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Li Y, Lyu J, Wang Y, Ye M, Wang H. Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions. Chem Res Toxicol 2024; 37:1-15. [PMID: 38146056 DOI: 10.1021/acs.chemrestox.3c00282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Adverse health outcomes caused by environmental chemicals are often initiated via their interactions with proteins. Essentially, one environmental chemical may interact with a number of proteins and/or a protein may interact with a multitude of environmental chemicals, forming an intricate interaction network. Omics-wide protein-environmental chemical interaction profiling (PECI) is of prominent importance for comprehensive understanding of these interaction networks, including the toxicity mechanisms of action (MoA), and for providing systematic chemical safety assessment. However, such information remains unknown for most environmental chemicals, partly due to their vast chemical diversity. In recent years, with the continuous efforts afforded, especially in mass spectrometry (MS) based omics technologies, several ligand modification-free methods have been developed, and new attention for systematic PECI profiling was gained. In this Review, we provide a comprehensive overview on these methodologies for the identification of ligand-protein interactions, including affinity interaction-based methods of affinity-driven purification, covalent modification profiling, and activity-based protein profiling (ABPP) in a competitive mode, physicochemical property changes assessment methods of ligand-directed nuclear magnetic resonance (ligand-directed NMR), MS integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS), thermal proteome profiling (TPP), limited proteolysis-coupled mass spectrometry (LiP-MS), stability of proteins from rates of oxidation (SPROX), and several intracellular downstream response characterization methods. We expect that the applications of these ligand modification-free technologies will drive a considerable increase in the number of PECI identified, facilitate unveiling the toxicological mechanisms, and ultimately contribute to systematic health risk assessment of environmental chemicals.
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Affiliation(s)
- Yanan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jiawen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- State Key Laboratory of Medical Proteomics, Beijing, 102206, China
| | - Hailin Wang
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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2
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Belcher BP, Ward CC, Nomura DK. Ligandability of E3 Ligases for Targeted Protein Degradation Applications. Biochemistry 2023; 62:588-600. [PMID: 34473924 PMCID: PMC8928483 DOI: 10.1021/acs.biochem.1c00464] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Targeted protein degradation (TPD) using proteolysis targeting chimeras (PROTACs) and molecular glue degraders has arisen as a powerful therapeutic modality for eliminating disease-causing proteins from cells. PROTACs and molecular glue degraders employ heterobifunctional or monovalent small molecules, respectively, to chemically induce the proximity of target proteins with E3 ubiquitin ligases to ubiquitinate and degrade specific proteins via the proteasome. Whereas TPD is an attractive therapeutic strategy for expanding the druggable proteome, only a relatively small number of E3 ligases out of the >600 E3 ligases encoded by the human genome have been exploited by small molecules for TPD applications. Here we review the existing E3 ligases that have thus far been successfully exploited for TPD and discuss chemoproteomics-enabled covalent screening strategies for discovering new E3 ligase recruiters. We also provide a chemoproteomic map of reactive cysteines within hundreds of E3 ligases that may represent potential ligandable sites that can be pharmacologically interrogated to uncover additional E3 ligase recruiters.
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Affiliation(s)
- Bridget P. Belcher
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720,Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Carl C. Ward
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720,Innovative Genomics Institute, Berkeley, CA 94720 USA,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720,Innovative Genomics Institute, Berkeley, CA 94720 USA,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA,correspondence to
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3
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Honeder SE, Tomin T, Schinagl M, Pfleger R, Hoehlschen J, Darnhofer B, Schittmayer M, Birner‐Gruenberger R. Research Advances Through Activity‐Based Lipid Hydrolase Profiling. Isr J Chem 2023. [DOI: 10.1002/ijch.202200078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sophie Elisabeth Honeder
- Research and Diagnostic Institute of Pathology Medical University of Graz Stiftingtalstraße 6 8036 Graz Austria
| | - Tamara Tomin
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
| | - Maximilian Schinagl
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
| | - Raphael Pfleger
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
| | - Julia Hoehlschen
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
| | - Barbara Darnhofer
- Core Facility Mass Spectrometry Center for Medical Research Medical University of Graz Neue Stiftingtalstraße 24 8036 Graz Austria
| | - Matthias Schittmayer
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
| | - Ruth Birner‐Gruenberger
- Research and Diagnostic Institute of Pathology Medical University of Graz Stiftingtalstraße 6 8036 Graz Austria
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
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4
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Deng N, Qiao M, Li Y, Liang F, Li J, Liu Y. Anticancer effects of licochalcones: A review of the mechanisms. Front Pharmacol 2023; 14:1074506. [PMID: 36755942 PMCID: PMC9900005 DOI: 10.3389/fphar.2023.1074506] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
Cancer is a disease with a high fatality rate representing a serious threat to human health. Researchers have tried to identify effective anticancer drugs. Licorice is a widely used traditional Chinese medicine with various pharmacological properties, and licorice-derived flavonoids include licochalcones like licochalcone A, licochalcone B, licochalcone C, licochalcone D, licochalcone E, and licochalcone H. By regulating the expression in multiple signaling pathways such as the EGFR/ERK, PI3K/Akt/mTOR, p38/JNK, JAK2/STAT3, MEK/ERK, Wnt/β-catenin, and MKK4/JNK pathways, and their downstream proteins, licochalcones can activate the mitochondrial apoptosis pathway and death receptor pathway, promote autophagy-related protein expression, inhibit the expression of cell cycle proteins and angiogenesis factors, regulate autophagy and apoptosis, and inhibit the proliferation, migration, and invasion of cancer cells. Among the licochalcones, the largest number of studies examined licochalcone A, far more than other licochalcones. Licochalcone A not only has prominent anticancer effects but also can be used to inhibit the efflux of antineoplastic drugs from cancer cells. Moreover, derivatives of licochalcone A exhibit strong antitumor effects. Currently, most results of the anticancer effects of licochalcones are derived from cell experiments. Thus, more clinical studies are needed to confirm the antineoplastic effects of licochalcones.
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Affiliation(s)
- Nan Deng
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Mingming Qiao
- Chongqing Institute for Food and Drug Control, Chongqing, China
| | - Ying Li
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Fengyan Liang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jingjing Li
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yanfeng Liu
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China,*Correspondence: Yanfeng Liu,
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5
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Li MT, Xie L, Jiang HM, Huang Q, Tong RS, Li X, Xie X, Liu HM. Role of Licochalcone A in Potential Pharmacological Therapy: A Review. Front Pharmacol 2022; 13:878776. [PMID: 35677438 PMCID: PMC9168596 DOI: 10.3389/fphar.2022.878776] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/20/2022] [Indexed: 12/16/2022] Open
Abstract
Licochalcone A (LA), a useful and valuable flavonoid, is isolated from Glycyrrhiza uralensis Fisch. ex DC. and widely used clinically in traditional Chinese medicine. We systematically updated the latest information on the pharmacology of LA over the past decade from several authoritative internet databases, including Web of Science, Elsevier, Europe PMC, Wiley Online Library, and PubMed. A combination of keywords containing “Licochalcone A,” “Flavonoid,” and “Pharmacological Therapy” was used to help ensure a comprehensive review. Collected information demonstrates a wide range of pharmacological properties for LA, including anticancer, anti-inflammatory, antioxidant, antibacterial, anti-parasitic, bone protection, blood glucose and lipid regulation, neuroprotection, and skin protection. LA activity is mediated through several signaling pathways, such as PI3K/Akt/mTOR, P53, NF-κB, and P38. Caspase-3 apoptosis, MAPK inflammatory, and Nrf2 oxidative stress signaling pathways are also involved with multiple therapeutic targets, such as TNF-α, VEGF, Fas, FasL, PI3K, AKT, and caspases. Recent studies mainly focus on the anticancer properties of LA, which suggests that the pharmacology of other aspects of LA will need additional study. At the end of this review, current challenges and future research directions on LA are discussed. This review is divided into three parts based on the pharmacological effects of LA for the convenience of readers. We anticipate that this review will inspire further research.
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Affiliation(s)
- Meng-Ting Li
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Long Xie
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy and College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hai-Mei Jiang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy and College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qun Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy and College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Rong-Sheng Tong
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiang Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy and College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xin Xie
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy and College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hong-Mei Liu
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
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6
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Wang X, Yin G, Zhang W, Song K, Zhang L, Guo Z. Prostaglandin Reductase 1 as a Potential Therapeutic Target for Cancer Therapy. Front Pharmacol 2021; 12:717730. [PMID: 34421612 PMCID: PMC8377670 DOI: 10.3389/fphar.2021.717730] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/29/2021] [Indexed: 12/12/2022] Open
Abstract
Altered tumor metabolism is a hallmark of cancer and targeting tumor metabolism has been considered as an attractive strategy for cancer therapy. Prostaglandin Reductase 1 (PTGR1) is a rate-limiting enzyme involved in the arachidonic acid metabolism pathway and mainly responsible for the deactivation of some eicosanoids, including prostaglandins and leukotriene B4. A growing evidence suggested that PTGR1 plays a significant role in cancer and has emerged as a novel target for cancer therapeutics. In this review, we summarize the progress made in recent years toward the understanding of PTGR1 function and structure, highlight the roles of PTGR1 in cancer, and describe potential inhibitors of PTGR1. Finally, we provide some thoughts on future directions that might facilitate the PTGR1 research and therapeutics development.
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Affiliation(s)
- Xing Wang
- Department of Breast and Thyroid Surgery, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Guobing Yin
- Department of Breast and Thyroid Surgery, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wei Zhang
- Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Kunlin Song
- Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Longbin Zhang
- Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Zufeng Guo
- Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University, Chongqing, China
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7
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Conway LP, Li W, Parker CG. Chemoproteomic-enabled phenotypic screening. Cell Chem Biol 2021; 28:371-393. [PMID: 33577749 DOI: 10.1016/j.chembiol.2021.01.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/26/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022]
Abstract
The ID of disease-modifying, chemically accessible targets remains a central priority of modern therapeutic discovery. The phenotypic screening of small-molecule libraries not only represents an attractive approach to identify compounds that may serve as drug leads but also serves as an opportunity to uncover compounds with novel mechanisms of action (MoAs). However, a major bottleneck of phenotypic screens continues to be the ID of pharmacologically relevant target(s) for compounds of interest. The field of chemoproteomics aims to map proteome-wide small-molecule interactions in complex, native systems, and has proved a key technology to unravel the protein targets of pharmacological modulators. In this review, we discuss the application of modern chemoproteomic methods to identify protein targets of phenotypic screening hits and investigate MoAs, with a specific focus on the development of chemoproteomic-enabled compound libraries to streamline target discovery.
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Affiliation(s)
- Louis P Conway
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Weichao Li
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.
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8
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Ma S, Wang F, Zhang C, Wang X, Wang X, Yu Z. Cell metabolomics to study the function mechanism of Cyperus rotundus L. on triple-negative breast cancer cells. BMC Complement Med Ther 2020; 20:262. [PMID: 32843016 PMCID: PMC7449030 DOI: 10.1186/s12906-020-02981-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 06/01/2020] [Indexed: 12/24/2022] Open
Abstract
Background Triple-negative breast cancer (TNBC) is a kind of malignant tumor with higher recurrence and metastasis rate. According to historical records, the dry rhizomes Cyperus rotundus L. could be ground into powder and mixed with ginger juice and wine for external application for breast cancer. We studied the effect of the ethanol extract of Cyperus rotundus L. (EECR) on TNBC cells and found its’ apoptosis-inducing effect with a dose-relationship. But the function mechanism of EECR on TNBC is still mysterious. Hence, the present research aimed to detect its function mechanism at the small molecule level through ultra-high performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF-MS/MS) metabolomics. Methods The CCK-8 assay and the Annexin V-FITC/PI assay were applied to test the effect of EECR on MDA-MB-231 cells and MDA-MB 468 cells at various concentrations of 0, 200, 400, and 600 μg/ml. UPLC-Q-TOF-MS/MS based metabolomics was used between the control group and the EECR treatment groups. Multivariate statistical analysis was used to visualize the apoptosis-inducing action of EECR and filtrate significantly changed metabolites. Results The apoptosis-inducing action was confirmed and forty-nine significantly changed metabolites (VIP > 1, p < 0.05, and FC > 1.2 or FC < 0.8) were identified after the interference of EECR. The level of significant differential metabolites between control group, middle dose group, and high dose group were compared and found that which supported the apoptosis-inducing action with dose-dependence. Conclusion By means of metabolism, we have detected the mechanism of EECR inducing apoptosis of TNBC cells at the level of small molecule metabolites and found that EECR impacted the energy metabolism of TNBC cells. In addition, we concluded that EECR induced apoptosis by breaking the balance between ATP-production and ATP-consumption: arresting the pathways of Carbohydrate metabolism such as Central carbon metabolism in cancer, aerobic glycolysis, and Amino sugar and nucleotide sugar metabolism, whereas accelerating the pathways of ATP-consumption including Amino Acids metabolism, Fatty acid metabolism, Riboflavin metabolism and Purine metabolism. Although further study is still needed, EECR has great potential in the clinical treatment of TNBC with fewer toxic and side effects.
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Affiliation(s)
- Shuangshuang Ma
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, No.440 jiyan road, Jinan, 250017, Shandong, China.,Shandong Hongjitang Pharmaceutical Group Co.,Ltd., Jinan, 250000, China
| | - Fukai Wang
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, No.440 jiyan road, Jinan, 250017, Shandong, China
| | - Caijuan Zhang
- School of life Science, Beijing University of Chinese Medicine, Northeast corner of intersection of Sunshine South Street and Baiyang East Road, Fang-Shan District, Beijing, 102488, China
| | - Xinzhao Wang
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, No.440 jiyan road, Jinan, 250017, Shandong, China
| | - Xueyong Wang
- School of Chinese Materia Medical, Beijing University of Chinese Medicine, No.11 North 3rd Ring East Road, Chao-Yang District, Beijing, 100029, China.
| | - Zhiyong Yu
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, No.440 jiyan road, Jinan, 250017, Shandong, China.
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Watt MJ, Clark AK, Selth LA, Haynes VR, Lister N, Rebello R, Porter LH, Niranjan B, Whitby ST, Lo J, Huang C, Schittenhelm RB, Anderson KE, Furic L, Wijayaratne PR, Matzaris M, Montgomery MK, Papargiris M, Norden S, Febbraio M, Risbridger GP, Frydenberg M, Nomura DK, Taylor RA. Suppressing fatty acid uptake has therapeutic effects in preclinical models of prostate cancer. Sci Transl Med 2020; 11:11/478/eaau5758. [PMID: 30728288 DOI: 10.1126/scitranslmed.aau5758] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/17/2018] [Accepted: 01/15/2019] [Indexed: 12/22/2022]
Abstract
Metabolism alterations are hallmarks of cancer, but the involvement of lipid metabolism in disease progression is unclear. We investigated the role of lipid metabolism in prostate cancer using tissue from patients with prostate cancer and patient-derived xenograft mouse models. We showed that fatty acid uptake was increased in human prostate cancer and that these fatty acids were directed toward biomass production. These changes were mediated, at least partly, by the fatty acid transporter CD36, which was associated with aggressive disease. Deleting Cd36 in the prostate of cancer-susceptible Pten-/- mice reduced fatty acid uptake and the abundance of oncogenic signaling lipids and slowed cancer progression. Moreover, CD36 antibody therapy reduced cancer severity in patient-derived xenografts. We further demonstrated cross-talk between fatty acid uptake and de novo lipogenesis and found that dual targeting of these pathways more potently inhibited proliferation of human cancer-derived organoids compared to the single treatments. These findings identify a critical role for CD36-mediated fatty acid uptake in prostate cancer and suggest that targeting fatty acid uptake might be an effective strategy for treating prostate cancer.
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Affiliation(s)
- Matthew J Watt
- Department of Physiology, University of Melbourne, Melbourne, VIC 3010, Australia. .,Monash Biomedicine Discovery Institute, Metabolic Disease and Obesity, Department of Physiology, Monash University, Clayton, VIC 3800, Australia
| | - Ashlee K Clark
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Physiology, Monash University, Clayton, VIC 3800, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - Luke A Selth
- Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's Health, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Vanessa R Haynes
- Department of Physiology, University of Melbourne, Melbourne, VIC 3010, Australia.,Monash Biomedicine Discovery Institute, Metabolic Disease and Obesity, Department of Physiology, Monash University, Clayton, VIC 3800, Australia
| | - Natalie Lister
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Physiology, Monash University, Clayton, VIC 3800, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - Richard Rebello
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Physiology, Monash University, Clayton, VIC 3800, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia.,Cancer Research UK Manchester Institute, University of Manchester, Manchester M20 4GJ, UK
| | - Laura H Porter
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Physiology, Monash University, Clayton, VIC 3800, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - Birunthi Niranjan
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Physiology, Monash University, Clayton, VIC 3800, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - Sarah T Whitby
- Monash Biomedicine Discovery Institute, Metabolic Disease and Obesity, Department of Physiology, Monash University, Clayton, VIC 3800, Australia.,Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Physiology, Monash University, Clayton, VIC 3800, Australia
| | - Jennifer Lo
- Monash Biomedicine Discovery Institute, Metabolic Disease and Obesity, Department of Physiology, Monash University, Clayton, VIC 3800, Australia
| | - Cheng Huang
- Monash Biomedical Proteomics Facility and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Ralf B Schittenhelm
- Monash Biomedical Proteomics Facility and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Kimberley E Anderson
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkley, Berkeley, CA, USA
| | - Luc Furic
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Physiology, Monash University, Clayton, VIC 3800, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Poornima R Wijayaratne
- Monash Biomedicine Discovery Institute, Metabolic Disease and Obesity, Department of Physiology, Monash University, Clayton, VIC 3800, Australia
| | - Maria Matzaris
- Monash Biomedicine Discovery Institute, Metabolic Disease and Obesity, Department of Physiology, Monash University, Clayton, VIC 3800, Australia
| | - Magdalene K Montgomery
- Department of Physiology, University of Melbourne, Melbourne, VIC 3010, Australia.,Monash Biomedicine Discovery Institute, Metabolic Disease and Obesity, Department of Physiology, Monash University, Clayton, VIC 3800, Australia
| | - Melissa Papargiris
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Physiology, Monash University, Clayton, VIC 3800, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - Sam Norden
- TissuPath, Mount Waverley, VIC 3149, Australia
| | - Maria Febbraio
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R7, Canada
| | - Gail P Risbridger
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Physiology, Monash University, Clayton, VIC 3800, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Mark Frydenberg
- Department of Surgery, Faculty of Medicine, Monash University, Clayton, VIC 3800, Australia
| | - Daniel K Nomura
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkley, Berkeley, CA, USA
| | - Renea A Taylor
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Physiology, Monash University, Clayton, VIC 3800, Australia. .,Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
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10
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Counihan JL, Wiggenhorn AL, Anderson KE, Nomura DK. Chemoproteomics-Enabled Covalent Ligand Screening Reveals ALDH3A1 as a Lung Cancer Therapy Target. ACS Chem Biol 2018; 13:1970-1977. [PMID: 30004670 DOI: 10.1021/acschembio.8b00381] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemical genetics is a powerful approach for identifying therapeutically active small molecules, but identifying the mechanisms of action underlying hit compounds remains challenging. Chemoproteomic platforms have arisen to tackle this challenge and enable rapid mechanistic deconvolution of small-molecule screening hits. Here, we have screened a cysteine-reactive covalent ligand library to identify hit compounds that impair cell survival and proliferation in nonsmall cell lung carcinoma cells, but not in primary human bronchial epithelial cells. Through this screen, we identified a covalent ligand hit, DKM 3-42, which impaired both in situ and in vivo lung cancer pathogenicity. We used activity-based protein profiling to discover that the primary target of DKM 3-42 was the catalytic cysteine in aldehyde dehydrogenase 3A1 (ALDH3A1). We performed further chemoproteomics-enabled covalent ligand screening directly against ALDH3A1, and identified a more potent and selective lead covalent ligand, EN40, which inhibits ALDH3A1 activity and impairs lung cancer pathogenicity. We show here that ALDH3A1 represents a potentially novel therapeutic target for lung cancers that express ALDH3A1 and put forth two selective ALDH3A1 inhibitors. Overall, we show the utility of combining chemical genetics screening of covalent ligand libraries with chemoproteomic approaches to rapidly identify anticancer leads and targets.
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Ye Z, Zhang X, Zhu Y, Song T, Chen X, Lei X, Wang C. Chemoproteomic Profiling Reveals Ethacrynic Acid Targets Adenine Nucleotide Translocases to Impair Mitochondrial Function. Mol Pharm 2018; 15:2413-2422. [PMID: 29763317 DOI: 10.1021/acs.molpharmaceut.8b00250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Ethacrynic acid (EA) is a diuretic drug that is widely used to treat high-blood pressure and swelling caused by congestive heart failure or kidney failure. It acts through noncovalent inhibition of the Na+-K+-2Cl- cotransporter in the thick ascending limb of Henle's loop. Chemically, EA contains a Michael acceptor group that can react covalently with nucleophilic residues in proteins; however, the proteome reactivity of EA remains unexplored. Herein, we took a quantitative chemoproteomic approach to globally profile EA's targets in cancer cells. We discovered that EA induces impaired mitochondrial function accompanied by increased ROS production. Our profiling revealed that EA targets functional proteins on mitochondrial membranes, including adenine nucleotide translocases (ANTs). Site-specific mapping identified that EA covalently modifies a functional cysteine in ANTs, a mutation of which resulted in the rescuing effect on EA-induced mitochondrial dysfunction. The newly discovered modes of action offer valuable information to repurpose EA for cancer treatment.
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Affiliation(s)
- Zi Ye
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of 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
| | - Xiaoyun Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Yuangang Zhu
- Institute of Molecular Medicine , Peking University , Beijing 100871 , China
| | - Tong Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Xiaowei Chen
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies , Peking University , Beijing 100871 , China.,Institute of Molecular Medicine , Peking University , Beijing 100871 , China
| | - Xiaoguang Lei
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of 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
| | - Chu Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of 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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Hoch DG, Abegg D, Adibekian A. Cysteine-reactive probes and their use in chemical proteomics. Chem Commun (Camb) 2018; 54:4501-4512. [PMID: 29645055 DOI: 10.1039/c8cc01485j] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Proteomic profiling using bioorthogonal chemical probes that selectively react with certain amino acids is now a widely used method in life sciences to investigate enzymatic activities, study posttranslational modifications and discover novel covalent inhibitors. Over the past two decades, researchers have developed selective probes for several different amino acids, including lysine, serine, cysteine, threonine, tyrosine, aspartate and glutamate. Among these amino acids, cysteines are particularly interesting due to their highly diverse and complex biochemical role in our cells. In this feature article, we focus on the chemical probes and methods used to study cysteines in complex proteomes.
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Affiliation(s)
- Dominic G Hoch
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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13
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Target Identification of Bioactive Covalently Acting Natural Products. Curr Top Microbiol Immunol 2018; 420:351-374. [PMID: 30105423 DOI: 10.1007/82_2018_121] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There are countless natural products that have been isolated from microbes, plants, and other living organisms that have been shown to possess therapeutic activities such as antimicrobial, anticancer, or anti-inflammatory effects. However, developing these bioactive natural products into drugs has remained challenging in part because of their difficulty in isolation, synthesis, mechanistic understanding, and off-target effects. Among the large pool of bioactive natural products lies classes of compounds that contain potential reactive electrophilic centers that can covalently react with nucleophilic amino acid hotspots on proteins and other biological molecules to modulate their biological action. Covalently acting natural products are more amenable to rapid target identification and mapping of specific druggable hotspots within proteins using activity-based protein profiling (ABPP)-based chemoproteomic strategies. In addition, the granular biochemical insights afforded by knowing specific sites of protein modifications of covalently acting natural products enable the pharmacological interrogation of these sites with more synthetically tractable covalently acting small molecules whose structures are more easily tuned. Both discovering binding pockets and targets hit by natural products and exploiting druggable modalities targeted by natural products with simpler molecules may overcome some of the challenges faced with translating natural products into drugs.
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Abstract
Cysteine thiols are involved in a diverse set of biological transformations, including nucleophilic and redox catalysis, metal coordination and formation of both dynamic and structural disulfides. Often posttranslationally modified, cysteines are also frequently alkylated by electrophilic compounds, including electrophilic metabolites, drugs, and natural products, and are attractive sites for covalent probe and drug development. Quantitative proteomics combined with activity-based protein profiling has been applied to annotate cysteine reactivity, susceptibility to posttranslational modifications, and accessibility to chemical probes, uncovering thousands of functional and small-molecule targetable cysteines across a diverse set of proteins, proteome-wide in an unbiased manner. Reactive cysteines have been targeted by high-throughput screening and fragment-based ligand discovery efforts. New cysteine-reactive electrophiles and compound libraries have been synthesized to enable inhibitor discovery broadly and to minimize nonspecific toxicity and off-target activity of compounds. With the recent blockbuster success of several covalent inhibitors, and the development of new chemical proteomic strategies to broadly identify reactive, ligandable and posttranslationally modified cysteines, cysteine profiling is poised to enable the development of new potent and selective chemical probes and even, in some cases, new drugs.
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Grossman EA, Ward CC, Spradlin JN, Bateman LA, Huffman TR, Miyamoto DK, Kleinman JI, Nomura DK. Covalent Ligand Discovery against Druggable Hotspots Targeted by Anti-cancer Natural Products. Cell Chem Biol 2017; 24:1368-1376.e4. [PMID: 28919038 DOI: 10.1016/j.chembiol.2017.08.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 07/10/2017] [Accepted: 08/15/2017] [Indexed: 01/30/2023]
Abstract
Many natural products that show therapeutic activities are often difficult to synthesize or isolate and have unknown targets, hindering their development as drugs. Identifying druggable hotspots targeted by covalently acting anti-cancer natural products can enable pharmacological interrogation of these sites with more synthetically tractable compounds. Here, we used chemoproteomic platforms to discover that the anti-cancer natural product withaferin A targets C377 on the regulatory subunit PPP2R1A of the tumor-suppressor protein phosphatase 2A (PP2A) complex leading to activation of PP2A activity, inactivation of AKT, and impaired breast cancer cell proliferation. We developed a more synthetically tractable cysteine-reactive covalent ligand, JNS 1-40, that selectively targets C377 of PPP2R1A to impair breast cancer signaling, proliferation, and in vivo tumor growth. Our study highlights the utility of using chemoproteomics to map druggable hotspots targeted by complex natural products and subsequently interrogating these sites with more synthetically tractable covalent ligands for cancer therapy.
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Affiliation(s)
- Elizabeth A Grossman
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Carl C Ward
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Jessica N Spradlin
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Leslie A Bateman
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Tucker R Huffman
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - David K Miyamoto
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Jordan I Kleinman
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Daniel K Nomura
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA.
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