1
|
Bai L, Deng Z, Xu M, Zhang Z, Guo G, Xue X, Wang S, Yang J, Xia Z. CETSA-MS-based target profiling of anti-aging natural compound quercetin. Eur J Med Chem 2024; 267:116203. [PMID: 38342014 DOI: 10.1016/j.ejmech.2024.116203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/18/2023] [Revised: 01/16/2024] [Accepted: 01/31/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND Quercetin is widely distributed in nature and abundant in the human diet, which exhibits diverse biological activities and potential medical benefits. However, there remains a lack of comprehensive understanding about its cellular targets, impeding its in-depth mechanistic studies and clinical applications. PURPOSE This study aimed to profile protein targets of quercetin at the proteome level. METHODS A label-free CETSA-MS proteomics technique was employed for target enrichment and identification. The R package Inflect was used for melting curve fitting and target selection. D3Pocket and LiBiSco tools were used for binding pocket prediction and binding pocket analysis. Western blotting, molecular docking, site-directed mutagenesis and pull-down assays were used for target verification and validation. RESULTS We curated a library of direct binding targets of quercetin in cells. This library comprises 37 proteins that show increased thermal stability upon quercetin binding and 33 proteins that display decreased thermal stability. Through Western blotting, molecular docking, site-directed mutagenesis and pull-down assays, we validated CBR1 and GSK3A from the stabilized protein group and MAPK1 from the destabilized group as direct binding targets of quercetin. Moreover, we characterized the shared chemical properties of the binding pockets of quercetin with targets. CONCLUSION Our findings deepen our understanding of the proteins pivotal to the bioactivity of quercetin and lay the groundwork for further exploration into its mechanisms of action and potential clinical applications.
Collapse
Affiliation(s)
- Lin Bai
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhifen Deng
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Mengfei Xu
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhehao Zhang
- Department of Biochemistry, Faculty of Life Science, Faculty of Natural Science, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Guangyu Guo
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China; Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China; Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xinli Xue
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Shaochi Wang
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jinghua Yang
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zongping Xia
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China; Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China; Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| |
Collapse
|
2
|
Wang L, Xu H, Li X, Chen H, Zhang H, Zhu X, Lin Z, Guo S, Bao Z, Rui H, He W, Zhang H. Cucurbitacin E reduces IL-1β-induced inflammation and cartilage degeneration by inhibiting the PI3K/Akt pathway in osteoarthritic chondrocytes. J Transl Med 2023; 21:880. [PMID: 38049841 PMCID: PMC10696753 DOI: 10.1186/s12967-023-04771-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Osteoarthritis is a degenerative joint disease. Cartilage degeneration is the earliest and most important pathological change in osteoarthritis, and persistent inflammation is one of the driving factors of cartilage degeneration. Cucurbitacin E, an isolated compound in the Cucurbitacin family, has been shown to have anti-inflammatory effects, but its role and mechanism in osteoarthritic chondrocytes are unclear. METHODS For in vitro experiments, human chondrocytes were stimulated with IL-1β, and the expression of inflammatory genes was measured by Western blotting and qPCR. The expression of extracellular matrix proteins was evaluated by immunofluorescence staining, Western blotting and saffron staining. Differences in gene expression between cartilage from osteoarthritis patients and normal cartilage were analysed by bioinformatics methods, and the relationship between Cucurbitacin E and its target was analysed by a cellular thermal shift assay, molecular docking analysis and molecular dynamics simulation. For in vivo experiments, knee osteoarthritis was induced by DMM in C57BL/6 mouse knee joints, and the effect of Cucurbitacin E on knee joint degeneration was evaluated. RESULTS The in vitro experiments confirmed that Cucurbitacin E effectively inhibited the production of the inflammatory cytokine interleukin-1β(IL-1β) and cyclooxygenase-2 (COX-2) by IL-1β-stimulated chondrocytes and alleviates extracellular matrix degradation. The in vivo experiments demonstrated that Cucurbitacin E had a protective effect on the knee cartilage of C57BL/6 mice with medial meniscal instability in the osteoarthritis model. Mechanistically, bioinformatic analysis of the GSE114007 and GSE117999 datasets showed that the PI3K/AKT pathway was highly activated in osteoarthritis. Immunohistochemical analysis of PI3K/Akt signalling pathway proteins in pathological slices of human cartilage showed that the level of p-PI3K in patients with osteoarthritis was higher than that in the normal group. PI3K/Akt were upregulated in IL-1β-stimulated chondrocytes, and Cucurbitacin E intervention reversed this phenomenon. The cellular thermal shift assay, molecular docking analysis and molecular dynamics experiment showed that Cucurbitacin E had a strong binding affinity for the inhibitory target PI3K. SC79 activated Akt phosphorylation and reversed the effect of Cucurbitacin E on IL-1β-induced chondrocyte degeneration, demonstrating that Cucurbitacin E inhibits IL-1β-induced chondrocyte inflammation and degeneration by inhibiting the PI3K/AKT pathway. CONCLUSION Cucurbitacin E inhibits the activation of the PI3K/AKT pathway, thereby alleviating the progression of OA. In summary, we believe that Cucurbitacin E is a potential drug for the treatment of OA.
Collapse
Affiliation(s)
- Lin Wang
- Department of Orthopaedics, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China
| | - Hui Xu
- Department of Orthopaedics, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China
| | - Xin Li
- School of Basic Medicine Sciences, Anhui Medical University, Hefei, Anhui Province, China
| | - Hongwei Chen
- Department of Orthopaedics, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China
| | - Haigang Zhang
- Department of Orthopaedics, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China
| | - Xunpeng Zhu
- Department of Orthopaedics, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China
| | - Zhijie Lin
- Anhui Medical University, Hefei, Anhui Province, China
| | - Shilei Guo
- Anhui Medical University, Hefei, Anhui Province, China
| | - Zhibo Bao
- Anhui Medical University, Hefei, Anhui Province, China
| | - Haicheng Rui
- Anhui Medical University, Hefei, Anhui Province, China
| | - Wei He
- School of Basic Medicine Sciences, Anhui Medical University, Hefei, Anhui Province, China.
| | - Hui Zhang
- Department of Orthopaedics, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China.
| |
Collapse
|
3
|
Silva J, Omar N, Sittaramane V, Cowell JK. Identification of small molecules that suppress cell invasion and metastasis promoted by WASF3 activation. Heliyon 2023; 9:e20662. [PMID: 37867831 PMCID: PMC10585217 DOI: 10.1016/j.heliyon.2023.e20662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/07/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/24/2023] Open
Abstract
The WASF3 gene promotes cancer cell invasion and metastasis, and genetic inactivation leads to suppression of metastasis. To identify small molecules that might interfere with WASF3 function, we performed an in silico docking study to the regulatory pocket of WASF3 using the National Cancer Institute (NCI) diversity set VI small molecule library. Compounds that showed the maximum likelihood of interaction with WASF3 were screened for their effect on cell movement in breast and prostate cancer cells, a well-established predictor of invasion and metastasis. Three hit compounds were identified that affected cell movement, and the same compounds also suppressed cell migration and invasion in vitro in both MDA-MB-231 breast cancer cells and Du145 prostate cancer cells. Using a zebrafish metastasis assay, one of these compounds, NSC670283, showed significant suppression of metastasis in vivo while not affecting cell proliferation. NSC670283 showed a consistent effect on suppression of invasion and metastasis, and cellular temperature shift assays provided support for physical interaction with WASF3. In addition, suppression of cell movement and invasion was accompanied by a decrease in actin filament polymerization. The data in this study suggest that these small molecules inhibit cancer cell invasion and metastasis, and to our knowledge, it is the first identification of a small molecule that can potentially inhibit WASF3-directed metastasis, laying the foundation for medicinal chemistry approaches to enhance the potency of the identified compounds.
Collapse
Affiliation(s)
- Jeane Silva
- The Georgia Cancer Center, 1410 Laney Walker Blvd., Augusta, GA 30912, Georgia
- Department of Interdisciplinary Health Sciences, College of Allied Sciences, Augusta University, GA, 30912, Georgia
| | - Nivin Omar
- Department of Pathology, Medical College of Georgia, Augusta University, GA, 30912, Georgia
| | - Vinoth Sittaramane
- Department of Biology, Georgia Southern University, Statesboro, GA 30458, Georgia
| | - John K. Cowell
- The Georgia Cancer Center, 1410 Laney Walker Blvd., Augusta, GA 30912, Georgia
| |
Collapse
|
4
|
Tu Y, Tan L, Tao H, Li Y, Liu H. CETSA and thermal proteome profiling strategies for target identification and drug discovery of natural products. Phytomedicine 2023; 116:154862. [PMID: 37216761 DOI: 10.1016/j.phymed.2023.154862] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Monitoring target engagement at various stages of drug development is essential for natural product (NP)-based drug discovery and development. The cellular thermal shift assay (CETSA) developed in 2013 is a novel, broadly applicable, label-free biophysical assay based on the principle of ligand-induced thermal stabilization of target proteins, which enables direct assessment of drug-target engagement in physiologically relevant contexts, including intact cells, cell lysates and tissues. This review aims to provide an overview of the work principles of CETSA and its derivative strategies and their recent progress in protein target validation, target identification and drug lead discovery of NPs. METHODS A literature-based survey was conducted using the Web of Science and PubMed databases. The required information was reviewed and discussed to highlight the important role of CETSA-derived strategies in NP studies. RESULTS After nearly ten years of upgrading and evolution, CETSA has been mainly developed into three formats: classic Western blotting (WB)-CETSA for target validation, thermal proteome profiling (TPP, also known as MS-CETSA) for unbiased proteome-wide target identification, and high-throughput (HT)-CETSA for drug hit discovery and lead optimization. Importantly, the application possibilities of a variety of TPP approaches for the target discovery of bioactive NPs are highlighted and discussed, including TPP-temperature range (TPP-TR), TPP-compound concentration range (TPP-CCR), two-dimensional TPP (2D-TPP), cell surface-TPP (CS-TPP), simplified TPP (STPP), thermal stability shift-based fluorescence difference in 2D gel electrophoresis (TS-FITGE) and precipitate supported TPP (PSTPP). In addition, the key advantages, limitations and future outlook of CETSA strategies for NP studies are discussed. CONCLUSION The accumulation of CETSA-based data can significantly accelerate the elucidation of the mechanism of action and drug lead discovery of NPs, and provide strong evidence for NP treatment against certain diseases. The CETSA strategy will certainly bring a great return far beyond the initial investment and open up more possibilities for future NP-based drug research and development.
Collapse
Affiliation(s)
- Yanbei Tu
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Lihua Tan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Hongxun Tao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Yanfang Li
- School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China.
| | - Hanqing Liu
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
| |
Collapse
|
5
|
Lu Q, Russinova E. Cellular Thermal Shift Assay for the Detection of Small Molecule-Target Interactions in Arabidopsis Cells. Methods Mol Biol 2023; 2554:21-34. [PMID: 36178618 DOI: 10.1007/978-1-0716-2624-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Indexed: 06/16/2023]
Abstract
Chemical genetics takes advantage of small molecule-protein interactions to explore various biological processes. Although an attractive alternative to classical genetics in plants, the identification of small-molecule targets remains a challenge and limits the broad use of the compounds. The cellular thermal shift assay (CETSA), based on the principle that binding of small molecules could affect the thermal stability of proteins, has been applied for target validation in plant cells. Combined with high-resolution mass spectrometry, CETSA can detect small-molecule targets by monitoring the changes in the protein thermal stability caused by the interactions with small molecules at the proteome level. Here we describe the small-molecule target validation as well as the target identification with mass spectrometry by means of CETSA.
Collapse
Affiliation(s)
- Qing Lu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
| |
Collapse
|
6
|
de Araujo ED, Orlova A, Ashraf QF, Moriggl R, Gunning PT. Inhibitor Library Screening of SH2 Domains Through Denaturation-Based Assays. Methods Mol Biol 2023; 2705:213-223. [PMID: 37668976 DOI: 10.1007/978-1-0716-3393-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Indexed: 09/06/2023]
Abstract
Screening of inhibitor libraries for candidate ligands is an important step in the drug discovery process. Thermal denaturation-based screening strategies are built on the premise that a protein-ligand complex has an altered stability profile compared to the protein alone. As such, these assays provide an accessible and rapid methodology for stratifying ligands that directly engage with the protein target of interest. Here, we describe three denaturation-based strategies for examining protein-inhibitor binding, in the context of SH2 domains. This includes conventional dye-based Thermal Shift Assays (TSA), nonconventional labeled ligand-based TSA, and Cellular Thermal Shift Assays (CETSA). Conventional dye-based TSA reports on the fluorescence of an external hydrophobic dye as it interacts with heat-exposed nonpolar protein surfaces as the temperature is incrementally increased. By contrast, nonconventional-labeled ligand TSA involves a fluorescence-tagged probe (phosphopeptide for SH2 domains) that is quenched as it dissociates from the protein during the denaturation process. CETSA involves monitoring the presence of the protein via Western blotting as the temperature is increased. In all three approaches, performing the assay in the presence of a candidate ligand can alter the melting profile of the protein. These assays offer primary screening tools to examine SH2 domain inhibitors libraries with varying chemical motifs, and a subset of the advantages and limitations of each approach is also discussed.
Collapse
Affiliation(s)
- Elvin D de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Anna Orlova
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Qirat F Ashraf
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada.
- Department of Chemistry, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
7
|
Chen J, Ma D, Zeng C, White LV, Zhang H, Teng Y, Lan P. Solasodine suppress MCF7 breast cancer stem-like cells via targeting Hedgehog/Gli1. Phytomedicine 2022; 107:154448. [PMID: 36116198 DOI: 10.1016/j.phymed.2022.154448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 08/25/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Recently, a novel therapy to treat cancer has been to target cancer stem-like cells (CSCs). The aim of this study was to investigate the effect of solasodine, a steroidal alkaloid isolated from Solanum incanum L., on MCF7 CSCs and to understand the compound's underlying mechanism of action. METHOD A tumorsphere formation assay was used to evaluate the effects of solasodine on the proliferation and self-renewal ability of MCF7 CSCs. The level of expression of proteins associated with cancer stemness markers and Hh signaling mediators was determined. The interaction between solasodine and Gli1 was calculated by molecular docking and further demonstrated by cellular thermal shift assay. RESULTS Solasodine significantly decreased the proliferation of MCF7 tumorspheres and showed a stronger cytotoxicity on breast cancer cells with higher levels of Gli1 expression. The results showed that the levels of CD44 and ALDH1 expression were suppressed. Furthermore, expression of CD24 was enhanced by solasodine, via a mechanism that involved dampening Gli1 expression and blocking the nuclear translocation of this protein in MCF7 tumorspheres. Computational studies predicted that solasodine showed a high affinity with the Gli1 zinc finger domain that resulted from hydrogen-bonds to the THR243 and ASP216 amino acids residues. In addition, solasodine specifically bound with Gli1 and enhanced Gli1 protein stability in MCF7 cells. CONCLUSION Here, our findings indicated that solasodine can directly suppresses Hh/Gli1 signaling, and is a novel anticancer candidate that targets CSCs.
Collapse
Affiliation(s)
- Jing Chen
- College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Da Ma
- College of Packaging engineering, Jinan University, Zhuhai, 519070, China.
| | - Cuicui Zeng
- College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Lorenzo V White
- College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Huanqing Zhang
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Yinglai Teng
- College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Ping Lan
- College of Pharmacy, Jinan University, Guangzhou, 510632, China.
| |
Collapse
|
8
|
Park DI, Novak B, Yan Y, Kaya ME, Turck CW. Paroxetine binding and activation of phosphofructokinase implicates energy metabolism in antidepressant mode of action. J Psychiatr Res 2020; 129:8-14. [PMID: 32540574 DOI: 10.1016/j.jpsychires.2020.05.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/30/2020] [Accepted: 05/31/2020] [Indexed: 12/16/2022]
Abstract
Selective serotonin reuptake inhibitors (SSRIs) are the predominant drugs prescribed for Major Depressive Disorder. The immediate pharmacological target of SSRIs is the serotonin transporter. However, the delayed therapeutic effect and high rate of patient non-response make it highly likely that SSRIs also have other molecular targets that are yet to be identified. Cellular thermal shift assay (CETSA) is a method based on thermal stabilization of target proteins upon drug binding. In the present study, we show that the SSRI paroxetine binds to phosphofructokinase (PFK) protein using CETSA. We found that mouse brain PFK and recombinant human PFK proteins are stabilized by paroxetine incubation. Chronic paroxetine treatment also significantly increased mouse brain PFK thermal stability. Paroxetine significantly elevated in vitro and in vivo PFK activity. Levels of several metabolites in glutamate- and energy metabolism-related pathways are significantly correlated with PFK activity in mouse hippocampus. Our data show that paroxetine can bind to PFK and affect its activity. Implications of these results for the antidepressant mode of action of paroxetine are discussed.
Collapse
Affiliation(s)
- Dong Ik Park
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, 80804, Munich, Germany; Danish Research Institute of Translational Neuroscience (DANDRITE), Department of Biomedicine, Aarhus University, Aarhus, Denmark; The Danish National Research Foundation Center, PROMEMO, Department of Biomedicine, Aarhus University, Aarhus, Denmark.
| | - Božidar Novak
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, 80804, Munich, Germany
| | - Yu Yan
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, 80804, Munich, Germany
| | - Melahat Ezgi Kaya
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, 80804, Munich, Germany
| | - Christoph W Turck
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, 80804, Munich, Germany
| |
Collapse
|
9
|
Abstract
Determining protein thermal stability is integral in biomedical research. Here, with the use of two thermal stability assays, we show the melting temperature of amyloid precursor protein, an Alzheimer's disease related protein. The average melting temperature for amyloid precursor protein of 55.9 °C was derived from differential scanning fluorometry (55.1 ± 0.3 °C) and cellular thermal melt (56.7 ± 0.7 °C). These experimental methods have significant application for Alzheimer's disease research including their use for amyloid precursor protein stability profiling and for the identification of additional binding partners to further elucidate novel protein functions.
Collapse
Affiliation(s)
- Alexandré Delport
- Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, 3201, South Africa
| | - Raymond Hewer
- Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, 3201, South Africa.
| |
Collapse
|
10
|
Sun W, Dai L, Yu H, Puspita B, Zhao T, Li F, Tan JL, Lim YT, Chen MW, Sobota RM, Tenen DG, Prabhu N, Nordlund P. Monitoring structural modulation of redox-sensitive proteins in cells with MS-CETSA. Redox Biol 2019; 24:101168. [PMID: 30925293 PMCID: PMC6439307 DOI: 10.1016/j.redox.2019.101168] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/07/2019] [Accepted: 03/10/2019] [Indexed: 12/31/2022] Open
Abstract
Reactive oxygen species (ROS) induce different cellular stress responses but can also mediate cellular signaling. Augmented levels of ROS are associated with aging, cancer as well as various metabolic and neurological disorders. ROS can also affect the efficacy and adverse effects of drugs. Although proteins are key mediators of most ROS effects, direct studies of ROS-modulated-protein function in the cellular context are very challenging. Therefore the understanding of specific roles of different proteins in cellular ROS responses is still relatively rudimentary. In the present work we show that Mass Spectrometry-Cellular Thermal Shift Assay (MS-CETSA) can directly monitor ROS and redox modulations of protein structure at the proteome level. By altering ROS levels in cultured human hepatocellular carcinoma cell lysates and intact cells, we detected CETSA responses in many proteins known to be redox sensitive, and also revealed novel candidate ROS sensitive proteins. Studies in intact cells treated with hydrogen peroxide and sulfasalazine, a ROS modulating drug, identified not only proteins that are directly modified, but also proteins reporting on downstream cellular effects. Comprehensive changes are seen on rate-limiting proteins regulating key cellular processes, including known redox control systems, protein degradation, epigenetic control and protein translational processes. Interestingly, concerted shifts on ATP-binding proteins revealed redox-induced modulation of ATP levels, which likely control many cellular processes. Collectively, these studies establish CETSA as a novel method for cellular studies of redox modulations of proteins, which implicated in a wide range of processes and for the discovery of CETSA-based biomarkers reporting on the efficacy as well as adverse effects of drugs.
Collapse
Affiliation(s)
- Wendi Sun
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Lingyun Dai
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Han Yu
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Brenda Puspita
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Tianyun Zhao
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Feng Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Justin L Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Genome Institute of Singapore, A*STAR, 138672, Singapore
| | - Yan Ting Lim
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Ming Wei Chen
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | | | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nayana Prabhu
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Pär Nordlund
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore; Institute of Molecular and Cell Biology, A*STAR, 138673, Singapore; Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden.
| |
Collapse
|
11
|
Liu YK, Chen HY, Chueh PJ, Liu PF. A one-pot analysis approach to simplify measurements of protein stability and folding kinetics. Biochim Biophys Acta Proteins Proteom 2018; 1867:184-193. [PMID: 30578861 DOI: 10.1016/j.bbapap.2018.12.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/16/2018] [Accepted: 12/17/2018] [Indexed: 10/27/2022]
Abstract
To achieve a good understanding of the characteristics of a protein, it is important to study its stability and folding kinetics. Investigations of protein stability have been recently applied to drug-target identification, drug screening, and proteomic studies. The efficiency of the experiments performed to study protein stability and folding kinetics is now a crucial factor that needs to be optimized for these potential applications. However, the standard procedures used to carry out these experiments are usually complicated and time consuming. Large number of measurements is the bottleneck that limits the application of protein folding to large-scale experiments. To overcome this limitation, we developed a method denoted as "one-pot analysis" which is based on taking a single measurement from a mixture of samples rather than from every sample. We combined one-pot analysis with pulse proteolysis to determine the effects of the binding of maltose to maltose-binding protein on the protein folding properties. After carrying out a simple optimization, we demonstrated that protein stability or unfolding kinetics could be measured accurately with just one detection measurement. We then further applied the optimized conditions to cellular thermal shift assay (CETSA). Combining one-pot analysis with CETSA led to a successful determination of the effects of the binding of methotrexate to dihydrofolate reductase in HCT116 cancer cells. Our results demonstrated the applicability of one-pot analysis to energetics-based methods for studying protein folding. We expect the combination of one-pot analysis and energetics-based methods to significantly benefit studies such as drug-target identification, proteomic investigations, and drug screening.
Collapse
Affiliation(s)
- Yi-Kai Liu
- Department of Food Science and Biotechnology, National Chung Hsing University, 145 Xingda Rd., South Dist., Taichung City 402, Taiwan, ROC
| | - Huei-Yu Chen
- Institute of Biomedical Science, National Chung Hsing University, 145 Xingda Rd., South Dist., Taichung City 402, Taiwan, ROC
| | - Pin Ju Chueh
- Institute of Biomedical Science, National Chung Hsing University, 145 Xingda Rd., South Dist., Taichung City 402, Taiwan, ROC
| | - Pei-Fen Liu
- Department of Food Science and Biotechnology, National Chung Hsing University, 145 Xingda Rd., South Dist., Taichung City 402, Taiwan, ROC.
| |
Collapse
|