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Ni Z, Shi Y, Liu Q, Wang L, Sun X, Rao Y. Degradation-Based Protein Profiling: A Case Study of Celastrol. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308186. [PMID: 38664976 PMCID: PMC11220716 DOI: 10.1002/advs.202308186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/28/2024] [Indexed: 07/04/2024]
Abstract
Natural products, while valuable for drug discovery, encounter limitations like uncertainty in targets and toxicity. As an important active ingredient in traditional Chinese medicine, celastrol exhibits a wide range of biological activities, yet its mechanism remains unclear. In this study, they introduced an innovative "Degradation-based protein profiling (DBPP)" strategy, which combined PROteolysis TArgeting Chimeras (PROTAC) technology with quantitative proteomics and Immunoprecipitation-Mass Spectrometry (IP-MS) techniques, to identify multiple targets of natural products using a toolbox of degraders. Taking celastrol as an example, they successfully identified its known targets, including inhibitor of nuclear factor kappa B kinase subunit beta (IKKβ), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PI3Kα), and cellular inhibitor of PP2A (CIP2A), as well as potential new targets such as checkpoint kinase 1 (CHK1), O-GlcNAcase (OGA), and DNA excision repair protein ERCC-6-like (ERCC6L). Furthermore, the first glycosidase degrader is developed in this work. Finally, by employing a mixed PROTAC toolbox in quantitative proteomics, they also achieved multi-target identification of celastrol, significantly reducing costs while improving efficiency. Taken together, they believe that the DBPP strategy can complement existing target identification strategies, thereby facilitating the rapid advancement of the pharmaceutical field.
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Affiliation(s)
- Zhihao Ni
- MOE Key Laboratory of Protein SciencesSchool of Pharmaceutical SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijing100084China
| | - Yi Shi
- MOE Key Laboratory of Protein SciencesSchool of Pharmaceutical SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijing100084China
| | - Qianlong Liu
- MOE Key Laboratory of Protein SciencesSchool of Pharmaceutical SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijing100084China
| | - Liguo Wang
- MOE Key Laboratory of Protein SciencesSchool of Pharmaceutical SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijing100084China
| | | | - Yu Rao
- MOE Key Laboratory of Protein SciencesSchool of Pharmaceutical SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijing100084China
- Changping LaboratoryBeijing102206China
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2
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Banahene N, Peters-Clarke TM, Biegas KJ, Shishkova E, Hart EM, McKitterick AC, Kambitsis NH, Johnson UG, Bernhardt TG, Coon JJ, Swarts BM. Chemical Proteomics Strategies for Analyzing Protein Lipidation Reveal the Bacterial O-Mycoloylome. J Am Chem Soc 2024; 146:12138-12154. [PMID: 38635392 PMCID: PMC11066868 DOI: 10.1021/jacs.4c02278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024]
Abstract
Protein lipidation dynamically controls protein localization and function within cellular membranes. A unique form of protein O-fatty acylation in Corynebacterium, termed protein O-mycoloylation, involves the attachment of mycolic acids─unusually large and hydrophobic fatty acids─to serine residues of proteins in these organisms' outer mycomembrane. However, as with other forms of protein lipidation, the scope and functional consequences of protein O-mycoloylation are challenging to investigate due to the inherent difficulties of enriching and analyzing lipidated peptides. To facilitate the analysis of protein lipidation and enable the comprehensive profiling and site mapping of protein O-mycoloylation, we developed a chemical proteomics strategy integrating metabolic labeling, click chemistry, cleavable linkers, and a novel liquid chromatography-tandem mass spectrometry (LC-MS/MS) method employing LC separation and complementary fragmentation methods tailored to the analysis of lipophilic, MS-labile O-acylated peptides. Using these tools in the model organism Corynebacterium glutamicum, we identified approximately 30 candidate O-mycoloylated proteins, including porins, mycoloyltransferases, secreted hydrolases, and other proteins with cell envelope-related functions─consistent with a role for O-mycoloylation in targeting proteins to the mycomembrane. Site mapping revealed that many of the proteins contained multiple spatially proximal modification sites, which occurred predominantly at serine residues surrounded by conformationally flexible peptide motifs. Overall, this study (i) discloses the putative protein O-mycoloylome for the first time, (ii) yields new insights into the undercharacterized proteome of the mycomembrane, which is a hallmark of important pathogens (e.g., Corynebacterium diphtheriae, Mycobacterium tuberculosis), and (iii) provides generally applicable chemical strategies for the proteomic analysis of protein lipidation.
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Affiliation(s)
- Nicholas Banahene
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
- Biochemistry,
Cell, and Molecular Biology Graduate Programs, Central Michigan University, Mount
Pleasant, Michigan 48859, United States
| | - Trenton M. Peters-Clarke
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53562, United States
- Department
of Biomolecular Chemistry, University of
Wisconsin, Madison, Wisconsin 53562, United States
- National
Center for Quantitative Biology of Complex Systems, University of Wisconsin, Madison, Wisconsin 53562, United States
| | - Kyle J. Biegas
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
- Biochemistry,
Cell, and Molecular Biology Graduate Programs, Central Michigan University, Mount
Pleasant, Michigan 48859, United States
| | - Evgenia Shishkova
- Department
of Biomolecular Chemistry, University of
Wisconsin, Madison, Wisconsin 53562, United States
- National
Center for Quantitative Biology of Complex Systems, University of Wisconsin, Madison, Wisconsin 53562, United States
| | - Elizabeth M. Hart
- Department
of Microbiology, Harvard Medical School, Boston, Massachusetts 02115 United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Amelia C. McKitterick
- Department
of Microbiology, Harvard Medical School, Boston, Massachusetts 02115 United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Nikolas H. Kambitsis
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
| | - Ulysses G. Johnson
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
- Biochemistry,
Cell, and Molecular Biology Graduate Programs, Central Michigan University, Mount
Pleasant, Michigan 48859, United States
| | - Thomas G. Bernhardt
- Department
of Microbiology, Harvard Medical School, Boston, Massachusetts 02115 United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Joshua J. Coon
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53562, United States
- Department
of Biomolecular Chemistry, University of
Wisconsin, Madison, Wisconsin 53562, United States
- National
Center for Quantitative Biology of Complex Systems, University of Wisconsin, Madison, Wisconsin 53562, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53562, United States
| | - Benjamin M. Swarts
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
- Biochemistry,
Cell, and Molecular Biology Graduate Programs, Central Michigan University, Mount
Pleasant, Michigan 48859, United States
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Chen J, Chu Z, Zhang Q, Wang C, Luo P, Zhang Y, Xia F, Gu L, Wong YK, Shi Q, Xu C, Tang H, Wang J. STEP: profiling cellular-specific targets and pathways of bioactive small molecules in tissues via integrating single-cell transcriptomics and chemoproteomics. Chem Sci 2024; 15:4313-4321. [PMID: 38516082 PMCID: PMC10952072 DOI: 10.1039/d3sc04826h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/06/2024] [Indexed: 03/23/2024] Open
Abstract
Identifying the cellular targets of bioactive small molecules within tissues has been a major concern in drug discovery and chemical biology research. Compared to cell line models, tissues consist of multiple cell types and complicated microenvironments. Therefore, elucidating the distribution and heterogeneity of targets across various cells in tissues would enhance the mechanistic understanding of drug or toxin action in real-life scenarios. Here, we present a novel multi-omics integration pipeline called Single-cell TargEt Profiling (STEP) that enables the global profiling of protein targets in mammalian tissues with single-cell resolution. This pipeline integrates single-cell transcriptome datasets with tissue-level protein target profiling using chemoproteomics. Taking well-established classic drugs such as aspirin, aristolochic acid, and cisplatin as examples, we confirmed the specificity and precision of cellular drug-target profiles and their associated molecular pathways in tissues using the STEP analysis. Our findings provide more informative insights into the action modes of bioactive molecules compared to in vitro models. Collectively, STEP represents a novel strategy for profiling cellular-specific targets and functional processes with unprecedented resolution.
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Affiliation(s)
- Jiayun Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700 China
| | - Zheng Chu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700 China
| | - Qian Zhang
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University Guangzhou 510515 China
| | - Chen Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700 China
| | - Piao Luo
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University Guangzhou 510515 China
| | - Ying Zhang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700 China
| | - Fei Xia
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700 China
| | - Liwei Gu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700 China
| | - Yin Kwan Wong
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology Shenzhen 518020 China
| | - Qiaoli Shi
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700 China
| | - Chengchao Xu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700 China
| | - Huan Tang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700 China
| | - Jigang Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700 China
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University Guangzhou 510515 China
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology Shenzhen 518020 China
- State Key Laboratory of Antiviral Drugs, School of Pharmacy, Henan University Kaifeng 475004 China
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4
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Kaur D, Choudhury C, Yadav R, Kumari L, Bhatia A. Aspirin as a potential drug repurposing candidate targeting estrogen receptor alpha in breast cancer: a molecular dynamics and in-vitro study. J Biomol Struct Dyn 2024:1-12. [PMID: 38279948 DOI: 10.1080/07391102.2024.2308780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 01/14/2024] [Indexed: 01/29/2024]
Abstract
Estrogen receptor alpha (ERα) is expressed by 70% of breast cancers (BCs). Any deregulation in ERα signaling is crucial for the initiation and progression of BC. Because of development of resistance to anti-estrogenic compounds, repurposing existing drugs is an apt strategy to avoid a long drug-discovery process. Substantial epidemiologic evidence suggests that Aspirin use reduces the risk of different cancers including BC, while its role as an adjuvant or a possible antineoplastic agent in cancer treatment is being investigated. In this study, we attempted to explore possibilities of ERα inhibition by Aspirin which may act through competitive binding to the ligand binding domain (LBD) of ERα. A list of 48 ERα-LBD crystal structures bound with agonists, antagonists, and selective ER modulators (SERMs) was thoroughly analysed to determine interaction patterns specific to each ligand category. Exhaustive docking and 500 ns molecular dynamics (MD) studies were performed on three ERα - Aspirin complexes generated using agonist, antagonist, and SERM-bound crystal structures. Besides, three ERα crystal structures bound to agonist, antagonist, and SERM respectively were also subjected to MD simulations. Aspirin showed good affinity to LBD of ERα. Comparative analyses of binding patterns, conformational changes and molecular interaction profiles from the docking results and MD trajectories suggests that Aspirin was most stable in complex generated using SERM bound crystal structure of ERα and showed interactions with Gly-521, Ala-350, Leu-525 and Thr-347 like SERMs. In addition, in-vitro assays, qPCR, and immunofluorescent assay demonstrated the decline in the expression of ERα in MCF-7 upon treatment with Aspirin. These preliminary bioinformatical and in-vitro findings may form the basis to consider Aspirin as a potential candidate for targeting ERα, especially in tamoxifen-resistant cancers.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Deepinder Kaur
- Department of Experimental Medicine and Biotechnology, PGIMER, Chandigarh, India
| | - Chinmayee Choudhury
- Department of Experimental Medicine and Biotechnology, PGIMER, Chandigarh, India
- Department of Biological Sciences, Indian Institute of Science Education and research, Mohali, India
| | - Reena Yadav
- Department of Experimental Medicine and Biotechnology, PGIMER, Chandigarh, India
| | - Laxmi Kumari
- Department of Experimental Medicine and Biotechnology, PGIMER, Chandigarh, India
| | - Alka Bhatia
- Department of Experimental Medicine and Biotechnology, PGIMER, Chandigarh, India
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5
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Xu M, Ma X, Ye Z, Wang F, Xu S, Zhang CJ. Concentration-Dependent Enrichment Identifies Primary Protein Targets of Multitarget Bioactive Molecules. J Proteome Res 2023; 22:802-811. [PMID: 36716354 DOI: 10.1021/acs.jproteome.2c00550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Multitarget bioactive molecules (MBMs) are of increasing importance in drug discovery as they could produce high efficacy and a low chance of resistance. Several advanced approaches of quantitative proteomics were developed to accurately identify the protein targets of MBMs, but little study has been carried out in a sequential manner to identify primary protein targets (PPTs) of MBMs. This set of proteins will first interact with MBMs in the temporal order and play an important role in the mode of action of MBMs, especially when MBMs are at low concentrations. Herein, we describe a valuable observation that the result of the enrichment process is highly dependent on concentrations of the probe and the proteome. Interestingly, high concentrations of probe and low concentrations of incubated proteome will readily miss the hyper-reactive protein targets and thereby increase the probability of rendering PPTs with false-negative results, while low concentrations of probe and high concentrations of incubated proteome more than likely will capture the PPTs. Based on this enlightening observation, we developed a proof-of-concept approach to identify the PPTs of iodoacetamide, a thiol-reactive MBM. This study will deepen our understanding of the enrichment process and improve the accuracy of pull-down-guided target identification.
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Affiliation(s)
- Manyi Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Xingyu Ma
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Zi Ye
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Fengge Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Shiqi Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Chong-Jing Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
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6
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Li X, Chai X, Lyu HN, Fu C, Tang H, Shi Q, Wang J, Xu C. Chemical proteomics reveals an ISR-like response elicited by salicylic acid in Arabidopsis. THE NEW PHYTOLOGIST 2023; 237:1486-1489. [PMID: 36444540 DOI: 10.1111/nph.18646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Xin Li
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xin Chai
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Hai-Ning Lyu
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Chunjin Fu
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China
| | - Huan Tang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qiaoli Shi
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jigang Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China
- Center for Reproductive Medicine, Dongguan Maternal and Child Health Care Hospital, Southern Medical University, Dongguan, 523125, Guangdong, China
| | - Chengchao Xu
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China
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7
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Hurben AK, Tretyakova NY. Role of Protein Damage Inflicted by Dopamine Metabolites in Parkinson's Disease: Evidence, Tools, and Outlook. Chem Res Toxicol 2022; 35:1789-1804. [PMID: 35994383 PMCID: PMC10225972 DOI: 10.1021/acs.chemrestox.2c00193] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dopamine is an important neurotransmitter that plays a critical role in motivational salience and motor coordination. However, dysregulated dopamine metabolism can result in the formation of reactive electrophilic metabolites which generate covalent adducts with proteins. Such protein damage can impair native protein function and lead to neurotoxicity, ultimately contributing to Parkinson's disease etiology. In this Review, the role of dopamine-induced protein damage in Parkinson's disease is discussed, highlighting the novel chemical tools utilized to drive this effort forward. Continued innovation of methodologies which enable detection, quantification, and functional response elucidation of dopamine-derived protein adducts is critical for advancing this field. Work in this area improves foundational knowledge of the molecular mechanisms that contribute to dopamine-mediated Parkinson's disease progression, potentially assisting with future development of therapeutic interventions.
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Affiliation(s)
- Alexander K. Hurben
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
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8
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Sharma A, Cipriano M, Ferrins L, Hajduk SL, Mensa-Wilmot K. Hypothesis-generating proteome perturbation to identify NEU-4438 and acoziborole modes of action in the African Trypanosome. iScience 2022; 25:105302. [PMID: 36304107 PMCID: PMC9593816 DOI: 10.1016/j.isci.2022.105302] [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: 03/07/2022] [Revised: 07/24/2022] [Accepted: 09/29/2022] [Indexed: 11/29/2022] Open
Abstract
NEU-4438 is a lead for the development of drugs against Trypanosoma brucei, which causes human African trypanosomiasis. Optimized with phenotypic screening, targets of NEU-4438 are unknown. Herein, we present a cell perturbome workflow that compares NEU-4438's molecular modes of action to those of SCYX-7158 (acoziborole). Following a 6 h perturbation of trypanosomes, NEU-4438 and acoziborole reduced steady-state amounts of 68 and 92 unique proteins, respectively. After analysis of proteomes, hypotheses formulated for modes of action were tested: Acoziborole and NEU-4438 have different modes of action. Whereas NEU-4438 prevented DNA biosynthesis and basal body maturation, acoziborole destabilized CPSF3 and other proteins, inhibited polypeptide translation, and reduced endocytosis of haptoglobin-hemoglobin. These data point to CPSF3-independent modes of action for acoziborole. In case of polypharmacology, the cell-perturbome workflow elucidates modes of action because it is target-agnostic. Finally, the workflow can be used in any cell that is amenable to proteomic and molecular biology experiments.
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Affiliation(s)
- Amrita Sharma
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA 30144, USA
| | - Michael Cipriano
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Lori Ferrins
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Stephen L. Hajduk
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Kojo Mensa-Wilmot
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA 30144, USA,Corresponding author
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9
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Hall DCN, Benndorf RA. Aspirin sensitivity of PIK3CA-mutated Colorectal Cancer: potential mechanisms revisited. Cell Mol Life Sci 2022; 79:393. [PMID: 35780223 PMCID: PMC9250486 DOI: 10.1007/s00018-022-04430-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/01/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022]
Abstract
PIK3CA mutations are amongst the most prevalent somatic mutations in cancer and are associated with resistance to first-line treatment along with low survival rates in a variety of malignancies. There is evidence that patients carrying PIK3CA mutations may benefit from treatment with acetylsalicylic acid, commonly known as aspirin, particularly in the setting of colorectal cancer. In this regard, it has been clarified that Class IA Phosphatidylinositol 3-kinases (PI3K), whose catalytic subunit p110α is encoded by the PIK3CA gene, are involved in signal transduction that regulates cell cycle, cell growth, and metabolism and, if disturbed, induces carcinogenic effects. Although PI3K is associated with pro-inflammatory cyclooxygenase-2 (COX-2) expression and signaling, and COX-2 is among the best-studied targets of aspirin, the mechanisms behind this clinically relevant phenomenon are still unclear. Indeed, there is further evidence that the protective, anti-carcinogenic effect of aspirin in this setting may be mediated in a COX-independent manner. However, until now the understanding of aspirin's prostaglandin-independent mode of action is poor. This review will provide an overview of the current literature on this topic and aims to analyze possible mechanisms and targets behind the aspirin sensitivity of PIK3CA-mutated cancers.
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Affiliation(s)
- Daniella C N Hall
- Department of Clinical Pharmacy and Pharmacotherapy, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Ralf A Benndorf
- Department of Clinical Pharmacy and Pharmacotherapy, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany.
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10
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Luo P, Zhang Q, Zhong TY, Chen JY, Zhang JZ, Tian Y, Zheng LH, Yang F, Dai LY, Zou C, Li ZJ, Liu JH, Wang JG. Celastrol mitigates inflammation in sepsis by inhibiting the PKM2-dependent Warburg effect. Mil Med Res 2022; 9:22. [PMID: 35596191 PMCID: PMC9121578 DOI: 10.1186/s40779-022-00381-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 04/12/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Sepsis involves life-threatening organ dysfunction and is caused by a dysregulated host response to infection. No specific therapies against sepsis have been reported. Celastrol (Cel) is a natural anti-inflammatory compound that shows potential against systemic inflammatory diseases. This study aimed to investigate the pharmacological activity and molecular mechanism of Cel in models of endotoxemia and sepsis. METHODS We evaluated the anti-inflammatory efficacy of Cel against endotoxemia and sepsis in mice and macrophage cultures treated with lipopolysaccharide (LPS). We screened for potential protein targets of Cel using activity-based protein profiling (ABPP). Potential targets were validated using biophysical methods such as cellular thermal shift assays (CETSA) and surface plasmon resonance (SPR). Residues involved in Cel binding to target proteins were identified through point mutagenesis, and the functional effects of such binding were explored through gene knockdown. RESULTS Cel protected mice from lethal endotoxemia and improved their survival with sepsis, and it significantly decreased the levels of pro-inflammatory cytokines in mice and macrophages treated with LPS (P < 0.05). Cel bound to Cys424 of pyruvate kinase M2 (PKM2), inhibiting the enzyme and thereby suppressing aerobic glycolysis (Warburg effect). Cel also bound to Cys106 in high mobility group box 1 (HMGB1) protein, reducing the secretion of inflammatory cytokine interleukin (IL)-1β. Cel bound to the Cys residues in lactate dehydrogenase A (LDHA). CONCLUSION Cel inhibits inflammation and the Warburg effect in sepsis via targeting PKM2 and HMGB1 protein.
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Affiliation(s)
- Piao Luo
- Artemisinin Research Center, and Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China.,Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Qian Zhang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China.,Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Tian-Yu Zhong
- Laboratory Medicine, the First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Jia-Yun Chen
- Artemisinin Research Center, and Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jun-Zhe Zhang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ya Tian
- Artemisinin Research Center, and Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liu-Hai Zheng
- Department of Geriatric Medicine, Shenzhen People's Hospital, the Second Clinical Medical College, Jinan University and the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, China
| | - Fan Yang
- Department of Geriatric Medicine, Shenzhen People's Hospital, the Second Clinical Medical College, Jinan University and the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, China
| | - Ling-Yun Dai
- Department of Geriatric Medicine, Shenzhen People's Hospital, the Second Clinical Medical College, Jinan University and the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, China
| | - Chang Zou
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Zhi-Jie Li
- Department of Geriatric Medicine, Shenzhen People's Hospital, the Second Clinical Medical College, Jinan University and the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, China.
| | - Jing-Hua Liu
- Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Ji-Gang Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China. .,Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China. .,Laboratory Medicine, the First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, China. .,Department of Geriatric Medicine, Shenzhen People's Hospital, the Second Clinical Medical College, Jinan University and the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, China. .,Center for Reproductive Medicine, Dongguan Maternal and Child Health Care Hospital, Southern Medical University, Dongguan, 523125, Guangdong, China. .,Central People's Hospital of Zhanjiang, Zhanjiang, 524037, Guangdong, China.
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11
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Grams RJ, Hsu KL. Reactive chemistry for covalent probe and therapeutic development. Trends Pharmacol Sci 2022; 43:249-262. [PMID: 34998611 PMCID: PMC8840975 DOI: 10.1016/j.tips.2021.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 02/06/2023]
Abstract
Bioactive small molecules that form covalent bonds with a target protein are important tools for basic research and can be highly effective drugs. This review highlights reactive groups found in a collection of thiophilic and oxophilic drugs that mediate pharmacological activity through a covalent mechanism of action (MOA). We describe the application of advanced proteomic and bioanalytical methodologies for assessing selectivity of these covalent agents to guide and inspire the search for additional electrophiles suitable for covalent probe and therapeutic development. While the emphasis is on chemistry for modifying catalytic serine, threonine or cysteine residues, we devote a substantial fraction of the review to a collection of exploratory reactive groups of understudied residues on proteins.
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Affiliation(s)
- R. Justin Grams
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA22908, USA; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; University of Virginia Cancer Center, University of Virginia, Charlottesville, VA 22903, USA.
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12
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Rosa A, Butt E, Hopper CP, Loroch S, Bender M, Schulze H, Sickmann A, Vorlova S, Seizer P, Heinzmann D, Zernecke A. Cyclophilin A Is Not Acetylated at Lysine-82 and Lysine-125 in Resting and Stimulated Platelets. Int J Mol Sci 2022; 23:ijms23031469. [PMID: 35163387 PMCID: PMC8836233 DOI: 10.3390/ijms23031469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/17/2022] [Accepted: 01/24/2022] [Indexed: 12/24/2022] Open
Abstract
Cyclophilin A (CyPA) is widely expressed by all prokaryotic and eukaryotic cells. Upon activation, CyPA can be released into the extracellular space to engage in a variety of functions, such as interaction with the CD147 receptor, that contribute to the pathogenesis of cardiovascular diseases. CyPA was recently found to undergo acetylation at K82 and K125, two lysine residues conserved in most species, and these modifications are required for secretion of CyPA in response to cell activation in vascular smooth muscle cells. Herein we addressed whether acetylation at these sites is also required for the release of CyPA from platelets based on the potential for local delivery of CyPA that may exacerbate cardiovascular disease events. Western blot analyses confirmed the presence of CyPA in human and mouse platelets. Thrombin stimulation resulted in CyPA release from platelets; however, no acetylation was observed-neither in cell lysates nor in supernatants of both untreated and activated platelets, nor after immunoprecipitation of CyPA from platelets. Shotgun proteomics detected two CyPA peptide precursors in the recombinant protein, acetylated at K28, but again, no acetylation was found in CyPA derived from resting or stimulated platelets. Our findings suggest that acetylation of CyPA is not a major protein modification in platelets and that CyPA acetylation is not required for its secretion from platelets.
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Affiliation(s)
- Annabelle Rosa
- Institute of Experimental Biomedicine, University Hospital Würzburg, 97080 Würzburg, Germany; (A.R.); (E.B.); (C.P.H.); (M.B.); (H.S.); (S.V.)
| | - Elke Butt
- Institute of Experimental Biomedicine, University Hospital Würzburg, 97080 Würzburg, Germany; (A.R.); (E.B.); (C.P.H.); (M.B.); (H.S.); (S.V.)
| | - Christopher P. Hopper
- Institute of Experimental Biomedicine, University Hospital Würzburg, 97080 Würzburg, Germany; (A.R.); (E.B.); (C.P.H.); (M.B.); (H.S.); (S.V.)
| | - Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften (ISAS), 44139 Dortmund, Germany; (S.L.); (A.S.)
| | - Markus Bender
- Institute of Experimental Biomedicine, University Hospital Würzburg, 97080 Würzburg, Germany; (A.R.); (E.B.); (C.P.H.); (M.B.); (H.S.); (S.V.)
| | - Harald Schulze
- Institute of Experimental Biomedicine, University Hospital Würzburg, 97080 Würzburg, Germany; (A.R.); (E.B.); (C.P.H.); (M.B.); (H.S.); (S.V.)
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften (ISAS), 44139 Dortmund, Germany; (S.L.); (A.S.)
- Medizinisches Proteom-Center, Ruhr-University Bochum, 44801 Bochum, Germany
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen AB24 3FX, UK
| | - Sandra Vorlova
- Institute of Experimental Biomedicine, University Hospital Würzburg, 97080 Würzburg, Germany; (A.R.); (E.B.); (C.P.H.); (M.B.); (H.S.); (S.V.)
| | | | - David Heinzmann
- Department of Cardiology and Angiology, University of Tübingen, 72076 Tübingen, Germany;
| | - Alma Zernecke
- Institute of Experimental Biomedicine, University Hospital Würzburg, 97080 Würzburg, Germany; (A.R.); (E.B.); (C.P.H.); (M.B.); (H.S.); (S.V.)
- Correspondence: ; Tel.: +49-(0)-931-201-48331
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13
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Tantry US, Schror K, Navarese EP, Jeong YH, Kubica J, Bliden KP, Gurbel PA. Aspirin as an Adjunctive Pharmacologic Therapy Option for COVID-19: Anti-Inflammatory, Antithrombotic, and Antiviral Effects All in One Agent. J Exp Pharmacol 2021; 13:957-970. [PMID: 34908882 PMCID: PMC8665864 DOI: 10.2147/jep.s330776] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/22/2021] [Indexed: 12/16/2022] Open
Abstract
Introduction Pharmacologic therapy options for COVID-19 should include antiviral, anti-inflammatory, and anticoagulant agents. With the limited effectiveness, currently available virus-directed therapies may have a substantial impact on global health due to continued reports of mutant variants affecting repeated waves of COVID-19 around the world. Methods We searched articles pertaining to aspirin, COVID-19, acute lung injury and pharmacology in PubMed and provide a comprehensive appraisal of potential use of aspirin in the management of patients with COVID-19. The scope of this article is to provide an overview of the rationale and currently available clinical evidence that supports aspirin as an effective therapeutic option in COVID-19. Results Experimental and clinical evidence are available for the potential use of aspirin in patients with COVID-19. Discussion Aspirin targets the intracellular signaling pathway that is essential for viral replication, and resultant inflammatory responses, hypercoagulability, and platelet activation. With these multiple benefits, aspirin can be a credible adjunctive therapeutic option for the treatment of COVID-19. In addition, inhaled formulation with its rapid effects may enhance direct delivery to the lung, which is the key organ damaged in COVID-19 during the critical initial course of the disease, whereas the 150-325 mg/day can be used for long-term treatment to prevent thrombotic event occurrences. Being economical and widely available, aspirin can be exploited globally, particularly in underserved communities and remote areas of the world to combat the ongoing COVID-19 pandemic.
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Affiliation(s)
- Udaya S Tantry
- Sinai Center for Thrombosis Research and Drug Development, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA
| | - Karsten Schror
- Department of Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Eliano Pio Navarese
- Department of Cardiology and Internal Medicine, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Young-Hoon Jeong
- Department of Internal Medicine, Gyeongsang National University School of Medicine and Cardiovascular Center, Gyeongsang National University Changwon Hospital, Changwon, South Korea
| | - Jacek Kubica
- Department of Cardiology and Internal Medicine, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Kevin P Bliden
- Sinai Center for Thrombosis Research and Drug Development, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA
| | - Paul A Gurbel
- Sinai Center for Thrombosis Research and Drug Development, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA
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14
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Myers RA, Ortel TL, Waldrop A, Dave S, Ginsburg GS, Voora D. Aspirin effects on platelet gene expression are associated with a paradoxical, increase in platelet function. Br J Clin Pharmacol 2021; 88:2074-2083. [PMID: 34705291 PMCID: PMC9007832 DOI: 10.1111/bcp.15127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/10/2021] [Accepted: 10/18/2021] [Indexed: 01/04/2023] Open
Abstract
Aspirin has known effects beyond inhibiting platelet cyclooxygenase-1 (COX-1) that have been incompletely characterized. Transcriptomics can comprehensively characterize the on- and off-target effects of medications. We used a systems pharmacogenomics approach of aspirin exposure in volunteers coupled with serial platelet function and purified platelet mRNA sequencing to test the hypothesis that aspirin's effects on the platelet transcriptome are associated with platelet function. We prospectively recruited 74 adult volunteers for a randomized crossover study of 81- vs. 325 mg/day, each for 4 weeks. Using mRNA sequencing of purified platelets collected before and after each 4-week exposure, we identified 208 aspirin-responsive genes with no evidence for dosage effects. In independent cohorts of healthy volunteers and patients with diabetes, we validated aspirin's effects on five genes: EIF2S3, CHRNB1, EPAS1, SLC9A3R2 and HLA-DRA. Functional characterization of the effects of aspirin on mRNA as well as platelet ribosomal RNA demonstrated that aspirin may act as an inhibitor of protein synthesis. Database searches for small molecules that mimicked the effects of aspirin on platelet gene expression in vitro identified aspirin but no other molecules that share aspirin's known mechanisms of action. The effects of aspirin on platelet mRNA were correlated with higher levels of platelet function both at baseline and after aspirin exposure-an effect that counteracts aspirin's known antiplatelet effect. In summary, this work collectively demonstrates a dose-independent effect of aspirin on the platelet transcriptome that counteracts the well-known antiplatelet effects of aspirin.
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Affiliation(s)
- Rachel A Myers
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Thomas L Ortel
- Division of Hematology, Department of Medicine, Duke University Medical Center, Durham, NC, United States
| | - Alexander Waldrop
- Center for Genomics and Computational Biology, Duke University, Durham, NC, United States
| | - Sandeep Dave
- Center for Genomics and Computational Biology, Duke University, Durham, NC, United States
| | - Geoffrey S Ginsburg
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Deepak Voora
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, United States
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15
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Gao J, Liu Y, Yang F, Chen X, Cravatt BF, Wang C. CIMAGE2.0: An Expanded Tool for Quantitative Analysis of Activity-Based Protein Profiling (ABPP) Data. J Proteome Res 2021; 20:4893-4900. [PMID: 34495668 DOI: 10.1021/acs.jproteome.1c00455] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Activity-based protein profiling (ABPP) is a powerful chemical proteomic method for studying protein activity, modifications, and interactions in a high-throughput manner. In ABPP experiments, accurate quantification is crucial to determine the extent of probe labeling at the level of either target proteins or specific amino acid side chains. CIMAGE has been developed as an in-house quantification software specifically designed for ABPP data analysis that incorporates (1) a relaxed peak extraction algorithm and (2) stringent post-quantification checks for efficient and accurate quantification. It also can generate table and image data for users to conveniently visualize their results. Here we provide a retrospective introduction of the software and describe our recent upgrade efforts to enable (1) interfacing with different database search engines as input, (2) triplex quantification of ABPP data by reductive dimethylation, and (3) envelope checking for chemical elements with special isotopic distributions. We show that the updated CIMAGE can maintain its ability to quantify ABPP data with dramatic depth and high accuracy, and it also has similar quantification performance in benchmarked SILAC data as compared with MaxQuant. We believe that CIMAGE2.0 will continue to serve as a powerful analytical tool for ABPP studies.
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Affiliation(s)
- Jinjun Gao
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yuan Liu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Fan Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xuemin Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Benjamin F Cravatt
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Chu Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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16
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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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17
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Cutolo G, Shankar SN, Pratt MR. Your mother was right, washing matters: An alkyne-analog of ibuprofen reveals unwanted reactivity of aromatic compounds with proteins during copper-catalyzed click chemistry. Bioorg Med Chem Lett 2021; 48:128260. [PMID: 34265422 DOI: 10.1016/j.bmcl.2021.128260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
Bioorthogonal chemistry, in particular the copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC), has enabled the robust identification of covalent protein targets of probes and drugs. Ibuprofen is commonly used pain and fever reducer and is sold as an enantiomeric racemate. Interestingly, the stereoisomers can be enzymatically converted through an ibuprofen-CoA thioester intermediate, which might non-specifically react with protein nucleophiles. Here, we use an alkyne-analog of ibuprofen to make two discoveries. First, we find that ibuprofen likely does not result in notable chemical labeling of proteins. However, we secondly find that aromatic compounds can react with proteins during the CuAAC reaction unless they are appropriately washed out of the mixture. This second discovery of false positive labeling has important technical implications for the application of this approach.
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Affiliation(s)
- Giuliano Cutolo
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, United States
| | - Sahiti N Shankar
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, United States
| | - Matthew R Pratt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, United States; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, United States.
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18
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Liu DD, Luo P, Gu L, Zhang Q, Gao P, Zhu Y, Chen X, Guo Q, Zhang J, Ma N, Wang J. Celastrol exerts a neuroprotective effect by directly binding to HMGB1 protein in cerebral ischemia-reperfusion. J Neuroinflammation 2021; 18:174. [PMID: 34372857 PMCID: PMC8353826 DOI: 10.1186/s12974-021-02216-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Celastrol (cel) was one of the earliest isolated and identified chemical constituents of Tripterygium wilfordii Hook. f. Based on a cel probe (cel-p) that maintained the bioactivity of the parent compound, the targets of cel in cerebral ischemia-reperfusion (I/R) injury were comprehensively analyzed by a quantitative chemical proteomics method. METHODS We constructed an oxygen-glucose deprivation (OGD) model in primary rat cortical neurons and a middle cerebral artery occlusion (MCAO) model in adult rats to detect the direct binding targets of cel in cerebral I/R. By combining various experimental methods, including tandem mass tag (TMT) labeling, mass spectrometry, and cellular thermal shift assay (CETSA), we revealed the targets to which cel directly bound to exert neuroprotective effects. RESULTS We found that cel inhibited the proinflammatory activity of high mobility group protein 1 (HMGB1) by directly binding to it and then blocking the binding of HMGB1 to its inflammatory receptors in the microenvironment of ischemia and hypoxia. In addition, cel rescued neurons from OGD injury in vitro and decreased cerebral infarction in vivo by targeting HSP70 and NF-κB p65. CONCLUSION Cel exhibited neuroprotective and anti-inflammatory effects by targeting HSP70 and NF-κB p65 and directly binding to HMGB1 in cerebral I/R injury.
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Affiliation(s)
- Dan-Dan Liu
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Piao Luo
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liwei Gu
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qian Zhang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Peng Gao
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yongping Zhu
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiao Chen
- School of Biopharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qiuyan Guo
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Junzhe Zhang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Nan Ma
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China. .,School of Pharmacy, Jinan University, Guangzhou , 510632, China.
| | - Jigang Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China. .,Central People's Hospital of Zhanjiang, Zhanjiang, China. .,Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China. .,Department of Physiology, School of Preclinical Medicine, Guangxi Medical University, Nanning, 530021, China. .,Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, China. .,Department of Urology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, 518020, Shenzhen, China.
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19
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Mensa-Wilmot K. How Physiologic Targets Can Be Distinguished from Drug-Binding Proteins. Mol Pharmacol 2021; 100:1-6. [PMID: 33941662 DOI: 10.1124/molpharm.120.000186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 04/09/2021] [Indexed: 01/04/2023] Open
Abstract
In clinical trials, some drugs owe their effectiveness to off-target activity. This and other observations raise a possibility that many studies identifying targets of drugs are incomplete. If off-target proteins are pharmacologically important, it will be worthwhile to identify them early in the development process to gain a better understanding of the molecular basis of drug action. Herein, we outline a multidisciplinary strategy for systematic identification of physiologic targets of drugs in cells. A drug-binding protein whose genetic disruption yields very similar molecular effects as treatment of cells with the drug may be defined as a physiologic target of the drug. For a drug developed with a rational approach, it is desirable to verify experimentally that a protein used for hit optimization in vitro remains the sole polypeptide recognized by the drug in a cell. SIGNIFICANCE STATEMENT: A body of evidence indicates that inactivation of many drug-binding proteins may not cause the pharmacological effects triggered by the drugs. A multidisciplinary cell-based approach can be of great value in identifying the physiologic targets of drugs, including those developed with target-based strategies.
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Affiliation(s)
- Kojo Mensa-Wilmot
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia, and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia
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20
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Joshi SN, Murphy EA, Olaniyi P, Bryant RJ. The multiple effects of aspirin in prostate cancer patients. Cancer Treat Res Commun 2020; 26:100267. [PMID: 33360326 DOI: 10.1016/j.ctarc.2020.100267] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/02/2020] [Accepted: 12/07/2020] [Indexed: 01/31/2023]
Abstract
Aspirin is a commonly used medication with anti-inflammatory and analgesic properties, and it is widely used to reduce the risk of ischaemic heart disease-related events and/or cerebrovascular accidents. However, there is also evidence from epidemiological and interventional studies to suggest that regular aspirin use can reduce the risk of prostate cancer development and progression, and can reduce the risk of disease recurrence following anti-prostate cancer therapy. Aspirin use in African-American men is associated with a reduced incidence of advanced PCa and reduced disease recurrence, and there is evidence from other studies of an association between regular aspirin use and decreased PCa-related mortality. The cyclooxygenase-2 enzyme inhibited by Aspirin and other NSAIDs, and which catalyses prostaglandin synthesis and mediates inflammation, is overexpressed in prostate cancer, therefore inhibition of cyclooxygenase-2 may have direct, and indirect, therapeutic effects. This review explores the evidence suggesting that aspirin use can modify prostate cancer biology and disease characteristics, and explores the potential mechanisms underpinning the observed associations between aspirin use and modification of prostate cancer risk. It also summarises the potential for adjuvant aspirin use to combine with other therapeutic approaches such as radical surgery and radiotherapy.
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Affiliation(s)
- S N Joshi
- Medical Sciences Divisional Office, University of Oxford, Level 3, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - E A Murphy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - P Olaniyi
- Department of Urology, Ipswich Hospital, East Suffolk and North Essex NHS Foundation Trust, Heath Road, Ipswich IP4 5PD, United Kingdom
| | - R J Bryant
- Department of Urology, Ipswich Hospital, East Suffolk and North Essex NHS Foundation Trust, Heath Road, Ipswich IP4 5PD, United Kingdom; Department of Urology, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, United Kingdom.
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21
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Karmakar S, Kostrhunova H, Ctvrtlikova T, Novohradsky V, Gibson D, Brabec V. Platinum(IV)-Estramustine Multiaction Prodrugs Are Effective Antiproliferative Agents against Prostate Cancer Cells. J Med Chem 2020; 63:13861-13877. [PMID: 33175515 DOI: 10.1021/acs.jmedchem.0c01400] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Herein, we describe the synthesis, characterization, and biological properties of Pt(IV) derivatives of cisplatin with estramustine at the first axial position, which is known to disrupt the microtubule assembly and act as an androgen antagonist, and varying the second axial position using an innocent ligand (acetate or hydroxyl) to prepare dual-action and triple-action prodrugs with known inhibitors of histone deacetylase, cyclooxygenase, and pyruvate dehydrogenase kinase. We demonstrate superior antiproliferative activity at submicromolar concentrations of the prodrugs against a panel of cancer cell lines, particularly against prostate cancer cell lines. The results obtained in this study exemplify the complex mode of action of "multiaction" Pt(IV) prodrugs. Interestingly, changing the second axial ligand in the Pt-estramustine complex has a significant effect on the mode of action, suggesting that all three components of the Pt(IV) prodrugs (platinum moiety and axial ligands) contribute to the killing of cells and not just one dominant component.
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Affiliation(s)
- Subhendu Karmakar
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Hana Kostrhunova
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, Brno CZ-61265, Czech Republic
| | - Tereza Ctvrtlikova
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, Brno CZ-61265, Czech Republic
| | - Vojtech Novohradsky
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, Brno CZ-61265, Czech Republic
| | - Dan Gibson
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Viktor Brabec
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, Brno CZ-61265, Czech Republic
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22
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Zhang X, Chen J, Cheng C, Li P, Cai F, Xu H, Lu Y, Cao N, Liu J, Wang J, Hua ZC, Zhuang H. Aspirin potentiates celecoxib-induced growth inhibition and apoptosis in human non-small cell lung cancer by targeting GRP78 activity. Ther Adv Med Oncol 2020; 12:1758835920947976. [PMID: 32994805 PMCID: PMC7502795 DOI: 10.1177/1758835920947976] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 07/13/2020] [Indexed: 12/24/2022] Open
Abstract
Background: Aspirin has recently emerged as an anticancer drug, but its therapeutic effect on lung cancer has been rarely reported, and the mechanism of action is still unclear. Long-term use of celecoxib in large doses causes serious side effects, and it is necessary to explore better ways to achieve curative effects. In this study, we evaluated the synergistic anticancer effects of celecoxib and aspirin in non-small cell lung cancer (NSCLC) cells. Methods: In vitro, we evaluated the combined effects of celecoxib (40 μM) and aspirin (8 mM) on cell apoptosis, cell cycle distribution, cell proliferation, cell migration and signaling pathways. Furthermore, the effect of aspirin (100 mg/kg body weight) and celecoxib (50 mg/kg body weight) on the growth of xenograft tumors was explored in vivo. Results: Our data suggest that cancer sensitivity to combined therapy using low concentrations of celecoxib and aspirin was higher than that of celecoxib or aspirin alone. Further research showed that the anti-tumor effect of celecoxib combined with aspirin was mainly produced by activating caspase-9/caspase-3, arresting cell cycle and inhibiting the ERK-MAPK signaling pathway. In addition, celecoxib alone or in combination with aspirin inhibited the migration and invasion of NSCLC cells by inhibiting MMP-9 and MMP-2 activity levels. Moreover, we identified GRP78 as a target protein of aspirin in NSCLC cells. Aspirin induced an endoplasmic reticulum stress response by inhibiting GRP78 activity. Furthermore, combination therapy also exhibited a better inhibitory effect on tumor growth in vivo. Conclusions: Our study provides a rationale for further detailed preclinical and potential clinical studies of the combination of celecoxib and aspirin for NSCLC therapy.
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Affiliation(s)
- Xiangyu Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R. China
| | - Jia Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R. China
| | - Cheng Cheng
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R. China
| | - Ping Li
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R. China
| | - Fangfang Cai
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R. China
| | - Huangru Xu
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R. China
| | - Yanyan Lu
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R. China
| | - Nini Cao
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R. China
| | - Jia Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R. China
| | - Jigang Wang
- Department of Biological Science, National University of Singapore, Singapore, 117543, Singapore
| | - Zi-Chun Hua
- School of Life Sciences, Nanjing University, 163 Xianlin Blvd., Nanjing, 210023, China
| | - Hongqin Zhuang
- School of Life Sciences, Nanjing University, 163 Xianlin Blvd., Nanjing, 210023, China
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23
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McConnell EW, Smythers AL, Hicks LM. Maleimide-Based Chemical Proteomics for Quantitative Analysis of Cysteine Reactivity. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1697-1705. [PMID: 32573231 DOI: 10.1021/jasms.0c00116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cysteine is the most intrinsically nucleophilic residue in proteins and serves as a mediator against increasing reactive oxygen species (ROS) via reversible thiol oxidation. Despite the importance of cysteine oxidation in understanding biological stress response, cysteine sites most reactive toward ROS remain largely unknown and are a major analytical challenge. Herein, a chemical proteomic method to quantify site-specific cysteine reactivity using a maleimide-activated, thiol-reactive probe (N-propargylmaleimide, NPM) is described. Implementation of a gel-based approach via conjugation of rhodamine-azide to NPM-labeled cysteine residues by copper-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry allowed simple and highly sensitive fluorescence profiling. Relative quantification of >1500 unique cysteine sites from greater than 800 proteins was achieved by conjugating dialkoxydiphenylsilane (DADPS) biotin-azide by the CuAAC reaction and subsequently performing biotin-streptavidin affinity purification and mass-spectrometry-based proteomics. Taken together, this work defines a novel role for the NPM probe in chemical proteomics and presents a robust method for determination of cysteine reactivity during oxidative stress response.
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Affiliation(s)
- Evan W McConnell
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Amanda L Smythers
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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24
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Yang X, Forster ER, Darabedian N, Kim AT, Pratt MR, Shen A, Hang HC. Translation of Microbiota Short-Chain Fatty Acid Mechanisms Affords Anti-infective Acyl-Salicylic Acid Derivatives. ACS Chem Biol 2020; 15:1141-1147. [PMID: 32091869 DOI: 10.1021/acschembio.9b01009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The discovery of specific microbiota metabolite mechanisms has begun to motivate new therapeutic approaches. Inspired by our mechanistic studies of microbiota-derived short chain fatty acid (SCFA) acylation of bacterial virulence factors, here we explored covalent protein acylation therapeutics as potential anti-infectives. For these studies, we focused on acetyl-salicylic acid, aspirin, and discovered that SCFA analogues such as butyryl-salicylic acid showed significantly improved anti-infective activity against Salmonella Typhimurium. Structure-activity studies showed that the ester functionality of butyryl-salicylic acid was crucial and associated with the acylation of key bacterial virulence factors and metabolic enzymes, which are important for Salmonella infection of host cells and bacterial growth. Beyond the Gram-negative bacterial pathogens, butyryl-salicylic acid also showed better antibacterial activity compared to aspirin against Clostridioides difficile, a clinically challenging Gram-positive bacterial pathogen. Notably, coadministration of butyryl-salicylic acid, but not aspirin, effectively attenuated Salmonella pathogenesis in vivo. This study highlights how the analysis of microbiota metabolite mechanisms may inspire the repurposing and development of new anti-infective agents.
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Affiliation(s)
- Xinglin Yang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Emily R. Forster
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, United States
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, United States
| | - Narek Darabedian
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Alexander T. Kim
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Matthew R. Pratt
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, United States
| | - Howard C. Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
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25
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Tian Y, Wang S, Shang H, Wang WQ, Wang BQ, Zhang X, Xu XD, Sun GB, Sun XB. The clickable activity-based probe of anti-apoptotic calenduloside E. PHARMACEUTICAL BIOLOGY 2019; 57:133-139. [PMID: 30843752 PMCID: PMC6407588 DOI: 10.1080/13880209.2018.1557699] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/04/2018] [Accepted: 12/04/2018] [Indexed: 05/27/2023]
Abstract
CONTEXT Calenduloside E (CE), one of the primary natural products found in Aralia elata (Miq.) Seem. (Araliaceae), possesses prominent anti-apoptotic potential. A previous study found that one of the anti-apoptotic CE targets is heat shock protein 90 AB1 (Hsp90AB1) by probe CE-P, while the other targets of CE still need to be identified with more efficient probes. OBJECTIVE This study investigates CE analogue (CEA) as one clickable activity-based probe for use in exploring anti-apoptotic CE targets. MATERIALS AND METHODS Pretreatment of HUVECs with CEA (1.25 μM) for 8 hr, followed by ox-LDL stimulation for 24 h. Flow cytometry analysis and JC-1 staining assays were performed The kinetic constant measurements were tested by the Biacore T200, CM5 Sensor Chip which was activated by using sulpho-NHS/EDC. Ligands were dissolved and injected with a concentration of 12.5, 6.25, 3.125, 1.56, 0.78 and 0 μM. RESULTS CEA was confirmed to possess an anti-apoptotic effect. The probable targets of CE/CEA were calculated, and as one of the higher scores proteins (Fit values: 0.88/0.86), Hsp90 properly got our attention. Molecular modelling study showed that both CE and CEA could bind to Hsp90 with the similar interaction, and the docking scores (S value) were -7.61 and -7.33. SPR assay provided more evidence to prove that CEA can interact with Hsp90 with the KD value 11.7 µM. DISCUSSION AND CONCLUSIONS Our results suggest that clickable probe CEA could alleviate ox-LDL induced apoptosis by a similar mechanism of anti-apoptotic CE, and afforded the possibility of identifying additional anti-apoptotic targets of CE.
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Affiliation(s)
- Yu Tian
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources, Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Efficacy Evaluation of Chinese Medicine against Glycolipid Metabolic Disorders, State Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Zhong guan cun Open Laboratory of the Research and Development of Natural Medicine and Health Products, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of new drug discovery based on Classic Chinese Academy of Medical Sciences
| | - Shan Wang
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources, Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Efficacy Evaluation of Chinese Medicine against Glycolipid Metabolic Disorders, State Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Zhong guan cun Open Laboratory of the Research and Development of Natural Medicine and Health Products, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of new drug discovery based on Classic Chinese Academy of Medical Sciences
| | - Hai Shang
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources, Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Efficacy Evaluation of Chinese Medicine against Glycolipid Metabolic Disorders, State Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Zhong guan cun Open Laboratory of the Research and Development of Natural Medicine and Health Products, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of new drug discovery based on Classic Chinese Academy of Medical Sciences
| | - Wen-Qian Wang
- Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Bao-Qi Wang
- Center of Research and Development on Life Sciences and Environment Sciences, Harbin University of Commerce, Harbin, China
| | - Xi Zhang
- Center of Research and Development on Life Sciences and Environment Sciences, Harbin University of Commerce, Harbin, China
| | - Xu-Dong Xu
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources, Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Efficacy Evaluation of Chinese Medicine against Glycolipid Metabolic Disorders, State Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Zhong guan cun Open Laboratory of the Research and Development of Natural Medicine and Health Products, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of new drug discovery based on Classic Chinese Academy of Medical Sciences
| | - Gui-Bo Sun
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources, Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Efficacy Evaluation of Chinese Medicine against Glycolipid Metabolic Disorders, State Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Zhong guan cun Open Laboratory of the Research and Development of Natural Medicine and Health Products, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of new drug discovery based on Classic Chinese Academy of Medical Sciences
| | - Xiao-Bo Sun
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources, Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Efficacy Evaluation of Chinese Medicine against Glycolipid Metabolic Disorders, State Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Zhong guan cun Open Laboratory of the Research and Development of Natural Medicine and Health Products, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of new drug discovery based on Classic Chinese Academy of Medical Sciences
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26
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Rabalski AJ, Bogdan AR, Baranczak A. Evaluation of Chemically-Cleavable Linkers for Quantitative Mapping of Small Molecule-Cysteinome Reactivity. ACS Chem Biol 2019; 14:1940-1950. [PMID: 31430117 DOI: 10.1021/acschembio.9b00424] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Numerous reagents have been developed to enable chemical proteomic analysis of small molecule-protein interactomes. However, the performance of these reagents has not been systematically evaluated and compared. Herein, we report our efforts to conduct a parallel assessment of two widely used chemically cleavable linkers equipped with dialkoxydiphenylsilane (DADPS linker) and azobenzene (AZO linker) moieties. Profiling a cellular cysteinome using the iodoacetamide alkyne probe demonstrated a significant discrepancy between the experimental results obtained through the application of each of the reagents. To better understand the source of observed discrepancy, we evaluated the key sample preparation steps. We also performed a mass tolerant database search strategy using MSFragger software. This resulted in identifying a previously unreported artifactual modification on the residual mass of the azobenzene linker. Furthermore, we conducted a comparative analysis of enrichment modes using both cleavable linkers. This effort determined that enrichment of proteolytic digests yielded a far greater number of identified cysteine residues than the enrichment conducted prior to protein digest. Inspired by recent studies where multiplexed quantitative labeling strategies were applied to cleavable biotin linkers, we combined this further optimized protocol using the DADPS cleavable linker with tandem mass tag (TMT) labeling to profile the FDA-approved covalent EGFR kinase inhibitor dacomitinib against the cysteinome of an epidermoid cancer cell line. Our analysis resulted in the detection and quantification of over 10,000 unique cysteine residues, a nearly 3-fold increase over previous studies that used cleavable biotin linkers for enrichment. Critically, cysteine residues corresponding to proteins directly as well as indirectly modulated by dacomitinib treatment were identified. Overall, our study suggests that the dialkoxydiphenylsilane linker could be broadly applied wherever chemically cleavable linkers are required for chemical proteomic characterization of cellular proteomes.
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Affiliation(s)
- Adam J. Rabalski
- Drug Discovery Science & Technology, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064-6101, United States
| | - Andrew R. Bogdan
- Drug Discovery Science & Technology, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064-6101, United States
| | - Aleksandra Baranczak
- Drug Discovery Science & Technology, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064-6101, United States
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27
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Kanikarla-Marie P, Kopetz S, Hawk ET, Millward SW, Sood AK, Gresele P, Overman M, Honn K, Menter DG. Bioactive lipid metabolism in platelet "first responder" and cancer biology. Cancer Metastasis Rev 2019; 37:439-454. [PMID: 30112590 DOI: 10.1007/s10555-018-9755-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Platelets can serve as "first responders" in cancer and metastasis. This is partly due to bioactive lipid metabolism that drives both platelet and cancer biology. The two primary eicosanoid metabolites that maintain platelet rapid response homeostasis are prostacyclin made by endothelial cells that inhibits platelet function, which is counterbalanced by thromboxane produced by platelets during activation, aggregation, and platelet recruitment. Both of these arachidonic acid metabolites are inherently unstable due to their chemical structure. Tumor cells by contrast predominantly make more chemically stable prostaglandin E2, which is the primary bioactive lipid associated with inflammation and oncogenesis. Pharmacological, clinical, and epidemiologic studies demonstrate that non-steroidal anti-inflammatory drugs (NSAIDs), which target cyclooxygenases, can help prevent cancer. Much of the molecular and biological impact of these drugs is generally accepted in the field. Cyclooxygenases catalyze the rate-limiting production of substrate used by all synthase molecules, including those that produce prostaglandins along with prostacyclin and thromboxane. Additional eicosanoid metabolites include lipoxygenases, leukotrienes, and resolvins that can also influence platelets, inflammation, and carcinogenesis. Our knowledge base and technology are now progressing toward identifying newer molecular and cellular interactions that are leading to revealing additional targets. This review endeavors to summarize new developments in the field.
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Affiliation(s)
- Preeti Kanikarla-Marie
- Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Scott Kopetz
- Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Ernest T Hawk
- Office of the Vice President Cancer Prevention and Population Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Steven W Millward
- Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Anil K Sood
- Gynocologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA.,Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Paolo Gresele
- Department of Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Via E. Dal Pozzo, 06126, Perugia, Italy
| | - Michael Overman
- Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Kenneth Honn
- Bioactive Lipids Research Program, Department of Pathology, Wayne State University, 5101 Cass Ave. 430 Chemistry, Detroit, MI, 48202, USA.,Department of Pathology, Wayne State University School of Medicine, 431 Chemistry Bldg, Detroit, MI, 48202, USA.,Cancer Biology Division, Wayne State University School of Medicine, 431 Chemistry Bldg, Detroit, MI, 48202, USA.,Department of Gastrointestinal Medical Oncology, M. D. Anderson Cancer Center, 1515 Holcombe Boulevard--Unit 0426, Houston, TX, 77030, USA
| | - David G Menter
- Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA.
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28
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Zacharias NM, Ornelas A, Lee J, Hu J, Davis JS, Uddin N, Pudakalakatti S, Menter DG, Karam JA, Wood CG, Hawk ET, Kopetz S, Vilar E, Bhattacharya PK, Millward SW. Real‐Time Interrogation of Aspirin Reactivity, Biochemistry, and Biodistribution by Hyperpolarized Magnetic Resonance Spectroscopy. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Niki M. Zacharias
- Department of Cancer Systems Imaging The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd. Houston TX 77030 USA
- Department of Urology The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd. Houston TX 77030 USA
| | - Argentina Ornelas
- Department of Cancer Systems Imaging The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd. Houston TX 77030 USA
| | - Jaehyuk Lee
- Department of Cancer Systems Imaging The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd. Houston TX 77030 USA
| | - Jingzhe Hu
- Department of Cancer Systems Imaging The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd. Houston TX 77030 USA
| | - Jennifer S. Davis
- Department of Epidemiology The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd. Houston TX 77030 USA
| | - Nasir Uddin
- Department of Cancer Systems Imaging The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd. Houston TX 77030 USA
| | - Shivanand Pudakalakatti
- Department of Cancer Systems Imaging The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd. Houston TX 77030 USA
| | - David G. Menter
- Department of Gastrointestinal Medical Oncology The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd. Houston TX 77030 USA
| | - Jose A. Karam
- Department of Urology The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd. Houston TX 77030 USA
| | - Christopher G. Wood
- Department of Urology The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd. Houston TX 77030 USA
| | - Ernest T. Hawk
- Department of Clinical Cancer Prevention The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd. Houston TX 77030 USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd. Houston TX 77030 USA
| | - Eduardo Vilar
- Department of Gastrointestinal Medical Oncology The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd. Houston TX 77030 USA
- Department of Clinical Cancer Prevention The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd. Houston TX 77030 USA
| | - Pratip K. Bhattacharya
- Department of Cancer Systems Imaging The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd. Houston TX 77030 USA
| | - Steven W. Millward
- Department of Cancer Systems Imaging The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd. Houston TX 77030 USA
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29
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Zacharias NM, Ornelas A, Lee J, Hu J, Davis JS, Uddin N, Pudakalakatti S, Menter DG, Karam JA, Wood CG, Hawk ET, Kopetz S, Vilar E, Bhattacharya PK, Millward SW. Real-Time Interrogation of Aspirin Reactivity, Biochemistry, and Biodistribution by Hyperpolarized Magnetic Resonance Spectroscopy. Angew Chem Int Ed Engl 2019; 58:4179-4183. [PMID: 30680862 PMCID: PMC6467058 DOI: 10.1002/anie.201812759] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/21/2019] [Indexed: 12/21/2022]
Abstract
Hyperpolarized magnetic resonance spectroscopy enables quantitative, non-radioactive, real-time measurement of imaging probe biodistribution and metabolism in vivo. Here, we investigate and report on the development and characterization of hyperpolarized acetylsalicylic acid (aspirin) and its use as a nuclear magnetic resonance (NMR) probe. Aspirin derivatives were synthesized with single- and double-13 C labels and hyperpolarized by dynamic nuclear polarization with 4.7 % and 3 % polarization, respectively. The longitudinal relaxation constants (T1 ) for the labeled acetyl and carboxyl carbonyls were approximately 30 seconds, supporting in vivo imaging and spectroscopy applications. In vitro hydrolysis, transacetylation, and albumin binding of hyperpolarized aspirin were readily monitored in real time by 13 C-NMR spectroscopy. Hyperpolarized, double-labeled aspirin was well tolerated in mice and could be observed by both 13 C-MR imaging and 13 C-NMR spectroscopy in vivo.
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Affiliation(s)
- Niki M. Zacharias
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030 (USA)
| | - Argentina Ornelas
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030 (USA)
| | - Jaehyuk Lee
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030 (USA)
| | - Jingzhe Hu
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030 (USA)
| | - Jennifer S. Davis
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030 (USA)
| | - Nasir Uddin
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030 (USA)
| | - Shivanand Pudakalakatti
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030 (USA)
| | - David G. Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030 (USA)
| | - Jose A. Karam
- Department of Urology, The University of Texas MD Anderson Cancer, 1515 Holcombe Blvd., Houston, TX 77030 (USA)
| | - Christopher G. Wood
- Department of Urology, The University of Texas MD Anderson Cancer, 1515 Holcombe Blvd., Houston, TX 77030 (USA)
| | - Ernest T. Hawk
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030 (USA)
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030 (USA)
| | - Eduardo Vilar
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030 (USA);Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030 (USA)
| | - Pratip K. Bhattacharya
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030 (USA)
| | - Steven W. Millward
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030 (USA)
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Qin Y, Liu HJ, Li M, Zhai DH, Tang YH, Yang L, Qiao KL, Yang JH, Zhong WL, Zhang Q, Liu YR, Yang G, Sun T, Yang C. Salidroside improves the hypoxic tumor microenvironment and reverses the drug resistance of platinum drugs via HIF-1α signaling pathway. EBioMedicine 2018; 38:25-36. [PMID: 30396856 PMCID: PMC6306459 DOI: 10.1016/j.ebiom.2018.10.069] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/27/2018] [Accepted: 10/28/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Hypoxia commonly occurs in solid tumors. The hypoxia in the center of solid tumors considerably decreases the chemosensitivity of tumor cells and induces epithelial-mesenchymal transition (EMT) as well as drug resistance of antitumor drugs. METHODS Here, the effects of salidroside (Sal) combined with platinum drugs on human hepatocellular carcinoma were examined in vitro and in vivo. We investigated the antitumor effects of Sal by inhibiting the drug resistance and explained its mechanism in inhibiting tumor growth. FINDINGS The results showed that Sal co-administration reverses the drug resistance of platinum drugs and suppressed metastasis induced by the hypoxic tumor microenvironment. Sal promoted the degradation of HIF-1α. In conclusion, Sal significantly increased the sensitivity to platinum drugs and inhibited hypoxia-induced EMT in hepatocellular carcinoma (HCC) through inhibiting HIF-1α signaling pathway. INTERPRETATION Therefore, Sal may be an effective platinum drug sensitizer that can improve the chemotherapeutic efficacy in patients with HCC.
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Affiliation(s)
- Yuan Qin
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Hui-Juan Liu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; College of Life Sciences, Nankai University, Tianjin, China
| | - Meng Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Deng-Hui Zhai
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Yuan-Hao Tang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Lan Yang
- Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Kai-Liang Qiao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Jia-Huan Yang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Wei-Long Zhong
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Qiang Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Yan-Rong Liu
- Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Guang Yang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China.
| | - Tao Sun
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China.
| | - Cheng Yang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China.
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31
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Qin Y, Liu HJ, Li M, Zhai DH, Tang YH, Yang L, Qiao KL, Yang JH, Zhong WL, Zhang Q, Liu YR, Yang G, Sun T, Yang C. Salidroside improves the hypoxic tumor microenvironment and reverses the drug resistance of platinum drugs via HIF-1α signaling pathway. EBioMedicine 2018. [PMID: 30396856 DOI: 10.1016/j.ebiom] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Hypoxia commonly occurs in solid tumors. The hypoxia in the center of solid tumors considerably decreases the chemosensitivity of tumor cells and induces epithelial-mesenchymal transition (EMT) as well as drug resistance of antitumor drugs. METHODS Here, the effects of salidroside (Sal) combined with platinum drugs on human hepatocellular carcinoma were examined in vitro and in vivo. We investigated the antitumor effects of Sal by inhibiting the drug resistance and explained its mechanism in inhibiting tumor growth. FINDINGS The results showed that Sal co-administration reverses the drug resistance of platinum drugs and suppressed metastasis induced by the hypoxic tumor microenvironment. Sal promoted the degradation of HIF-1α. In conclusion, Sal significantly increased the sensitivity to platinum drugs and inhibited hypoxia-induced EMT in hepatocellular carcinoma (HCC) through inhibiting HIF-1α signaling pathway. INTERPRETATION Therefore, Sal may be an effective platinum drug sensitizer that can improve the chemotherapeutic efficacy in patients with HCC.
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Affiliation(s)
- Yuan Qin
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Hui-Juan Liu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; College of Life Sciences, Nankai University, Tianjin, China
| | - Meng Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Deng-Hui Zhai
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Yuan-Hao Tang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Lan Yang
- Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Kai-Liang Qiao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Jia-Huan Yang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Wei-Long Zhong
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Qiang Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Yan-Rong Liu
- Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Guang Yang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China.
| | - Tao Sun
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China.
| | - Cheng Yang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China.
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Chemoproteomics reveals baicalin activates hepatic CPT1 to ameliorate diet-induced obesity and hepatic steatosis. Proc Natl Acad Sci U S A 2018; 115:E5896-E5905. [PMID: 29891721 DOI: 10.1073/pnas.1801745115] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Obesity and related metabolic diseases are becoming worldwide epidemics that lead to increased death rates and heavy health care costs. Effective treatment options have not been found yet. Here, based on the observation that baicalin, a flavonoid from the herbal medicine Scutellaria baicalensis, has unique antisteatosis activity, we performed quantitative chemoproteomic profiling and identified carnitine palmitoyltransferase 1 (CPT1), the controlling enzyme for fatty acid oxidation, as the key target of baicalin. The flavonoid directly activated hepatic CPT1 with isoform selectivity to accelerate the lipid influx into mitochondria for oxidation. Chronic treatment of baicalin ameliorated diet-induced obesity (DIO) and hepatic steatosis and led to systemic improvement of other metabolic disorders. Disruption of the predicted binding site of baicalin on CPT1 completely abolished the beneficial effect of the flavonoid. Our discovery of baicalin as an allosteric CPT1 activator opens new opportunities for pharmacological treatment of DIO and associated sequelae.
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33
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Ornelas A, Zacharias-Millward N, Menter DG, Davis JS, Lichtenberger L, Hawke D, Hawk E, Vilar E, Bhattacharya P, Millward S. Beyond COX-1: the effects of aspirin on platelet biology and potential mechanisms of chemoprevention. Cancer Metastasis Rev 2018; 36:289-303. [PMID: 28762014 PMCID: PMC5557878 DOI: 10.1007/s10555-017-9675-z] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
After more than a century, aspirin remains one of the most commonly used drugs in western medicine. Although mainly used for its anti-thrombotic, anti-pyretic, and analgesic properties, a multitude of clinical studies have provided convincing evidence that regular, low-dose aspirin use dramatically lowers the risk of cancer. These observations coincide with recent studies showing a functional relationship between platelets and tumors, suggesting that aspirin's chemopreventive properties may result, in part, from direct modulation of platelet biology and biochemistry. Here, we present a review of the biochemistry and pharmacology of aspirin with particular emphasis on its cyclooxygenase-dependent and cyclooxygenase-independent effects in platelets. We also correlate the results of proteomic-based studies of aspirin acetylation in eukaryotic cells with recent developments in platelet proteomics to identify non-cyclooxygenase targets of aspirin-mediated acetylation in platelets that may play a role in its chemopreventive mechanism.
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Affiliation(s)
- Argentina Ornelas
- Department of Cancer Systems Imaging, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Niki Zacharias-Millward
- Department of Cancer Systems Imaging, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David G Menter
- Department of Gastrointestinal (GI) Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer S Davis
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lenard Lichtenberger
- McGovern Medical School, Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - David Hawke
- Department of Systems Biology, Proteomics and Metabolomics Facility, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ernest Hawk
- Department of Clinical Cancer Prevention, Division of OVP, Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, Division of OVP, Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pratip Bhattacharya
- Department of Cancer Systems Imaging, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Steven Millward
- Department of Cancer Systems Imaging, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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34
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Baroni MD, Colombo S, Martegani E. Antagonism between salicylate and the cAMP signal controls yeast cell survival and growth recovery from quiescence. MICROBIAL CELL (GRAZ, AUSTRIA) 2018; 5:344-356. [PMID: 29992130 PMCID: PMC6035838 DOI: 10.15698/mic2018.07.640] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 03/14/2018] [Indexed: 12/18/2022]
Abstract
Aspirin and its main metabolite salicylate are promising molecules in preventing cancer and metabolic diseases. S. cerevisiae cells have been used to study some of their effects: (i) salicylate induces the reversible inhibition of both glucose transport and the biosyntheses of glucose-derived sugar phosphates, (ii) Aspirin/salicylate causes apoptosis associated with superoxide radical accumulation or early cell necrosis in MnSOD-deficient cells growing in ethanol or in glucose, respectively. So, treatment with (acetyl)-salicylic acid can alter the yeast metabolism and is associated with cell death. We describe here the dramatic effects of salicylate on cellular control of the exit from a quiescence state. The growth recovery of long-term stationary phase cells was strongly inhibited in the presence of salicylate, to a degree proportional to the drug concentration. At high salicylate concentration, growth reactivation was completely repressed and associated with a dramatic loss of cell viability. Strikingly, both of these phenotypes were fully suppressed by increasing the cAMP signal without any variation of the exponential growth rate. Upon nutrient exhaustion, salicylate induced a premature lethal cell cycle arrest in the budded-G2/M phase that cannot be suppressed by PKA activation. We discuss how the dramatic antagonism between cAMP and salicylate could be conserved and impinge common targets in yeast and humans. Targeting quiescence of cancer cells with stem-like properties and their growth recovery from dormancy are major challenges in cancer therapy. If mechanisms underlying cAMP-salicylate antagonism will be defined in our model, this might have significant therapeutic implications.
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Affiliation(s)
| | - Sonia Colombo
- Dipartimento di Biotecnologie e Bioscienze, Università Milano Bicocca, 20126 Milano, Italy
| | - Enzo Martegani
- Dipartimento di Biotecnologie e Bioscienze, Università Milano Bicocca, 20126 Milano, Italy
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35
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Hewings DS, Heideker J, Ma TP, AhYoung AP, El Oualid F, Amore A, Costakes GT, Kirchhofer D, Brasher B, Pillow T, Popovych N, Maurer T, Schwerdtfeger C, Forrest WF, Yu K, Flygare J, Bogyo M, Wertz IE. Reactive-site-centric chemoproteomics identifies a distinct class of deubiquitinase enzymes. Nat Commun 2018; 9:1162. [PMID: 29563501 PMCID: PMC5862848 DOI: 10.1038/s41467-018-03511-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/20/2018] [Indexed: 11/25/2022] Open
Abstract
Activity-based probes (ABPs) are widely used to monitor the activity of enzyme families in biological systems. Inferring enzyme activity from probe reactivity requires that the probe reacts with the enzyme at its active site; however, probe-labeling sites are rarely verified. Here we present an enhanced chemoproteomic approach to evaluate the activity and probe reactivity of deubiquitinase enzymes, using bioorthogonally tagged ABPs and a sequential on-bead digestion protocol to enhance the identification of probe-labeling sites. We confirm probe labeling of deubiquitinase catalytic Cys residues and reveal unexpected labeling of deubiquitinases on non-catalytic Cys residues and of non-deubiquitinase proteins. In doing so, we identify ZUFSP (ZUP1) as a previously unannotated deubiquitinase with high selectivity toward cleaving K63-linked chains. ZUFSP interacts with and modulates ubiquitination of the replication protein A (RPA) complex. Our reactive-site-centric chemoproteomics method is broadly applicable for identifying the reaction sites of covalent molecules, which may expand our understanding of enzymatic mechanisms. Deubiquitinases are proteases that cleave after the C-terminus of ubiquitin to hydrolyze ubiquitin chains and cleave ubiquitin from substrates. Here the authors describe a reactive-site-centric chemoproteomics approach to studying deubiquitinase activity, and expand the repertoire of known deubiquitinases.
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Affiliation(s)
- David S Hewings
- Discovery Oncology, Genentech, South San Francisco, California, 94080, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA.,Discovery Chemistry, Genentech, South San Francisco, California, 94080, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Johanna Heideker
- Discovery Oncology, Genentech, South San Francisco, California, 94080, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA
| | - Taylur P Ma
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, 94080, USA
| | - Andrew P AhYoung
- Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA
| | - Farid El Oualid
- UbiQ Bio BV, Science Park 408, 1098 XH, Amsterdam, The Netherlands
| | - Alessia Amore
- UbiQ Bio BV, Science Park 408, 1098 XH, Amsterdam, The Netherlands
| | - Gregory T Costakes
- Boston Biochem Inc., 840 Memorial Drive, Cambridge, Massachussetts, 02139, USA
| | - Daniel Kirchhofer
- Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA
| | - Bradley Brasher
- Boston Biochem Inc., 840 Memorial Drive, Cambridge, Massachussetts, 02139, USA
| | - Thomas Pillow
- Discovery Chemistry, Genentech, South San Francisco, California, 94080, USA
| | - Nataliya Popovych
- Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA
| | - Till Maurer
- Structural Biology, Genentech, South San Francisco, California, 94080, USA
| | | | - William F Forrest
- Bioinformatics, Genentech, South San Francisco, California, 94080, USA
| | - Kebing Yu
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, 94080, USA
| | - John Flygare
- Discovery Chemistry, Genentech, South San Francisco, California, 94080, USA.,Merck, 630 Gateway Boulevard, South San Francisco, California, 94080, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Ingrid E Wertz
- Discovery Oncology, Genentech, South San Francisco, California, 94080, USA. .,Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA.
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36
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Huang Z, Fang W, Liu W, Wang L, Liu B, Liu S, Liu S. Aspirin induces Beclin-1-dependent autophagy of human hepatocellular carcinoma cell. Eur J Pharmacol 2018; 823:58-64. [PMID: 29408091 DOI: 10.1016/j.ejphar.2018.01.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 01/20/2018] [Accepted: 01/23/2018] [Indexed: 12/11/2022]
Abstract
Aspirin not only reduces the incidence of hepatocellular carcinoma (HCC) but also plays a synergistic role with chemotherapy for HCC treatment. However, the underlying mechanisms remain incompletely elucidated. Given that autophagy triggers cancer cell death, the present study examined the autophagic effect of aspirin on HCC cells. Results showed that aspirin increased LC3II/LC3I ratio, decreased p62 expression, and enhanced autophagic flux (autophagosome and autolysosome puncta) in Hep3B, HepG2, or SMMC-7721 cells, reflecting the autophagy of HCC cells. The autophagic effects of aspirin depended on Beclin-1 expression. Aspirin disrupted the interaction between Bcl-2 and Beclin-1. In addition to activating the AMP-activated protein kinase, c-Jun N-terminal kinase, and Glycogen synthase kinase-3 pathways, aspirin inhibited the mammalian-target-of rapamycin-S6K1/4E-BP1 signaling. Aspirin induced autophagy of HCC cell. This study contributes to understanding the chemoprotective and inhibitory effects of aspirin on HCC development.
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Affiliation(s)
- Zhenjun Huang
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, PR China; Experiment Center, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510700, PR China
| | - Weilun Fang
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, PR China
| | - Weihua Liu
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, PR China
| | - Li Wang
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, PR China
| | - Bin Liu
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, PR China
| | - Shiming Liu
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, PR China
| | - Shaojun Liu
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, PR China.
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37
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Beclin 1 acetylation impairs the anticancer effect of aspirin in colorectal cancer cells. Oncotarget 2017; 8:74781-74790. [PMID: 29088823 PMCID: PMC5650378 DOI: 10.18632/oncotarget.20367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/25/2017] [Indexed: 12/21/2022] Open
Abstract
Regular use of aspirin can reduce cancer incidence, recurrence, metastasis and cancer-related mortality. Aspirin suppresses proliferation and induces apoptosis and autophagy in colorectal cancer cells, but the precise mechanism is not clear. In this study, we demonstrated that aspirin induced autophagosome formation in colorectal cancer cells, but autophagic degradation was blocked through aspirin-mediated Beclin 1 acetylation. Blocked autophagic degradation weakened aspirin-induced cell death. Collectively, our findings indicate the dual roles of aspirin on autophagy, and demonstrate a new mechanism by which Beclin 1 acetylation impairs the anticancer effect of aspirin in colorectal cancer cells.
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38
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Wong YK, Zhang J, Hua ZC, Lin Q, Shen HM, Wang J. Recent advances in quantitative and chemical proteomics for autophagy studies. Autophagy 2017; 13:1472-1486. [PMID: 28820289 DOI: 10.1080/15548627.2017.1313944] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Macroautophagy/autophagy is an evolutionarily well-conserved cellular degradative process with important biological functions that is closely implicated in health and disease. In recent years, quantitative mass spectrometry-based proteomics and chemical proteomics have emerged as important tools for the study of autophagy, through large-scale unbiased analysis of the proteome or through highly specific and accurate analysis of individual proteins of interest. At present, a variety of approaches have been successfully applied, including (i) expression and interaction proteomics for the study of protein post-translational modifications, (ii) investigating spatio-temporal dynamics of protein synthesis and degradation, and (iii) direct determination of protein activity and profiling molecular targets in the autophagic process. In this review, we attempted to provide an overview of principles and techniques relevant to the application of quantitative and chemical proteomics methods to autophagy, and outline the current landscape as well as future outlook of these methods in autophagy research.
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Affiliation(s)
- Yin-Kwan Wong
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore
| | - Jianbin Zhang
- b Department of Oncology, Clinical Research Institute , Zhejiang Provincial People's Hospital , Hangzhou , China
| | - Zi-Chun Hua
- c Changzhou High-Tech Research Institute of Nanjing University and the State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences , Nanjing University , Nanjing , China
| | - Qingsong Lin
- d Department of Biological Sciences , National University of Singapore , Singapore
| | - Han-Ming Shen
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore.,e NUS Graduate School for Integrative Sciences and Engineering , National University of Singapore , Singapore
| | - Jigang Wang
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore.,c Changzhou High-Tech Research Institute of Nanjing University and the State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences , Nanjing University , Nanjing , China
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39
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Chen X, Wong YK, Lim TK, Lim WH, Lin Q, Wang J, Hua Z. Artesunate Activates the Intrinsic Apoptosis of HCT116 Cells through the Suppression of Fatty Acid Synthesis and the NF-κB Pathway. Molecules 2017; 22:E1272. [PMID: 28786914 PMCID: PMC6152404 DOI: 10.3390/molecules22081272] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 07/27/2017] [Accepted: 07/27/2017] [Indexed: 11/16/2022] Open
Abstract
The artemisinin compounds, which are well-known for their potent therapeutic antimalarial activity, possess in vivo and in vitro antitumor effects. Although the anticancer effect of artemisinin compounds has been extensively reported, the precise mechanisms underlying its cytotoxicity remain under intensive study. In the present study, a high-throughput quantitative proteomics approach was applied to identify differentially expressed proteins of HCT116 colorectal cancer cell line with artesunate (ART) treatment. Through Ingenuity Pathway Analysis, we discovered that the top-ranked ART-regulated biological pathways are abrogation of fatty acid biosynthetic pathway and mitochondrial dysfunction. Subsequent assays showed that ART inhibits HCT116 cell proliferation through suppressing the fatty acid biosynthetic pathway and activating the mitochondrial apoptosis pathway. In addition, ART also regulates several proteins that are involved in NF-κB pathway, and our subsequent assays showed that ART suppresses the NF-κB pathway. These proteomic findings will contribute to improving our understanding of the underlying molecular mechanisms of ART for its therapeutic cytotoxic effect towards cancer cells.
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Affiliation(s)
- Xiao Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
| | - Yin Kwan Wong
- Department of Biological Science, National University of Singapore, Singapore 117543, Singapore.
| | - Teck Kwang Lim
- Department of Biological Science, National University of Singapore, Singapore 117543, Singapore.
| | - Wei Hou Lim
- Department of Biological Science, National University of Singapore, Singapore 117543, Singapore.
| | - Qingsong Lin
- Department of Biological Science, National University of Singapore, Singapore 117543, Singapore.
| | - Jigang Wang
- Department of Biological Science, National University of Singapore, Singapore 117543, Singapore.
- Changzhou High-Tech Research Institute of Nanjing University, Institute of Biotechnology, Jiangsu Industrial Technology Research Institute and Jiangsu TargetPharma Laboratories Inc., Changzhou 213164, China.
| | - Zichun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
- Changzhou High-Tech Research Institute of Nanjing University, Institute of Biotechnology, Jiangsu Industrial Technology Research Institute and Jiangsu TargetPharma Laboratories Inc., Changzhou 213164, China.
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40
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Chen J, Stark LA. Aspirin Prevention of Colorectal Cancer: Focus on NF-κB Signalling and the Nucleolus. Biomedicines 2017; 5:biomedicines5030043. [PMID: 28718829 PMCID: PMC5618301 DOI: 10.3390/biomedicines5030043] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/07/2017] [Accepted: 07/13/2017] [Indexed: 02/06/2023] Open
Abstract
Overwhelming evidence indicates that aspirin and related non-steroidal anti-inflammatory drugs (NSAIDs) have anti-tumour activity and the potential to prevent cancer, particularly colorectal cancer. However, the mechanisms underlying this effect remain hypothetical. Dysregulation of the nuclear factor-kappaB (NF-κB) transcription factor is a common event in many cancer types which contributes to tumour initiation and progression by driving expression of pro-proliferative/anti-apoptotic genes. In this review, we will focus on the current knowledge regarding NSAID effects on the NF-κB signalling pathway in pre-cancerous and cancerous lesions, and the evidence that these effects contribute to the anti-tumour activity of the agents. The nuclear organelle, the nucleolus, is emerging as a central regulator of transcription factor activity and cell growth and death. Nucleolar function is dysregulated in the majority of cancers which promotes cancer growth through direct and indirect mechanisms. Hence, this organelle is emerging as a promising target for novel therapeutic agents. Here, we will also discuss evidence for crosstalk between the NF-κB pathway and nucleoli, the role that this cross-talk has in the anti-tumour effects of NSAIDs and ways forward to exploit this crosstalk for therapeutic purpose.
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Affiliation(s)
- Jingyu Chen
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Rd., Edinburgh, Scotland EH4 2XU, UK.
| | - Lesley A Stark
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Rd., Edinburgh, Scotland EH4 2XU, UK.
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41
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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: 256] [Impact Index Per Article: 36.6] [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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42
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Isgut M, Rao M, Yang C, Subrahmanyam V, Rida PCG, Aneja R. Application of Combination High-Throughput Phenotypic Screening and Target Identification Methods for the Discovery of Natural Product-Based Combination Drugs. Med Res Rev 2017; 38:504-524. [DOI: 10.1002/med.21444] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 02/06/2017] [Accepted: 03/01/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Monica Isgut
- Department of Biology; Georgia State University; Atlanta GA 30303
| | - Mukkavilli Rao
- Department of Biology; Georgia State University; Atlanta GA 30303
| | - Chunhua Yang
- Department of Biology; Georgia State University; Atlanta GA 30303
| | | | - Padmashree C. G. Rida
- Department of Biology; Georgia State University; Atlanta GA 30303
- Novazoi Theranostics; Rolling Hills Estates CA 90274
| | - Ritu Aneja
- Department of Biology; Georgia State University; Atlanta GA 30303
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43
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Thai VC, Lim TK, Le KPU, Lin Q, Nguyen TTH. iTRAQ-based proteome analysis of fluoroquinolone-resistant Staphylococcus aureus. J Glob Antimicrob Resist 2017; 8:82-89. [DOI: 10.1016/j.jgar.2016.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/25/2016] [Accepted: 11/05/2016] [Indexed: 12/12/2022] Open
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44
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Tatham MH, Cole C, Scullion P, Wilkie R, Westwood NJ, Stark LA, Hay RT. A Proteomic Approach to Analyze the Aspirin-mediated Lysine Acetylome. Mol Cell Proteomics 2017; 16:310-326. [PMID: 27913581 PMCID: PMC5294217 DOI: 10.1074/mcp.o116.065219] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 11/23/2016] [Indexed: 12/14/2022] Open
Abstract
Aspirin, or acetylsalicylic acid is widely used to control pain, inflammation and fever. Important to this function is its ability to irreversibly acetylate cyclooxygenases at active site serines. Aspirin has the potential to acetylate other amino acid side-chains, leading to the possibility that aspirin-mediated lysine acetylation could explain some of its as-yet unexplained drug actions or side-effects. Using isotopically labeled aspirin-d3, in combination with acetylated lysine purification and LC-MS/MS, we identified over 12000 sites of lysine acetylation from cultured human cells. Although aspirin amplifies endogenous acetylation signals at the majority of detectable endogenous sites, cells tolerate aspirin mediated acetylation very well unless cellular deacetylases are inhibited. Although most endogenous acetylations are amplified by orders of magnitude, lysine acetylation site occupancies remain very low even after high doses of aspirin. This work shows that while aspirin has enormous potential to alter protein function, in the majority of cases aspirin-mediated acetylations do not accumulate to levels likely to elicit biological effects. These findings are consistent with an emerging model for cellular acetylation whereby stoichiometry correlates with biological relevance, and deacetylases act to minimize the biological consequences of nonspecific chemical acetylations.
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Affiliation(s)
- Michael H Tatham
- From the ‡Centre for Gene Regulation and Expression, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH. UK
| | - Christian Cole
- §Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH. UK
| | - Paul Scullion
- ¶Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH. UK
| | - Ross Wilkie
- ‖School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, North Haugh, St Andrews, Fife. KY16 9ST. UK
| | - Nicholas J Westwood
- ‖School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, North Haugh, St Andrews, Fife. KY16 9ST. UK
| | - Lesley A Stark
- **Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU UK
| | - Ronald T Hay
- From the ‡Centre for Gene Regulation and Expression, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH. UK;
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45
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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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46
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Tian Y, Wang S, Shang H, Wang M, Sun G, Xu X, Sun X. The proteomic profiling of calenduloside E targets in HUVEC: design, synthesis and application of biotinylated probe BCEA. RSC Adv 2017. [DOI: 10.1039/c6ra25572h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The proteomic profiling of calenduloside E targets was researched by employing the biotinylated probe BCEA of natural product calenduloside E.
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Affiliation(s)
- Yu Tian
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine
- Key Laboratory of efficacy evaluation of Chinese Medicine against glyeolipid metabolism disorder disease, State Administration of Traditional Chinese Medicine
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine
- Ministry of Education, Institute of Medicinal Plant Development
- Chinese Academy of Medical Sciences
| | - Shan Wang
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine
- Key Laboratory of efficacy evaluation of Chinese Medicine against glyeolipid metabolism disorder disease, State Administration of Traditional Chinese Medicine
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine
- Ministry of Education, Institute of Medicinal Plant Development
- Chinese Academy of Medical Sciences
| | - Hai Shang
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine
- Key Laboratory of efficacy evaluation of Chinese Medicine against glyeolipid metabolism disorder disease, State Administration of Traditional Chinese Medicine
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine
- Ministry of Education, Institute of Medicinal Plant Development
- Chinese Academy of Medical Sciences
| | - Min Wang
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine
- Key Laboratory of efficacy evaluation of Chinese Medicine against glyeolipid metabolism disorder disease, State Administration of Traditional Chinese Medicine
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine
- Ministry of Education, Institute of Medicinal Plant Development
- Chinese Academy of Medical Sciences
| | - Guibo Sun
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine
- Key Laboratory of efficacy evaluation of Chinese Medicine against glyeolipid metabolism disorder disease, State Administration of Traditional Chinese Medicine
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine
- Ministry of Education, Institute of Medicinal Plant Development
- Chinese Academy of Medical Sciences
| | - Xudong Xu
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine
- Key Laboratory of efficacy evaluation of Chinese Medicine against glyeolipid metabolism disorder disease, State Administration of Traditional Chinese Medicine
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine
- Ministry of Education, Institute of Medicinal Plant Development
- Chinese Academy of Medical Sciences
| | - Xiaobo Sun
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine
- Key Laboratory of efficacy evaluation of Chinese Medicine against glyeolipid metabolism disorder disease, State Administration of Traditional Chinese Medicine
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine
- Ministry of Education, Institute of Medicinal Plant Development
- Chinese Academy of Medical Sciences
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47
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Zhang J, Wang J, Lee YM, Lim TK, Lin Q, Shen HM. Proteomic Profiling of De Novo Protein Synthesis in Starvation-Induced Autophagy Using Bioorthogonal Noncanonical Amino Acid Tagging. Methods Enzymol 2016; 588:41-59. [PMID: 28237112 DOI: 10.1016/bs.mie.2016.09.075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Autophagy is an intracellular degradation process activated by stress factors such as nutrient starvation to maintain cellular homeostasis. There is emerging evidence demonstrating that de novo protein synthesis is involved in the autophagic process. However, up-to-date characterizing of these de novo proteins is technically difficult. In this chapter, we describe a novel method to identify newly synthesized proteins during starvation-mediated autophagy by bioorthogonal noncanonical amino acid tagging (BONCAT), in conjunction with isobaric tagging for relative and absolute quantification (iTRAQ)-based quantitative proteomics. l-azidohomoalanine (AHA) is an analog of methionine, and it can be readily incorporated into the newly synthesized proteins. The AHA-containing proteins can be enriched with avidin beads after a "click" reaction between alkyne-bearing biotin and the azide moiety of AHA. The enriched proteins are then subjected to iTRAQ™ labeling for protein identification and quantification using liquid chromatography-tandem mass spectrometry (LC-MS/MS). By using this technique, we have successfully profiled more than 700 proteins that are synthesized during starvation-induced autophagy. We believe that this approach is effective in identification of newly synthesized proteins in the process of autophagy and provides useful insights to the molecular mechanisms and biological functions of autophagy.
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Affiliation(s)
- J Zhang
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - J Wang
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; National University of Singapore, Singapore, Singapore; Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research & Technology (SMART), Singapore
| | - Y-M Lee
- National University of Singapore, Singapore, Singapore
| | - T-K Lim
- National University of Singapore, Singapore, Singapore
| | - Q Lin
- National University of Singapore, Singapore, Singapore.
| | - H-M Shen
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore.
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48
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Strmiskova M, Desrochers GF, Shaw TA, Powdrill MH, Lafreniere MA, Pezacki JP. Chemical Methods for Probing Virus-Host Proteomic Interactions. ACS Infect Dis 2016; 2:773-786. [PMID: 27933785 DOI: 10.1021/acsinfecdis.6b00084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Interactions between host and pathogen proteins constitute an important aspect of both infectivity and the host immune response. Different viruses have evolved complex mechanisms to hijack host-cell machinery and metabolic pathways to redirect resources and energy flow toward viral propagation. These interactions are often critical to the virus, and thus understanding these interactions at a molecular level gives rise to opportunities to develop novel antiviral strategies for therapeutic intervention. This review summarizes current advances in chemoproteomic methods for studying these molecular altercations between different viruses and their hosts.
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Affiliation(s)
- Miroslava Strmiskova
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Geneviève F. Desrochers
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Tyler A. Shaw
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Megan H. Powdrill
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Matthew A. Lafreniere
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
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49
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Chuh KN, Batt AR, Pratt MR. Chemical Methods for Encoding and Decoding of Posttranslational Modifications. Cell Chem Biol 2016; 23:86-107. [PMID: 26933738 DOI: 10.1016/j.chembiol.2015.11.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 11/25/2015] [Accepted: 11/25/2015] [Indexed: 12/13/2022]
Abstract
A large array of posttranslational modifications can dramatically change the properties of proteins and influence different aspects of their biological function such as enzymatic activity, binding interactions, and proteostasis. Despite the significant knowledge that has been gained about the function of posttranslational modifications using traditional biological techniques, the analysis of the site-specific effects of a particular modification, the identification of the full complement of modified proteins in the proteome, and the detection of new types of modifications remains challenging. Over the years, chemical methods have contributed significantly in both of these areas of research. This review highlights several posttranslational modifications where chemistry-based approaches have made significant contributions to our ability to both prepare homogeneously modified proteins and identify and characterize particular modifications in complex biological settings. As the number and chemical diversity of documented posttranslational modifications continues to rise, we believe that chemical strategies will be essential to advance the field in years to come.
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Affiliation(s)
- Kelly N Chuh
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Anna R Batt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Matthew R Pratt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
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50
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Roberts AM, Ward CC, Nomura DK. Activity-based protein profiling for mapping and pharmacologically interrogating proteome-wide ligandable hotspots. Curr Opin Biotechnol 2016; 43:25-33. [PMID: 27568596 DOI: 10.1016/j.copbio.2016.08.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/04/2016] [Accepted: 08/11/2016] [Indexed: 11/19/2022]
Abstract
Despite the completion of human genome sequencing efforts nearly 15 years ago that brought with it the promise of genome-based discoveries that would cure human diseases, most protein targets that control human diseases have remained largely untranslated, in-part because they represent difficult protein targets to drug. In addition, many of these protein targets lack screening assays or accessible binding pockets, making the development of small-molecule modulators very challenging. Here, we discuss modern methods for activity-based protein profiling-based chemoproteomic strategies to map 'ligandable' hotspots in proteomes using activity and reactivity-based chemical probes to allow for pharmacological interrogation of these previously difficult targets. We will showcase several recent examples of how these technologies have been used to develop highly selective small-molecule inhibitors against disease-related protein targets.
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Affiliation(s)
- Allison M Roberts
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Carl C Ward
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Daniel K Nomura
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, United States.
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