1
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Li G, Peng X, Guo Y, Gong S, Cao S, Qiu F. Currently Available Strategies for Target Identification of Bioactive Natural Products. Front Chem 2021; 9:761609. [PMID: 34660543 PMCID: PMC8515416 DOI: 10.3389/fchem.2021.761609] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
In recent years, biologically active natural products have gradually become important agents in the field of drug research and development because of their wide availability and variety. However, the target sites of many natural products are yet to be identified, which is a setback in the pharmaceutical industry and has seriously hindered the translation of research findings of these natural products as viable candidates for new drug exploitation. This review systematically describes the commonly used strategies for target identification via the application of probe and non-probe approaches. The merits and demerits of each method were summarized using recent examples, with the goal of comparing currently available methods and selecting the optimum techniques for identifying the targets of bioactive natural products.
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Affiliation(s)
- Gen Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xuling Peng
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yajing Guo
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shaoxuan Gong
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shijie Cao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Feng Qiu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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2
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Bhukta S, Gopinath P, Dandela R. Target identification of anticancer natural products using a chemical proteomics approach. RSC Adv 2021; 11:27950-27964. [PMID: 35480761 PMCID: PMC9038044 DOI: 10.1039/d1ra04283a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
In recent years, there has been a strong demand worldwide for the identification and development of potential anticancer drugs based on natural products. Natural products have been explored for their diverse biological and therapeutic applications from ancient time. In order to enhance the efficacy and selectivity and to minimize the undesired side effects of anti cancer natural products (ANPs), it is essential to understand their target proteins and their mechanistic pathway. Chemical proteomics is one of the most powerful tools to connect ANP target identification and quantification where labeling and non-labeling based approaches have been used. Herein, we have discussed the various strategies to systemically develop selective ANP based chemical probes to characterise their specific and non-specific target proteins using a chemical proteomic approach in various cancer cell lysates.
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Affiliation(s)
- Swadhapriya Bhukta
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology Indianoil Odisha Campus, Samantpuri Bhubaneswar 751013 India
| | - Pushparathinam Gopinath
- Department of Chemistry, SRM-Institute of Science and Technology Kattankulathur 603203 Chennai Tamilnadu India
| | - Rambabu Dandela
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology Indianoil Odisha Campus, Samantpuri Bhubaneswar 751013 India
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3
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Chen X, Wang Y, Tian J, Shao Y, Zhu B, Wang J, Hua Z. Quantitative Chemical Proteomics Reveals Resveratrol Inhibition of A549 Cell Migration Through Binding Multiple Targets to Regulate Cytoskeletal Remodeling and Suppress EMT. Front Pharmacol 2021; 12:636213. [PMID: 33867987 PMCID: PMC8044895 DOI: 10.3389/fphar.2021.636213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/10/2021] [Indexed: 12/03/2022] Open
Abstract
Resveratrol (RSV), a health-promoting natural product, has been shown to affect various cellular processes in tumor cells. However, the specific protein targets of RSV and the mechanism of action (MOA) of its anticancer effect remain elusive. In this study, the pharmacological activity of RSV was first evaluated in A549 cells, and the results showed that RSV significantly inhibited A549 cell migration but did not affect cell viability. To elucidate the underlying mechanism, a quantitative chemical proteomics approach was employed to identify the protein targets of RSV. A total of 38 target proteins were identified, and proteomic analysis showed that the targets were mainly involved in cytoskeletal remodeling and EMT, which were verified by subsequent in vitro and in vivo assays. In conclusion, RSV inhibits A549 cell migration by binding to multiple targets to regulate cytoskeletal remodeling and suppress EMT.
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Affiliation(s)
- Xiao Chen
- School of Medicine and Holistic Integrative Medicine and College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,School of Biopharmacy, China Pharmaceutical University, Nanjing, China
| | - Yutong Wang
- School of Medicine and Holistic Integrative Medicine and College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jing Tian
- School of Medicine and Holistic Integrative Medicine and College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yurou Shao
- School of Medicine and Holistic Integrative Medicine and College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Bo Zhu
- School of Medicine and Holistic Integrative Medicine and College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,School of Biopharmacy, China Pharmaceutical University, Nanjing, China
| | - Jigang Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zichun Hua
- School of Medicine and Holistic Integrative Medicine and College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,School of Biopharmacy, China Pharmaceutical University, Nanjing, China.,The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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4
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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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5
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Panyain N, Godinat A, Lanyon-Hogg T, Lachiondo-Ortega S, Will EJ, Soudy C, Mondal M, Mason K, Elkhalifa S, Smith LM, Harrigan JA, Tate EW. Discovery of a Potent and Selective Covalent Inhibitor and Activity-Based Probe for the Deubiquitylating Enzyme UCHL1, with Antifibrotic Activity. J Am Chem Soc 2020; 142:12020-12026. [PMID: 32579346 PMCID: PMC7366380 DOI: 10.1021/jacs.0c04527] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Indexed: 12/22/2022]
Abstract
Ubiquitin carboxy-terminal hydrolase L1 (UCHL1) is a deubiquitylating enzyme that is proposed as a potential therapeutic target in neurodegeneration, cancer, and liver and lung fibrosis. Herein we report the discovery of the most potent and selective UCHL1 probe (IMP-1710) to date based on a covalent inhibitor scaffold and apply this probe to identify and quantify target proteins in intact human cells. IMP-1710 stereoselectively labels the catalytic cysteine of UCHL1 at low nanomolar concentration in cells. We further demonstrate that potent and selective UCHL1 inhibitors block pro-fibrotic responses in a cellular model of idiopathic pulmonary fibrosis, supporting the potential of UCHL1 as a potential therapeutic target in fibrotic diseases.
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Affiliation(s)
- Nattawadee Panyain
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
| | - Aurélien Godinat
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
| | - Thomas Lanyon-Hogg
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
| | - Sofía Lachiondo-Ortega
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
| | - Edward J. Will
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
| | | | - Milon Mondal
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
| | - Katie Mason
- Mission
Therapeutics Ltd, Moneta, Babraham Research Campus, Cambridge, CB22 3AT, U.K.
| | - Sarah Elkhalifa
- Mission
Therapeutics Ltd, Moneta, Babraham Research Campus, Cambridge, CB22 3AT, U.K.
| | - Lisa M. Smith
- Mission
Therapeutics Ltd, Moneta, Babraham Research Campus, Cambridge, CB22 3AT, U.K.
| | - Jeanine A. Harrigan
- Mission
Therapeutics Ltd, Moneta, Babraham Research Campus, Cambridge, CB22 3AT, U.K.
| | - Edward W. Tate
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
- The
Francis Crick Institute, London, NW1 1AT, U.K.
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6
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Chen X, Wang Y, Ma N, Tian J, Shao Y, Zhu B, Wong YK, Liang Z, Zou C, Wang J. Target identification of natural medicine with chemical proteomics approach: probe synthesis, target fishing and protein identification. Signal Transduct Target Ther 2020; 5:72. [PMID: 32435053 PMCID: PMC7239890 DOI: 10.1038/s41392-020-0186-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 12/14/2022] Open
Abstract
Natural products are an important source of new drugs for the treatment of various diseases. However, developing natural product-based new medicines through random moiety modification is a lengthy and costly process, due in part to the difficulties associated with comprehensively understanding the mechanism of action and the side effects. Identifying the protein targets of natural products is an effective strategy, but most medicines interact with multiple protein targets, which complicate this process. In recent years, an increasing number of researchers have begun to screen the target proteins of natural products with chemical proteomics approaches, which can provide a more comprehensive array of the protein targets of active small molecules in an unbiased manner. Typically, chemical proteomics experiments for target identification consist of two key steps: (1) chemical probe design and synthesis and (2) target fishing and identification. In recent decades, five different types of chemical proteomic probes and their respective target fishing methods have been developed to screen targets of molecules with different structures, and a variety of protein identification approaches have been invented. Presently, we will classify these chemical proteomics approaches, the application scopes and characteristics of the different types of chemical probes, the different protein identification methods, and the advantages and disadvantages of these strategies.
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Affiliation(s)
- Xiao Chen
- School of Medicine & Holistic Integrative Medicine, and College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- School of Biopharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yutong Wang
- School of Medicine & Holistic Integrative Medicine, and College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Nan Ma
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jing Tian
- School of Medicine & Holistic Integrative Medicine, and College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yurou Shao
- School of Medicine & Holistic Integrative Medicine, and College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Bo Zhu
- School of Medicine & Holistic Integrative Medicine, and College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- School of Biopharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yin Kwan Wong
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, 518020, China
| | - Zhen Liang
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, 518020, China.
| | - Chang Zou
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, 518020, China.
| | - Jigang Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, 518020, China.
- Department of Toxicology, School of Public Health, Guangxi Medical University, Nanning, 530021, China.
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7
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Storck EM, Morales-Sanfrutos J, Serwa RA, Panyain N, Lanyon-Hogg T, Tolmachova T, Ventimiglia LN, Martin-Serrano J, Seabra MC, Wojciak-Stothard B, Tate EW. Dual chemical probes enable quantitative system-wide analysis of protein prenylation and prenylation dynamics. Nat Chem 2019; 11:552-561. [PMID: 30936521 PMCID: PMC6544531 DOI: 10.1038/s41557-019-0237-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 02/27/2019] [Indexed: 12/14/2022]
Abstract
Post-translational farnesylation or geranylgeranylation at a C-terminal cysteine residue regulates the localization and function of over 100 proteins, including the Ras isoforms, and is a therapeutic target in diseases including cancer and infection. Here, we report global and selective profiling of prenylated proteins in living cells enabled by the development of isoprenoid analogues YnF and YnGG in combination with quantitative chemical proteomics. Eighty prenylated proteins were identified in a single human cell line, 64 for the first time at endogenous abundance without metabolic perturbation. We further demonstrate that YnF and YnGG enable direct identification of post-translationally processed prenylated peptides, proteome-wide quantitative analysis of prenylation dynamics and alternative prenylation in response to four different prenyltransferase inhibitors, and quantification of defective Rab prenylation in a model of the retinal degenerative disease choroideremia.
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Affiliation(s)
- Elisabeth M Storck
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Julia Morales-Sanfrutos
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Remigiusz A Serwa
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Nattawadee Panyain
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
| | - Thomas Lanyon-Hogg
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
| | - Tanya Tolmachova
- Molecular Medicine Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Leandro N Ventimiglia
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Juan Martin-Serrano
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Miguel C Seabra
- Molecular Medicine Section, National Heart and Lung Institute, Imperial College London, London, UK
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Beata Wojciak-Stothard
- Centre for Pharmacology and Therapeutics, Department of Medicine, Imperial College London, London, UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK.
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8
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Utaka Y, Kashiwazaki G, Tajima S, Fujiwara Y, Sumi K, Itoh T, Kitayama T. Antiproliferative effects of zerumbone-pendant derivatives on human T-cell lymphoid cell line Jurkat cells. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.01.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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9
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Girisa S, Shabnam B, Monisha J, Fan L, Halim CE, Arfuso F, Ahn KS, Sethi G, Kunnumakkara AB. Potential of Zerumbone as an Anti-Cancer Agent. Molecules 2019; 24:molecules24040734. [PMID: 30781671 PMCID: PMC6413012 DOI: 10.3390/molecules24040734] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/15/2019] [Accepted: 02/16/2019] [Indexed: 12/26/2022] Open
Abstract
Cancer is still a major risk factor to public health globally, causing approximately 9.8 million deaths worldwide in 2018. Despite advances in conventional treatment modalities for cancer treatment, there are still few effective therapies available due to the lack of selectivity, adverse side effects, non-specific toxicities, and tumour recurrence. Therefore, there is an immediate need for essential alternative therapeutics, which can prove to be beneficial and safe against cancer. Various phytochemicals from natural sources have been found to exhibit beneficial medicinal properties against various human diseases. Zerumbone is one such compound isolated from Zingiber zerumbet Smith that possesses diverse pharmacological properties including those of antioxidant, antibacterial, antipyretic, anti-inflammatory, immunomodulatory, as well as anti-neoplastic. Zerumbone has shown its anti-cancer effects by causing significant suppression of proliferation, survival, angiogenesis, invasion, and metastasis through the molecular modulation of different pathways such as NF-κB, Akt, and IL-6/JAK2/STAT3 (interleukin-6/janus kinase-2/signal transducer and activator of transcription 3) and their downstream target proteins. The current review briefly summarizes the modes of action and therapeutic potential of zerumbone against various cancers.
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Affiliation(s)
- Sosmitha Girisa
- Cancer Biology Laboratory, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Department of Biosciences & Bioengineering, Indian Institute of Technology, Guwahati, Assam 781039, India.
| | - Bano Shabnam
- Cancer Biology Laboratory, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Department of Biosciences & Bioengineering, Indian Institute of Technology, Guwahati, Assam 781039, India.
| | - Javadi Monisha
- Cancer Biology Laboratory, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Department of Biosciences & Bioengineering, Indian Institute of Technology, Guwahati, Assam 781039, India.
| | - Lu Fan
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore.
| | - Clarissa Esmeralda Halim
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore.
| | - Frank Arfuso
- Stem Cell and Cancer Biology Laboratory, School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia.
| | - Kwang Seok Ahn
- College of Korean Medicine, Kyung Hee University, 24 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea.
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore.
| | - Ajaikumar B Kunnumakkara
- Cancer Biology Laboratory, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Department of Biosciences & Bioengineering, Indian Institute of Technology, Guwahati, Assam 781039, India.
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10
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Stimulation of the ATPase activity of Hsp90 by zerumbone modification of its cysteine residues destabilizes its clients and causes cytotoxicity. Biochem J 2018; 475:2559-2576. [DOI: 10.1042/bcj20180230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 12/14/2022]
Abstract
Hsp90 is an ATP-dependent molecular chaperone that assists folding and conformational maturation/maintenance of many proteins. It is a potential cancer drug target because it chaperones oncoproteins. A prokaryotic homolog of Hsp90 (HtpG) is essential for thermo-tolerance in some bacteria and virulence of zoonotic pathogens. To identify a new class of small molecules which target prokaryotic and eukaryotic Hsp90s, we studied the effects of a naturally occurring cyclic sesquiterpene, zerumbone, which inhibits proliferation of a wide variety of tumor cells, on the activity of Hsp90. Zerumbone enhanced the ATPase activity of cyanobacterial Hsp90 (Hsp90SE), yeast Hsp90, and human Hsp90α. It also enhanced the catalytic efficiency of Hsp90SE by greatly increasing kcat. Mass analysis showed that zerumbone binds to cysteine side chains of Hsp90SE covalently. Mutational studies identified 3 cysteine residues (one per each domain of Hsp90SE) that are involved in the enhancement, suggesting the presence of allosteric sites in the middle and C-terminal domains of Hsp90SE. Treatment of cyanobacterial cells with zerumbone caused them to become very temperature-sensitive, a phenotype reminiscent of cyanobacterial Hsp90 mutants, and also decreased the cellular level of linker polypeptides that are clients for Hsp90SE. Zerumbone showed cellular toxicity on cancer-derived mammalian cells by inducing apoptosis. In addition, zerumbone inhibited the binding of Hsp90/Cdc37 to client kinases. Altogether, we conclude that modification of cysteine residues of Hsp90 by zerumbone enhances its ATPase activity and inhibits physiological Hsp90 function. The activation of Hsp90 may provide new strategies to inhibit its chaperone function in cells.
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11
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Target Identification of Bioactive Covalently Acting Natural Products. Curr Top Microbiol Immunol 2018; 420:351-374. [PMID: 30105423 DOI: 10.1007/82_2018_121] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There are countless natural products that have been isolated from microbes, plants, and other living organisms that have been shown to possess therapeutic activities such as antimicrobial, anticancer, or anti-inflammatory effects. However, developing these bioactive natural products into drugs has remained challenging in part because of their difficulty in isolation, synthesis, mechanistic understanding, and off-target effects. Among the large pool of bioactive natural products lies classes of compounds that contain potential reactive electrophilic centers that can covalently react with nucleophilic amino acid hotspots on proteins and other biological molecules to modulate their biological action. Covalently acting natural products are more amenable to rapid target identification and mapping of specific druggable hotspots within proteins using activity-based protein profiling (ABPP)-based chemoproteomic strategies. In addition, the granular biochemical insights afforded by knowing specific sites of protein modifications of covalently acting natural products enable the pharmacological interrogation of these sites with more synthetically tractable covalently acting small molecules whose structures are more easily tuned. Both discovering binding pockets and targets hit by natural products and exploiting druggable modalities targeted by natural products with simpler molecules may overcome some of the challenges faced with translating natural products into drugs.
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12
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Wright MH, Sieber SA. Chemical proteomics approaches for identifying the cellular targets of natural products. Nat Prod Rep 2017; 33:681-708. [PMID: 27098809 PMCID: PMC5063044 DOI: 10.1039/c6np00001k] [Citation(s) in RCA: 258] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This review focuses on chemical probes to identify the protein binding partners of natural products in living systems.
Covering: 2010 up to 2016 Deconvoluting the mode of action of natural products and drugs remains one of the biggest challenges in chemistry and biology today. Chemical proteomics is a growing area of chemical biology that seeks to design small molecule probes to understand protein function. In the context of natural products, chemical proteomics can be used to identify the protein binding partners or targets of small molecules in live cells. Here, we highlight recent examples of chemical probes based on natural products and their application for target identification. The review focuses on probes that can be covalently linked to their target proteins (either via intrinsic chemical reactivity or via the introduction of photocrosslinkers), and can be applied “in situ” – in living systems rather than cell lysates. We also focus here on strategies that employ a click reaction, the copper-catalysed azide–alkyne cycloaddition reaction (CuAAC), to allow minimal functionalisation of natural product scaffolds with an alkyne or azide tag. We also discuss ‘competitive mode’ approaches that screen for natural products that compete with a well-characterised chemical probe for binding to a particular set of protein targets. Fuelled by advances in mass spectrometry instrumentation and bioinformatics, many modern strategies are now embracing quantitative proteomics to help define the true interacting partners of probes, and we highlight the opportunities this rapidly evolving technology provides in chemical proteomics. Finally, some of the limitations and challenges of chemical proteomics approaches are discussed.
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Affiliation(s)
- M H Wright
- Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany.
| | - S A Sieber
- Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany.
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13
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Clulow JA, Storck EM, Lanyon-Hogg T, Kalesh KA, Jones LH, Tate EW. Competition-based, quantitative chemical proteomics in breast cancer cells identifies new target profiles for sulforaphane. Chem Commun (Camb) 2017; 53:5182-5185. [PMID: 28439590 PMCID: PMC6034444 DOI: 10.1039/c6cc08797c] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/13/2017] [Indexed: 01/03/2023]
Abstract
Sulforaphane is a small molecule isothiocyanate which exhibits anticancer potential, yet its biological targets remain poorly understood. Here we employ a competition-based chemical proteomics strategy to profile sulforaphane's targets and identify over 500 targets along with their relative affinities. These targets provide a new set of mediators for sulforaphane's bioactivity, and aid understanding of its complex mode of action.
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Affiliation(s)
- James A Clulow
- Department of Chemistry, Imperial College London, London, UKSW7 2AZ.
| | | | | | | | - Lyn H Jones
- Medicine Design, Pfizer, 610 Main Street, Cambridge, MA 02139, USA
| | - Edward W Tate
- Department of Chemistry, Imperial College London, London, UKSW7 2AZ.
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Drug Target Identification Using an iTRAQ-Based Quantitative Chemical Proteomics Approach—Based on a Target Profiling Study of Andrographolide. Methods Enzymol 2017; 586:291-309. [DOI: 10.1016/bs.mie.2016.09.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Chen X, Wong YK, Wang J, Zhang J, Lee YM, Shen HM, Lin Q, Hua ZC. Target identification with quantitative activity based protein profiling (ABPP). Proteomics 2016; 17. [PMID: 27723264 DOI: 10.1002/pmic.201600212] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/14/2016] [Accepted: 10/06/2016] [Indexed: 12/20/2022]
Abstract
As many small bioactive molecules fulfill their functions through interacting with protein targets, the identification of such targets is crucial in understanding their mechanisms of action (MOA) and side effects. With technological advancements in target identification, it has become possible to accurately and comprehensively study the MOA and side effects of small molecules. While small molecules with therapeutic potential were derived solely from nature in the past, the remodeling and synthesis of such molecules have now been made possible. Presently, while some small molecules have seen successful application as drugs, the majority remain undeveloped, requiring further understanding of their MOA and side effects to fully tap into their potential. Given the typical promiscuity of many small molecules and the complexity of the cellular proteome, a high-flux and high-accuracy method is necessary. While affinity chromatography approaches combined with MS have had successes in target identification, limitations associated with nonspecific results remain. To overcome these complications, quantitative chemical proteomics approaches have been developed including metabolic labeling, chemical labeling, and label-free methods. These new approaches are adopted in conjunction with activity-based protein profiling (ABPP), allowing for a rapid process and accurate results. This review will briefly introduce the principles involved in ABPP, then summarize current advances in quantitative chemical proteomics approaches as well as illustrate with examples how ABPP coupled with quantitative chemical proteomics has been used to detect the targets of drugs and other bioactive small molecules including natural products.
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Affiliation(s)
- Xiao Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China
| | - Yin Kwan Wong
- Department of Biological Sciences, National University of Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jigang Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China.,Department of Biological Sciences, National University of Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research & Technology (SMART), Singapore
| | - Jianbin Zhang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, P. R., China
| | - Yew-Mun Lee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Han-Ming Shen
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Zi-Chun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China
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16
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Ward JA, McLellan L, Stockley M, Gibson KR, Whitlock GA, Knights C, Harrigan JA, Jacq X, Tate EW. Quantitative Chemical Proteomic Profiling of Ubiquitin Specific Proteases in Intact Cancer Cells. ACS Chem Biol 2016; 11:3268-3272. [PMID: 27779380 DOI: 10.1021/acschembio.6b00766] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Deubiquitinating enzymes play an important role in a plethora of therapeutically relevant processes and are emerging as pioneering drug targets. Herein, we present a novel probe, Ubiquitin Specific Protease (USP) inhibitor, alongside an alkyne-tagged activity-based probe analogue. Activity-based proteome profiling identified 12 USPs, including USP4, USP16, and USP33, as inhibitor targets using submicromolar probe concentrations. This represents the first intact cell activity-based profiling of deubiquitinating enzymes. Further analysis demonstrated functional inhibition of USP33 and identified a synergistic relationship in combination with ATR inhibition, consistent with USP4 inhibition.
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Affiliation(s)
- Jennifer A. Ward
- Department of Chemistry, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Lauren McLellan
- MISSION Therapeutics, Ltd., Moneta,
Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Martin Stockley
- MISSION Therapeutics, Ltd., Moneta,
Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Karl R. Gibson
- Sandexis Medicinal Chemistry, Ltd., Innovation House, Discovery Park, Ramsgate Road, Sandwich, Kent, CT13 9ND, United Kingdom
| | - Gavin A. Whitlock
- Sandexis Medicinal Chemistry, Ltd., Innovation House, Discovery Park, Ramsgate Road, Sandwich, Kent, CT13 9ND, United Kingdom
| | - Charlotte Knights
- MISSION Therapeutics, Ltd., Moneta,
Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Jeanine A. Harrigan
- MISSION Therapeutics, Ltd., Moneta,
Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Xavier Jacq
- MISSION Therapeutics, Ltd., Moneta,
Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Edward W. Tate
- Department of Chemistry, Imperial College London, London, SW7 2AZ, United Kingdom
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17
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Pechalrieu D, Etievant C, Arimondo PB. DNA methyltransferase inhibitors in cancer: From pharmacology to translational studies. Biochem Pharmacol 2016; 129:1-13. [PMID: 27956110 DOI: 10.1016/j.bcp.2016.12.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/07/2016] [Indexed: 12/31/2022]
Abstract
DNA methylation is a mammalian epigenetic mark that participates to define where and when genes are expressed, both in normal cells and in the context of diseases. Like other epigenetic marks, it is reversible and can be modulated by chemical agents. Because it plays an important role in cancer by silencing certain genes, such as tumour suppressor genes, it is a promising therapeutic target. Two compounds are already approved to treat haematological cancers, and many efforts have been carried out to discover new molecules that inhibit DNA methyltransferases, the enzymes responsible for DNA methylation. Here, we analyse the molecular mechanisms and cellular pharmacology of these inhibitors, pointing out the necessity for new pharmacological models and paradigms. The parameters of pharmacological responses need to be redefined: the aim is cellular reprogramming rather than general cytotoxicity. Thus, "epigenetic" rather than cytotoxic dosages are defined. Another issue is the delay of the response: cellular reprogramming can take several generations to produce observable phenotypes. Is this compatible with laboratory scale experiments? Finally, it is important to consider the specificity for cancer cells compared to normal cells and the appearance of resistance. We also discuss different techniques that are used and the selection of pharmacological models.
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Affiliation(s)
- Dany Pechalrieu
- Unité de Service et de Recherche CNRS-Pierre Fabre USR3388, CNRS FRE3600, ETaC, Epigenetic Targeting of Cancer, Toulouse, France
| | - Chantal Etievant
- Unité de Service et de Recherche CNRS-Pierre Fabre USR3388, CNRS FRE3600, ETaC, Epigenetic Targeting of Cancer, Toulouse, France
| | - Paola B Arimondo
- Unité de Service et de Recherche CNRS-Pierre Fabre USR3388, CNRS FRE3600, ETaC, Epigenetic Targeting of Cancer, Toulouse, France.
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18
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Rana VS, Ahluwalia V, Shakil NA, Prasad L. Essential oil composition, antifungal, and seedling growth inhibitory effects of zerumbone from Zingiber zerumbet Smith. JOURNAL OF ESSENTIAL OIL RESEARCH 2016. [DOI: 10.1080/10412905.2016.1261051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Virendra S. Rana
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Vivek Ahluwalia
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Najam A. Shakil
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Lakshman Prasad
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi, India
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19
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Target identification of natural and traditional medicines with quantitative chemical proteomics approaches. Pharmacol Ther 2016; 162:10-22. [DOI: 10.1016/j.pharmthera.2016.01.010] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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20
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Wang J, Zhang J, Zhang CJ, Wong YK, Lim TK, Hua ZC, Liu B, Tannenbaum SR, Shen HM, Lin Q. In situ Proteomic Profiling of Curcumin Targets in HCT116 Colon Cancer Cell Line. Sci Rep 2016; 6:22146. [PMID: 26915414 PMCID: PMC4768257 DOI: 10.1038/srep22146] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/08/2016] [Indexed: 01/02/2023] Open
Abstract
To date, the exact targets and mechanism of action of curcumin, a natural product with anti-inflammatory and anti-cancer properties, remain elusive. Here we synthesized a cell permeable curcumin probe (Cur-P) with an alkyne moiety, which can be tagged with biotin for affinity enrichment, or with a fluorescent dye for visualization of the direct-binding protein targets of curcumin in situ. iTRAQTM quantitative proteomics approach was applied to distinguish the specific binding targets from the non-specific ones. In total, 197 proteins were confidently identified as curcumin binding targets from HCT116 colon cancer cell line. Gene Ontology analysis showed that the targets are broadly distributed and enriched in the nucleus, mitochondria and plasma membrane, and they are involved in various biological functions including metabolic process, regulation, response to stimulus and cellular process. Ingenuity Pathway AnalysisTM (IPA) suggested that curcumin may exert its anticancer effects over multiple critical biological pathways including the EIF2, eIF4/p70S6K, mTOR signaling and mitochondrial dysfunction pathways. Functional validations confirmed that curcumin downregulates cellular protein synthesis, and induces autophagy, lysosomal activation and increased ROS production, thus leading to cell death.
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Affiliation(s)
- Jigang Wang
- Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research &Technology (SMART), 138602, Singapore.,Department of Biological Sciences, National University of Singapore, 117543, Singapore.,The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jianbin Zhang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Chong-Jing Zhang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117585, Singapore
| | - Yin Kwan Wong
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Teck Kwang Lim
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Zi-Chun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Bin Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117585, Singapore
| | - Steven R Tannenbaum
- Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research &Technology (SMART), 138602, Singapore.,Departments of Biological Engineering &Chemistry, Massachusetts Institute of Technology, 02139, United States of America
| | - Han-Ming Shen
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
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21
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Abstract
Chemical biology has a significant role to play in the discovery and validation of new therapeutic targets. Activity- and affinity-based probes have demonstrated considerable promise in the drug discovery setting as they provide a chemoproteomic means to confirm and quantify target engagement and selectivity of small molecule drug candidates. Many of these technologies have been developed using cell lysate (through the use of resin-immobilized enzyme inhibitors for example), but this does not represent the biology of an intact cell. This review highlights recent advances made in the design and application of cell-permeable probes that report on target activity and drug-target occupancy in living cells, thus providing a means to decipher molecular pharmacology and pathology in a more physiologically relevant manner.
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