1
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Fang PW, Lin YC, Fan SY, Panja A, Xu SQ, Lee SH, Tan KT. Protein-Labeling Fluorescent Probe for Folate Receptor α. Anal Chem 2023; 95:11535-11541. [PMID: 37479992 DOI: 10.1021/acs.analchem.3c02215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
GPI-anchored folate receptor α (FRα) is an attractive anticancer drug target and diagnosis marker in fundamental biology and medical research due to its significant expression on many cancer cells. Currently, analyses of FRα expression levels are usually achieved using immunological methods. Due to the continual FRα synthesis and degradation, immunological methods are not suitable for studying real-time dynamic activities of FRα in living cells. In this paper, we introduce a rapid and specific FRα protein-labeling fluorescent probe, FR1, to facilitate the study of the dynamics of expression and degradation processes of endogenous FRα in living cells. With this labeling probe, insights on FRα protein lifetime and shedding from the cell surface can be obtained using fluorescence live-cell imaging and electrophoresis techniques. We revealed that FRα undergoes soluble domain release and endocytosis degradation simultaneously. Imaging results showed that most of the membrane FRα are transported to the lysosomes after 2 h of incubation. Furthermore, we also showed that the secretion of a FRα soluble domain into the environment is most likely accomplished by phospholipase. We believe that this protein-labeling approach can be an important tool for analyzing various dynamic processes involving FRα.
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Affiliation(s)
- Pin-Wen Fang
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, Republic of China
| | - Yu-Chun Lin
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, Republic of China
| | - Syuan-Yun Fan
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, Republic of China
| | - Avijit Panja
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, Republic of China
| | - Shun-Qiang Xu
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, Republic of China
| | - Szu-Hsien Lee
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, Republic of China
| | - Kui-Thong Tan
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, Republic of China
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101 Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, Republic of China
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, Republic of China
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2
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Liu Y, Liu J, Zhang X, Guo C, Xing X, Zhang ZM, Ding K, Li Z. Oxidant-Induced Bioconjugation for Protein Labeling in Live Cells. ACS Chem Biol 2023; 18:112-122. [PMID: 36543757 DOI: 10.1021/acschembio.2c00740] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chemical proteomics is a powerful technology that can be used in the studies of the functions of uncharacterized proteins in the human proteome. It relies on a suitable bioconjugation strategy for protein labeling. This could be either a UV-responsive photo-crosslinker or an electrophilic warhead embedded in chemical probes that can form covalent bonds with target proteins. Here, we report a new protein-labeling strategy in which a nitrile oxide, a highly reactive intermediate that reacts with proteins, can be efficiently generated by the treatment of oximes with a water-soluble and a minimally toxic oxidant, phenyliodine bis (trifluoroacetate) (PIFA). The resulting intermediate can rapidly bioconjugate with amino acid residues of target proteins, thus enabling target identification of oxime-containing bioactive molecules. Excellent chemoselectivity of cysteine residues by the nitrile oxide was observed, and over 4000 reactive and/or accessible cysteines, including KRAS G12C, have been successfully characterized by quantitative chemical proteomics. Some of these residues could not be detected by conventional cysteine reagents, thus demonstrating the complementary utility of this method.
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Affiliation(s)
- Yue Liu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Jiacong Liu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Xianfang Zhang
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Cuiping Guo
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Xiwen Xing
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhi-Min Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
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3
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Ali R, Parelkar SS, Thompson PR, Mitroka-Batsford S, Yerramilli S, Scarlata SF, Mistretta KS, Coburn JM, Mattson AE. Phomoxanthone A Targets ATP Synthase. Chemistry 2022; 28:e202202397. [PMID: 36082977 PMCID: PMC9942271 DOI: 10.1002/chem.202202397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Indexed: 11/06/2022]
Abstract
Phomoxanthone A is a naturally occurring molecule and a powerful anti-cancer agent, although its mechanism of action is unknown. To facilitate the determination of its biological target(s), we used affinity-based labelling using a phomoxanthone A probe. Labelled proteins were pulled down, subjected to chemoproteomics analysis using LC-MS/MS and ATP synthase was identified as a likely target. Mitochondrial ATP synthase was validated in cultured cells lysates and in live intact cells. Our studies show sixty percent inhibition of ATP synthase by 260 μM phomoxanthone A.
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Affiliation(s)
- Rameez Ali
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St., Worcester, MA 01609, USA
| | - Sangram S Parelkar
- Department of Chemical Biology, University of Massachusetts Medical School, 364 Plantation St., Wocester, MA 01605, USA
| | - Paul R Thompson
- Department of Chemical Biology, University of Massachusetts Medical School, 364 Plantation St., Wocester, MA 01605, USA
| | - Susan Mitroka-Batsford
- Department of Chemistry and Biochemistry, Worcester State University, 486 Chandler St., Worcester, MA 10602, USA
| | - Siddartha Yerramilli
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St., Worcester, MA 01609, USA
| | - Suzanne F Scarlata
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St., Worcester, MA 01609, USA
| | - Katelyn S Mistretta
- Department of Biomedical Engineering, Worcester Polytechnic Institute, 60 Prescott St., Worcester, MA 01609, USA
| | - Jeannine M Coburn
- Department of Biomedical Engineering, Worcester Polytechnic Institute, 60 Prescott St., Worcester, MA 01609, USA
| | - Anita E Mattson
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St., Worcester, MA 01609, USA
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4
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Yu H, Wang S, Huang J, Fu Y, Wagner M, Weil T, Zhong F, Zhao W, Wu Y. Light-Controlled Traceless Protein Labeling via Decaging Thio- o-naphthoquinone Methide Chemistry. Org Lett 2022; 24:6816-6821. [PMID: 36099167 DOI: 10.1021/acs.orglett.2c02742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the molecular design of a novel multifunctional reagent and its application for light-controlled selective protein labeling. This molecule integrates functions of protein-ligand recognition, bioconjugation, ligand cleavage, and photoactivation by merging the photochemistries of 2-nitrophenylpropyloxycarbonyl and 3-hydroxymethyl-2-naphthol with an affinity ligand and fluorescein. Highly electrophilic o-naphthoquinone methide was photochemically released and underwent proximity-driven selective labeling with the protein of interest (e.g., carbonic anhydrases), which retains its native function after labeling.
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Affiliation(s)
- Huaibin Yu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Shuangshuang Wang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Jianjian Huang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Yu Fu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
| | - Manfred Wagner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Fangrui Zhong
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Weining Zhao
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
| | - Yuzhou Wu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
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5
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Li S, Zhang P, Xu F, Hu S, Liu J, Tan Y, Tu Z, Sun H, Zhang ZM, He QY, Sun P, Ding K, Li Z. Ynamide Electrophile for the Profiling of Ligandable Carboxyl Residues in Live Cells and the Development of New Covalent Inhibitors. J Med Chem 2022; 65:10408-10418. [PMID: 35880853 DOI: 10.1021/acs.jmedchem.2c00272] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covalent inhibitors with an electrophilic warhead have received considerable attention due to their remarkable pharmacological properties. However, the electrophilic warhead in covalent drugs is often an α, β-unsaturated amide, and the targets are mainly cysteine or lysine residues. Thus, the development of novel electrophiles that can target other amino acids is highly desirable. Ynamide, a useful and versatile building block, is commonly employed in the construction of various compounds in organic synthesis. The performance of this functional group in a proteome-wide environment has been studied here for the first time, and it has been shown that it can efficiently modify carboxyl residues in situ and in vitro. Upon incorporation of this ynamide warhead into the pharmacophores of kinase inhibitors, the resulting compound showed moderate inhibition against the EGFR L858R mutant but not against EGFR WT. This novel electrophilic group can be used in the development of new types of covalent inhibitors.
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Affiliation(s)
- Shengrong Li
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Pengwei Zhang
- Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, Guangdong, China.,Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, Guangdong, China
| | - Fang Xu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Shengcao Hu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Jiacong Liu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Yi Tan
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Zhengchao Tu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Hongyan Sun
- Department of Chemistry, City University of Hong Kong, Hong Kong 999077, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Qing-Yu He
- Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, Guangdong, China.,MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510120, China
| | - Pinghua Sun
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Ke Ding
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632.,MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510120, China
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6
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Chemical Probes and Activity-Based Protein Profiling for Cancer Research. Int J Mol Sci 2022; 23:ijms23115936. [PMID: 35682614 PMCID: PMC9180054 DOI: 10.3390/ijms23115936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/10/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022] Open
Abstract
Chemical probes can be used to understand the complex biological nature of diseases. Due to the diversity of cancer types and dynamic regulatory pathways involved in the disease, there is a need to identify signaling pathways and associated proteins or enzymes that are traceable or detectable in tests for cancer diagnosis and treatment. Currently, fluorogenic chemical probes are widely used to detect cancer-associated proteins and their binding partners. These probes are also applicable in photodynamic therapy to determine drug efficacy and monitor regulating factors. In this review, we discuss the synthesis of chemical probes for different cancer types from 2016 to the present time and their application in monitoring the activity of transferases, hydrolases, deacetylases, oxidoreductases, and immune cells. Moreover, we elaborate on their potential roles in photodynamic therapy.
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7
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Tan Y, Fu S, Yang T, Xie Y, Shen G, Yan J, Zhao Y, Ni F. Evaluation of Site-Diversified, Fully Functionalized Diazirine Probes for Chemical Proteomic Applications. Chem Commun (Camb) 2022; 58:9532-9535. [DOI: 10.1039/d2cc03868d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of site-diversified, fully functionalized diazirine probes are constructed based on a scaffold shared by several marketed EGFR-targeted drugs. The integrated analysis of protein targets of site-diversified probe toolkit...
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8
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Fan Y, Si H, Zhang Z, Zhong L, Sun H, Zhu C, Yin Z, Li H, Tang G, Yao SQ, Sun P, Zhang ZM, Ding K, Li Z. Novel Electrophilic Warhead Targeting a Triple-Negative Breast Cancer Driver in Live Cells Revealed by "Inverse Drug Discovery". J Med Chem 2021; 64:15582-15592. [PMID: 34623802 DOI: 10.1021/acs.jmedchem.0c02024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The "inverse drug discovery" strategy is a potent means of exploring the cellular targets of latent electrophiles not typically used in medicinal chemistry. Cyclopropenone, a powerful electrophile, is generally used in bio-orthogonal reactions mediated by triarylphosphine or in photo-triggered cycloaddition reactions. Here, we have studied, for the first time, the proteome reactivity of cyclopropenones in live cells and discovered that the cyclopropenone warhead can specifically and efficiently modify a triple-negative breast cancer driver, glutathione S-transferase pi-1 (GSTP1), by covalently binding at the catalytic active site. Further structure optimization and signaling pathway validation have led to the discovery of potent inhibitors of GSTP1.
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Affiliation(s)
- Youlong Fan
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Hongfei Si
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhang Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Liang Zhong
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Hongyan Sun
- Department of Chemistry, City University of Hong Kong, Hong Kong 999077, China
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhibin Yin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Pinghua Sun
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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9
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Burton NR, Kim P, Backus KM. Photoaffinity labelling strategies for mapping the small molecule-protein interactome. Org Biomol Chem 2021; 19:7792-7809. [PMID: 34549230 PMCID: PMC8489259 DOI: 10.1039/d1ob01353j] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nearly all FDA approved drugs and bioactive small molecules exert their effects by binding to and modulating proteins. Consequently, understanding how small molecules interact with proteins at an molecular level is a central challenge of modern chemical biology and drug development. Complementary to structure-guided approaches, chemoproteomics has emerged as a method capable of high-throughput identification of proteins covalently bound by small molecules. To profile noncovalent interactions, established chemoproteomic workflows typically incorporate photoreactive moieties into small molecule probes, which enable trapping of small molecule-protein interactions (SMPIs). This strategy, termed photoaffinity labelling (PAL), has been utilized to profile an array of small molecule interactions, including for drugs, lipids, metabolites, and cofactors. Herein we describe the discovery of photocrosslinking chemistries, including a comparison of the strengths and limitations of implementation of each chemotype in chemoproteomic workflows. In addition, we highlight key examples where photoaffinity labelling has enabled target deconvolution and interaction site mapping.
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Affiliation(s)
- Nikolas R Burton
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA.
| | - Phillip Kim
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Keriann M Backus
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA.
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
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10
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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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11
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Zhang X, Spiegel J, Martínez Cuesta S, Adhikari S, Balasubramanian S. Chemical profiling of DNA G-quadruplex-interacting proteins in live cells. Nat Chem 2021; 13:626-633. [PMID: 34183817 PMCID: PMC8245323 DOI: 10.1038/s41557-021-00736-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022]
Abstract
DNA-protein interactions regulate critical biological processes. Identifying proteins that bind to specific, functional genomic loci is essential to understand the underlying regulatory mechanisms on a molecular level. Here we describe a co-binding-mediated protein profiling (CMPP) strategy to investigate the interactome of DNA G-quadruplexes (G4s) in native chromatin. CMPP involves cell-permeable, functionalized G4-ligand probes that bind endogenous G4s and subsequently crosslink to co-binding G4-interacting proteins in situ. We first showed the robustness of CMPP by proximity labelling of a G4 binding protein in vitro. Employing this approach in live cells, we then identified hundreds of putative G4-interacting proteins from various functional classes. Next, we confirmed a high G4-binding affinity and selectivity for several newly discovered G4 interactors in vitro, and we validated direct G4 interactions for a functionally important candidate in cellular chromatin using an independent approach. Our studies provide a chemical strategy to map protein interactions of specific nucleic acid features in living cells.
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Affiliation(s)
- Xiaoyun Zhang
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Jochen Spiegel
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Sergio Martínez Cuesta
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Data Sciences and Quantitative Biology, Discovery Sciences, AstraZeneca, Cambridge, UK
| | | | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge, UK.
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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12
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Smolinski MP, Urgaonkar S, Pitzonka L, Cutler M, Lee G, Suh KH, Lau JYN. Discovery of Encequidar, First-in-Class Intestine Specific P-glycoprotein Inhibitor. J Med Chem 2021; 64:3677-3693. [PMID: 33729781 DOI: 10.1021/acs.jmedchem.0c01826] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Many chemotherapeutics, such as paclitaxel, are administered intravenously as they suffer from poor oral bioavailability, partly because of efflux mechanism of P-glycoprotein in the intestinal epithelium. To date, no drug has been approved by the U.S. Food and Drug Administration (FDA) that selectively blocks this efflux pump. We sought to identify a compound that selectively inhibits P-glycoprotein in the gastrointestinal mucosa with poor oral bioavailability, thus eliminating the issues such as bone marrow toxicity associated with systemic inhibition of P-glycoprotein. Here, we describe the discovery of highly potent, selective, and poorly orally bioavailable P-glycoprotein inhibitor 14 (encequidar). Clinically, encequidar was found to be well tolerated and minimally absorbed; and importantly, it enabled the oral delivery of paclitaxel.
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Affiliation(s)
- Michael P Smolinski
- Athenex Inc., Conventus Building, 1001 Main Street, Suite 600, Buffalo, New York 14203, United States
| | - Sameer Urgaonkar
- Athenex Inc., Conventus Building, 1001 Main Street, Suite 600, Buffalo, New York 14203, United States
| | - Laura Pitzonka
- Athenex Inc., Conventus Building, 1001 Main Street, Suite 600, Buffalo, New York 14203, United States
| | - Murray Cutler
- Athenex Inc., Conventus Building, 1001 Main Street, Suite 600, Buffalo, New York 14203, United States
| | - GwanSun Lee
- Hanmi Pharmaceutical Co. Ltd., 14, Wiryeseong-daero, Songpa-gu, Seoul, 05545, Korea
| | - Kwee Hyun Suh
- Hanmi Pharmaceutical Co. Ltd., 14, Wiryeseong-daero, Songpa-gu, Seoul, 05545, Korea
| | - Johnson Y N Lau
- Athenex Inc., Conventus Building, 1001 Main Street, Suite 600, Buffalo, New York 14203, United States
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13
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Xu B, Liu D, Wang Z, Tian R, Zuo Y. Multi-substrate selectivity based on key loops and non-homologous domains: new insight into ALKBH family. Cell Mol Life Sci 2021; 78:129-141. [PMID: 32642789 PMCID: PMC11072825 DOI: 10.1007/s00018-020-03594-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/24/2020] [Accepted: 07/03/2020] [Indexed: 12/16/2022]
Abstract
AlkB homologs (ALKBH) are a family of specific demethylases that depend on Fe2+ and α-ketoglutarate to catalyze demethylation on different substrates, including ssDNA, dsDNA, mRNA, tRNA, and proteins. Previous studies have made great progress in determining the sequence, structure, and molecular mechanism of the ALKBH family. Here, we first review the multi-substrate selectivity of the ALKBH demethylase family from the perspective of sequence and structural evolution. The construction of the phylogenetic tree and the comparison of key loops and non-homologous domains indicate that the paralogs with close evolutionary relationship have similar domain compositions. The structures show that the lack and variations of four key loops change the shape of clefts to cause the differences in substrate affinity, and non-homologous domains may be related to the compatibility of multiple substrates. We anticipate that the new insights into selectivity determinants of the ALKBH family are useful for understanding the demethylation mechanisms.
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Affiliation(s)
- Baofang Xu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Dongyang Liu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zerong Wang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ruixia Tian
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yongchun Zuo
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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Larsson M, Rudqvist N, Spetz J, Shubbar E, Parris TZ, Langen B, Helou K, Forssell-Aronsson E. Long-term transcriptomic and proteomic effects in Sprague Dawley rat thyroid and plasma after internal low dose 131I exposure. PLoS One 2021; 15:e0244098. [PMID: 33382739 PMCID: PMC7774980 DOI: 10.1371/journal.pone.0244098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/03/2020] [Indexed: 02/08/2023] Open
Abstract
Background Radioiodide (131I) is commonly used to treat thyroid cancer and hyperthyroidis.131I released during nuclear accidents, have resulted in increased incidence of thyroid cancer in children. Therefore, a better understanding of underlying cellular mechanisms behind 131I exposure is of great clinical and radiation protection interest. The aim of this work was to study the long-term dose-related effects of 131I exposure in thyroid tissue and plasma in young rats and identify potential biomarkers. Materials and methods Male Sprague Dawley rats (5-week-old) were i.v. injected with 0.5, 5.0, 50 or 500 kBq 131I (Dthyroid ca 1–1000 mGy), and killed after nine months at which time the thyroid and blood samples were collected. Gene expression microarray analysis (thyroid samples) and LC-MS/MS analysis (thyroid and plasma samples) were performed to assess differential gene and protein expression profiles in treated and corresponding untreated control samples. Bioinformatics analyses were performed using the DAVID functional annotation tool and Ingenuity Pathway Analysis (IPA). The gene expression microarray data and LC-MS/MS data were validated using qRT-PCR and ELISA, respectively. Results Nine 131I exposure-related candidate biomarkers (transcripts: Afp and RT1-Bb, and proteins: ARF3, DLD, IKBKB, NONO, RAB6A, RPN2, and SLC25A5) were identified in thyroid tissue. Two dose-related protein candidate biomarkers were identified in thyroid (APRT and LDHA) and two in plasma (DSG4 and TGM3). Candidate biomarkers for thyroid function included the ACADL and SORBS2 (all activities), TPO and TG proteins (low activities). 131I exposure was shown to have a profound effect on metabolism, immune system, apoptosis and cell death. Furthermore, several signalling pathways essential for normal cellular function (actin cytoskeleton signalling, HGF signalling, NRF2-mediated oxidative stress, integrin signalling, calcium signalling) were also significantly regulated. Conclusion Exposure-related and dose-related effects on gene and protein expression generated few expression patterns useful as biomarkers for thyroid function and cancer.
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Affiliation(s)
- Malin Larsson
- Departments of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- * E-mail:
| | - Nils Rudqvist
- Departments of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Johan Spetz
- Departments of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Emman Shubbar
- Departments of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Toshima Z. Parris
- Departments of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Britta Langen
- Departments of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Khalil Helou
- Departments of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Eva Forssell-Aronsson
- Departments of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
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15
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Yu H, Li C, Wang X, Duan J, Yang N, Xie L, Yuan Y, Li S, Bi C, Yang B, Li Y. Techniques and Strategies for Potential Protein Target Discovery and Active Pharmaceutical Molecule Screening in a Pandemic. J Proteome Res 2020; 19:4242-4258. [PMID: 32957788 PMCID: PMC7640955 DOI: 10.1021/acs.jproteome.0c00372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Indexed: 12/12/2022]
Abstract
Viruses remain a major challenge in the fierce fight against diseases. There have been many pandemics caused by various viruses throughout the world over the years. Recently, the global outbreak of COVID-19 has had a catastrophic impact on human health and the world economy. Antiviral drug treatment has become another essential means to overcome pandemics in addition to vaccine development. How to quickly find effective drugs that can control the development of a pandemic is a hot issue that still needs to be resolved in medical research today. To accelerate the development of drugs, it is necessary to target the key target proteins in the development of the pandemic, screen active molecules, and develop reliable methods for the identification and characterization of target proteins based on the active ingredients of drugs. This article discusses key target proteins and their biological mechanisms in the progression of COVID-19 and other major epidemics. We propose a model based on these foundations, which includes identifying potential core targets, screening potential active molecules of core targets, and verifying active molecules. This article summarizes the related innovative technologies and methods. We hope to provide a reference for the screening of drugs related to pandemics and the development of new drugs.
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Affiliation(s)
| | | | | | - Jingyi Duan
- Tianjin University of Traditional
Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin, 301617, China
| | - Na Yang
- Tianjin University of Traditional
Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin, 301617, China
| | - Lijuan Xie
- Tianjin University of Traditional
Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin, 301617, China
| | - Yu Yuan
- Tianjin University of Traditional
Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin, 301617, China
| | - Shanze Li
- Tianjin University of Traditional
Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin, 301617, China
| | - Chenghao Bi
- Tianjin University of Traditional
Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin, 301617, China
| | - Bin Yang
- Tianjin University of Traditional
Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin, 301617, China
| | - Yubo Li
- Tianjin University of Traditional
Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin, 301617, China
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16
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Wu X, Luo L, Kong R, Song Y, Li Q, Nice EC, Wang K. Recent advances in autophagic machinery: a proteomic perspective. Expert Rev Proteomics 2020; 17:561-579. [PMID: 32772586 DOI: 10.1080/14789450.2020.1808464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Autophagy is an evolutionarily conserved cellular clearance process, by which cytosolic components are delivered to autolysosomes for breakdown and recycling to maintain cellular homeostasis. During the past decades, autophagy has been found to be tightly implicated in various physiological and pathological progresses. Unraveling the regulatory mechanisms of the autophagy process will contribute to the development of emerging autophagy-targeting strategies for the treatment of various diseases. Recently, the rapid development of proteomics approaches has enabled the use of large-scale unbiased strategies to unravel autophagy machinery. AREAS COVERED In this review, we will highlight the recent contributions of proteomics strategies in clarifying the autophagy machinery, with an emphasis on the three different types of autophagy (namely macroautophagy, microautophagy, and chaperone-mediated autophagy). We will also discuss the emerging role of proteomics approaches in investigating the mechanism of the autophagy-based unconventional secretory pathway (secretory autophagy). EXPERT OPINION Proteomics has provided an effective strategy for the comprehensive analysis of the autophagy process, which will broaden our understanding of autophagy machinery, and holds great promise for developing clinical therapies targeting autophagy.
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Affiliation(s)
- Xingyun Wu
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China
| | - Li Luo
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education , Chengdu, P.R. China
| | - Ruxin Kong
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China
| | - Yabing Song
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China
| | - Qifu Li
- Department of Neurology, the First Affiliated Hospital of Hainan Medical University, and Key Laboratory of Brain Science Research & Transformation in Tropical Environment of Hainan Province, Hainan Medical University , Haikou, P.R. China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University , Clayton, Australia
| | - Kui Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China
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17
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Xu J, Zhang Z, Lin L, Sun H, White LV, Ding K, Li Z. Quantitative Proteomics Reveals Cellular Off-Targets of a DDR1 Inhibitor. ACS Med Chem Lett 2020; 11:535-540. [PMID: 32292561 DOI: 10.1021/acsmedchemlett.9b00658] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/05/2020] [Indexed: 12/17/2022] Open
Abstract
Target identification of small molecules is a great challenge but an essential step in drug discovery. Here, a quantitative proteomics approach has been used to characterize the cellular targets of DR, a DDR1 inhibitor. By taking advantage of competitive affinity-based protein profiling coupled with bioimaging, Cathepsin D (CTSD) was found to be the principle off-target of DR in human cancer cells. Further findings suggest the potential of DR as a novel CTSD inhibitor for breast cancer treatment. In addition, a trans-cyclooctene (TCO) containing probe was developed to track the binding between DR and its target proteins in living systems and could be a useful tool for DDR1 detection.
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Affiliation(s)
- Jiaqian Xu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, Guangzhou Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- Department of Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Hong Kong SAR 999077, China
| | - Zhang Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, Guangzhou Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ligen Lin
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau, China
| | - Hongyan Sun
- Department of Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Hong Kong SAR 999077, China
| | - Lorenzo V. White
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, Guangzhou Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, Guangzhou Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, Guangzhou Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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