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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 : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 116:154862. [PMID: 37216761 DOI: 10.1016/j.phymed.2023.154862] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [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.
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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.
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Jung J, Park J, Kim M, Ha J, Cho H, Park SB. SB2301-mediated perturbation of membrane composition in lipid droplets induces lipophagy and lipid droplets ubiquitination. Commun Biol 2023; 6:300. [PMID: 36944894 PMCID: PMC10030462 DOI: 10.1038/s42003-023-04682-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/09/2023] [Indexed: 03/23/2023] Open
Abstract
Lipid droplets (LDs) are involved in various biological events in cells along with their primary role as a storage center for neutral lipids. Excessive accumulation of LDs is highly correlated with various diseases, including metabolic diseases. Therefore, a basic understanding of the molecular mechanism of LD degradation would be beneficial in both academic and industrial research. Lipophagy, a selective autophagy mechanism/LD degradation process, has gained increased attention in the research community. Herein, we sought to elucidate a novel lipophagy mechanism by utilizing the LD-degrading small molecule, SB2301, which activates ubiquitin-mediated lipophagy. Using a label-free target identification method, we revealed that ethanolamine-phosphate cytidylyltransferase 2 (PCYT2) is a potential target protein of SB2301. We also demonstrated that although SB2301 does not modulate PCYT2 function, it induces the cellular translocation of PCYT2 to the LD surface and spatially increases the phosphatidylethanolamine (PE)/phosphatidylcholine (PC) ratio of the LD membrane, causing LD coalescence, leading to the activation of lipophagy process to maintain energy homeostasis.
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Affiliation(s)
- Jinjoo Jung
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Jongbeom Park
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Mingi Kim
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Jaeyoung Ha
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, South Korea
| | - Hana Cho
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, South Korea
| | - Seung Bum Park
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, South Korea.
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, South Korea.
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3
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Abstract
Protein-protein interactions and multiprotein assemblies of water-soluble and membrane proteins are inherent features of the proteome, which also impart functional heterogeneity. One needs to consider this aspect while studying changes in abundance and activities of proteins in response to any physiological stimulus. Abundance changes in the components of a given proteome can be best visualized and efficiently quantified using electrophoresis-based approaches. Here, we describe the method of Blue Native Difference Gel Electrophoresis to quantify changes in abundance and activity of proteins in the context of protein-protein interactions. This method confers an additional advantage to monitor quantitative changes in membrane proteins, which otherwise is a difficult task.
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Affiliation(s)
- Diksha Dani
- Institut für Biochemie und Biologie, Universität Potsdam, Potsdam-Golm, Germany
- Physical Biochemistry, Department of Chemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Norbert A Dencher
- Physical Biochemistry, Department of Chemistry, Technische Universität Darmstadt, Darmstadt, Germany.
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4
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Zhang X, Wang K, Wu S, Ruan C, Li K, Wang Y, Zhu H, Liu X, Liu Z, Li G, Hu L, Ye M. Highly effective identification of drug targets at the proteome level by pH-dependent protein precipitation. Chem Sci 2022; 13:12403-12418. [PMID: 36382280 PMCID: PMC9629037 DOI: 10.1039/d2sc03326g] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/20/2022] [Indexed: 09/09/2023] Open
Abstract
Fully understanding the target spaces of drugs is essential for investigating the mechanism of drug action and side effects, as well as for drug discovery and repurposing. In this study, we present an energetics-based approach, termed pH-dependent protein precipitation (pHDPP), to probe the ligand-induced protein stability shift for proteome-wide drug target identification. We demonstrate that pHDPP works for a diverse array of ligands, including a folate derivative, an ATP analog, a CDK inhibitor and an immunosuppressant, enabling highly specific identification of target proteins from total cell lysates. This approach is compared to thermal and solvent-induced denaturation approaches with a pan-kinase inhibitor as the model drug, demonstrating its high sensitivity and high complementarity to other approaches. Dihydroartemisinin (DHA), a dominant derivative of artemisinin to treat malaria, is known to have an extraordinary effect on the treatment of various cancers. However, the anti-tumor mechanisms remain unknown. pHDPP was applied to reveal the target space of DHA and 45 potential target proteins were identified. Pathway analysis indicated that these target proteins were mainly involved in metabolism and apoptosis pathways. Two cancer-related target proteins, ALDH7A1 and HMGB1, were validated by structural simulation and AI-based target prediction methods. And they were further validated to have strong affinity to DHA by using cellular thermal shift assay (CETSA). In summary, pHDPP is a powerful tool to construct the target protein space to reveal the mechanism of drug action and would have broad application in drug discovery studies.
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Affiliation(s)
- Xiaolei Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University Changchun 130012 China
| | - Keyun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Sijin Wu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Chengfei Ruan
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Kejia Li
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Yan Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - He Zhu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Xiaoyan Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Zhen Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Guohui Li
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Lianghai Hu
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University Changchun 130012 China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
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Yim J, Park SB. Label-Free Target Identification Reveals the Anticancer Mechanism of a Rhenium Isonitrile Complex. Front Chem 2022; 10:850638. [PMID: 35372261 PMCID: PMC8964423 DOI: 10.3389/fchem.2022.850638] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/25/2022] [Indexed: 01/21/2023] Open
Abstract
Elucidation of the molecular mechanism of therapeutic agents and potential candidates is in high demand. Interestingly, rhenium-based complexes have shown a highly selective anticancer effect, only on cancer cells, unlike platinum-based drugs, such as cisplatin and carboplatin. These differences might be attributed to their different molecular targets. We confirmed that the target of tricarbonyl rhenium isonitrile polypyridyl (TRIP) complex is a protein, not DNA, using ICP-MS analysis and identified heat shock protein 60 (HSP60) as its target protein using a label-free target identification method. The subsequent biological evaluation revealed that TRIP directly inhibits the chaperone function of HSP60 and induces the accumulation of misfolded proteins in mitochondria, thereby leading to the activation of mitochondrial unfolded protein response (mtUPR)-mediated JNK2/AP-1/CHOP apoptotic pathway.
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Affiliation(s)
- Junhyeong Yim
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, South Korea
| | - Seung Bum Park
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, South Korea
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, South Korea
- *Correspondence: Seung Bum Park,
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Ruan C, Ning W, Liu Z, Zhang X, Fang Z, Li Y, Dang Y, Xue Y, Ye M. Precipitate-Supported Thermal Proteome Profiling Coupled with Deep Learning for Comprehensive Screening of Drug Target Proteins. ACS Chem Biol 2022; 17:252-262. [PMID: 34989232 DOI: 10.1021/acschembio.1c00936] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although thermal proteome profiling (TPP) acts as a popular modification-free approach for drug target deconvolution, some key problems are still limiting screening sensitivity. In the prevailing TPP workflow, only the soluble fractions are analyzed after thermal treatment, while the precipitate fractions that also contain abundant information of drug-induced stability shifts are discarded; the sigmoid melting curve fitting strategy used for data processing suffers from discriminations for a part of human proteome with multiple transitions. In this study, a precipitate-supported TPP (PSTPP) assay was presented for unbiased and comprehensive analysis of protein-drug interactions at the proteome level. In PSTPP, only these temperatures where significant precipitation is observed were applied to induce protein denaturation and the complementary information contained in both supernatant fractions and precipitate fractions was used to improve the screening specificity and sensitivity. In addition, a novel image recognition algorithm based on deep learning was developed to recognize the target proteins, which circumvented the problems that exist in the sigmoid curve fitting strategy. PSTPP assay was validated by identifying the known targets of methotrexate, raltitrexed, and SNS-032 with good performance. Using a promiscuous kinase inhibitor, staurosporine, we delineated 99 kinase targets with a specificity up to 83% in K562 cell lysates, which represented a significant improvement over the existing thermal shift methods. Furthermore, the PSTPP strategy was successfully applied to analyze the binding targets of rapamycin, identifying the well-known targets, FKBP1A, as well as revealing a few other potential targets.
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Affiliation(s)
- Chengfei Ruan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanshan Ning
- MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, Hubei 430074, China
| | - Zhen Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Xiaolei Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Zheng Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Yongjun Dang
- Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yu Xue
- MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, Hubei 430074, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
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7
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Muroi M, Osada H. Two-dimensional electrophoresis–cellular thermal shift assay (2DE-CETSA) for target identification of bioactive compounds. Methods Enzymol 2022; 675:425-437. [DOI: 10.1016/bs.mie.2022.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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8
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Muroi M, Osada H. Proteomics-based target identification of natural products affecting cancer metabolism. J Antibiot (Tokyo) 2021; 74:639-650. [PMID: 34282314 DOI: 10.1038/s41429-021-00437-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
The Warburg effect, a widely known characteristic of cancer cells, refers to the utilization of glycolysis under aerobic conditions for extended periods of time. Recent studies have revealed that cancer cells are capable of reprogramming their metabolic pathways to meet vigorous metabolic demands. New anticancer drugs that target the complicated metabolic systems of cancer cells are being developed. Identifying the potential targets of novel compounds that affect cancer metabolism may enable the discovery of new therapeutic targets for cancer treatment, and hasten the development of anticancer drugs. Historically, various drug screening techniques such as the analysis of a compound's antiproliferative effect on cancer cells and proteomic methods, that enable target identification have been used to obtain many useful drugs from natural products. Here, we review proteomics-based target identification methods applicable to natural products that affect cancer metabolism.
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Affiliation(s)
- Makoto Muroi
- Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama, Japan.
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9
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Ha J, Park SB. Callyspongiolide kills cells by inducing mitochondrial dysfunction via cellular iron depletion. Commun Biol 2021; 4:1123. [PMID: 34556786 PMCID: PMC8460830 DOI: 10.1038/s42003-021-02643-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/01/2021] [Indexed: 12/15/2022] Open
Abstract
The highly cytotoxic marine natural product callyspongiolide holds great promise as a warhead of antibody-drug conjugate in cancer therapeutics; however, the mechanism underlying its cytotoxicity remains unclear. To elucidate how callyspongiolide kills cells, we employed label-free target identification with thermal stability-shift-based fluorescence difference in two-dimensional (2-D) gel electrophoresis (TS-FITGE), which allowed observation of a unique phenomenon of protein-spot separation on 2-D gels upon treatment with callyspongiolide at increasing temperatures. During our exploration of what proteins were associated with this phenomenon as well as why it happens, we found that callyspongiolide induces mitochondrial/lysosomal dysfunction and autophagy inhibition. Moreover, molecular biology studies revealed that callyspongiolide causes lysosomal dysfunction, which induces cellular iron depletion and leads to mitochondrial dysfunction and subsequent cytotoxicity. Notably, these effects were rescued through iron supplementation. Although our approach was unable to reveal the direct protein targets of callyspongiolide, unique phenomena observed only by TS-FITGE provided critical insight into the mechanism of action of callyspongiolide and specifically its cytotoxic activity via induction of mitochondrial dysfunction through cellular iron depletion caused by lysosomal deacidification, which occurred independent of known programmed cell death pathways. In order to elucidate how callyspongiolide, a potent cytotoxic marine natural product, kills human lung cancer cells, Ha and Park employed TS-FITGE technique, a label-free target identification method with thermal stability-shift-based fluorescence difference in 2-D gel electrophoresis, allowing them to observe protein-spot separation upon treatment in increasing temperatures. They found that callyspongiolide induces lysosomal dysfunction followed by mitochondrial dysfunction as well as iron depletion, which sheds light on the mechanism of action of callyspongiolide.
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Affiliation(s)
- Jaeyoung Ha
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, Korea
| | - Seung Bum Park
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, Korea. .,CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, Korea. .,SPARK Biopharma, Inc, Seoul, 08791, Korea.
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10
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Jo A, Kim M, Kim JI, Ha J, Hwang YS, Nam H, Hwang I, Kim JB, Park SB. Phenotypic Discovery of SB1501, an Anti-obesity Agent, through Modulating Mitochondrial Activity. ChemMedChem 2021; 16:1104-1115. [PMID: 33538065 DOI: 10.1002/cmdc.202100062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 11/08/2022]
Abstract
Obesity has become a pandemic that threatens the quality of life and discovering novel therapeutic agents that can reverse obesity and obesity-related metabolic disorders are necessary. Here, we aimed to identify new anti-obesity agents using a phenotype-based approach. We performed image-based high-content screening with a fluorogenic bioprobe (SF44), which visualizes cellular lipid droplets (LDs), to identify initial hit compounds. A structure-activity relationship study led us to yield a bioactive compound SB1501, which reduces cellular LDs in 3T3-L1 adipocytes without cytotoxicity. SB1501 induced the expression of gene products that regulate mitochondrial biogenesis and fatty acid oxidation in 3T3-L1 adipocytes. Daily treatment with SB1501 improved the metabolic states of db/db mice by reducing body fat mass, adipose tissue mass, food intake, and increasing glucose tolerance. The anti-obesity effect of SB1501 may result from perturbation of the PGC-1α-UCP1 regulatory axis in inguinal white adipose tissue and brown adipose tissue. These data suggest the therapeutic potential of SB1501 as an anti-obesity agent via modulating mitochondrial activities.
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Affiliation(s)
- Ala Jo
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Mingi Kim
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Jong In Kim
- CRI Center for Adipocyte Structure-Function, School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Jaeyoung Ha
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, Korea
| | - Yoon Soo Hwang
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Hyunsung Nam
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Injae Hwang
- CRI Center for Adipocyte Structure-Function, School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Jae Bum Kim
- CRI Center for Adipocyte Structure-Function, School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Seung Bum Park
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, Korea.,Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, Korea
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11
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Conway LP, Li W, Parker CG. Chemoproteomic-enabled phenotypic screening. Cell Chem Biol 2021; 28:371-393. [PMID: 33577749 DOI: 10.1016/j.chembiol.2021.01.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/26/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022]
Abstract
The ID of disease-modifying, chemically accessible targets remains a central priority of modern therapeutic discovery. The phenotypic screening of small-molecule libraries not only represents an attractive approach to identify compounds that may serve as drug leads but also serves as an opportunity to uncover compounds with novel mechanisms of action (MoAs). However, a major bottleneck of phenotypic screens continues to be the ID of pharmacologically relevant target(s) for compounds of interest. The field of chemoproteomics aims to map proteome-wide small-molecule interactions in complex, native systems, and has proved a key technology to unravel the protein targets of pharmacological modulators. In this review, we discuss the application of modern chemoproteomic methods to identify protein targets of phenotypic screening hits and investigate MoAs, with a specific focus on the development of chemoproteomic-enabled compound libraries to streamline target discovery.
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Affiliation(s)
- Louis P Conway
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Weichao Li
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.
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12
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Shin YH, Cho H, Choi BY, Kim J, Ha J, Suh SW, Park SB. Phenotypic Discovery of Neuroprotective Agents by Regulation of Tau Proteostasis via Stress-Responsive Activation of PERK Signaling. Angew Chem Int Ed Engl 2021; 60:1831-1838. [PMID: 33210431 PMCID: PMC7898623 DOI: 10.1002/anie.202013915] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Indexed: 02/06/2023]
Abstract
Tau protein aggregates are a recognized neuropathological feature in Alzheimer's disease as well as many other neurodegenerative disorders, known as tauopathies. The development of tau-targeting therapies is therefore extremely important but efficient strategies or protein targets are still unclear. Here, we performed a cell-based phenotypic screening under endoplasmic reticulum (ER) stress conditions and identified a small molecule, SB1617, capable of suppressing abnormal tau protein aggregation. By applying label-free target identification technology, we revealed that the transient enhancement of protein kinase-like endoplasmic reticulum kinase (PERK) signaling pathway through the inhibition of stress-responsive SB1617 targets, PDIA3 and DNAJC3, is an effective strategy for regulating proteostasis in tauopathies. The molecular mechanism and the promising efficacy of SB1617 were demonstrated in neuronal cells and a mouse model with traumatic brain injury, a tauopathy known to involve ER stress.
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Affiliation(s)
- Young-Hee Shin
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Hana Cho
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, Korea
| | - Bo Young Choi
- Department of Physiology, College of Medicine, Hallym University, Chuncheon, 24252, Korea
| | - Jonghoon Kim
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, Korea.,Present address: Department of Chemistry, Soongsil University, Seoul, 06978, Korea
| | - Jaeyoung Ha
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, Korea
| | - Sang Won Suh
- Department of Physiology, College of Medicine, Hallym University, Chuncheon, 24252, Korea
| | - Seung Bum Park
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, Korea.,Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, Korea
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13
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Shin Y, Cho H, Choi BY, Kim J, Ha J, Suh SW, Park SB. Phenotypic Discovery of Neuroprotective Agents by Regulation of Tau Proteostasis via Stress‐Responsive Activation of PERK Signaling. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202013915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Young‐Hee Shin
- CRI Center for Chemical Proteomics Department of Chemistry Seoul National University Seoul 08826 Korea
| | - Hana Cho
- Department of Biophysics and Chemical Biology Seoul National University Seoul 08826 Korea
| | - Bo Young Choi
- Department of Physiology College of Medicine Hallym University Chuncheon 24252 Korea
| | - Jonghoon Kim
- CRI Center for Chemical Proteomics Department of Chemistry Seoul National University Seoul 08826 Korea
- Present address: Department of Chemistry Soongsil University Seoul 06978 Korea
| | - Jaeyoung Ha
- Department of Biophysics and Chemical Biology Seoul National University Seoul 08826 Korea
| | - Sang Won Suh
- Department of Physiology College of Medicine Hallym University Chuncheon 24252 Korea
| | - Seung Bum Park
- CRI Center for Chemical Proteomics Department of Chemistry Seoul National University Seoul 08826 Korea
- Department of Biophysics and Chemical Biology Seoul National University Seoul 08826 Korea
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14
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Ha J, Park H, Park J, Park SB. Recent advances in identifying protein targets in drug discovery. Cell Chem Biol 2020; 28:394-423. [PMID: 33357463 DOI: 10.1016/j.chembiol.2020.12.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/11/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023]
Abstract
Phenotype-based screening has emerged as an alternative route for discovering new chemical entities toward first-in-class therapeutics. However, clarifying their mode of action has been a significant bottleneck for drug discovery. For target protein identification, conventionally bioactive small molecules are conjugated onto solid supports and then applied to isolate target proteins from whole proteome. This approach requires a high binding affinity between bioactive small molecules and their target proteins. Besides, the binding affinity can be significantly hampered after structural modifications of bioactive molecules with linkers. To overcome these limitations, two major strategies have recently been pursued: (1) the covalent conjugation between small molecules and target proteins using photoactivatable moieties or electrophiles, and (2) label-free target identification through monitoring target engagement by tracking the thermal, proteolytic, or chemical stability of target proteins. This review focuses on recent advancements in target identification from covalent capturing to label-free strategies.
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Affiliation(s)
- Jaeyoung Ha
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea
| | - Hankum Park
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jongmin Park
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Korea.
| | - Seung Bum Park
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea; CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea.
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15
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Pasquer QTL, Tsakoumagkos IA, Hoogendoorn S. From Phenotypic Hit to Chemical Probe: Chemical Biology Approaches to Elucidate Small Molecule Action in Complex Biological Systems. Molecules 2020; 25:E5702. [PMID: 33287212 PMCID: PMC7730769 DOI: 10.3390/molecules25235702] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 01/22/2023] Open
Abstract
Biologically active small molecules have a central role in drug development, and as chemical probes and tool compounds to perturb and elucidate biological processes. Small molecules can be rationally designed for a given target, or a library of molecules can be screened against a target or phenotype of interest. Especially in the case of phenotypic screening approaches, a major challenge is to translate the compound-induced phenotype into a well-defined cellular target and mode of action of the hit compound. There is no "one size fits all" approach, and recent years have seen an increase in available target deconvolution strategies, rooted in organic chemistry, proteomics, and genetics. This review provides an overview of advances in target identification and mechanism of action studies, describes the strengths and weaknesses of the different approaches, and illustrates the need for chemical biologists to integrate and expand the existing tools to increase the probability of evolving screen hits to robust chemical probes.
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Affiliation(s)
| | | | - Sascha Hoogendoorn
- Department of Organic Chemistry, University of Geneva, Quai Ernest-Ansermet 30, 1211 Genève, Switzerland; (Q.T.L.P.); (I.A.T.)
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16
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Dai L, Li Z, Chen D, Jia L, Guo J, Zhao T, Nordlund P. Target identification and validation of natural products with label-free methodology: A critical review from 2005 to 2020. Pharmacol Ther 2020; 216:107690. [PMID: 32980441 DOI: 10.1016/j.pharmthera.2020.107690] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 02/08/2023]
Abstract
Natural products (NPs) have been an important source of therapeutic drugs in clinic use and contributed many chemical probes for research. The usefulness of NPs is however often marred by the incomplete understanding of their direct cellular targets. A number of experimental methods for drug target identification have been developed over the years. One class of methods, termed "label-free" methodology, exploits the energetic and biophysical features accompanying the association of macromolecules with drugs and other compounds in their native forms. Herein we review the working principles, assay implementations, and key applications of the most important approaches, and also give examples where they have been applied to NPs. We also assess the key advantages and limitations of each method. Furthermore, we address when and how the label-free methodology can be particularly useful considering some of the unique features of NP chemistry and bioactivation.
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Affiliation(s)
- Lingyun Dai
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China; Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, Guangdong, China; Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.
| | - Zhijie Li
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China; Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, Guangdong, China
| | - Dan Chen
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Lin Jia
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Jinan Guo
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China
| | - Tianyun Zhao
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Pär Nordlund
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore; Department of Oncology and Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden.
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17
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Zhang X, Ruan C, Zhu H, Li K, Zhang W, Wang K, Hu L, Ye M. A Simplified Thermal Proteome Profiling Approach to Screen Protein Targets of a Ligand. Proteomics 2020; 20:e1900372. [PMID: 32578935 DOI: 10.1002/pmic.201900372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 06/10/2020] [Indexed: 01/10/2023]
Abstract
Thermal proteome profiling is a powerful energetic-based chemical proteomics method to reveal the ligand-protein interaction. However, the costly multiplexed isotopic labeling reagent, mainly Multiplexed isobaric tandem mass tag (TMT), and the long mass spectrometric time limits the wide application of this method. Here a simple and cost-effective strategy by using dimethyl labeling technique instead of TMT labeling is reported to quantify proteins and by using the peptides derived from the same protein to determine significantly changed proteins in one LC-MS run. This method is validated by identifying the known targets of methotrexate and geldanamycin. In addition, several potential off-targets involved in detoxification of reactive oxygen species pathway are also discovered for geldanamycin. This method is further applied to map the interactome of adenosine triphosphate (ATP) in the 293T cell lysate by using ATP analogue, adenylyl imidodiphosphate (AMP-PNP), as the ligand. As a result, a total of 123 AMP-PNP-sensitive proteins are found, of which 59 proteins are stabilized by AMP-PNP. Approximately 53% and 20% of these stabilized candidate protein targets are known as ATP and RNA binding proteins. Overall, above results demonstrated that this approach could be a valuable platform for the unbiased target proteins identification with reduced reagent cost and mass spectrometric time.
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Affiliation(s)
- Xiaolei Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Key Laboratory Molecular Enzymology and Engineering, the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Chengfei Ruan
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - He Zhu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Kejia Li
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Wenbo Zhang
- Key Laboratory Molecular Enzymology and Engineering, the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Keyun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Lianghai Hu
- Key Laboratory Molecular Enzymology and Engineering, the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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18
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Yamaguchi T. [Development of a Novel Affinity Labeling Method for Target Identification of Bioactive Small Molecules]. YAKUGAKU ZASSHI 2020; 139:1513-1521. [PMID: 31787638 DOI: 10.1248/yakushi.19-00171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Target identification (target-ID) is an important step in elucidating the mechanisms of action of bioactive small molecules. In the past few decades, a number of target-ID methods have been developed. Among these, affinity labeling has been reliably used for specific modifications, as well as for the identification of weakly interacting protein targets, membrane-associated protein targets, and target-interacting proteins under native cellular conditions, which are generally difficult to achieve by conventional pull-down methods. In general, affinity labeling utilizes chemical probes composed of a bioactive small molecule, a reactive group, and a detection unit. However, the design and synthesis of highly functionalized chemical probes is often time-consuming. To address this issue, we have recently developed some simple affinity labeling methods using small fluorogenic tags, such as 4-alkoxy-7-nitro-2,1,3-benzoxadiazole (O-NBD), 2,3-dichloromaleimide (diCMI), and 4-azidophthalimide (AzPI), and successfully achieved the specific fluorescent labeling of target proteins, even in living cells. These methods should be useful for target-ID in phenotypic drug discovery.
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Affiliation(s)
- Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University
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19
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Nagasawa I, Muroi M, Kawatani M, Ohishi T, Ohba SI, Kawada M, Osada H. Identification of a Small Compound Targeting PKM2-Regulated Signaling Using 2D Gel Electrophoresis-Based Proteome-wide CETSA. Cell Chem Biol 2020; 27:186-196.e4. [PMID: 31813846 DOI: 10.1016/j.chembiol.2019.11.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/01/2019] [Accepted: 11/14/2019] [Indexed: 02/07/2023]
Abstract
The cellular thermal shift assay (CETSA) has recently been devised as a label-free method for target validation of small compounds and monitoring the thermal stabilization or destabilization of proteins due to binding with the compound. Herein, we developed a modified method by combining the CETSA and proteomics analysis based on 2D gel electrophoresis, namely 2DE-CETSA, to identify the thermal stability-shifted proteins by binding with a new compound. We applied the 2DE-CETSA for analysis of a target-unknown compound, NPD10084, which exerts anti-proliferative activity against colorectal cancer cells in vitro and in vivo, and identified pyruvate kinase muscle isoform 2 (PKM2) as a candidate target protein. Interestingly, NPD10084 interrupted protein-protein interactions between PKM2 and β-catenin or STAT3, with subsequent suppression of downstream signaling. We thus demonstrate that our 2DE-CETSA method is applicable for identification of target compounds discovered by phenotypic screening.
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Affiliation(s)
- Ikuko Nagasawa
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Makoto Muroi
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Makoto Kawatani
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tomokazu Ohishi
- Institute of Microbial Chemistry (BIKAKEN), Numazu, Microbial Chemistry Research Foundation, 18-24 Miyamoto, Numazu, Shizuoka 410-0301, Japan
| | - Shun-Ichi Ohba
- Institute of Microbial Chemistry (BIKAKEN), Numazu, Microbial Chemistry Research Foundation, 18-24 Miyamoto, Numazu, Shizuoka 410-0301, Japan
| | - Manabu Kawada
- Institute of Microbial Chemistry (BIKAKEN), Numazu, Microbial Chemistry Research Foundation, 18-24 Miyamoto, Numazu, Shizuoka 410-0301, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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20
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Gaetani M, Sabatier P, Saei AA, Beusch CM, Yang Z, Lundström SL, Zubarev RA. Proteome Integral Solubility Alteration: A High-Throughput Proteomics Assay for Target Deconvolution. J Proteome Res 2019; 18:4027-4037. [DOI: 10.1021/acs.jproteome.9b00500] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Massimiliano Gaetani
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
- SciLifeLab, SE-17 177 Stockholm, Sweden
| | - Pierre Sabatier
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
| | - Amir A. Saei
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
| | - Christian M. Beusch
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
| | - Zhe Yang
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
| | - Susanna L. Lundström
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
- SciLifeLab, SE-17 177 Stockholm, Sweden
| | - Roman A. Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
- SciLifeLab, SE-17 177 Stockholm, Sweden
- Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, 119146, Russia
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21
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Liang X, Luo D, Luesch H. Advances in exploring the therapeutic potential of marine natural products. Pharmacol Res 2019; 147:104373. [PMID: 31351913 PMCID: PMC6839689 DOI: 10.1016/j.phrs.2019.104373] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/26/2022]
Abstract
Marine natural products represent novel and diverse chemotypes that serve as templates for the discovery and development of therapeutic agents with distinct mechanisms of action. These genetically encoded compounds produced by an evolutionary optimized biosynthetic machinery are usually quite complex and can be difficult to recreate in the laboratory. The isolation from the source organism results in limited amount of material; however, the development of advanced NMR technologies and dereplication strategies has enabled the structure elucidation on small scale. In order to rigorously explore the therapeutic potential of marine natural products and advance them further, the biological characterization has to keep pace with the chemical characterization. The limited marine natural product supply has been a serious challenge for thorough investigation of the biological targets. Several marine drugs have reached the markets or are in clinical trials, where those challenges have been overcome, including through the development of scalable syntheses. However, the identification of mechanisms of action of marine natural products early in the discovery process is potentially game changing, since effectively linking marine natural products to potential therapeutic applications in turn triggers motivation to tackle challenging syntheses and solve the supply problem. An increasing number of sensitive technologies and methods have been developed in recent years, some of which have been successfully applied to marine natural products, increasing the value of these compounds with respect to their biomedical utility. In this review, we discuss advances in overcoming the bottlenecks in marine natural product research, emphasizing on the development and advances of diverse target identification technologies applicable for marine natural product research.
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Affiliation(s)
- Xiao Liang
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, Florida, 32610, United States
| | - Danmeng Luo
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, Florida, 32610, United States
| | - Hendrik Luesch
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, Florida, 32610, United States.
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22
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Park H, Ha J, Park SB. Label-free target identification in drug discovery via phenotypic screening. Curr Opin Chem Biol 2019; 50:66-72. [DOI: 10.1016/j.cbpa.2019.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/28/2019] [Accepted: 02/06/2019] [Indexed: 11/25/2022]
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23
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Xiao X, Li BX. Identification of lamins as the molecular targets of LBL1 using a clickable photoaffinity probe. Methods Enzymol 2019; 633:185-201. [PMID: 32046845 DOI: 10.1016/bs.mie.2019.02.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Phenotypic screening is a powerful approach to discover small molecules targeting pathways or disease biology with complex genetic causes. Following the initial discovery of these small molecules is their target identification, which is at the cornerstone in addressing their biological and clinical utility. Yet, finding the needle in the haystack remains a challenge. Nuclear lamins are type V intermediate filament proteins that form a filamentous structure underneath the inner nuclear envelope to support the mechanical stability of the mammalian cell nucleus. They also participate a myriad of other cellular signaling processes with incompletely understood molecular mechanisms. Small molecules that can directly bind to nuclear lamins will be incredible tools to address lamins' roles in different aspects of biology. However, these small molecules did not exist until recently. We previously discovered an acylpyrroloquinazoline called LBL1 that selectively killed breast cancer cells without harming normal human cells. To help understand the mechanism of action of LBL1, we recently took an unbiased chemical proteomics approach to identify its direct binding targets from the entire human cellular proteome. In this chapter, we describe our detailed methods to identify and validate lamins as the direct targets of LBL1. In this approach, we developed a clickable photoaffinity probe called LBL1-P that contains acylpyrroloquinazoline, trifluoromethyldiazirine and alkyne groups. Furthermore, we described a fluorescence microscopic method to validate that LBL1 directly targets lamin A in living cells. When properly designed, this approach should be broadly applicable to other bioactive small molecules.
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Affiliation(s)
- Xiangshu Xiao
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States
| | - Bingbing X Li
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States.
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24
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Park H, Park SB. Label-free target identification reveals oxidative DNA damage as the mechanism of a selective cytotoxic agent. Chem Sci 2019; 10:3449-3458. [PMID: 30996934 PMCID: PMC6438152 DOI: 10.1039/c8sc05465g] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/09/2019] [Indexed: 12/14/2022] Open
Abstract
Phenotypic screening can not only identify promising first-in-class drug candidates, but can also reveal potential therapeutic targets or neomorphic functions of known proteins. In this study, we identified target proteins of SB2001, a cytotoxic agent that acts specifically against HeLa human cervical cancer cells. Because SB2001 lacks chemical modification sites, label-free target identification methods including thermal stability shift-based fluorescence difference in two-dimensional gel electrophoresis (TS-FITGE) and thermal proteome profiling (TPP) were applied to characterize its mechanism of action. Owing to their differences, the two label-free target identification methods uncovered complementary target candidates. Candidates from both methods were prioritized according to their selective lethality upon the knockdown of those genes in HeLa cells, compared to CaSki cells which were used as a negative control cell line from the human cervix. LTA4H was identified only by TS-FITGE, but not by TPP, because only one isoform was stabilized by SB2001. Furthermore, it was implied that a non-canonical function of LTA4H was involved in the SB2001 activity. MTH1 was identified by both TS-FITGE and TPP, and SB2001 inhibited the function of MTH1 in hydrolyzing oxidized nucleotides. Compared to CaSki cells, HeLa cells displayed downregulated DNA mismatch repair pathways, which made HeLa cells more susceptible to the oxidative stress caused by SB2001, resulting in increased 8-oxoG concentrations, DNA damage, and subsequent cell death.
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Affiliation(s)
- Hankum Park
- CRI Center for Chemical Proteomics , Department of Chemistry , Seoul National University , Seoul 08826 , Korea
| | - Seung Bum Park
- CRI Center for Chemical Proteomics , Department of Chemistry , Seoul National University , Seoul 08826 , Korea.,Department of Biophysics and Chemical Biology , Seoul National University , Seoul 08826 , Korea .
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25
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Kubota K, Funabashi M, Ogura Y. Target deconvolution from phenotype-based drug discovery by using chemical proteomics approaches. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:22-27. [DOI: 10.1016/j.bbapap.2018.08.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/19/2018] [Accepted: 08/09/2018] [Indexed: 11/16/2022]
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26
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Kaur U, Meng H, Lui F, Ma R, Ogburn RN, Johnson JHR, Fitzgerald MC, Jones LM. Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale. J Proteome Res 2018; 17:3614-3627. [PMID: 30222357 DOI: 10.1021/acs.jproteome.8b00341] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past decade, a suite of new mass-spectrometry-based proteomics methods has been developed that now enables the conformational properties of proteins and protein-ligand complexes to be studied in complex biological mixtures, from cell lysates to intact cells. Highlighted here are seven of the techniques in this new toolbox. These techniques include chemical cross-linking (XL-MS), hydroxyl radical footprinting (HRF), Drug Affinity Responsive Target Stability (DARTS), Limited Proteolysis (LiP), Pulse Proteolysis (PP), Stability of Proteins from Rates of Oxidation (SPROX), and Thermal Proteome Profiling (TPP). The above techniques all rely on conventional bottom-up proteomics strategies for peptide sequencing and protein identification. However, they have required the development of unconventional proteomic data analysis strategies. Discussed here are the current technical challenges associated with these different data analysis strategies as well as the relative analytical capabilities of the different techniques. The new biophysical capabilities that the above techniques bring to bear on proteomic research are also highlighted in the context of several different application areas in which these techniques have been used, including the study of protein ligand binding interactions (e.g., protein target discovery studies and protein interaction network analyses) and the characterization of biological states.
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Affiliation(s)
- Upneet Kaur
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - He Meng
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0346 , United States
| | | | - Renze Ma
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0346 , United States
| | - Ryenne N Ogburn
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0346 , United States
| | - Julia H R Johnson
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0346 , United States
| | - Michael C Fitzgerald
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0346 , United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
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27
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Phenotype-Based High-Content Screening Using Fluorescent Chemical Bioprobes: Lipid Droplets and Glucose Uptake Quantification in Live Cells. Methods Mol Biol 2018. [PMID: 29736722 DOI: 10.1007/978-1-4939-7847-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Phenotypic screening in live cells has emerged as a promising strategy for drug discovery in pharmaceutical communities. For relevant phenotype-based screening setups, it is critical to develop adequate reporters in order to selectively visualize subcellular compartments or phenotypic changes that represent disease-related characteristics during compound screening. In this chapter, we introduce two phenotype-based high-content/high-throughput assays using fluorescent bioprobes that have been designed and refined to selectively stain cellular lipid droplets (LDs) and to show cellular glucose uptake. In conjunction with target identification process for the hit compounds from phenotypic screening, these fluorescent chemical probe-based screening techniques are expected to drive a great advancement for the discovery of novel first-in-class therapeutics.
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28
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29
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Chiba K, Asanuma M, Ishikawa M, Hashimoto Y, Dodo K, Sodeoka M, Yamaguchi T. Specific fluorescence labeling of target proteins by using a ligand–4-azidophthalimide conjugate. Chem Commun (Camb) 2017; 53:8751-8754. [DOI: 10.1039/c7cc03252h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two distinct model studies demonstrate that the ligand–4-azidophthalimide conjugate strategy is useful for specific fluorescence labeling of target proteins.
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Affiliation(s)
- Kosuke Chiba
- Institute of Molecular and Cellular Biosciences
- The University of Tokyo
- Tokyo 113-0032
- Japan
| | - Miwako Asanuma
- Synthetic Organic Chemistry Laboratory
- RIKEN
- Wako
- Japan
- AMED-CREST
| | - Minoru Ishikawa
- Institute of Molecular and Cellular Biosciences
- The University of Tokyo
- Tokyo 113-0032
- Japan
| | - Yuichi Hashimoto
- Institute of Molecular and Cellular Biosciences
- The University of Tokyo
- Tokyo 113-0032
- Japan
| | - Kosuke Dodo
- Synthetic Organic Chemistry Laboratory
- RIKEN
- Wako
- Japan
- AMED-CREST
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory
- RIKEN
- Wako
- Japan
- AMED-CREST
| | - Takao Yamaguchi
- Institute of Molecular and Cellular Biosciences
- The University of Tokyo
- Tokyo 113-0032
- Japan
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