1
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Shen L, Yang Y, Lu L, Huang J, He W, Zhao C, Guo F, Zhang C, Zhong H, Liao F. Design and synthesis of piperine-based photoaffinity probes for revealing potential targets of piperine in neurological disease. Chem Commun (Camb) 2024. [PMID: 39628399 DOI: 10.1039/d4cc04330h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2024]
Abstract
Piperine (PIP) has attracted extensive attention due to its diverse biological activities. In this study, we developed two photoaffinity probes PIP-1 and PIP-2, which are biologically safe and retain PIP's bioactivity, to investigate its protein targets in vivo. Using in situ labeling and cell imaging, we were able to effectively detect and visualize the drug targets of PIP with our probes. Additionally, a series of protein targets of PIP were fished using PIP-2 through proteome profiling, with further validation suggesting that TGFβ1 might be a potential target involved in PIP's effects on neurological diseases. These findings demonstrate that PIP-2 is a valuable tool for identifying the targets of PIP.
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Affiliation(s)
- Li Shen
- Department of Pharmaceutics, College of Pharmacy, Nanchang University, Nanchang 330006, Jiangxi, China.
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, Jiangxi Province Key Laboratory of Drug Target Discovery and Validation, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
| | - Yue Yang
- Department of Pharmaceutics, College of Pharmacy, Nanchang University, Nanchang 330006, Jiangxi, China.
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, Jiangxi Province Key Laboratory of Drug Target Discovery and Validation, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
| | - Lijun Lu
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jili Huang
- Department of Pharmaceutics, College of Pharmacy, Nanchang University, Nanchang 330006, Jiangxi, China.
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, Jiangxi Province Key Laboratory of Drug Target Discovery and Validation, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
| | - Wen He
- Department of Pharmaceutics, College of Pharmacy, Nanchang University, Nanchang 330006, Jiangxi, China.
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, Jiangxi Province Key Laboratory of Drug Target Discovery and Validation, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
| | - Chunfang Zhao
- Department of Pharmaceutics, College of Pharmacy, Nanchang University, Nanchang 330006, Jiangxi, China.
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, Jiangxi Province Key Laboratory of Drug Target Discovery and Validation, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
| | - Feng Guo
- Department of Pharmaceutics, College of Pharmacy, Nanchang University, Nanchang 330006, Jiangxi, China.
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, Jiangxi Province Key Laboratory of Drug Target Discovery and Validation, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
| | - Chunbo Zhang
- Department of Pharmaceutics, College of Pharmacy, Nanchang University, Nanchang 330006, Jiangxi, China.
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, Jiangxi Province Key Laboratory of Drug Target Discovery and Validation, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
| | - Haijun Zhong
- Department of Pharmaceutics, College of Pharmacy, Nanchang University, Nanchang 330006, Jiangxi, China.
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, Jiangxi Province Key Laboratory of Drug Target Discovery and Validation, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
| | - Fan Liao
- Department of Pharmaceutics, College of Pharmacy, Nanchang University, Nanchang 330006, Jiangxi, China.
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, Jiangxi Province Key Laboratory of Drug Target Discovery and Validation, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
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2
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Huang C, Yang T, Jia J, Fu S, Hong B, Wu F, Ni F. Selenium-catalyzed allylic C-H phosphoramidation of alkenes. Org Biomol Chem 2024; 22:4882-4887. [PMID: 38809155 DOI: 10.1039/d4ob00638k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
We report herein a synthesis of allylic phosphoramidates from alkenes by selenium-catalyzed allylic C-H derivatization. This method features mild conditions, broad substrate scope, and high functional group tolerance, enabling late-stage modification of a number of complex substrates. In addition, this protocol was applied to modify caryophyllene and produced a photoaffinity probe capable of proteomic target labeling in live HeLa cells.
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Affiliation(s)
- Chengjie Huang
- Institute of Drug Discovery Technology and Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Tao Yang
- Institute of Drug Discovery Technology and Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Jingyang Jia
- Institute of Drug Discovery Technology and Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Songsen Fu
- Institute of Drug Discovery Technology and Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Bang Hong
- LeadArt Technologies Ltd, Ningbo, 315211, China
| | - Fan Wu
- Institute of Drug Discovery Technology and Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Feng Ni
- Institute of Drug Discovery Technology and Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, Zhejiang 315211, China.
- LeadArt Technologies Ltd, Ningbo, 315211, China
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3
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Zhang S, Liu P, Li L, Liu Z, Qian X, Jiang X, Sun W, Wang L, Akkaya EU. Upconverting Nanoparticle-Based Photoactive Probes for Highly Efficient Labeling and Isolation of Target Proteins. ACS APPLIED MATERIALS & INTERFACES 2023; 15:40280-40291. [PMID: 37585283 DOI: 10.1021/acsami.3c08397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Photoaffinity labeling (PAL) has blossomed into a powerful and versatile tool for capture and identification of biomolecular targets. However, low labeling efficiency for specific targets such as lectins, the tedious process for protein purification, inevitable cellular photodamage, and less tissue penetration of UV light are significant challenges. Herein, we reported a near-infrared (NIR) light-driven photoaffinity labeling approach using upconverting nanoparticle (UCNP)-based photoactive probes, which were constructed by assembling photoactive groups and ligands onto NaYF4:Yb,Tm nanoparticles. The novel probes were easily prepared and functionalized, and the labeled proteins can be isolated and purified through simple centrifugation and washing. The advantages of this approach were demonstrated by labeling and isolation of peanut agglutinin (PNA), asialoglycoprotein receptor (ASGPR), and human carbonic anhydrase II (hCAII) from mixed proteins or cell lysates with good selectivity and efficiency, especially for PNA and ASGPR, two lectins that showed low binding affinity to their ligands. More importantly, successful labeling of PNA through pork tissues and ASGPR in mice strongly proved the good tissue penetrating capacity of NIR light and the application potential of UCNP-based photoactive probes for protein labeling in vivo. Biosafety of this approach was experimentally validated by enzyme, cell, and animal work, and we demonstrated that NIR light caused minimal photodamage to enzyme activity compared to UV light, and the UCNP-based photoactive probe presents good biosafety both in vitro and in vivo. We believe that this novel PAL approach will provide a promising tool for study of ligand-protein interactions and identification of biomolecular targets.
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Affiliation(s)
- Shengli Zhang
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Peng Liu
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Li Li
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Ziang Liu
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Xiao Qian
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Xueying Jiang
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Wen Sun
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Lei Wang
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Engin U Akkaya
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
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4
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Zhu L, Hu S, Yan X, Zeng Q, Zhang B, Jiang L, Yao SQ, Ge J. Ugi reaction-assisted assembly of covalent PROTACs against glutathione peroxidase 4. Bioorg Chem 2023; 134:106461. [PMID: 36924654 DOI: 10.1016/j.bioorg.2023.106461] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/06/2022] [Accepted: 03/07/2023] [Indexed: 03/12/2023]
Abstract
Inducing cell ferroptosis by inactivating glutathione peroxidase 4 (GPX4) is a popular cancer treatment strategy. However, only few GPX4 inhibitors have been developed to date. PROteolysis Targeting Chimera (PROTAC) is a promising approach to provide new opportunities to overcome limitations of traditional therapeutics. Herein, a PROTAC-like activity-based probe PD-Q2 was first assembled using Ugi reaction, consisting of a known GPX4 inhibitor ML-162 homolog to the E3 ligase cereblon ligand-pomalidomide. Pull-down and immunoblotting analysis revealed that GPX4 was a covalent target of PD-Q2, but the degradation efficiency was weak. Therefore, a series of degraders was further synthesized by varying the linkers of heterofunctional PROTACs. Among these degraders, PD-4 and PD-P2 were found to promote effective GPX4 degradation via the ubiquitin-proteasome system and cause lipid ROS accumulation. PD-4 and PD-P2 showed potent inhibitory of colony formation and cell growth. Furthermore, we found that with pomalidomide, the degraders exhibit a high fluorescent signal that is mostly localized in the lysosome, which may affect the effectiveness of anti-cell proliferation. Overall, we provide GPX4 degraders for further exploring therapeutic potential of regulating ferroptosis.
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Affiliation(s)
- Liquan Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Shiqi Hu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xiaoqiao Yan
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Qian Zeng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Bei Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Linye Jiang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117544, Singapore.
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China.
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5
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Lv S, Xu F, Fan Y, Ding K, Li Z. Cyclopropenone, Cyclopropeniminium Ion, and Cyclopropenethione as Novel Electrophilic Warheads for Potential Target Discovery of Triple-Negative Breast Cancer. J Med Chem 2023; 66:2851-2864. [PMID: 36762554 DOI: 10.1021/acs.jmedchem.2c01889] [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: 02/11/2023]
Abstract
Because very few targets are currently available for drug development, triple-negative breast cancer (TNBC) has been defined as one of the most difficult diseases for chemotherapy. Herein, we describe a suite of novel electrophilic warheads, which we have used in chemical proteomics studies in a search for potential targets for TNBC. Binding site analysis revealed that these warheads can modify not only highly nucleophilic residues, including cysteine and lysine, but also weakly nucleophilic residues. Cys12 of Kirsten rat sarcoma (KRASG12C) was successfully labeled by cyclopropenone and the cyclopropeniminium ions. Moderate inhibitory activity against TNBC cells was achieved with these novel electrophile-based probes. Activity-based protein profiling reveals that these electrophiles can covalently label a series of essential protein targets, including ALDH2, LRPPRC, and FABP5 from MDA-MB-231 cells. Further functional validation experiments demonstrated that FABP5 might be a potential target for TNBC.
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Affiliation(s)
- Shumin Lv
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Fang Xu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Youlong Fan
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
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6
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Liu Y, Liu J, Zhang X, Guo C, Xing X, Zhang ZM, Ding K, Li Z. Oxidant-Induced Bioconjugation for Protein Labeling in Live Cells. ACS Chem Biol 2023; 18:112-122. [PMID: 36543757 DOI: 10.1021/acschembio.2c00740] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chemical proteomics is a powerful technology that can be used in the studies of the functions of uncharacterized proteins in the human proteome. It relies on a suitable bioconjugation strategy for protein labeling. This could be either a UV-responsive photo-crosslinker or an electrophilic warhead embedded in chemical probes that can form covalent bonds with target proteins. Here, we report a new protein-labeling strategy in which a nitrile oxide, a highly reactive intermediate that reacts with proteins, can be efficiently generated by the treatment of oximes with a water-soluble and a minimally toxic oxidant, phenyliodine bis (trifluoroacetate) (PIFA). The resulting intermediate can rapidly bioconjugate with amino acid residues of target proteins, thus enabling target identification of oxime-containing bioactive molecules. Excellent chemoselectivity of cysteine residues by the nitrile oxide was observed, and over 4000 reactive and/or accessible cysteines, including KRAS G12C, have been successfully characterized by quantitative chemical proteomics. Some of these residues could not be detected by conventional cysteine reagents, thus demonstrating the complementary utility of this method.
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Affiliation(s)
- Yue Liu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Jiacong Liu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Xianfang Zhang
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Cuiping Guo
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Xiwen Xing
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhi-Min Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
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7
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Xu J, Peng L, Guo C, Xu F, Lin DS, Tang Y, Li Z. Comparison of Different Competitive Proteome Profiling Approaches in Target Identification of Covalent Inhibitors. Chembiochem 2022; 23:e202200389. [PMID: 36271784 DOI: 10.1002/cbic.202200389] [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: 07/11/2022] [Revised: 10/17/2022] [Indexed: 01/25/2023]
Abstract
Competitive proteome profiling is a powerful approach for the identification of targets of small molecules. This approach usually employs an inhibitor-derived probe or a cysteine-reactive probe such as an IA-alkyne in a comparison between inhibitor-treated and untreated samples, thus enabling distinction between genuine targets and nonspecific labeling. We have developed an active probe derived from an EGFR inhibitor, afatinib, and a cysteine reactive probe, an alkyne-containing α,β-unsaturated amide, to compare their characterization of cellular targets. In both approaches, myosin heavy chain 9 (MYH9) was identified as an off-target. Subsequent functional validation experiments suggested that MYH9 might be involved in the function of afatinib.
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Affiliation(s)
- Jiaqian Xu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Lijie Peng
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Cuiping Guo
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Fang Xu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Dong-Shi Lin
- Department of Pharmacy, Guangdong Provincial Corps Hospital of Chinese People's Armed Police Forces, Guangzhou, Guangdong, 510507, P. R. China
| | - Yi Tang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou, 510632, China
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8
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Challis MP, Devine SM, Creek DJ. Current and emerging target identification methods for novel antimalarials. Int J Parasitol Drugs Drug Resist 2022; 20:135-144. [PMID: 36410177 PMCID: PMC9771836 DOI: 10.1016/j.ijpddr.2022.11.001] [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] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
New antimalarial compounds with novel mechanisms of action are urgently needed to combat the recent rise in antimalarial drug resistance. Phenotypic high-throughput screens have proven to be a successful method for identifying new compounds, however, do not provide mechanistic information about the molecular target(s) responsible for antimalarial action. Current and emerging target identification methods such as in vitro resistance generation, metabolomics screening, chemoproteomic approaches and biophysical assays measuring protein stability across the whole proteome have successfully identified novel drug targets. This review provides an overview of these techniques, comparing their strengths and weaknesses and how they can be utilised for antimalarial target identification.
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Affiliation(s)
- Matthew P. Challis
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Shane M. Devine
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Darren J. Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia,Corresponding author. Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia.
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9
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Page ACS, Scholz SO, Keenan KN, Spradlin JN, Belcher BP, Brittain SM, Tallarico JA, McKenna JM, Schirle M, Nomura DK, Toste FD. Photo-Brook rearrangement of acyl silanes as a strategy for photoaffinity probe design. Chem Sci 2022; 13:3851-3856. [PMID: 35432890 PMCID: PMC8966736 DOI: 10.1039/d2sc00426g] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/02/2022] [Indexed: 01/14/2023] Open
Abstract
Photoaffinity labeling (PAL) is a powerful tool for the identification of non-covalent small molecule–protein interactions that are critical to drug discovery and medicinal chemistry, but this approach is limited to only a small subset of robust photocrosslinkers. The identification of new photoreactive motifs capable of covalent target capture is therefore highly desirable. Herein, we report the design, synthesis, and evaluation of a new class of PAL warheads based on the UV-triggered 1,2-photo-Brook rearrangement of acyl silanes, which hitherto have not been explored for PAL workflows. Irradiation of a series of probes in cell lysate revealed an iPr-substituted acyl silane with superior photolabeling and minimal thermal background labeling compared to other substituted acyl silanes. Further, small molecule (+)-JQ1- and rapamycin-derived iPr acyl silanes were shown to selectively label recombinant BRD4-BD1 and FKBP12, respectively, with minimal background. Together, these data highlight the untapped potential of acyl silanes as a novel, tunable scaffold for photoaffinity labeling. Irradiation initiated 1,2-photo Brook rearrangement of acyl silanes generated α-siloxycarbene intermediates that were used for photoaffinity labeling. Optimization of the acyl silane group produced a probe capable of capturing small molecule–protein interactions.![]()
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Affiliation(s)
- Annika C S Page
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA
| | - Spencer O Scholz
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA
| | - Katherine N Keenan
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA
| | - Jessica N Spradlin
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Innovative Genomics Institute, University of California Berkeley California 94720 USA
| | - Bridget P Belcher
- Department of Chemistry, University of California Berkeley California 94720 USA .,Innovative Genomics Institute, University of California Berkeley California 94720 USA
| | - Scott M Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Novartis Institute for BioMedical Research Cambridge Massachusetts 02139 USA
| | - John A Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Novartis Institute for BioMedical Research Cambridge Massachusetts 02139 USA
| | - Jeffrey M McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Novartis Institute for BioMedical Research Cambridge Massachusetts 02139 USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Novartis Institute for BioMedical Research Cambridge Massachusetts 02139 USA
| | - Daniel K Nomura
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Innovative Genomics Institute, University of California Berkeley California 94720 USA.,Department of Molecular and Cellular Biology, University of California Berkeley California 94720 USA
| | - F Dean Toste
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA
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10
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Asiimwe N, Lee J, Hong K, murale D, Haque MM, Kim DH, Lee JS. Temporal control of protein labeling by photo-caged benzaldehyde motif and discovery of host cell factors of avian influenza virus infection. Chem Commun (Camb) 2022; 58:9345-9348. [DOI: 10.1039/d2cc04091c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photo-caged benzaldehyde probes using o-nitrophenylethylene glycol were designed for photo-activated electrophile generation. Unlike radical reaction that produce uncontrolled multiple reaction paths resulting low yield of crosslinking, reaction of electrophile has...
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11
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Liu Y, Lv S, Peng L, Xie C, Gao L, Sun H, Lin L, Ding K, Li Z. Development and application of novel electrophilic warheads in target identification and drug discovery. Biochem Pharmacol 2021; 190:114636. [PMID: 34062128 DOI: 10.1016/j.bcp.2021.114636] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
Nucleophilic amino acids play important roles in maintenance of protein structure and function, covalent modification of such amino acid residues by therapeutic agents is an efficient way to treat human diseases. Most of current clinical drugs are structurally limited to α,β-unsaturated amide as an electrophilic warhead. To alleviate this issue, many novel electrophiles have been developed in recent years that can covalently bind to different amino acid residues and provides a unique way to interrogate proteins, including "undruggable" targets. With an activity-based protein profiling (ABPP) approach, the activity and functionality of a protein and its binding sites can be assessed. This facilitates an understanding of protein function, and contributes to the discovery of new druggable targets and lead compounds. Meanwhile, many novel inhibitors bearing new reactive warhead were developed and displayed remarkable pharmaceutical properties. In this perspective, we have reviewed the recent remarkable progress of novel electrophiles and their applications in target identification and drug discovery.
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Affiliation(s)
- Yue Liu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Shumin Lv
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Lijie Peng
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Chengliang Xie
- School of Pharmaceutical Science (Shenzhen), Sun Yat-sen University, Guangzhou 510000, China
| | - Liqian Gao
- School of Pharmaceutical Science (Shenzhen), Sun Yat-sen University, Guangzhou 510000, China
| | - Hongyan Sun
- Department of Chemistry, City University of Hong Kong, Hong Kong 999077, China
| | - Ligen Lin
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, China
| | - Ke Ding
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China; MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, China.
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12
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Fang H, Peng B, Ong SY, Wu Q, Li L, Yao SQ. Recent advances in activity-based probes (ABPs) and affinity-based probes (A fBPs) for profiling of enzymes. Chem Sci 2021; 12:8288-8310. [PMID: 34221311 PMCID: PMC8221178 DOI: 10.1039/d1sc01359a] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/11/2021] [Indexed: 12/14/2022] Open
Abstract
Activity-based protein profiling (ABPP) is a technique that uses highly selective active-site targeted chemical probes to label and monitor the state of proteins. ABPP integrates the strengths of both chemical and biological disciplines. By utilizing chemically synthesized or modified bioactive molecules, ABPP is able to reveal complex physiological and pathological enzyme-substrate interactions at molecular and cellular levels. It is also able to provide critical information of the catalytic activity changes of enzymes, annotate new functions of enzymes, discover new substrates of enzymes, and allow real-time monitoring of the cellular location of enzymes. Based on the mechanism of probe-enzyme interaction, two types of probes that have been used in ABPP are activity-based probes (ABPs) and affinity-based probes (AfBPs). This review highlights the recent advances in the use of ABPs and AfBPs, and summarizes their design strategies (based on inhibitors and substrates) and detection approaches.
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Affiliation(s)
- Haixiao Fang
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE), Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University 127 West Youyi Road Xi'an 710072 P. R. China
| | - Sing Yee Ong
- Department of Chemistry, National University of Singapore 4 Science Drive 2 117544 Singapore
| | - Qiong Wu
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore 4 Science Drive 2 117544 Singapore
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13
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Electrophilic Natural Products as Drug Discovery Tools. Trends Pharmacol Sci 2021; 42:434-447. [PMID: 33902949 DOI: 10.1016/j.tips.2021.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/22/2022]
Abstract
Electrophilic natural products (ENPs) are a rich source of bioactive molecules with tremendous therapeutic potential. While their synthetic complexity may hinder their direct use as therapeutics, they represent tools for elucidation of suitable molecular targets and serve as inspiration for the design of simplified synthetic counterparts. Here, we review the recent use of various activity-based protein profiling methods to uncover molecular targets of ENPs. Beyond target identification, these examples also showcase further development of synthetic ligands from natural product starting points. Two examples demonstrate how ENPs can progress the emerging fields of targeted protein degradation and molecular glues. Though challenges still remain in the synthesis of ENP-based probes, and in their synthetic simplification, their potential for discovery of novel mechanisms of action makes it well worth the effort.
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14
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Jörg M, Madden KS. The right tools for the job: the central role for next generation chemical probes and chemistry-based target deconvolution methods in phenotypic drug discovery. RSC Med Chem 2021; 12:646-665. [PMID: 34124668 PMCID: PMC8152813 DOI: 10.1039/d1md00022e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/15/2021] [Indexed: 12/15/2022] Open
Abstract
The reconnection of the scientific community with phenotypic drug discovery has created exciting new possibilities to develop therapies for diseases with highly complex biology. It promises to revolutionise fields such as neurodegenerative disease and regenerative medicine, where the development of new drugs has consistently proved elusive. Arguably, the greatest challenge in readopting the phenotypic drug discovery approach exists in establishing a crucial chain of translatability between phenotype and benefit to patients in the clinic. This remains a key stumbling block for the field which needs to be overcome in order to fully realise the potential of phenotypic drug discovery. Excellent quality chemical probes and chemistry-based target deconvolution techniques will be a crucial part of this process. In this review, we discuss the current capabilities of chemical probes and chemistry-based target deconvolution methods and evaluate the next advances necessary in order to fully support phenotypic screening approaches in drug discovery.
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Affiliation(s)
- Manuela Jörg
- School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville Victoria 3052 Australia
| | - Katrina S Madden
- School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville Victoria 3052 Australia
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15
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Friedman Ohana R, Levin S, Hurst R, Rosenblatt MM, Zimmerman K, Machleidt T, Wood KV, Kirkland TA. Streamlined Target Deconvolution Approach Utilizing a Single Photoreactive Chloroalkane Capture Tag. ACS Chem Biol 2021; 16:404-413. [PMID: 33543920 DOI: 10.1021/acschembio.0c00987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Identification of physiologically relevant targets for lead compounds emerging from drug discovery screens is often the rate-limiting step toward understanding their mechanism of action and potential for undesired off-target effects. To this end, we developed a streamlined chemical proteomic approach utilizing a single, photoreactive cleavable chloroalkane capture tag, which upon attachment to bioactive compounds facilitates selective isolation of their respective cellular targets for subsequent identification by mass spectrometry. When properly positioned, the tag does not significantly affect compound potency and membrane permeability, allowing for binding interactions with the tethered compound (probe) to be established within intact cells under physiological conditions. Subsequent UV-induced covalent photo-cross-linking "freezes" the interactions between the probe and its cellular targets and prevents their dissociation upon cell lysis. Targets cross-linked to the capture tag are then efficiently enriched through covalent capture onto HaloTag coated beads and subsequent selective chemical release from the solid support. The tag's built-in capability for selective enrichment eliminates the need for ligation of a capture tag, thereby simplifying the workflow and reducing variability introduced through additional operational steps. At the same time, the capacity for adequate cross-linking without structural optimization permits modular assembly of photoreactive chloroalkane probes, which reduces the burden of customized chemistry. Using three model compounds, we demonstrate the capability of this approach to identify known and novel cellular targets, including those with low affinity and/or low abundance as well as membrane targets with several transmembrane domains.
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Affiliation(s)
| | - Sergiy Levin
- Promega Biosciences LLC, 277 Granada Drive, San Luis Obispo, California 93401, United States
| | - Robin Hurst
- Promega Corporation, 2800 Woods Hollow, Fitchburg, Wisconsin 53711, United States
| | | | - Kristopher Zimmerman
- Promega Corporation, 2800 Woods Hollow, Fitchburg, Wisconsin 53711, United States
| | - Thomas Machleidt
- Promega Corporation, 2800 Woods Hollow, Fitchburg, Wisconsin 53711, United States
| | - Keith V. Wood
- Promega Corporation, 2800 Woods Hollow, Fitchburg, Wisconsin 53711, United States
| | - Thomas A. Kirkland
- Promega Biosciences LLC, 277 Granada Drive, San Luis Obispo, California 93401, United States
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16
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Lim Y, Kuang Y, Wu J, Yao SQ. Late‐Stage C(sp
2
)−H Functionalization: A Powerful Toolkit To Arm Natural Products for In Situ Proteome Profiling? Chemistry 2020; 27:3575-3580. [DOI: 10.1002/chem.202004373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/04/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Ying‐Jie Lim
- Department of Chemistry National University of Singapore 3 Science Drive 3 Singapore 117543 Singapore
| | - Yulong Kuang
- Department of Chemistry National University of Singapore 3 Science Drive 3 Singapore 117543 Singapore
| | - Jie Wu
- Department of Chemistry National University of Singapore 3 Science Drive 3 Singapore 117543 Singapore
| | - Shao Q. Yao
- Department of Chemistry National University of Singapore 3 Science Drive 3 Singapore 117543 Singapore
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17
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Yang J, He Y, Li Y, Zhang X, Wong YK, Shen S, Zhong T, Zhang J, Liu Q, Wang J. Advances in the research on the targets of anti-malaria actions of artemisinin. Pharmacol Ther 2020; 216:107697. [PMID: 33035577 PMCID: PMC7537645 DOI: 10.1016/j.pharmthera.2020.107697] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/30/2020] [Accepted: 09/30/2020] [Indexed: 01/01/2023]
Abstract
Malaria has been a global epidemic health threat since ancient times. It still claims roughly half a million lives every year in this century. Artemisinin and its derivatives, are frontline antimalarial drugs known for their efficacy and low toxicity. After decades of wide use, artemisinins remain our bulwark against malaria. Here, we review decades of efforts that aim to understand the mechanism of action (MOA) of artemisinins, which help explain the specificity and potency of this anti-malarial drug. We summarize the methods and approaches employed to unravel the MOA of artemisinin over the last three decades, showing how the development of advanced techniques can help provide mechanistic insights and resolve some long-standing questions in the field of artemisinin research. We also provide examples to illustrate how to better repurpose artemisinins for anti-cancer therapies by leveraging on MOA. These examples point out a practical direction to engineer artemisinin for broader applications beyond malaria.
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Affiliation(s)
- Jing Yang
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, China; Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yingke He
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, China; Department of Anaesthesiology, Singapore General Hospital, Singapore
| | - Yinbao Li
- School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, JiangXi 341000, China
| | - Xing Zhang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yin-Kwan Wong
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shengnan Shen
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Tianyu Zhong
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, China; Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China.
| | - Jianbin Zhang
- Department of Oncology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China.
| | - Qian Liu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, China.
| | - Jigang Wang
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, China; Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China; Central People's Hospital of Zhanjiang, Zhanjiang, Guangdong, China; Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China.
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18
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Voorneveld J, Florea BI, Bakkum T, Mendowicz RJ, van der Veer MS, Gagestein B, van Kasteren SI, van der Stelt M, Overkleeft HS, Filippov DV. Olaparib-Based Photoaffinity Probes for PARP-1 Detection in Living Cells. Chembiochem 2020; 21:2431-2434. [PMID: 32282108 PMCID: PMC7496120 DOI: 10.1002/cbic.202000042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/11/2020] [Indexed: 12/31/2022]
Abstract
The poly-ADP-ribose polymerase (PARP) is a protein from the family of ADP-ribosyltransferases that catalyzes polyadenosine diphosphate ribose (ADPR) formation in order to attract the DNA repair machinery to sites of DNA damage. The inhibition of PARP activity by olaparib can cause cell death, which is of clinical relevance in some tumor types. This demonstrates that quantification of PARP activity in the context of living cells is of great importance. In this work, we present the design, synthesis and biological evaluation of photo-activatable affinity probes inspired by the olaparib molecule that are equipped with a diazirine for covalent attachment upon activation by UV light and a ligation handle for the addition of a reporter group of choice. SDS-PAGE, western blotting and label-free LC-MS/MS quantification analysis show that the probes target the PARP-1 protein and are selectively outcompeted by olaparib; this suggests that they bind in the same enzymatic pocket. Proteomics data are available via ProteomeXchange with identifier PXD018661.
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Affiliation(s)
- Jim Voorneveld
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Bogdan I. Florea
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Thomas Bakkum
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Rafal J. Mendowicz
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Miriam S. van der Veer
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Berend Gagestein
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Sander I. van Kasteren
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Mario van der Stelt
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Herman S. Overkleeft
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Dmitri V. Filippov
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
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19
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Xu J, Zhang Z, Lin L, Sun H, White LV, Ding K, Li Z. Quantitative Proteomics Reveals Cellular Off-Targets of a DDR1 Inhibitor. ACS Med Chem Lett 2020; 11:535-540. [PMID: 32292561 DOI: 10.1021/acsmedchemlett.9b00658] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/05/2020] [Indexed: 12/17/2022] Open
Abstract
Target identification of small molecules is a great challenge but an essential step in drug discovery. Here, a quantitative proteomics approach has been used to characterize the cellular targets of DR, a DDR1 inhibitor. By taking advantage of competitive affinity-based protein profiling coupled with bioimaging, Cathepsin D (CTSD) was found to be the principle off-target of DR in human cancer cells. Further findings suggest the potential of DR as a novel CTSD inhibitor for breast cancer treatment. In addition, a trans-cyclooctene (TCO) containing probe was developed to track the binding between DR and its target proteins in living systems and could be a useful tool for DDR1 detection.
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Affiliation(s)
- Jiaqian Xu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, Guangzhou Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- Department of Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Hong Kong SAR 999077, China
| | - Zhang Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, Guangzhou Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ligen Lin
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau, China
| | - Hongyan Sun
- Department of Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Hong Kong SAR 999077, China
| | - Lorenzo V. White
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, Guangzhou Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, Guangzhou Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, Guangzhou Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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20
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Hong KT, Lee JS. Label-Free Proteome Profiling as a Quantitative Target Identification Technique for Bioactive Small Molecules. Biochemistry 2020; 59:213-215. [PMID: 31746590 DOI: 10.1021/acs.biochem.9b00975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kyung Tae Hong
- Molecular Recognition Research Center , Korea Institute of Science and Technology (KIST) , Hwarangro 14 gil 5 , Seunbguk-gu, Seoul 02792 , Republic of Korea.,Bio-Med Program , KIST-School UST , Hwarangro 14 gil 5 , Seungbuk-gu, Seoul 02792 , Republic of Korea
| | - Jun-Seok Lee
- Molecular Recognition Research Center , Korea Institute of Science and Technology (KIST) , Hwarangro 14 gil 5 , Seunbguk-gu, Seoul 02792 , Republic of Korea.,Bio-Med Program , KIST-School UST , Hwarangro 14 gil 5 , Seungbuk-gu, Seoul 02792 , Republic of Korea
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21
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Ma N, Zhang ZM, Lee JS, Cheng K, Lin L, Zhang DM, Hao P, Ding K, Ye WC, Li Z. Affinity-Based Protein Profiling Reveals Cellular Targets of Photoreactive Anticancer Inhibitors. ACS Chem Biol 2019; 14:2546-2552. [PMID: 31742988 DOI: 10.1021/acschembio.9b00784] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Affinity-based protein profiling has proven to be a powerful method in target identification of bioactive molecules. Here, this technology was applied in two photoreactive anticancer inhibitors, arenobufagin and HM30181. Using UV irradiation, these photoreactive reagents can covalently cross-link to target proteins, leading to a covalent binding with target proteins. Moreover, the cellular on/off targets of these two molecules, including ATP1A1, MDR1, PARP1, DDX5, NOP2, RAB6A, and ERGIC1 were first identified by affinity-based protein profiling and bioimaging approaches. The protein hit, PARP1, was further validated to be involved in the function of the anticancer effects.
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Affiliation(s)
- Nan Ma
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine, Modernization and Innovative Drug Development Ministry of Education (MOE) of People’s Republic of China, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine, Modernization and Innovative Drug Development Ministry of Education (MOE) of People’s Republic of China, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 136-791, Korea
| | - Ke Cheng
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine, Modernization and Innovative Drug Development Ministry of Education (MOE) of People’s Republic of China, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ligen Lin
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China
| | - Dong-Mei Zhang
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine, Modernization and Innovative Drug Development Ministry of Education (MOE) of People’s Republic of China, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Ke Ding
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine, Modernization and Innovative Drug Development Ministry of Education (MOE) of People’s Republic of China, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Wen-Cai Ye
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine, Modernization and Innovative Drug Development Ministry of Education (MOE) of People’s Republic of China, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine, Modernization and Innovative Drug Development Ministry of Education (MOE) of People’s Republic of China, 601 Huangpu Avenue West, Guangzhou 510632, China
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22
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Xu J, Li X, Ding K, Li Z. Applications of Activity-Based Protein Profiling (ABPP) and Bioimaging in Drug Discovery. Chem Asian J 2019; 15:34-41. [PMID: 31762171 DOI: 10.1002/asia.201901500] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Indexed: 01/12/2023]
Abstract
Activity-based protein profiling (ABPP) and bioimaging have been developed in recent years as powerful technologies in drug discovery. Specifically, both approaches can be applied in critical steps of drug development, such as therapy target discovery, high-throughput drug screening and target identification of bioactive molecules. We have been focused on the development of various strategies that enable simultaneous activity-based protein profiling and bioimaging studies, thus facilitating an understanding of drug actions and potential toxicities. In this Minireview, we summarize these novel strategies and applications, with the aim of promoting these technologies in drug discovery.
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Affiliation(s)
- Jiaqian Xu
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China.,Department of Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Hong Kong SAR, 999077, China
| | - Xiaoqian Li
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Ke Ding
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China
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23
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Lang W, Yuan C, Zhu B, Pan S, Liu J, Luo J, Nie S, Zhu Q, Lee JS, Ge J. Expanding the "minimalist" small molecule tagging approach to different bioactive compounds. Org Biomol Chem 2019; 17:3010-3017. [PMID: 30816385 DOI: 10.1039/c8ob03175d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
"Minimalist" small molecule tagging (MSMT) is a promising approach that easily converts bioactive compounds into affinity-based probes (AfBPs) for proteomic studies. In this work, seven bioactive compounds targeting diversified protein classes were installed with "minimalist" linkers through common reactions to generate the corresponding AfBPs. These probes were evaluated for cell-based protein profiling and target validation. Among them, the entinostat-derived probe EN and the camptothecin-derived probe CA were further utilized in cellular imaging and SILAC-based large-scale target identification. Our extensive studies suggest that the "minimalist" small molecule tagging approach could be expanded to different classes of bioactive compounds for modification into AfBPs as a dual functional tool for both proteomics and cellular imaging.
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Affiliation(s)
- Wenjie Lang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China.
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24
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Dong J, Hong D, Lang W, Huang J, Qian L, Zhu Q, Li L, Ge J. Differently Tagged Probes for Protein Profiling of Mitochondria. Chembiochem 2019; 20:1155-1160. [PMID: 30600897 DOI: 10.1002/cbic.201800735] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 11/10/2022]
Abstract
The mitochondrion is one of the most important organelles in the eukaryotic cell. Characterization of the mitochondrial proteome is a prerequisite for understanding its cellular functions at the molecular level. Here we report a proteomics method based on mitochondrion-targeting groups and click chemistry. In our strategy, three different mitochondrion-targeting moieties were each augmented with a clickable handle and a cysteine-reactive group. Fluorescence-based bioimaging and fractionation experiments clearly showed that most signals arising from the labels were localized in the mitochondria of cells, as a result of covalent attachment between probe and target proteins. The three probes had distinct profiling characteristics. Furthermore, we successfully identified more than two hundred mitochondrial proteins. The results showed that different mitochondrion-targeting groups targeted distinct proteins with partial overlap. Most of the labeled proteins were localized in the mitochondrial matrix and inner mitochondrial membrane. Our results provide a tool for chemoproteomic analysis of mitochondrion-related proteins.
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Affiliation(s)
- Jia Dong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Danqi Hong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Wenjie Lang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Jintao Huang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Linghui Qian
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Qing Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, China
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
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25
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Hyun JY, Park SH, Park CW, Kim HB, Cho JW, Shin I. Trifunctional Fluorogenic Probes for Fluorescence Imaging and Isolation of Glycosidases in Cells. Org Lett 2019; 21:4439-4442. [DOI: 10.1021/acs.orglett.9b01147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Li L, Zhao Y, Cao R, Li L, Cai G, Li J, Qi X, Chen S, Zhang Z. Activity-based protein profiling reveals GSTO1 as the covalent target of piperlongumine and a promising target for combination therapy for cancer. Chem Commun (Camb) 2019; 55:4407-4410. [PMID: 30916079 DOI: 10.1039/c9cc00917e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Through systematic target identification for piperlongumine, a cancer-selective killing molecule, we identified GSTO1 as its major covalent target for cancer cell death induction. We also reveal that GSTO1 inhibition is a promising combination strategy with other anti-cancer agents by drug combination screening in which piperlongumine exhibits broad-spectrum synergistic effects with a large proportion of the tested anti-cancer agents, especially with PI3K/Akt/mTOR pathway inhibitors.
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Affiliation(s)
- Li Li
- National Institute of Biological Sciences (NIBS), Beijing, 7 Science Park Rd., ZGC Life Science Park, Beijing, P. R. China.
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Vil’ VA, Gorlov ES, Bityukov OV, Krylov IB, Nikishin GI, Pivnitsky KK, Terent’ev AO. Oxidative C–O coupling as a new idea in the ‘click-like chemistry’: malonyl peroxides for the conjugation of two molecules. MENDELEEV COMMUNICATIONS 2019. [DOI: 10.1016/j.mencom.2019.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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28
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Abstract
Natural products (NPs) are important sources of clinical drugs due to their structural diversity and biological prevalidation. However, the structural complexity of NPs leads to synthetic difficulties, unfavorable pharmacokinetic profiles, and poor drug-likeness. Structural simplification by truncating unnecessary substructures is a powerful strategy for overcoming these limitations and improving the efficiency and success rate of NP-based drug development. Herein, we will provide a comprehensive review of the structural simplification of NPs with a focus on design strategies, case studies, and new technologies. In particular, a number of successful examples leading to marketed drugs or drug candidates will be discussed in detail to illustrate how structural simplification is applied in lead optimization of NPs.
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Affiliation(s)
- Shengzheng Wang
- Department of Medicinal Chemistry, School of Pharmacy , Second Military Medical University , 325 Guohe Road , Shanghai , 200433 , P.R. China.,Department of Medicinal Chemistry, School of Pharmacy , Fourth Military Medical University , 169 Changle West Road , Xi'an , 710032 , P.R. China
| | - Guoqiang Dong
- Department of Medicinal Chemistry, School of Pharmacy , Second Military Medical University , 325 Guohe Road , Shanghai , 200433 , P.R. China
| | - Chunquan Sheng
- Department of Medicinal Chemistry, School of Pharmacy , Second Military Medical University , 325 Guohe Road , Shanghai , 200433 , P.R. China
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Catalyst-free cycloaddition of 1,3-diene-1-carbamates with azodicarboxylates: A rapid click reaction. Bioorg Med Chem 2019; 27:2438-2443. [PMID: 30755349 DOI: 10.1016/j.bmc.2019.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/02/2019] [Indexed: 11/21/2022]
Abstract
Novel click reactions are of continued interest in many scientific research areas and applications. Herein, we report a novel practical, catalyst-free, azo-Diels-Alder reaction between dienecarbamates and azodicarboxylates exhibiting a remarkable functional group tolerance. The availability of starting materials, mild reaction conditions, chemoselectivity and scalability make this cycloaddition a viable supplement to the other reactions in "click" chemistry.
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30
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Ying S, Du S, Dong J, Ng BX, Zhang C, Li L, Ge J, Zhu Q. Intracellular effects of prodrug-like wortmannin probes. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2018.05.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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31
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Wang Z, Guo Z, Song T, Zhang X, He N, Liu P, Wang P, Zhang Z. Proteome-Wide Identification of On- and Off-Targets of Bcl-2 Inhibitors in Native Biological Systems by Using Affinity-Based Probes (AfBPs). Chembiochem 2018; 19:2312-2320. [DOI: 10.1002/cbic.201800380] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Ziqian Wang
- Zhang Dayu School of Chemistry; State Key Laboratory of Fine Chemicals; Dalian University of Technology; No. 2 Linggong Road Dalian 116024 P.R. China
| | - Zongwei Guo
- School of Life Science and Technology; Dalian University of Technology; No. 2 Linggong Road Dalian 116024 P.R. China
| | - Ting Song
- State Key Laboratory of Fine Chemicals; School of Chemistry; Dalian University of Technology; No. 2 Linggong Road Dalian 116024 P.R. China
| | - Xiaodong Zhang
- State Key Laboratory of Fine Chemicals; School of Chemistry; Dalian University of Technology; No. 2 Linggong Road Dalian 116024 P.R. China
| | - Nianzhe He
- State Key Laboratory of Fine Chemicals; School of Chemistry; Dalian University of Technology; No. 2 Linggong Road Dalian 116024 P.R. China
| | - Peng Liu
- School of Life Science and Technology; Dalian University of Technology; No. 2 Linggong Road Dalian 116024 P.R. China
| | - Peiran Wang
- State Key Laboratory of Fine Chemicals; School of Chemistry; Dalian University of Technology; No. 2 Linggong Road Dalian 116024 P.R. China
| | - Zhichao Zhang
- State Key Laboratory of Fine Chemicals; School of Chemistry; Dalian University of Technology; No. 2 Linggong Road Dalian 116024 P.R. China
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Zheng B, Guo H, Ma N, Ni Y, Xu J, Li L, Hao P, Ding K, Li Z. Cell- and Tissue-Based Proteome Profiling and Bioimaging with Probes Derived from a Potent AXL Kinase Inhibitor. Chem Asian J 2018; 13:2601-2605. [PMID: 29939481 DOI: 10.1002/asia.201800605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/17/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Binbin Zheng
- School of Pharmacy, Jinan University; Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China; 601 Huangpu Avenue West Guangzhou 510632 China
| | - Haijun Guo
- School of Pharmacy, Jinan University; Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China; 601 Huangpu Avenue West Guangzhou 510632 China
| | - Nan Ma
- School of Pharmacy, Jinan University; Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China; 601 Huangpu Avenue West Guangzhou 510632 China
| | - Yun Ni
- Institute of Advanced Materials (IAM); Nanjing Tech University; China
| | - Jiaqian Xu
- School of Pharmacy, Jinan University; Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China; 601 Huangpu Avenue West Guangzhou 510632 China
| | - Lin Li
- Institute of Advanced Materials (IAM); Nanjing Tech University; China
| | - Piliang Hao
- School of Life Science and Technology; ShanghaiTech University; China
| | - Ke Ding
- School of Pharmacy, Jinan University; Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China; 601 Huangpu Avenue West Guangzhou 510632 China
| | - Zhengqiu Li
- School of Pharmacy, Jinan University; Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China; 601 Huangpu Avenue West Guangzhou 510632 China
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33
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Target identification reveals protein arginine methyltransferase 1 is a potential target of phenyl vinyl sulfone and its derivatives. Biosci Rep 2018. [PMID: 29540535 PMCID: PMC5968187 DOI: 10.1042/bsr20171717] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Phenyl vinyl sulfone (PVS) and phenyl vinyl sulfonate (PVSN) inactivate protein tyrosine phosphatases (PTPs) by mimicking the phosphotyrosine structure and providing a Michael addition acceptor for the active-site cysteine residue of PTPs, thus forming covalent adducts between PVS (or PVSN) and PTPs. We developed a specific antiserum against PVS. This antiserum can be used in general antibody-based assays such as immunoblotting, immunofluorescence staining, and immunoprecipitation. Target identification through immunoprecipitation and mass spectrometry analysis reveals potential targets of PVS, mostly proteins with reactive cysteine residues or low-pKa cysteine residues that are prone to reversible redox modifications. Target identification of PVSN has been conducted because the anti-PVS antiserum can also recognize PVSN. Among the targets, protein arginine methyltransferase 1 (PRMT1), inosine-5'-monophosphate dehydrogenase 1, vimentin, and glutathione reductase (GR) were further confirmed by immunoprecipitation followed by immunoblotting. In addition, PVSN and Bay11-7082 inhibited GR activity, and PVS, PVSN, and Bay 11-7082 inhibited PRMT1 activity in in vitro assays. In addition, treatment of PVSN, Bay11-7082, or Bay 11-7085 in cultured HeLa cells can cause the quick decline in the levels of protein asymmetric dimethylarginine. These results indicate that the similar moiety among PVS, PVSN, Bay 11-7082, and Bay 11-7085 can be the key structure of lead compounds of PRMT1. Therefore, we expect to use this approach in the identification of potential targets of other covalent drugs.
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Tian C, Sun R, Liu K, Fu L, Liu X, Zhou W, Yang Y, Yang J. Multiplexed Thiol Reactivity Profiling for Target Discovery of Electrophilic Natural Products. Cell Chem Biol 2017; 24:1416-1427.e5. [PMID: 28988947 DOI: 10.1016/j.chembiol.2017.08.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/06/2017] [Accepted: 08/30/2017] [Indexed: 02/09/2023]
Abstract
Electrophilic groups, such as Michael acceptors, expoxides, are common motifs in natural products (NPs). Electrophilic NPs can act through covalent modification of cysteinyl thiols on functional proteins, and exhibit potent cytotoxicity and anti-inflammatory/cancer activities. Here we describe a new chemoproteomic strategy, termed multiplexed thiol reactivity profiling (MTRP), and its use in target discovery of electrophilic NPs. We demonstrate the utility of MTRP by identifying cellular targets of gambogic acid, an electrophilic NP that is currently under evaluation in clinical trials as anticancer agent. Moreover, MTRP enables simultaneous comparison of seven structurally diversified α,β-unsaturated γ-lactones, which provides insights into the relative proteomic reactivity and target preference of diverse structural scaffolds coupled to a common electrophilic motif and reveals various potential druggable targets with liganded cysteines. We anticipate that this new method for thiol reactivity profiling in a multiplexed manner will find broad application in redox biology and drug discovery.
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Affiliation(s)
- Caiping Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences - Beijing, Beijing 102206, China
| | - Rui Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences - Beijing, Beijing 102206, China; State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Keke Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences - Beijing, Beijing 102206, China
| | - Ling Fu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences - Beijing, Beijing 102206, China
| | - Xiaoyu Liu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Wanqi Zhou
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Yong Yang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Jing Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences - Beijing, Beijing 102206, China.
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35
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Chen X, Zhang J, Yuan L, Lay Y, Wong YK, Lim TK, Ong CS, Lin Q, Wang J, Hua Z. Andrographolide Suppresses MV4-11 Cell Proliferation through the Inhibition of FLT3 Signaling, Fatty Acid Synthesis and Cellular Iron Uptake. Molecules 2017; 22:molecules22091444. [PMID: 28858244 PMCID: PMC6151431 DOI: 10.3390/molecules22091444] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 12/28/2022] Open
Abstract
Background: Andrographolide (ADR), the main active component of Andrographis paniculata, displays anticancer activity in various cancer cell lines, among which leukemia cell lines exhibit the highest sensitivity to ADR. In particular, ADR was also reported to have reduced drug resistance in multidrug resistant cell lines. However, the mechanism of action (MOA) of ADR’s anticancer and anti-drug-resistance activities remain elusive. Methods: In this study, we used the MV4-11 cell line, a FLT3 positive acute myeloid leukemia (AML) cell line that displays multidrug resistance, as our experimental system. We first evaluated the effect of ADR on MV4-11 cell proliferation. Then, a quantitative proteomics approach was applied to identify differentially expressed proteins in ADR-treated MV4-11 cells. Finally, cellular processes and signal pathways affected by ADR in MV4-11 cell were predicted with proteomic analysis and validated with in vitro assays. Results: ADR inhibits MV4-11 cell proliferation in a dose- and time-dependent manner. With a proteomic approach, we discovered that ADR inhibited fatty acid synthesis, cellular iron uptake and FLT3 signaling pathway in MV4-11 cells. Conclusions: ADR inhibits MV4-11 cell proliferation through inhibition of fatty acid synthesis, iron uptake and protein synthesis. Furthermore, ADR reduces drug resistance by blocking FLT3 signaling.
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Affiliation(s)
- Xiao Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
| | - Jianbin Zhang
- Department of Oncology, Clinical Research Institute, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310014, China.
| | - Lixia Yuan
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China.
| | - Yifei Lay
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Yin Kwan Wong
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Teck Kwang Lim
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Chye Sun Ong
- Institute of Mental Health, Education Office, Singapore 539747, Singapore.
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Jigang Wang
- Department of Biological Sciences, 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 Target Pharma 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 Target Pharma Laboratories Inc., Changzhou 213164, China.
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36
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Pan S, Jang SY, Wang D, Liew SS, Li Z, Lee JS, Yao SQ. A Suite of “Minimalist” Photo-Crosslinkers for Live-Cell Imaging and Chemical Proteomics: Case Study with BRD4 Inhibitors. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706076] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sijun Pan
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Se-Young Jang
- Molecular Recognition Research Center; Bio-Med Program of KIST-School UST; Korea Institute of Science & Technology; Hwarangno 14-gil 5, Seongbuk-gu Seoul 136-791 Korea
| | - Danyang Wang
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Si Si Liew
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Zhengqiu Li
- College of Pharmacy; Jinan University; Guangzhou 510632 China
| | - Jun-Seok Lee
- Molecular Recognition Research Center; Bio-Med Program of KIST-School UST; Korea Institute of Science & Technology; Hwarangno 14-gil 5, Seongbuk-gu Seoul 136-791 Korea
| | - Shao Q. Yao
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
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37
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Pan S, Jang SY, Wang D, Liew SS, Li Z, Lee JS, Yao SQ. A Suite of "Minimalist" Photo-Crosslinkers for Live-Cell Imaging and Chemical Proteomics: Case Study with BRD4 Inhibitors. Angew Chem Int Ed Engl 2017; 56:11816-11821. [PMID: 28783236 DOI: 10.1002/anie.201706076] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/28/2017] [Indexed: 11/08/2022]
Abstract
Affinity-based probes (AfBPs) provide a powerful tool for large-scale chemoproteomic studies of drug-target interactions. The development of high-quality probes capable of recapitulating genuine drug-target engagement, however, could be challenging. "Minimalist" photo-crosslinkers, which contain an alkyl diazirine group and a chemically tractable tag, could alleviate such challenges, but few are currently available. Herein, we have developed new alkyl diazirine-containing photo-crosslinkers with different bioorthogonal tags. They were subsequently used to create a suite of AfBPs based on GW841819X (a small molecule inhibitor of BRD4). Through in vitro and in situ studies under conditions that emulated native drug-target interactions, we have obtained better insights into how a tag might affect the probe's performance. Finally, SILAC-based chemoproteomic studies have led to the discovery of a novel off-target, APEX1. Further studies showed GW841819X binds to APEX1 and caused up-regulation of endogenous DNMT1 expression under normoxia conditions.
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Affiliation(s)
- Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Se-Young Jang
- Molecular Recognition Research Center, Bio-Med Program of KIST-School UST, Korea Institute of Science & Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 136-791, Korea
| | - Danyang Wang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Si Si Liew
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Zhengqiu Li
- College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Bio-Med Program of KIST-School UST, Korea Institute of Science & Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 136-791, Korea
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
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38
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Guo H, Li Z. Developments of bioorthogonal handle-containing photo-crosslinkers for photoaffinity labeling. MEDCHEMCOMM 2017; 8:1585-1591. [PMID: 30108869 PMCID: PMC6071706 DOI: 10.1039/c7md00217c] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 06/14/2017] [Indexed: 01/14/2023]
Abstract
Photoaffinity labeling (PAL) has been widely applied in various research areas such as medicinal chemistry, chemical biology and structural biology, owing to its capability of investigating non-covalent ligand-protein interactions under native environments and elucidating protein structures, functions etc. One important application of this technique is to use affinity-based proteome profiling (AfBP) coupled with bioimaging for profiling drug-target interactions in situ. In order to accurately report drug-target interactions via these approaches, several considerations as follows need to be made: (1) maximally retaining bioactivities of photoprobes upon functionalization with a photoreactive group and a reporter tag from a parental compound; (2) performing proteome profiling and imaging in situ simultaneously, to monitor drug-target interactions in different manners; and (3) developing excellent photo-crosslinkers capable of photo-crosslinking and fluorescence turn-on at the same time. With these considerations in mind, we have developed three versions of "minimalist" bioorthogonal handle-containing photo-crosslinkers (L3-L6) during the years and successfully applied them in all kinds of small bioactive molecules for protein labeling and cellular imaging studies. In this mini-review, the features and functions of these linkers are specifically highlighted and summarized.
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Affiliation(s)
- Haijun Guo
- College of Pharmacy , Jinan University , Guangzhou , 510632 China .
| | - Zhengqiu Li
- College of Pharmacy , Jinan University , Guangzhou , 510632 China .
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39
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Wang DY, Cao Y, Zheng LY, Chen LD, Chen XF, Hong ZY, Zhu ZY, Li X, Chai YF. Target Identification of Kinase Inhibitor Alisertib (MLN8237) by Using DNA-Programmed Affinity Labeling. Chemistry 2017; 23:10906-10914. [DOI: 10.1002/chem.201702033] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Dong-Yao Wang
- School of Pharmacy; Second Military Medical University; No. 325 Guohe Road Shanghai 200433 P.R. China
| | - Yan Cao
- School of Pharmacy; Second Military Medical University; No. 325 Guohe Road Shanghai 200433 P.R. China
| | - Le-Yi Zheng
- School of Pharmacy; Second Military Medical University; No. 325 Guohe Road Shanghai 200433 P.R. China
| | - Lang-Dong Chen
- School of Pharmacy; Second Military Medical University; No. 325 Guohe Road Shanghai 200433 P.R. China
| | - Xiao-Fei Chen
- School of Pharmacy; Second Military Medical University; No. 325 Guohe Road Shanghai 200433 P.R. China
| | - Zhan-Ying Hong
- School of Pharmacy; Second Military Medical University; No. 325 Guohe Road Shanghai 200433 P.R. China
| | - Zhen-Yu Zhu
- School of Pharmacy; Second Military Medical University; No. 325 Guohe Road Shanghai 200433 P.R. China
| | - Xiaoyu Li
- Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong SAR China
| | - Yi-Feng Chai
- School of Pharmacy; Second Military Medical University; No. 325 Guohe Road Shanghai 200433 P.R. China
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40
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Pan S, Zhang H, Wang C, Yao SCL, Yao SQ. Target identification of natural products and bioactive compounds using affinity-based probes. Nat Prod Rep 2017; 33:612-20. [PMID: 26580476 DOI: 10.1039/c5np00101c] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Covering: 2010 to 2014.Advances in isolation, synthesis and screening strategies have made many bioactive substances available. However, in most cases their putative biological targets remain unknown. Herein, we highlight recent advances in target identification of natural products and bioactive compounds by using affinity-based probes. Aided by photoaffinity labelling, this strategy can capture potential cellular targets (on and off) of a natural product or bioactive compound in live cells directly, even when the compound-target interaction is reversible with moderate affinity. The knowledge of these targets may help uncover molecular pathways and new therapeutics for currently untreatable diseases. In this highlight, we will introduce the development of various photoactivatable groups, their synthesis and applications in target identification of natural products and bioactive compounds, with a focus on work done in recent years and from our laboratory. We will further discuss the strengths and weaknesses of each group and the outlooks for this novel proteome-wide profiling strategy.
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Affiliation(s)
- Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Hailong Zhang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Chenyu Wang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Samantha C L Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
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41
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Kang K, Park J, Kim E. Tetrazine ligation for chemical proteomics. Proteome Sci 2017; 15:15. [PMID: 28674480 PMCID: PMC5485739 DOI: 10.1186/s12953-017-0121-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 06/15/2017] [Indexed: 12/12/2022] Open
Abstract
Determining small molecule-target protein interaction is essential for the chemical proteomics. One of the most important keys to explore biological system in chemical proteomics field is finding first-class molecular tools. Chemical probes can provide great spatiotemporal control to elucidate biological functions of proteins as well as for interrogating biological pathways. The invention of bioorthogonal chemistry has revolutionized the field of chemical biology by providing superior chemical tools and has been widely used for investigating the dynamics and function of biomolecules in live condition. Among 20 different bioorthogonal reactions, tetrazine ligation has been spotlighted as the most advanced bioorthogonal chemistry because of their extremely faster kinetics and higher specificity than others. Therefore, tetrazine ligation has a tremendous potential to enhance the proteomic research. This review highlights the current status of tetrazine ligation reaction as a molecular tool for the chemical proteomics.
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Affiliation(s)
- Kyungtae Kang
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi 17104 Republic of Korea
| | - Jongmin Park
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge St, CPZN 5206, Boston, Massachusetts 02114 USA
| | - Eunha Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499 Republic of Korea
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Terent'ev AO, Vil' VA, Gorlov ES, Rusina ON, Korlyukov AA, Nikishin GI, Adam W. Selective Oxidative Coupling of 3H-Pyrazol-3-ones, Isoxazol-5(2H)-ones, Pyrazolidine-3,5-diones, and Barbituric Acids with Malonyl Peroxides: An Effective C-O Functionalization. ChemistrySelect 2017. [DOI: 10.1002/slct.201700720] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alexander O. Terent'ev
- N. D. Zelinsky Institute of Organic Chemistry; Russian Academy of Sciences; Leninsky Prospekt 47 Moscow 119991 Russian Federation
- D. I. Mendeleev University of Chemical Technology of Russia; 9 Miusskaya square Moscow 125047 Russian Federation
- All-Russian Research Institute for Phytopathology; B. Vyazyomy Moscow Region 143050 Russian Federation
| | - Vera A. Vil'
- N. D. Zelinsky Institute of Organic Chemistry; Russian Academy of Sciences; Leninsky Prospekt 47 Moscow 119991 Russian Federation
- D. I. Mendeleev University of Chemical Technology of Russia; 9 Miusskaya square Moscow 125047 Russian Federation
- All-Russian Research Institute for Phytopathology; B. Vyazyomy Moscow Region 143050 Russian Federation
| | - Evgenii S. Gorlov
- N. D. Zelinsky Institute of Organic Chemistry; Russian Academy of Sciences; Leninsky Prospekt 47 Moscow 119991 Russian Federation
- D. I. Mendeleev University of Chemical Technology of Russia; 9 Miusskaya square Moscow 125047 Russian Federation
| | - Olga N. Rusina
- N. D. Zelinsky Institute of Organic Chemistry; Russian Academy of Sciences; Leninsky Prospekt 47 Moscow 119991 Russian Federation
- D. I. Mendeleev University of Chemical Technology of Russia; 9 Miusskaya square Moscow 125047 Russian Federation
| | - Alexander A. Korlyukov
- A. N. Nesmeyanov Institute of Organoelement Compounds; Russian Academy of Sciences; 28 Vavilova ul Moscow 119991 Russian Federation
- Pirogov Russian National Research Medical University; Ostrovitianov str. 1 Moscow 117997 Russian Federation
| | - Gennady I. Nikishin
- N. D. Zelinsky Institute of Organic Chemistry; Russian Academy of Sciences; Leninsky Prospekt 47 Moscow 119991 Russian Federation
| | - Waldemar Adam
- Institute of Organic Chemistry; University of Würzburg; Am Hubland, D- 97074 Würzburg Germany
- Department of Chemistry, Faculty of Natural Sciences; University of Puerto Rico; Rio Piedras Puerto Rico 00931 USA
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43
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Fung SK, Zou T, Cao B, Lee PY, Fung YME, Hu D, Lok CN, Che CM. Cyclometalated Gold(III) Complexes Containing N-Heterocyclic Carbene Ligands Engage Multiple Anti-Cancer Molecular Targets. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612583] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sin Ki Fung
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Taotao Zou
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Bei Cao
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Pui-Yan Lee
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Yi Man Eva Fung
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Di Hu
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Chun-Nam Lok
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Chi-Ming Che
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
- HKU Shenzhen Institute of Research and Innovation; Shenzhen 518053 China
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44
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Fung SK, Zou T, Cao B, Lee PY, Fung YME, Hu D, Lok CN, Che CM. Cyclometalated Gold(III) Complexes Containing N-Heterocyclic Carbene Ligands Engage Multiple Anti-Cancer Molecular Targets. Angew Chem Int Ed Engl 2017; 56:3892-3896. [PMID: 28247451 DOI: 10.1002/anie.201612583] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Indexed: 01/03/2023]
Abstract
Metal N-heterocyclic carbene (NHC) complexes are a promising class of anti-cancer agents displaying potent in vitro and in vivo activities. Taking a multi-faceted approach employing two clickable photoaffinity probes, herein we report the identification of multiple molecular targets for anti-cancer active pincer gold(III) NHC complexes. These complexes display potent and selective cytotoxicity against cultured cancer cells and in vivo anti-tumor activities in mice bearing xenografts of human cervical and lung cancers. Our experiments revealed the specific engagement of the gold(III) complexes with multiple cellular targets, including HSP60, vimentin, nucleophosmin, and YB-1, accompanied by expected downstream mechanisms of action. Additionally, PtII and PdII analogues can also bind the cellular proteins targeted by the gold(III) complexes, uncovering a distinct pincer cyclometalated metal-NHC scaffold in the design of anti-cancer metal medicines with multiple molecular targets.
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Affiliation(s)
- Sin Ki Fung
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Taotao Zou
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Bei Cao
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Pui-Yan Lee
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yi Man Eva Fung
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Di Hu
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chun-Nam Lok
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chi-Ming Che
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.,HKU Shenzhen Institute of Research and Innovation, Shenzhen, 518053, China
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45
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Zhou Y, Li W, Wang M, Zhang X, Zhang H, Tong X, Xiao Y. Competitive profiling of celastrol targets in human cervical cancer HeLa cells via quantitative chemical proteomics. MOLECULAR BIOSYSTEMS 2017; 13:83-91. [DOI: 10.1039/c6mb00691d] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We reported the proteome-wide profiling of cellular targets of celastrol in HeLa cellsviacompetitive chemoproteomics approach utilizing a cysteine-targeting activity-based probe.
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Affiliation(s)
- Yiqing Zhou
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Weichao Li
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Mingli Wang
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Xixi Zhang
- University of Chinese Academy of Sciences
- Beijing 100039
- China
- Institute for Nutritional Sciences
- Shanghai Institutes for Biological Sciences
| | - Haibing Zhang
- Institute for Nutritional Sciences
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Xiaofeng Tong
- Department of Chemistry
- East China University of Science and Technology
- Shanghai 200001
- China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
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46
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Wang D, Cao Y, Zheng L, Lv D, Chen L, Xing X, Zhu Z, Li X, Chai Y. Identification of Annexin A2 as a target protein for plant alkaloid matrine. Chem Commun (Camb) 2017; 53:5020-5023. [DOI: 10.1039/c7cc02227a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The cellular target of matrine is identified.
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Affiliation(s)
- Dongyao Wang
- School of Pharmacy
- Second Military Medical University
- Shanghai
- China
| | - Yan Cao
- School of Pharmacy
- Second Military Medical University
- Shanghai
- China
| | - Leyi Zheng
- School of Pharmacy
- Second Military Medical University
- Shanghai
- China
| | - Diya Lv
- School of Pharmacy
- Second Military Medical University
- Shanghai
- China
| | - Langdong Chen
- School of Pharmacy
- Second Military Medical University
- Shanghai
- China
| | - Xinrui Xing
- School of Pharmacy
- Second Military Medical University
- Shanghai
- China
| | - Zhenyu Zhu
- School of Pharmacy
- Second Military Medical University
- Shanghai
- China
| | - Xiaoyu Li
- Department of Chemistry
- The University of Hong Kong
- Hong Kong SAR
- China
| | - Yifeng Chai
- School of Pharmacy
- Second Military Medical University
- Shanghai
- China
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47
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Guo H, Xu J, Hao P, Ding K, Li Z. Competitive affinity-based proteome profiling and imaging to reveal potential cellular targets of betulinic acid. Chem Commun (Camb) 2017; 53:9620-9623. [DOI: 10.1039/c7cc04190j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Affinity-based proteome profiling (AfBP) coupled with bioimaging to uncover cellular targets of betulinic acid.
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Affiliation(s)
- Haijun Guo
- College of Pharmacy
- Jinan University
- Guangzhou
- China
| | - Jiaqian Xu
- College of Pharmacy
- Jinan University
- Guangzhou
- China
| | - Piliang Hao
- School of Life Science and Technology
- ShanghaiTech University
- Shanghai 201210
- China
| | - Ke Ding
- College of Pharmacy
- Jinan University
- Guangzhou
- China
| | - Zhengqiu Li
- College of Pharmacy
- Jinan University
- Guangzhou
- China
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48
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de S. Vilhena F, de M. Carneiro JW. Reactivity and regioselectivity in reactions of methyl and ethyl azides with cyclooctynes: activation strain model and energy decomposition analysis. J Mol Model 2016; 23:14. [DOI: 10.1007/s00894-016-3178-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 11/28/2016] [Indexed: 10/20/2022]
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49
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Xie Y, Ge J, Lei H, Peng B, Zhang H, Wang D, Pan S, Chen G, Chen L, Wang Y, Hao Q, Yao SQ, Sun H. Fluorescent Probes for Single-Step Detection and Proteomic Profiling of Histone Deacetylases. J Am Chem Soc 2016; 138:15596-15604. [DOI: 10.1021/jacs.6b07334] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yusheng Xie
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Jingyan Ge
- College
of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People’s Republic of China
| | - Haipeng Lei
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Bo Peng
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Huatang Zhang
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Danyang Wang
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Sijun Pan
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Ganchao Chen
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Lanfang Chen
- Department
of Physiology, University of Hong Kong, Pok Fu Lam, Hong Kong, People’s Republic of China
| | - Yi Wang
- Department
of Physiology, University of Hong Kong, Pok Fu Lam, Hong Kong, People’s Republic of China
| | - Quan Hao
- Department
of Physiology, University of Hong Kong, Pok Fu Lam, Hong Kong, People’s Republic of China
| | - Shao Q. Yao
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Hongyan Sun
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
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50
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Problems and Solutions in Click Chemistry Applied to Drug Probes. Sci Rep 2016; 6:35579. [PMID: 27782133 PMCID: PMC5080546 DOI: 10.1038/srep35579] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/30/2016] [Indexed: 01/24/2023] Open
Abstract
Small-molecule fluorescent probes have been widely used in target identification, but this method has many disadvantages. For example, the identified proteins are usually complex, and additional biochemical studies are needed to distinguish real targets from interference results. To address this problem, we propose a series of strategies for improving the efficiency of target identification. First, pretreatment with a lower concentration of hydrogen peroxide can shield against thiol interference. Second, the use of benzophenone as a photo-affinity group is not appropriate, and diazirines are preferred. Third, if cytoskeleton proteins or stress proteins are captured, the interference must be carefully eliminated. The specificity of target identification can be improved by optimizing these three strategies. In this paper, we discuss the problems associated with the use of the click reaction in living cells and provide important complementary techniques for photo-affinity probes based on the click chemistry reaction.
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