012] [Indexed: 02/03/2023]
Affiliation(s)
- Lilian C. Russo
- Department of Cell Biology and Development; Biomedical Sciences Institute; University of São Paulo; São Paulo Brazil
| | - Amanda F. Asega
- Laboratory of Applied Toxinology (LETA); Butantan Institute; SP Brazil
| | - Leandro M. Castro
- Department of Cell Biology and Development; Biomedical Sciences Institute; University of São Paulo; São Paulo Brazil
| | - Priscilla D. Negraes
- Biochemistry Department; Chemistry Institute; University of São Paulo; São Paulo Brazil
| | - Lilian Cruz
- Department of Cell Biology and Development; Biomedical Sciences Institute; University of São Paulo; São Paulo Brazil
| | - Fabio C. Gozzo
- Chemistry Institute; Campinas State University; Campinas SP Brazil
| | - Henning Ulrich
- Biochemistry Department; Chemistry Institute; University of São Paulo; São Paulo Brazil
| | | | - Vanessa Rioli
- Laboratory of Applied Toxinology (LETA); Butantan Institute; SP Brazil
| | - Emer S. Ferro
- Department of Cell Biology and Development; Biomedical Sciences Institute; University of São Paulo; São Paulo Brazil
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11
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Hamdi A, Colas P. Yeast two-hybrid methods and their applications in drug discovery. Trends Pharmacol Sci 2012; 33:109-18. [DOI: 10.1016/j.tips.2011.10.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 10/21/2011] [Accepted: 10/24/2011] [Indexed: 01/08/2023]
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12
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Laurenson S, Pett M, Hoppe-Seyler K, Denk C, Hoppe-Seyler F, Coleman N, Ko Ferrigno P. Development of peptide aptamer microarrays for detection of HPV16 oncoproteins in cell extracts. Anal Biochem 2011; 410:161-70. [DOI: 10.1016/j.ab.2010.10.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 10/12/2010] [Accepted: 10/30/2010] [Indexed: 01/06/2023]
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13
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Wickramasinghe RD, Ko Ferrigno P, Roghi C. Peptide aptamers as new tools to modulate clathrin-mediated internalisation--inhibition of MT1-MMP internalisation. BMC Cell Biol 2010; 11:58. [PMID: 20653933 PMCID: PMC2919464 DOI: 10.1186/1471-2121-11-58] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 07/23/2010] [Indexed: 12/23/2022] Open
Abstract
Background Peptide aptamers are combinatorial protein reagents that bind to targets with a high specificity and a strong affinity thus providing a molecular tool kit for modulating the function of their targets in vivo. Results Here we report the isolation of a peptide aptamer named swiggle that interacts with the very short (21 amino acid long) intracellular domain of membrane type 1-metalloproteinase (MT1-MMP), a key cell surface protease involved in numerous and crucial physiological and pathological cellular events. Expression of swiggle in mammalian cells was found to increase the cell surface expression of MT1-MMP by impairing its internalisation. Swiggle interacts with the LLY573 internalisation motif of MT1-MMP intracellular domain, thus disrupting the interaction with the μ2 subunit of the AP-2 internalisation complex required for endocytosis of the protease. Interestingly, swiggle-mediated inhibition of MT1-MMP clathrin-mediated internalisation was also found to promote MT1-MMP-mediated cell migration. Conclusions Taken together, our results provide further evidence that peptide aptamers can be used to dissect molecular events mediated by individual protein domains, in contrast to the pleiotropic effects of RNA interference techniques.
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Affiliation(s)
- Rochana D Wickramasinghe
- Department of Oncology, Cambridge Research Centre, University of Cambridge, Cambridge CB2 0RE, UK
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14
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Barreto K, Bharathikumar VM, Ricardo A, DeCoteau JF, Luo Y, Geyer CR. A genetic screen for isolating "lariat" Peptide inhibitors of protein function. ACTA ACUST UNITED AC 2010; 16:1148-57. [PMID: 19942138 DOI: 10.1016/j.chembiol.2009.10.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 09/30/2009] [Accepted: 10/19/2009] [Indexed: 10/20/2022]
Abstract
Functional genomic analyses provide information that allows hypotheses to be formulated on protein function. These hypotheses, however, need to be validated using reverse genetic approaches, which are difficult to perform on a large scale and in diploid organisms. We developed a genetic screen for isolating "lariat" peptides that function as trans dominant inhibitors of protein function. A lariat consists of a lactone-cyclized peptide with a covalently attached transcription activation domain, which allows combinatorial lariat libraries to be screened for protein interactions using the yeast two-hybrid assay. We isolated lariats against the bacterial repressor protein LexA. LexA regulates bacterial SOS response and LexA mutants that cannot undergo autoproteolysis make bacteria more sensitive to, and inhibit resistance against, cytotoxic reagents. We showed that an anti-LexA lariat blocked LexA autoproteolysis and potentiated the antimicrobial activity of mitomycin C.
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15
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16
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Abstract
Prion diseases are fatal neurodegenerative and infectious disorders of humans and animals, characterized by structural transition of the host-encoded cellular prion protein (PrP(c)) into the aberrantly folded pathologic isoform PrP(Sc). RNA, DNA or peptide aptamers are classes of molecules which can be selected from complex combinatorial libraries for high affinity and specific binding to prion proteins and which might therefore be useful in diagnosis and therapy of prion diseases. Nucleic acid aptamers, which can be chemically synthesized, stabilized and immobilized, appear more suitable for diagnostic purposes, allowing use of PrP(Sc) as selection target. Peptide aptamers facilitate appropriate intracellular expression, targeting and re-routing without losing their binding properties to PrP, a requirement for potential therapeutic gene transfer experiments in vivo. Elucidation of structural properties of peptide aptamers might be used as basis for rational drug design, providing another attractive application of peptide aptamers in the search for effective anti-prion strategies.
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Affiliation(s)
- Sabine Gilch
- Institute of Virology, Technische Universität München, Trogerstr. 30, 81675 Munich, Germany
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17
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Saccucci L, Crance J, Colas P, Bickle M, Garin D, Iseni F. Inhibition of vaccinia virus replication by peptide aptamers. Antiviral Res 2009; 82:134-40. [DOI: 10.1016/j.antiviral.2009.02.191] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Revised: 01/22/2009] [Accepted: 02/16/2009] [Indexed: 11/17/2022]
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18
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Berti DA, Morano C, Russo LC, Castro LM, Cunha FM, Zhang X, Sironi J, Klitzke CF, Ferro ES, Fricker LD. Analysis of intracellular substrates and products of thimet oligopeptidase in human embryonic kidney 293 cells. J Biol Chem 2009; 284:14105-16. [PMID: 19282285 PMCID: PMC2682859 DOI: 10.1074/jbc.m807916200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Revised: 02/05/2009] [Indexed: 01/03/2023] Open
Abstract
Thimet oligopeptidase (EC 3.4.24.15; EP24.15) is an intracellular enzyme that has been proposed to metabolize peptides within cells, thereby affecting antigen presentation and G protein-coupled receptor signal transduction. However, only a small number of intracellular substrates of EP24.15 have been reported previously. Here we have identified over 100 peptides in human embryonic kidney 293 (HEK293) cells that are derived from intracellular proteins; many but not all of these peptides are substrates or products of EP24.15. First, cellular peptides were extracted from HEK293 cells and incubated in vitro with purified EP24.15. Then the peptides were labeled with isotopic tags and analyzed by mass spectrometry to obtain quantitative data on the extent of cleavage. A related series of experiments tested the effect of overexpression of EP24.15 on the cellular levels of peptides in HEK293 cells. Finally, synthetic peptides that corresponded to 10 of the cellular peptides were incubated with purified EP24.15 in vitro, and the cleavage was monitored by high pressure liquid chromatography and mass spectrometry. Many of the EP24.15 substrates identified by these approaches are 9-11 amino acids in length, supporting the proposal that EP24.15 can function in the degradation of peptides that could be used for antigen presentation. However, EP24.15 also converts some peptides into products that are 8-10 amino acids, thus contributing to the formation of peptides for antigen presentation. In addition, the intracellular peptides described here are potential candidates to regulate protein interactions within cells.
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Affiliation(s)
- Denise A Berti
- Department of Cell Biology and Development , Biomedical Science Institute, University of São Paulo, São Paulo SP 05508-900, Brazil
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19
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Borghouts C, Kunz C, Delis N, Groner B. Monomeric Recombinant Peptide Aptamers Are Required for Efficient Intracellular Uptake and Target Inhibition. Mol Cancer Res 2008; 6:267-81. [DOI: 10.1158/1541-7786.mcr-07-0245] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Abed N, Bickle M, Mari B, Schapira M, Sanjuan-España R, Robbe Sermesant K, Moncorgé O, Mouradian-Garcia S, Barbry P, Rudkin BB, Fauvarque MO, Michaud-Soret I, Colas P. A comparative analysis of perturbations caused by a gene knock-out, a dominant negative allele, and a set of peptide aptamers. Mol Cell Proteomics 2007; 6:2110-21. [PMID: 17785351 DOI: 10.1074/mcp.m700105-mcp200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The study of protein function mostly relies on perturbing regulatory networks by acting upon protein expression levels or using transdominant negative agents. Here we used the Escherichia coli global transcription regulator Fur (ferric uptake regulator) as a case study to compare the perturbations exerted by a gene knock-out, the expression of a dominant negative allele of a gene, and the expression of peptide aptamers that bind a gene product. These three perturbations caused phenotypes that differed quantitatively and qualitatively from one another. The Fur peptide aptamers inhibited the activity of their target to various extents and reduced the virulence of a pathogenic E. coli strain in Drosophila. A genome-wide transcriptome analysis revealed that the "penetrance" of a peptide aptamer was comparable to that of a dominant negative allele but lower than the penetrance of the gene knock-out. Our work shows that comparative analysis of phenotypic and transcriptome responses to different types of perturbation can help decipher complex regulatory networks that control various biological processes.
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Affiliation(s)
- Nadia Abed
- Differentiation and Cell Cycle Group, Laboratoire de Biologie Moléculaire de la Cellule, UMR 5239 CNRS/ENS Lyon, Université Lyon 1, Ecole Normale Supérieure de Lyon, IFR 128 BioSciences Lyon-Gerland, 46 allée d'Italie, 69364 Lyon cedex 07, France
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21
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Gilch S, Kehler C, Schätzl HM. Peptide Aptamers Expressed in the Secretory Pathway Interfere with Cellular PrPSc Formation. J Mol Biol 2007; 371:362-73. [PMID: 17574575 DOI: 10.1016/j.jmb.2007.05.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2007] [Revised: 05/11/2007] [Accepted: 05/17/2007] [Indexed: 11/22/2022]
Abstract
Prion diseases are rare and obligatory fatal neurodegenerative disorders caused by the accumulation of a misfolded isoform (PrPSc) of the host-encoded prion protein (PrPc). Prophylactic and therapeutic regimens against prion diseases are very limited. To extend such strategies we selected peptide aptamers binding to PrP from a combinatorial peptide library presented on the Escherichia coli thioredoxin A (trxA) protein as a scaffold. In a yeast two-hybrid screen employing full-length murine PrP (aa 23-231) as a bait we identified three peptide aptamers that reproducibly bind to PrP. Treatment of prion-infected cells with recombinantly expressed aptamers added to the culture medium abolished PrPSc conversion with an IC50 between 350 and 700 nM. For expression in eukaryotic cells, peptide aptamers were fused to an N-terminal signal peptide for entry of the secretory pathway. The C terminus was modified by a glycosyl-phosphatidyl-inositol-(GPI) anchoring signal, a KDEL retention motif and the transmembrane and cytosolic domain of LAMP-I, respectively. These peptide aptamers retained their binding properties to PrPc and, depending on peptide sequence and C-terminal modification, interfered with endogenous PrPSc conversion upon expression in prion-infected cells. Notably, infection of cell cultures could be prevented by expression of KDEL peptide aptamers. For the first time, we show that trxA-based peptide aptamers can be targeted to the secretory pathway, thereby not losing the affinity for their target protein. Beside their inhibitory effect on prion conversion, these molecules could be used as fundament for rational drug design.
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Affiliation(s)
- Sabine Gilch
- Institute of Virology, Prion Research Group, Technical University Munich, Trogerstr. 30, 81675 Munich, Germany
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22
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Bickle MBT, Dusserre E, Moncorgé O, Bottin H, Colas P. Selection and characterization of large collections of peptide aptamers through optimized yeast two-hybrid procedures. Nat Protoc 2007; 1:1066-91. [PMID: 17406388 DOI: 10.1038/nprot.2006.32] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Peptide aptamers are combinatorial proteins that specifically bind intracellular proteins and modulate their function. They are powerful tools to study protein function within complex regulatory networks and to guide small-molecule drug discovery. Here we describe methodological improvements that enhance the yeast two-hybrid selection and characterization of large collections of peptide aptamers. We provide a detailed protocol to perform high-efficiency transformation of peptide aptamer libraries, in-depth validation experiments of the bait proteins, high-efficiency mating to screen large numbers of peptide aptamers and streamlined confirmation of the positive clones. We also describe yeast two-hybrid mating assays, which can be used to determine the specificity of the selected aptamers, map their binding sites on target proteins and provide structural insights on their target-binding surface. Overall, 12 weeks are required to perform the protocols. The improvements on the yeast two-hybrid method can be also usefully applied to the screening of cDNA libraries to identify protein interactions.
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Affiliation(s)
- Marc B T Bickle
- Aptanomics, 181-203, Avenue Jean Jaurès, 69007 Lyon, France.
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23
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Kunz C, Borghouts C, Buerger C, Groner B. Peptide Aptamers with Binding Specificity for the Intracellular Domain of the ErbB2 Receptor Interfere with AKT Signaling and Sensitize Breast Cancer Cells to Taxol. Mol Cancer Res 2006; 4:983-98. [PMID: 17189388 DOI: 10.1158/1541-7786.mcr-06-0046] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The ErbB2 receptor tyrosine kinase is overexpressed in approximately 30% of breast tumor cases and its overexpression correlates with an unfavorable prognosis. A major contributor for this course of the disease is the insensitivity of these tumors toward chemotherapy. Monoclonal antibodies, inhibiting the ligand-induced activation of the receptor and tyrosine kinase inhibitors acting on the intrinsic enzymatic activity of the intracellular domain, have been developed as targeted drugs. Both have been shown to be beneficial for breast cancer patients. We targeted a third aspect of receptor function: its association with intracellular signaling components. For this purpose, we selected peptide aptamers, which specifically interact with defined domains of the intracellular part of the receptor. The peptide aptamers were selected from a random peptide library using a yeast two-hybrid system with the intracellular tyrosine kinase domain of ErbB2 as a bait construct. The peptide aptamer AII-7 interacts with high specificity with the ErbB2 receptor in vitro and in vivo. The aptamers colocalized with the intracellular domain of ErbB2 within cells. We investigated the functional consequences of the aptamer interaction with the ErbB2 receptor within tumor cells. The aptamer sequences were either expressed intracellularly or introduced into the cells as recombinant aptamer proteins. The phosphorylation of p42/44 mitogen-activated protein kinase was nearly unaffected and the activation of signal transducers and activators of transcription-3 was only modestly reduced. In contrast, they strongly inhibited the induction of AKT kinase in MCF7 breast cancer cells treated with heregulin, whereas AKT activation downstream of insulin-like growth factor I or epidermal growth factor receptor was not or only slightly affected. High AKT activity is responsible for the enhanced resistance of ErbB2-overexpressing cancer cells toward chemotherapeutic agents. Peptide aptamer interference with AKT activation resulted in the restoration of regular sensitivity of breast cancer cells toward Taxol.
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Affiliation(s)
- Christian Kunz
- Georg-Speyer-Haus, Institute for Biomedical Research, Frankfurt am Main, Germany
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24
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Watt PM, Heinrich TK, Thomas WR. Protein silencing with Phylomers: a new tool for target validation and generating lead biologicals targeting protein interactions. Expert Opin Drug Discov 2006; 1:491-502. [DOI: 10.1517/17460441.1.5.491] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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25
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Tomai E, Butz K, Lohrey C, von Weizsäcker F, Zentgraf H, Hoppe-Seyler F. Peptide Aptamer-mediated Inhibition of Target Proteins by Sequestration into Aggresomes. J Biol Chem 2006; 281:21345-21352. [PMID: 16717089 DOI: 10.1074/jbc.m604258200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peptide aptamers (PAs) can be employed to block the intracellular function of target proteins. Little is known about the mechanism of PA-mediated protein inhibition. Here, we generated PAs that specifically bound to the duck hepatitis B virus (HBV) core protein. Among them, PA34 strongly blocked duck HBV replication by inhibiting viral capsid formation. We found that PA34 led to a dramatic intracellular redistribution of its target protein into perinuclear inclusion bodies, which exhibit the typical characteristics of aggresomes. As a result, the core protein is efficiently removed from the viral life cycle. Corresponding findings were obtained for bioactive PAs that bind to the HBV core protein or to the human papillomavirus-16 (HPV16) E6 protein, respectively. The observation that PAs induce the specific sequestration of bound proteins into aggresomes defines a novel mechanism as to how this new class of intracellular inhibitors blocks the function of their target proteins.
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Affiliation(s)
- Evangelia Tomai
- Molecular Therapy of Virus-Associated Cancers Group (F065), German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Karin Butz
- Molecular Therapy of Virus-Associated Cancers Group (F065), German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Claudia Lohrey
- Molecular Therapy of Virus-Associated Cancers Group (F065), German Cancer Research Center, D-69120 Heidelberg, Germany
| | | | - Hanswalter Zentgraf
- Electron Microcopy Group (F090), German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Felix Hoppe-Seyler
- Molecular Therapy of Virus-Associated Cancers Group (F065), German Cancer Research Center, D-69120 Heidelberg, Germany.
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26
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Baines IC, Colas P. Peptide aptamers as guides for small-molecule drug discovery. Drug Discov Today 2006; 11:334-41. [PMID: 16580975 DOI: 10.1016/j.drudis.2006.02.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Revised: 12/21/2005] [Accepted: 02/17/2006] [Indexed: 11/17/2022]
Abstract
Peptide aptamers are combinatorial protein reagents that bind to target proteins with a high specificity and a strong affinity. By so doing, they can modulate the function of their cognate targets. Because peptide aptamers introduce perturbations that are similar to those caused by therapeutic molecules, their use identifies and/or validates therapeutic targets with a higher confidence level than is typically provided by methods that act upon protein expression levels. The unbiased combinatorial nature of peptide aptamers enables them to 'decorate' numerous polymorphic protein surfaces, whose biological relevance can be inferred through characterization of the peptide aptamers. Bioactive aptamers that bind druggable surfaces can be used in displacement screening assays to identify small-molecule hits to the surfaces. The peptide aptamer technology has a positive impact on drug discovery by addressing major causes of failure and by offering a seamless, cost-effective process from target validation to hit identification.
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Affiliation(s)
- Ivan C Baines
- Aptanomics, 181-203 avenue Jean Jaurès, 69007 Lyon, France
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27
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Matsuzawa SI, Cuddy M, Fukushima T, Reed JC. Method for targeting protein destruction by using a ubiquitin-independent, proteasome-mediated degradation pathway. Proc Natl Acad Sci U S A 2005; 102:14982-7. [PMID: 16219697 PMCID: PMC1257734 DOI: 10.1073/pnas.0507512102] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
With the euchromatic portion of several mammalian genomes now sequenced, emphasis has turned to ascertaining the functions of gene products. A method for targeting destruction of selected proteins in mammalian cells is described, based on the ubiquitin-independent mechanism by which ornithine decarboxylase (ODC) is degraded by the 26S proteasome in collaboration with antizyme (AZ). We show that expressing whole proteins, protein domains, or peptide ligands fused to the N terminus of ODC promotes proteasome-dependent degradation of these chimeric fusion proteins and their interacting cellular target proteins. Moreover, the degradation of the interacting (targeted) protein depends on coexpression of AZ in about half of cases, providing an inducible switch for triggering the degradation process. By using 12 pairs of interacting proteins for testing, direct comparisons with several alternative strategies for achieving targeted protein destruction based on the concept of induced ubiquitination revealed advantages of the ODC/AZ system, which does not require posttranslational attachment of ubiquitin to target proteins. As proof of concept, the ODC/AZ system was used to ablate expression of specific endogenous proteins (e.g., TRAF6; Rb), and was shown to create the expected lesions in cellular pathways that require these proteins. Altogether, these findings reveal a strategy for achieving targeted destruction of cellular proteins, thus providing an additional tool for revealing the cellular phenotypes of gene products.
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28
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Woodman R, Yeh JTH, Laurenson S, Ko Ferrigno P. Design and Validation of a Neutral Protein Scaffold for the Presentation of Peptide Aptamers. J Mol Biol 2005; 352:1118-33. [PMID: 16139842 DOI: 10.1016/j.jmb.2005.08.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Accepted: 08/03/2005] [Indexed: 10/25/2022]
Abstract
Peptide aptamers are peptides constrained and presented by a scaffold protein that are used to study protein function in cells. They are able to disrupt protein-protein interactions and to constitute recognition modules that allow the creation of a molecular toolkit for the intracellular analysis of protein function. The success of peptide aptamer technology is critically dependent on the performance of the scaffold. Here, we describe a rational approach to the design of a new peptide aptamer scaffold. We outline the qualities that an ideal scaffold would need to possess to be broadly useful for in vitro and in vivo studies and apply these criteria to the design of a new scaffold, called STM. Starting from the small, stable intracellular protease inhibitor stefin A, we have engineered a biologically neutral scaffold that retains the stable conformation of the parent protein. We show that STM is able to present peptides that bind to targets of interest, both in the context of known interactors and in library screens. Molecular tools based on our scaffold are likely to be used in a wide range of studies of biological pathways, and in the validation of drug targets.
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Affiliation(s)
- Robbie Woodman
- MRC Cancer Cell Unit Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 2 XZ, UK
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29
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Amstutz P, Binz HK, Parizek P, Stumpp MT, Kohl A, Grütter MG, Forrer P, Plückthun A. Intracellular Kinase Inhibitors Selected from Combinatorial Libraries of Designed Ankyrin Repeat Proteins. J Biol Chem 2005; 280:24715-22. [PMID: 15851475 DOI: 10.1074/jbc.m501746200] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The specific intracellular inhibition of protein activity at the protein level allows the determination of protein function in the cellular context. We demonstrate here the use of designed ankyrin repeat proteins as tailor-made intracellular kinase inhibitors. The target was aminoglycoside phosphotransferase (3')-IIIa (APH), which mediates resistance to aminoglycoside antibiotics in pathogenic bacteria and shares structural homology with eukaryotic protein kinases. Combining a selection and screening approach, we isolated 198 potential APH inhibitors from highly diverse combinatorial libraries of designed ankyrin repeat proteins. A detailed analysis of several inhibitors revealed that they bind APH with high specificity and with affinities down to the subnanomolar range. In vitro, the most potent inhibitors showed complete enzyme inhibition, and in vivo, a phenotype comparable with the gene knockout was observed, fully restoring antibiotic sensitivity in resistant bacteria. These results underline the great potential of designed ankyrin repeat proteins for modulation of intracellular protein function.
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Affiliation(s)
- Patrick Amstutz
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, Zürich CH-8057, Switzerland
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30
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Abstract
Transforming growth factor beta (TGF-beta) stimulation results in the assembly of Smad-containing protein complexes that mediate activation or repression of TGF-beta responsive genes. To determine if disruption of specific Smad protein-protein interactions would selectively inhibit responses to TGF-beta or generally interfere with Smad-dependent signaling, we developed three Smad-binding peptide aptamers by introducing Smad interaction motifs from Smad-binding proteins CBP, FoxH1 and Lef1 into the scaffold protein E. coli thioredoxin A (Trx). All three classes of aptamers bound to Smads by GST pulldown assays and co-immunoprecipitation from mammalian cells. Expression of the aptamers in HepG2 cells did not generally inhibit Smad-dependent signaling as evaluated using seven TGF-beta responsive luciferase reporter genes. The Trx-xFoxH1b aptamer inhibited TGF-beta-induced expression from a reporter dependent on the Smad-FoxH1 interaction, A3-lux, by 50%. Trx-xFoxH1b also partially inhibited two reporters not dependent on a Smad-FoxH1 interaction, 3TP-lux and Twntop, and endogenous PAI-1 expression. Trx-Lef1 aptamer only inhibited expression of the Smad-Lef1 responsive reporter gene TwnTop. The Trx-CBP aptamer had no significant effect on reporter gene expression. The results suggest that Smad-binding peptide aptamers can be developed to selectively inhibit TGF-beta-induced gene expression.
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Affiliation(s)
- Qiqi Cui
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
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31
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Abstract
The ubiquitin-proteasome pathway plays a major role in cellular protein destruction and regulates fundamental cellular processes such as the cell cycle, cell signaling, and development. By altering the substrate recognition of ubiquitin-protein ligases, their robust proteolytic activity can be re-directed to recruit and accelerate the degradation of other cellular targets. Two approaches have been applied for targeted proteolysis: one entails designing a chimeric substrate receptor for recruitment of the target protein, the other involves the construction of peptide-small-molecule hybrids that bridge the interaction between the intended target and the substrate receptor of the known ubiquitin-protein ligases. The engineered ubiquitin-proteolytic apparatus operates at the post-translational level, and thus provides a new tool of reverse genetics to dissect complicated protein functions at a higher resolution than knockout or knockdown approaches functioning at the level of DNA or RNA. It also sheds light on novel therapeutic strategies for the amelioration of human disease.
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Affiliation(s)
- Pengbo Zhou
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA.
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32
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Abstract
Comprehensive dissection of protein functions entails more complicated manipulations than simply eliminating the protein of interest. Established knockdown technologies, such as RNA interference, antisense oligodeoxynucleotides, or ribozymes, are limited for specific applications such as modulating protein levels or specific targeting of a posttranslationally modified subpopulation. Here we show that the engineered Skp1, Cullin 1, and F-box-containing betaTrCP substrate receptor ubiquitin-proteolytic system, designated protein knockout, could achieve not only total elimination but also rapid and systematic reduction of a given cellular protein. Stable expression of a single engineered betaTrCP demonstrated simultaneous and sustained degradation of the entire retinoblastoma family proteins. Furthermore, the engineered betaTrCP was capable of selecting hypo- but not hyperphosphorylated forms of retinoblastoma for degradation. The engineered betaTrCP has been extensively modified to increase its specificity in substrate selection. This optimized protein-knockout system offers a powerful and versatile proteomic tool to dissect diverse functional properties of cellular proteins in somatic cells.
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Affiliation(s)
- Jianxuan Zhang
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
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33
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Bradbury A, Velappan N, Verzillo V, Ovecka M, Chasteen L, Sblattero D, Marzari R, Lou J, Siegel R, Pavlik P. Antibodies in proteomics II: screening, high-throughput characterization and downstream applications. Trends Biotechnol 2003; 21:312-7. [PMID: 12837616 DOI: 10.1016/s0167-7799(03)00117-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There are many ways in which the use of antibodies and antibody selection can be improved and developed for high-throughput characterization. Standard protocols, such as immunoprecipitation, western blotting and immunofluorescence, can be used with antibody fragments generated by display technologies. Together with novel approaches, such as antibody chips and intracellular immunization, these methods will yield useful proteomic data following adaptation of the protocols for increased reliability and robustness. To date, most work has focused on the use of standard, well-characterized commercial antibodies. Such protocols need to be adapted for broader use, for example, with antibody fragments or other binders generated by display technologies, because it is unlikely that traditional approaches will provide the required throughput.
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Affiliation(s)
- Andrew Bradbury
- B Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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34
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Abstract
The function of many key proteins and transcription factors involved in cell growth can be regulated by their cellular localization. Such proteins include the tumor suppressor p53 and the nuclear factor kappaB. Although the idea of trapping such proteins in either the nucleus or cytoplasm has been introduced as a potential therapeutic target, only two nuclear transport inhibitors have been reported. Here, we explore the roles of small-molecule inhibitors that cause target proteins to sequester in either the nucleus or cytoplasm. Methods of artificially targeting proteins to the nucleus or cytoplasm using peptide aptamer technology are also discussed.
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Affiliation(s)
- Tweeny R Kau
- Dept of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Dept of Cancer Biology, The Dana Farber Cancer Institute, Boston, MA 02115, USA
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35
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Golemis EA, Ochs MF, Pugacheva EN. Signal transduction driving technology driving signal transduction: factors in the design of targeted therapies. J Cell Biochem 2002; Suppl 37:42-52. [PMID: 11842427 DOI: 10.1002/jcb.10064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A significant number of human diseases can be attributed to defects in cellular signal transduction pathways. Large-scale proteomics projects now in progress seek to better define critical components of signal transduction networks, to enable more intelligent design of therapeutic agents that can specifically correct disease-specific signaling alterations by targeting individual proteins. A complicating factor in this endeavor is the fact that intracellular signaling involves many diverse mechanisms that in sum finely modulate the activity of individual proteins in response to different biological inputs. Ability to develop reagents that selectively correct disease-associated signaling activities, while leaving intact benign or essential activities, encompassed within a single protein requires an intimate knowledge of pathway-specific control mechanisms. To illustrate these points, we provide examples of some of the complex control mechanisms regulating the Cas proteins, which contribute to integrin-dependent biological response. We then discuss issues involved in systematically incorporating information related to complex control mechanisms in proteomic databases. Finally, we describe some recent instances in which protein interaction technologies have been specifically adapted to identify small molecule agents that regulate protein response in physiologically desirable ways, and discuss issues relevant to future drug discovery efforts.
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Affiliation(s)
- E A Golemis
- Cell and Developmental Biology Working Group, Division of Basic Science, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, Pennsylvania 19111, USA.
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