151
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Flaxman HA, Chang CF, Wu HY, Nakamoto CH, Woo CM. A Binding Site Hotspot Map of the FKBP12-Rapamycin-FRB Ternary Complex by Photoaffinity Labeling and Mass Spectrometry-Based Proteomics. J Am Chem Soc 2019; 141:11759-11764. [PMID: 31309829 DOI: 10.1021/jacs.9b03764] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Structural characterization of small molecule binding site hotspots within the global proteome is uniquely enabled by photoaffinity labeling (PAL) coupled with chemical enrichment and unbiased analysis by mass spectrometry (MS). MS-based binding site maps provide structural resolution of interaction sites in conjunction with identification of target proteins. However, binding site hotspot mapping has been confined to relatively simple small molecules to date; extension to more complex compounds would enable the structural definition of new binding modes in the proteome. Here, we extend PAL and MS methods to derive a binding site hotspot map for the immunosuppressant rapamycin, a complex macrocyclic natural product that forms a ternary complex with the proteins FKBP12 and FRB. Photo-rapamycin was developed as a diazirine-based PAL probe for rapamycin, and the FKBP12-photo-rapamycin-FRB ternary complex formed readily in vitro. Photoirradiation, digestion, and MS analysis of the ternary complex revealed a McLafferty rearrangement product of photo-rapamycin conjugated to specific surfaces on FKBP12 and FRB. Molecular modeling based on the binding site map revealed two distinct conformations of complex-bound photo-rapamycin, providing a 5.0 Å distance constraint between the conjugated residues and the diazirine carbon and a 9.0 Å labeling radius for the diazirine upon photoactivation. These measurements may be broadly useful in the interpretation of binding site measurements from PAL. Thus, in characterizing the ternary complex of photo-rapamycin by MS, we applied binding site hotspot mapping to a macrocyclic natural product and extracted precise structural measurements for interpretation of PAL products that may enable the discovery of new binding sites in the "undruggable" proteome.
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Affiliation(s)
- Hope A Flaxman
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Chia-Fu Chang
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Hung-Yi Wu
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Carter H Nakamoto
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Christina M Woo
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
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152
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Lim B, Lee J, Kim B, Lee R, Park J, Oh D, Gam J, Lee J. Target Identification of a 1,3,4‐Oxadiazin‐5(6
H
)‐One Anticancer Agent via Photoaffinity Labelling. ASIAN J ORG CHEM 2019. [DOI: 10.1002/ajoc.201900258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Bumhee Lim
- College of PharmacyResearch Institute of Pharmaceutical sciencesSeoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Korea
| | - Jinah Lee
- College of PharmacyResearch Institute of Pharmaceutical sciencesSeoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Korea
| | - Byungjin Kim
- College of PharmacyResearch Institute of Pharmaceutical sciencesSeoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Korea
| | - Rang Lee
- College of PharmacyResearch Institute of Pharmaceutical sciencesSeoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Korea
| | - Jaehyun Park
- College of PharmacyResearch Institute of Pharmaceutical sciencesSeoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Korea
| | - Dong‐Chan Oh
- College of PharmacyResearch Institute of Pharmaceutical sciencesSeoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Korea
| | - Jongsik Gam
- Department of Medicinal BioscienceCollege of Interdisciplinary & Creative StudiesKonyang University 2121 Daehak-ro Nonsan, Chungnam 32992 Korea
| | - Jeeyeon Lee
- College of PharmacyResearch Institute of Pharmaceutical sciencesSeoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Korea
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153
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Martyloga OV, Myronenko A, Tkachenko AM, Matvienko VO, Kuchkovska YO, Grygorenko OO. Multigram Synthesis of Functionalized Spirocyclic Diazirines. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900485] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | - Artamon Myronenko
- Enamine Ltd. (www.enamine.net); Chervonotkatska Street 78 02094 Kyiv Ukraine
| | - Anton M. Tkachenko
- Enamine Ltd. (www.enamine.net); Chervonotkatska Street 78 02094 Kyiv Ukraine
| | | | - Yuliya O. Kuchkovska
- Enamine Ltd. (www.enamine.net); Chervonotkatska Street 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
| | - Oleksandr O. Grygorenko
- Enamine Ltd. (www.enamine.net); Chervonotkatska Street 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
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154
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Wang P, Li Z, Jiang L, Zhou L, Ye D. Design and Synthesis of the Diazirine-based Clickable Photo-affinity Probe Targeting Sphingomyelin Synthase 2. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180816666181106154601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:SMS family plays a very important role in sphingolipids metabolism and is involved in the membrane mobility and signaling transduction.Methods:SMS2 subtype was related to a variety of diseases and could be regarded as a promising potential drug target. However, the uncertainty of the binding sites and the molecular mechanism of action limited the development of SMS2 inhibitors. Herein, we discovered a photo-affinity probe PAL-1 targeting SMS2.Results:The enzyme inhibitory activity and the photo-affinity labeling experiments showed that PAL-1 could be mono-labeled on SMS2.Conclusion:In summary, starting from the N-arylbenzamides core structure and the minimalist terminal alkyne-containing diazirine photo-crosslinker, we designed and synthesized a photoaffinity probe PAL-1 targeting SMS2. The enzymatic inhibitory activity study showed that PAL-1 exhibited superior selectivities for SMS2 with an IC50 of 0.37 µM over SMS1.
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Affiliation(s)
- Penghui Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Zhining Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Lulu Jiang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Lu Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Deyong Ye
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
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155
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Stepek IA, Cao T, Koetemann A, Shimura S, Wollscheid B, Bode JW. Antibiotic Discovery with Synthetic Fermentation: Library Assembly, Phenotypic Screening, and Mechanism of Action of β-Peptides Targeting Penicillin-Binding Proteins. ACS Chem Biol 2019; 14:1030-1040. [PMID: 30990649 DOI: 10.1021/acschembio.9b00227] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In analogy to biosynthetic pathways leading to bioactive natural products, synthetic fermentation generates mixtures of molecules from simple building blocks under aqueous, biocompatible conditions, allowing the resulting cultures to be directly screened for biological activity. In this work, a novel β-peptide antibiotic was successfully identified using the synthetic fermentation platform. Phenotypic screening was carried out in an initially random fashion, allowing simple identification of active cultures. Subsequent deconvolution, focused screening, and structure-activity relationship studies led to the identification of a potent antimicrobial peptide, showing strong selectivity for our model system Bacillus subtilis over human HEK293 cells. To determine the antibacterial mechanism of action, a peptide probe bearing a photoaffinity tag was readily synthesized through the use of appropriate synthetic fermentation building blocks and utilized for target identification using a quantitative mass spectrometry-based strategy. The chemoproteomic approach led to the identification of a number of bacterial membrane proteins as prospective targets. These findings were validated through binding affinity studies with penicillin-binding protein 4 using microscale thermophoresis, with the bioactive peptide showing a dissociation constant ( Kd) in the nanomolar range. Through these efforts, we provide a proof of concept for the synthetic fermentation approach presented here as a new strategy for the phenotypic discovery of novel bioactive compounds.
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Affiliation(s)
- Iain A. Stepek
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
| | - Trung Cao
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
| | - Anika Koetemann
- Department of Health Sciences and Technology, Institute of Molecular Systems Biology, and BioMedical Proteomics Platform (BMPP), ETH Zurich, 8093 Zurich, Switzerland
| | - Satomi Shimura
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
| | - Bernd Wollscheid
- Department of Health Sciences and Technology, Institute of Molecular Systems Biology, and BioMedical Proteomics Platform (BMPP), ETH Zurich, 8093 Zurich, Switzerland
| | - Jeffrey W. Bode
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8602, Japan
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156
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Yang Y, Cao L, Gao H, Wu Y, Wang Y, Fang F, Lan T, Lou Z, Rao Y. Discovery, Optimization, and Target Identification of Novel Potent Broad-Spectrum Antiviral Inhibitors. J Med Chem 2019; 62:4056-4073. [DOI: 10.1021/acs.jmedchem.9b00091] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yiqing Yang
- Tsinghua University−Peking University Joint Center for Life Sciences, Beijing 100084, P. R. China
| | - Lin Cao
- College of Life Sciences, Nankai University, Tianjin 300071, P. R. China
| | - Hongying Gao
- Tsinghua University−Peking University Joint Center for Life Sciences, Beijing 100084, P. R. China
| | | | - Yaxin Wang
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, P. R. China
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157
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Qian L, Pan S, Lee JS, Ge J, Li L, Yao SQ. Live-cell imaging and profiling of c-Jun N-terminal kinases using covalent inhibitor-derived probes. Chem Commun (Camb) 2019; 55:1092-1095. [PMID: 30620026 DOI: 10.1039/c8cc09558b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
c-Jun N-terminal kinases (JNKs) are involved in critical cellular functions. Herein, small-molecule JNK-targeting probes are reported based on a covalent inhibitor. Together with newly developed two-photon fluorescence Turn-ON reporters and chemoproteomic studies, we showed that some probes may be suitable for live-cell imaging and profiling of JNKs.
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Affiliation(s)
- Linghui Qian
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore. and Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - 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 02792, South Korea
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211800, China.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
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158
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Halloran MW, Lumb JP. Recent Applications of Diazirines in Chemical Proteomics. Chemistry 2019; 25:4885-4898. [PMID: 30444029 DOI: 10.1002/chem.201805004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/12/2018] [Indexed: 02/06/2023]
Abstract
The elucidation of substrate-protein interactions is an important component of the drug development process. Due to the complexity of native cellular environments, elucidating these fundamental biochemical interactions remains challenging. Photoaffinity labeling (PAL) is a versatile technique that can provide insight into ligand-target interactions. By judicious modification of substrates with a photoreactive group, PAL creates a covalent crosslink between a substrate and its biological target following UV-irradiation. Among the commonly employed photoreactive groups, diazirines have emerged as the gold standard. In this Minireview, recent developments in the field of diazirine-based photoaffinity labeling will be discussed, with emphasis being placed on their applications in chemical proteomic studies.
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Affiliation(s)
- Matthew W Halloran
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Jean-Philip Lumb
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
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159
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Wang AC, Pham HT, Lipps JM, Brittain SM, Harrington E, Wang Y, King FJ, Russ C, Pan X, Hoepfner D, Tallarico J, Feng Y, Jain RK, Schirle M, Thomas JR. Previously Uncharacterized Vacuolar-type ATPase Binding Site Discovered from Structurally Similar Compounds with Distinct Mechanisms of Action. ACS Chem Biol 2019; 14:20-26. [PMID: 30461263 DOI: 10.1021/acschembio.8b00656] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Using a comprehensive chemical genetics approach, we identified a member of the lignan natural product family, HTP-013, which exhibited significant cytotoxicity across various cancer cell lines. Correlation of compound activity across a panel of reporter gene assays suggested the vacuolar-type ATPase (v-ATPase) as a potential target for this compound. Additional cellular studies and a yeast haploinsufficiency screen strongly supported this finding. Competitive photoaffinity labeling experiments demonstrated that the ATP6V0A2 subunit of the v-ATPase complex binds directly to HTP-013, and further mutagenesis library screening identified resistance-conferring mutations in ATP6V0A2. The positions of these mutations suggest the molecule binds a novel pocket within the domain of the v-ATPase complex responsible for proton translocation. While other mechanisms of v-ATPase regulation have been described, such as dissociation of the complex or inhibition by natural products including bafilomycin A1 and concanamycin, this work provides detailed insight into a distinct binding pocket within the v-ATPase complex.
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Affiliation(s)
- Andrew C. Wang
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Helen T. Pham
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jennifer M. Lipps
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Scott M. Brittain
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Edmund Harrington
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Yuan Wang
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Fred J. King
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Carsten Russ
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Xuewen Pan
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Dominic Hoepfner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056 Basel, Switzerland
| | - John Tallarico
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Yan Feng
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Rishi K. Jain
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jason R. Thomas
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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160
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Zhu T, Chen C, Wang S, Zhang Y, Zhu D, Li L, Luo J, Kong L. Cellular target identification of Withangulatin A using fluorescent analogues and subsequent chemical proteomics. Chem Commun (Camb) 2019; 55:8231-8234. [DOI: 10.1039/c9cc03653a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Find the target of Withangulatin A with the combination of fluorescent probes and chemical proteomics.
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Affiliation(s)
- Tianyu Zhu
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Chen Chen
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Sisi Wang
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Yi Zhang
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Dongrong Zhu
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Lingnan Li
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Jianguang Luo
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Lingyi Kong
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing 210009
- China
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161
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Guo C, Chang Y, Wang X, Zhang C, Hao P, Ding K, Li Z. Minimalist linkers suitable for irreversible inhibitors in simultaneous proteome profiling, live-cell imaging and drug screening. Chem Commun (Camb) 2019; 55:834-837. [DOI: 10.1039/c8cc08685k] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A series of minimalist linkers were developed and have been demonstrated to be suitable for irreversible inhibitors in simultaneous proteome profiling, live-cell imaging and drug screening, thus facilitating the discovery of first-in-class anticancer drugs.
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Affiliation(s)
- Cuiping 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
- Guangzhou
- China
| | - Yu Chang
- 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
- Guangzhou
- China
| | - Xin Wang
- 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
- Guangzhou
- China
| | - Chengqian Zhang
- School of Life Science and Technology, ShanghaiTech University
- Shanghai 201210
- China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University
- 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
- Guangzhou
- 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
- Guangzhou
- China
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162
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Walko M, Hewitt E, Radford SE, Wilson AJ. Design and synthesis of cysteine-specific labels for photo-crosslinking studies. RSC Adv 2019; 9:7610-7614. [PMID: 35521201 PMCID: PMC9061181 DOI: 10.1039/c8ra10436k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/23/2019] [Indexed: 12/31/2022] Open
Abstract
Chemical cross-linking mass-spectrometry (XL-MS) represents a powerful methodology to map ligand/biomacromolecule interactions, particularly where conventional methods such as X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy or cryo-electron microscopy (EM) are not feasible. In this manuscript, we describe the design and synthesis of two new photo-crosslinking reagents that can be used to specifically label free thiols through either maleimido or methanethiosulfonate groups and facilitate PXL-MS workflows. Both crosslinkers are based on light sensitive diazirines – precursors of highly reactive carbenes which offer additional advantages over alternative crosslinking groups such as benzophenones and aryl nitrenes given the controlled rapid and more indiscriminate reactivity. The design and synthesis of cysteine specific diazirine containing labels is described.![]()
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Affiliation(s)
- Martin Walko
- School of Chemistry
- University of Leeds
- Leeds
- UK
- Astbury Centre for Structural Molecular Biology
| | - Eric Hewitt
- Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds
- UK
- School of Molecular and Cellular Biology
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds
- UK
- School of Molecular and Cellular Biology
| | - Andrew J. Wilson
- School of Chemistry
- University of Leeds
- Leeds
- UK
- Astbury Centre for Structural Molecular Biology
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163
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Zhang C, Shi Z, Han Y, Ren Y, Hao P. Multiparameter Optimization of Two Common Proteomics Quantification Methods for Quantifying Low-Abundance Proteins. J Proteome Res 2018; 18:461-468. [PMID: 30394099 DOI: 10.1021/acs.jproteome.8b00769] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Quantitative proteomics has been extensively applied in the screening of differentially regulated proteins in various research areas for decades, but its sensitivity and accuracy have been a bottleneck for many applications. Every step in the proteomics workflow can potentially affect the quantification of low-abundance proteins, but a systematic evaluation of their effects has not been done yet. In this work, to improve the sensitivity and accuracy of label-free quantification and tandem mass tags (TMT) labeling in quantifying low-abundance proteins, multiparameter optimization was carried out using a complex 2-proteome artificial sample mixture for a series of steps from sample preparation to data analysis, including the desalting of peptides, peptide injection amount for LC-MS/MS, MS1 resolution, the length of LC-MS/MS gradient, AGC targets, ion accumulation time, MS2 resolution, precursor coisolation threshold, data analysis software, statistical calculation methods, and protein fold changes, and the best settings for each parameter were defined. The suitable cutoffs for detecting low-abundance proteins with at least 1.5-fold and 2-fold changes were identified for label-free and TMT methods, respectively. The use of optimized parameters will significantly improve the overall performance of quantitative proteomics in quantifying low-abundance proteins and thus promote its application in other research areas.
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Affiliation(s)
- Chengqian Zhang
- School of Life Science and Technology , ShanghaiTech University , 393 Middle Huaxia Road , Shanghai 201210 , China
| | - Zhaomei Shi
- School of Life Science and Technology , ShanghaiTech University , 393 Middle Huaxia Road , Shanghai 201210 , China
| | - Ying Han
- School of Life Science and Technology , ShanghaiTech University , 393 Middle Huaxia Road , Shanghai 201210 , China
| | - Yan Ren
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,China National GeneBank , BGI-Shenzhen , Jinsha Road , Shenzhen 518120 , China
| | - Piliang Hao
- School of Life Science and Technology , ShanghaiTech University , 393 Middle Huaxia Road , Shanghai 201210 , China
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164
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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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165
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Thinking Outside the Box-Novel Antibacterials To Tackle the Resistance Crisis. Angew Chem Int Ed Engl 2018; 57:14440-14475. [PMID: 29939462 DOI: 10.1002/anie.201804971] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Indexed: 12/13/2022]
Abstract
The public view on antibiotics as reliable medicines changed when reports about "resistant superbugs" appeared in the news. While reasons for this resistance development are easily spotted, solutions for re-establishing effective antibiotics are still in their infancy. This Review encompasses several aspects of the antibiotic development pipeline from very early strategies to mature drugs. An interdisciplinary overview is given of methods suitable for mining novel antibiotics and strategies discussed to unravel their modes of action. Select examples of antibiotics recently identified by using these platforms not only illustrate the efficiency of these measures, but also highlight promising clinical candidates with therapeutic potential. Furthermore, the concept of molecules that disarm pathogens by addressing gatekeepers of virulence will be covered. The Review concludes with an evaluation of antibacterials currently in clinical development. Overall, this Review aims to connect select innovative antimicrobial approaches to stimulate interdisciplinary partnerships between chemists from academia and industry.
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Affiliation(s)
- Markus Lakemeyer
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Weining Zhao
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Franziska A Mandl
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases, Sanofi-Aventis (Deutschland) GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
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166
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Über bisherige Denkweisen hinaus - neue Wirkstoffe zur Überwindung der Antibiotika-Krise. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804971] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Markus Lakemeyer
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Weining Zhao
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Franziska A. Mandl
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases; Sanofi-Aventis (Deutschland) GmbH; Industriepark Höchst 65926 Frankfurt am Main Deutschland
| | - Stephan A. Sieber
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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167
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Tetracyclines Modify Translation by Targeting Key Human rRNA Substructures. Cell Chem Biol 2018; 25:1506-1518.e13. [PMID: 30318461 DOI: 10.1016/j.chembiol.2018.09.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/29/2018] [Accepted: 09/14/2018] [Indexed: 02/07/2023]
Abstract
Apart from their antimicrobial properties, tetracyclines demonstrate clinically validated effects in the amelioration of pathological inflammation and human cancer. Delineation of the target(s) and mechanism(s) responsible for these effects, however, has remained elusive. Here, employing quantitative mass spectrometry-based proteomics, we identified human 80S ribosomes as targets of the tetracyclines Col-3 and doxycycline. We then developed in-cell click selective crosslinking with RNA sequence profiling (icCL-seq) to map binding sites for these tetracyclines on key human rRNA substructures at nucleotide resolution. Importantly, we found that structurally and phenotypically variant tetracycline analogs could chemically discriminate these rRNA binding sites. We also found that tetracyclines both subtly modify human ribosomal translation and selectively activate the cellular integrated stress response (ISR). Together, the data reveal that targeting of specific rRNA substructures, activation of the ISR, and inhibition of translation are correlated with the anti-proliferative properties of tetracyclines in human cancer cell lines.
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168
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Opportunities for Lipid-Based Probes in the Field of Immunology. Curr Top Microbiol Immunol 2018; 420:283-319. [PMID: 30242513 DOI: 10.1007/82_2018_127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Lipids perform a wide range of functions inside the cell, ranging from structural building block of membranes and energy storage to cell signaling. The mode of action of many signaling lipids has remained elusive due to their low abundance, high lipophilicity, and inherent instability. Various chemical biology approaches, such as photoaffinity or activity-based protein profiling methods, have been employed to shed light on the biological role of lipids and the lipid-protein interaction profile. In this review, we will summarize the recent developments in the field of chemical probes to study lipid biology, especially in immunology, and indicate potential avenues for future research.
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169
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Jackson P, Lapinsky DJ. Appendage and Scaffold Diverse Fully Functionalized Small-Molecule Probes via a Minimalist Terminal Alkyne-Aliphatic Diazirine Isocyanide. J Org Chem 2018; 83:11245-11253. [DOI: 10.1021/acs.joc.8b01831] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paul Jackson
- Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - David J. Lapinsky
- Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
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170
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Li W, Zhou Y, You W, Yang M, Ma Y, Wang M, Wang Y, Yuan S, Xiao Y. Development of Photoaffinity Probe for the Discovery of Steviol Glycosides Biosynthesis Pathway in Stevia rebuadiana and Rapid Substrate Screening. ACS Chem Biol 2018; 13:1944-1949. [PMID: 29863335 DOI: 10.1021/acschembio.8b00285] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Functional discovery and characterization of the target enzymes responsible for the biosynthesis pathway coded for the genes is ongoing, and the unknown functional diversity of this class of enzymes has been revealed by genome sequencing. Commonly, it is feasible in annotating of biosynthetic genes of prokaryotes due to the existence of gene clusters of secondary metabolites. However, in eukaryotes, the biosynthetic genes are not compactly clustered in the way of prokaryotes. Hence, it remains challenging to identify the biosynthetic pathways of newly discovered natural products in plants. Steviol glycosides are one class of natural sweeteners found in high abundance in the herb Stevia rebaudiana. Here, we applied the chemoproteomic strategy for the proteomic profiling of the biosynthetic enzymes of steviol glycosides in Stevia rebaudiana. We not only identified a steviol-catalyzing UDP-glycosyltransferase (UGT) UGT73E1 involved in steviol glycoside biosynthesis but also built up a probe-based platform for the screening of potential substrates of functional uncharacterized UGT rapidly. This approach would be a complementary tool in mining novel synthetic parts for assembling of synthetic biological systems for the biosynthesis of other complex natural products.
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Affiliation(s)
- Weichao Li
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yiqing Zhou
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wenjing You
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Mengquan Yang
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yanrong Ma
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mingli Wang
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yong Wang
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Shuguang Yuan
- Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH B3 495 (Bâtiment CH) Station 6, CH-1015 Lausanne, Switzerland
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100039, China
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171
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Ge SS, Chen B, Wu YY, Long QS, Zhao YL, Wang PY, Yang S. Current advances of carbene-mediated photoaffinity labeling in medicinal chemistry. RSC Adv 2018; 8:29428-29454. [PMID: 35547988 PMCID: PMC9084484 DOI: 10.1039/c8ra03538e] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/07/2018] [Indexed: 12/21/2022] Open
Abstract
Photoaffinity labeling (PAL) in combination with a chemical probe to covalently bind its target upon UV irradiation has demonstrated considerable promise in drug discovery for identifying new drug targets and binding sites. In particular, carbene-mediated photoaffinity labeling (cmPAL) has been widely used in drug target identification owing to its excellent photolabeling efficiency, minimal steric interference and longer excitation wavelength. Specifically, diazirines, which are among the precursors of carbenes and have higher carbene yields and greater chemical stability than diazo compounds, have proved to be valuable photolabile reagents in a diverse range of biological systems. This review highlights current advances of cmPAL in medicinal chemistry, with a focus on structures and applications for identifying small molecule-protein and macromolecule-protein interactions and ligand-gated ion channels, coupled with advances in the discovery of targets and inhibitors using carbene precursor-based biological probes developed in recent decades.
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Affiliation(s)
- Sha-Sha Ge
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Biao Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Yuan-Yuan Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Qing-Su Long
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Yong-Liang Zhao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Pei-Yi Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
- College of Pharmacy, East China University of Science & Technology Shanghai 200237 China
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172
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Kasak L, Näks M, Eek P, Piirsoo A, Bhadoria R, Starkov P, Saarma M, Kasvandik S, Piirsoo M. Characterization of Protein Kinase ULK3 Regulation by Phosphorylation and Inhibition by Small Molecule SU6668. Biochemistry 2018; 57:5456-5465. [DOI: 10.1021/acs.biochem.8b00356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lagle Kasak
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Mihkel Näks
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Priit Eek
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Alla Piirsoo
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Rohit Bhadoria
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Pavel Starkov
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Merilin Saarma
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Sergo Kasvandik
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Marko Piirsoo
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
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173
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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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174
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Berkowitz AJ, Abdelmessih RG, Murelli RP. Amidation Strategy for Final-Step α-Hydroxytropolone Diversification. Tetrahedron Lett 2018; 59:3026-3028. [PMID: 30872871 PMCID: PMC6411066 DOI: 10.1016/j.tetlet.2018.06.063] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
α-Hydroxytropolones (αHTs) are excellent metalloenzyme-inhibiting fragments that have been the basis for the development of potent inhibitors of various therapeutically important enzymes. The following manuscript describes a final-step amidation approach for αHT diversification. The method takes advantage of a scalable, chromatography-free synthesis of a carboxylic acid-appended αHT, and in the present manuscript we describe the synthesis of eight amide-containing αHTs, three of which we envision using as chemical probes. We expect that the general strategy will find widespread usage in both chemical biology and medicinal chemistry studies on αHTs.
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Affiliation(s)
- Alex J. Berkowitz
- Department of Chemistry, Brooklyn College, The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, United States
- Ph.D. Program in Chemistry, The Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY, 10016, United States
| | - Rudolf G. Abdelmessih
- Department of Chemistry, Brooklyn College, The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, United States
| | - Ryan P. Murelli
- Department of Chemistry, Brooklyn College, The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, United States
- Ph.D. Program in Chemistry, The Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY, 10016, United States
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175
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DeMeester KE, Liang H, Jensen MR, Jones ZS, D'Ambrosio EA, Scinto SL, Zhou J, Grimes CL. Synthesis of Functionalized N-Acetyl Muramic Acids To Probe Bacterial Cell Wall Recycling and Biosynthesis. J Am Chem Soc 2018; 140:9458-9465. [PMID: 29986130 DOI: 10.1021/jacs.8b03304] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Uridine diphosphate N-acetyl muramic acid (UDP NAM) is a critical intermediate in bacterial peptidoglycan (PG) biosynthesis. As the primary source of muramic acid that shapes the PG backbone, modifications installed at the UDP NAM intermediate can be used to selectively tag and manipulate this polymer via metabolic incorporation. However, synthetic and purification strategies to access large quantities of these PG building blocks, as well as their derivatives, are challenging. A robust chemoenzymatic synthesis was developed using an expanded NAM library to produce a variety of 2 -N-functionalized UDP NAMs. In addition, a synthetic strategy to access bio-orthogonal 3-lactic acid NAM derivatives was developed. The chemoenzymatic UDP synthesis revealed that the bacterial cell wall recycling enzymes MurNAc/GlcNAc anomeric kinase (AmgK) and NAM α-1 phosphate uridylyl transferase (MurU) were permissive to permutations at the two and three positions of the sugar donor. We further explored the utility of these derivatives in the fluorescent labeling of both Gram (-) and Gram (+) PG in whole cells using a variety of bio-orthogonal chemistries including the tetrazine ligation. This report allows for rapid and scalable access to a variety of functionalized NAMs and UDP NAMs, which now can be used in tandem with other complementary bio-orthogonal labeling strategies to address fundamental questions surrounding PG's role in immunology and microbiology.
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176
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Li W, Zhou Y, Tang G, Wong NK, Yang M, Tan D, Xiao Y. Chemoproteomics Reveals the Antiproliferative Potential of Parkinson’s Disease Kinase Inhibitor LRRK2-IN-1 by Targeting PCNA Protein. Mol Pharm 2018; 15:3252-3259. [DOI: 10.1021/acs.molpharmaceut.8b00325] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- 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, Shanghai 200032, China
| | - 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, Shanghai 200032, China
| | - Guanghui Tang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Nai-Kei Wong
- State Key Discipline of Infection Diseases, Shenzhen Third People’s Hospital, The Second Affiliated Hospital, Shenzhen University, Shenzhen 518112, China
| | - Mengquan Yang
- 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, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Dan Tan
- Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, 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, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100039, China
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177
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Soethoudt M, Alachouzos G, van Rooden EJ, Moya-Garzón MD, van den Berg RJ, Heitman LH, van der Stelt M. Development of a Cannabinoid-Based Photoaffinity Probe to Determine the Δ 8/9-Tetrahydrocannabinol Protein Interaction Landscape in Neuroblastoma Cells. Cannabis Cannabinoid Res 2018; 3:136-151. [PMID: 29992186 PMCID: PMC6038054 DOI: 10.1089/can.2018.0003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Introduction: Δ9-Tetrahydrocannabinol (THC), the principle psychoactive ingredient in Cannabis, is widely used for its therapeutic effects in a large variety of diseases, but it also has numerous neurological side effects. The cannabinoid receptors (CBRs) are responsible to a large extent for these, but not all biological responses are mediated via the CBRs. Objectives: The identification of additional target proteins of THC to enable a better understanding of the (adverse) physiological effects of THC. Methods: In this study, a chemical proteomics approach using a two-step photoaffinity probe is applied to identify potential proteins that may interact with THC. Results: Photoaffinity probe 1, containing a diazirine as a photocrosslinker, and a terminal alkyne as a ligation handle, was synthesized in 14 steps. It demonstrated high affinity for both CBRs. Subsequently, two-step photoaffinity labeling in neuroblastoma cells led to identification of four potential novel protein targets of THC. The identification of these putative protein hits is a first step towards a better understanding of the protein interaction profile of THC, which could ultimately lead to the development of novel therapeutics based on THC.
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Affiliation(s)
- Marjolein Soethoudt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Georgios Alachouzos
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Eva J. van Rooden
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - María Dolores Moya-Garzón
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | - Laura H. Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
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178
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Zhu D, Guo H, Chang Y, Ni Y, Li L, Zhang ZM, Hao P, Xu Y, Ding K, Li Z. Cell- and Tissue-Based Proteome Profiling and Dual Imaging of Apoptosis Markers with Probes Derived from Venetoclax and Idasanutlin. Angew Chem Int Ed Engl 2018; 57:9284-9289. [PMID: 29768700 DOI: 10.1002/anie.201802003] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Indexed: 01/17/2023]
Affiliation(s)
- Dongsheng Zhu
- Guangdong Provincial Key Laboratory of Biocomputing; Guangzhou Institutes of Biomedicine and Health; Chinese Academy of Sciences; 190 Kaiyuan Avenue, Science Park Guangzhou 510530 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Beijing 100049 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
| | - Yu Chang
- 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
| | - Lin Li
- Institute of Advanced Materials (IAM); Nanjing Tech University; 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
| | - Piliang Hao
- School of Life Science and Technology; ShanghaiTech University; China
| | - Yong Xu
- Guangdong Provincial Key Laboratory of Biocomputing; Guangzhou Institutes of Biomedicine and Health; Chinese Academy of Sciences; 190 Kaiyuan Avenue, Science Park Guangzhou 510530 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Beijing 100049 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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179
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Zhu D, Guo H, Chang Y, Ni Y, Li L, Zhang ZM, Hao P, Xu Y, Ding K, Li Z. Cell- and Tissue-Based Proteome Profiling and Dual Imaging of Apoptosis Markers with Probes Derived from Venetoclax and Idasanutlin. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dongsheng Zhu
- Guangdong Provincial Key Laboratory of Biocomputing; Guangzhou Institutes of Biomedicine and Health; Chinese Academy of Sciences; 190 Kaiyuan Avenue, Science Park Guangzhou 510530 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Beijing 100049 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
| | - Yu Chang
- 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
| | - Lin Li
- Institute of Advanced Materials (IAM); Nanjing Tech University; 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
| | - Piliang Hao
- School of Life Science and Technology; ShanghaiTech University; China
| | - Yong Xu
- Guangdong Provincial Key Laboratory of Biocomputing; Guangzhou Institutes of Biomedicine and Health; Chinese Academy of Sciences; 190 Kaiyuan Avenue, Science Park Guangzhou 510530 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Beijing 100049 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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180
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Synthesis of an electronically-tuned minimally interfering alkynyl photo-affinity label to measure small molecule–protein interactions. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.03.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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181
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Hill JR, Robertson AAB. Fishing for Drug Targets: A Focus on Diazirine Photoaffinity Probe Synthesis. J Med Chem 2018; 61:6945-6963. [PMID: 29683660 DOI: 10.1021/acs.jmedchem.7b01561] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Target identification is a high-priority, albeit challenging, aspect of drug discovery. Diazirine-based photoaffinity probes (PAPs) can facilitate the process by covalently capturing transient molecular interactions. This can help identify target proteins and map the ligand's interactome. Diazirine probes have even been incorporated by cellular machinery into proteins. Embarking on the synthesis of customized PAPs, containing either an aliphatic or trifluoromethyl phenyl diazirine, can be a considerable endeavor, particularly for medicinal chemists and chemical biologists new to the field. This review takes a synthetic focus, aiming to summarize available routes, propose new avenues, and illuminate recent advances in diazirine synthesis. Select examples of diazirine photoaffinity labeling applications have been included throughout to provide instructive definition of the advantages and limitations of the technology while simultaneously highlighting how these reagents can be applied in a practical sense.
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Affiliation(s)
- James R Hill
- Institute for Molecular Bioscience , The University of Queensland , St. Lucia , Queensland 4072 , Australia
| | - Avril A B Robertson
- Institute for Molecular Bioscience , The University of Queensland , St. Lucia , Queensland 4072 , Australia.,School of Chemistry and Molecular Biosciences , The University of Queensland , St. Lucia QLD4072 , Australia
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182
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Dissection of Protein Kinase Pathways in Live Cells Using Photoluminescent Probes: Surveillance or Interrogation? CHEMOSENSORS 2018. [DOI: 10.3390/chemosensors6020019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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183
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Gao J, Mfuh A, Amako Y, Woo CM. Small Molecule Interactome Mapping by Photoaffinity Labeling Reveals Binding Site Hotspots for the NSAIDs. J Am Chem Soc 2018. [DOI: 10.1021/jacs.7b11639] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jinxu Gao
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138, United States
| | - Adelphe Mfuh
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138, United States
| | - Yuka Amako
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138, United States
| | - Christina M. Woo
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138, United States
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184
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Hofmans S, Devisscher L, Martens S, Van Rompaey D, Goossens K, Divert T, Nerinckx W, Takahashi N, De Winter H, Van Der Veken P, Goossens V, Vandenabeele P, Augustyns K. Tozasertib Analogues as Inhibitors of Necroptotic Cell Death. J Med Chem 2018; 61:1895-1920. [DOI: 10.1021/acs.jmedchem.7b01449] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Sam Hofmans
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk-Antwerp 2610, Belgium
| | - Lars Devisscher
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk-Antwerp 2610, Belgium
| | - Sofie Martens
- Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 927, Zwijnaarde-Ghent 9052, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Technologiepark 927, Zwijnaarde-Ghent 9052, Belgium
| | - Dries Van Rompaey
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk-Antwerp 2610, Belgium
| | - Kenneth Goossens
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk-Antwerp 2610, Belgium
| | - Tatyana Divert
- Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 927, Zwijnaarde-Ghent 9052, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Technologiepark 927, Zwijnaarde-Ghent 9052, Belgium
| | - Wim Nerinckx
- Unit for Medical Biotechnology, Center for Medical Biotechnology, VIB, Technologiepark 927, Zwijnaarde-Ghent 9052, Belgium
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, K.L.-Ledeganckstraat 35, Ghent 9000, Belgium
| | - Nozomi Takahashi
- Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 927, Zwijnaarde-Ghent 9052, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Technologiepark 927, Zwijnaarde-Ghent 9052, Belgium
| | - Hans De Winter
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk-Antwerp 2610, Belgium
| | - Pieter Van Der Veken
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk-Antwerp 2610, Belgium
| | - Vera Goossens
- Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 927, Zwijnaarde-Ghent 9052, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Technologiepark 927, Zwijnaarde-Ghent 9052, Belgium
| | - Peter Vandenabeele
- Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 927, Zwijnaarde-Ghent 9052, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Technologiepark 927, Zwijnaarde-Ghent 9052, Belgium
- Methusalem Program, Ghent University, Ghent 9000, Belgium
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk-Antwerp 2610, Belgium
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185
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Zhao B, Burgess K. Click-Addressable Cassette for Photoaffinity Labeling. ACS Med Chem Lett 2018; 9:155-158. [PMID: 29456805 DOI: 10.1021/acsmedchemlett.7b00516] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 01/24/2018] [Indexed: 12/17/2022] Open
Abstract
A small molecule 1 was designed to contain an alkyne, a trifluoromethyl phenyldiazirine, and a free piperidine-NH for facile conjugation to protein binding ligands. This "cassette" 1 was synthesized via a relatively direct route involving only routine steps. In this proof-of-concept study, putative ligands for carbonic anhydrase IX and for TrkC were conjugated to 1. Photoaffinity labeling was performed using purified extracellular regions of both these protein-receptors, and using cells that express these receptors (isolation via a pull-down procedure), labeling of the protein was observed in all four experiments.
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Affiliation(s)
- Bosheng Zhao
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
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186
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Keohane CE, Steele AD, Fetzer C, Khowsathit J, Tyne DV, Moynié L, Gilmore MS, Karanicolas J, Sieber SA, Wuest WM. Promysalin Elicits Species-Selective Inhibition of Pseudomonas aeruginosa by Targeting Succinate Dehydrogenase. J Am Chem Soc 2018; 140:1774-1782. [PMID: 29300464 PMCID: PMC5869686 DOI: 10.1021/jacs.7b11212] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural products have served as an inspiration to scientists both for their complex three-dimensional architecture and exquisite biological activity. Promysalin is one such Pseudomonad secondary metabolite that exhibits narrow-spectrum antibacterial activity, originally isolated from the rhizosphere. We herein utilize affinity-based protein profiling (AfBPP) to identify succinate dehydrogenase (Sdh) as the biological target of the natural product. The target was further validated in silico, in vitro, in vivo, and through the selection, and sequencing, of a resistant mutant. Succinate dehydrogenase plays an essential role in primary metabolism of Pseudomonas aeruginosa as the only enzyme that is involved both in the tricarboxylic acid cycle (TCA) and in respiration via the electron transport chain. These findings add credence to other studies that suggest that the TCA cycle is an understudied target in the development of novel therapeutics to combat P. aeruginosa, a significant pathogen in clinical settings.
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Affiliation(s)
- Colleen E. Keohane
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Andrew D. Steele
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Christian Fetzer
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Jittasak Khowsathit
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Daria Van Tyne
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02115, United States
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Lucile Moynié
- Division of Structural Biology, The University of Oxford, Headington Oxford, OX3 7BN, United Kingdom
- Biomedical Sciences Research Complex, University of St. Andrews, Fife Scotland, KY16 9ST, United Kingdom
| | - Michael S. Gilmore
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02115, United States
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - John Karanicolas
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
| | - Stephan A. Sieber
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - William M. Wuest
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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187
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Zhou Y, Li W, You W, Di Z, Wang M, Zhou H, Yuan S, Wong NK, Xiao Y. Discovery of Arabidopsis UGT73C1 as a steviol-catalyzing UDP-glycosyltransferase with chemical probes. Chem Commun (Camb) 2018; 54:7179-7182. [DOI: 10.1039/c7cc09951g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A strategy for rapidly mining biological parts from plants for synthetic biology utilizing natural product-derived chemical probes has been reported.
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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
| | - Wenjing You
- 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
| | - Zhengao Di
- 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
| | - Haiyan 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
| | - Shuguang Yuan
- Laboratory of Physical Chemistry of Polymers and Membranes
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- Switzerland
| | - Nai-Kei Wong
- State Key Discipline of Infection Diseases
- Shenzhen Third People's Hospital
- The Second Affiliated Hospital
- Shenzhen University
- Shenzhen 518112
| | - 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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188
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Parker CG, Kuttruff CA, Galmozzi A, Jørgensen L, Yeh CH, Hermanson DJ, Wang Y, Artola M, McKerrall SJ, Josyln CM, Nørremark B, Dünstl G, Felding J, Saez E, Baran PS, Cravatt BF. Chemical Proteomics Identifies SLC25A20 as a Functional Target of the Ingenol Class of Actinic Keratosis Drugs. ACS CENTRAL SCIENCE 2017; 3:1276-1285. [PMID: 29296668 PMCID: PMC5746860 DOI: 10.1021/acscentsci.7b00420] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Indexed: 05/29/2023]
Abstract
The diterpenoid ester ingenol mebutate (IngMeb) is the active ingredient in the topical drug Picato, a first-in-class treatment for the precancerous skin condition actinic keratosis. IngMeb is proposed to exert its therapeutic effects through a dual mode of action involving (i) induction of cell death that is associated with mitochondrial dysfunction followed by (ii) stimulation of a local inflammatory response, at least partially driven by protein kinase C (PKC) activation. Although this therapeutic model has been well characterized, the complete set of molecular targets responsible for mediating IngMeb activity remains ill-defined. Here, we have synthesized a photoreactive, clickable analogue of IngMeb and used this probe in quantitative proteomic experiments to map several protein targets of IngMeb in human cancer cell lines and primary human keratinocytes. Prominent among these targets was the mitochondrial carnitine-acylcarnitine translocase SLC25A20, which we show is inhibited in cells by IngMeb and the more stable analogue ingenol disoxate (IngDsx), but not by the canonical PKC agonist 12-O-tetradecanoylphorbol-13-acetate (TPA). SLC25A20 blockade by IngMeb and IngDsx leads to a buildup of cellular acylcarnitines and blockade of fatty acid oxidation (FAO), pointing to a possible mechanism for IngMeb-mediated perturbations in mitochondrial function.
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Affiliation(s)
- Christopher G. Parker
- Department
of Molecular Medicine, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Christian A. Kuttruff
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Andrea Galmozzi
- Department
of Molecular Medicine, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Lars Jørgensen
- Research
& Development, LEO Pharma, DK-2750 Ballerup, Denmark
| | - Chien-Hung Yeh
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Daniel J. Hermanson
- Department
of Molecular Medicine, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Yujia Wang
- Department
of Molecular Medicine, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Marta Artola
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Steven J. McKerrall
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Christopher M. Josyln
- Department
of Molecular Medicine, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | | | - Georg Dünstl
- Research
& Development, LEO Pharma, DK-2750 Ballerup, Denmark
| | - Jakob Felding
- Research
& Development, LEO Pharma, DK-2750 Ballerup, Denmark
| | - Enrique Saez
- Department
of Molecular Medicine, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Phil S. Baran
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Benjamin F. Cravatt
- Department
of Molecular Medicine, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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189
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Cheng K, Lee JS, Hao P, Yao SQ, Ding K, Li Z. Tetrazole-Based Probes for Integrated Phenotypic Screening, Affinity-Based Proteome Profiling, and Sensitive Detection of a Cancer Biomarker. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709584] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ke Cheng
- School of Pharmacy; Jinan University; 601 Huangpu Avenue West Guangzhou 510632 China
| | - Jun-Seok Lee
- Molecular Recognition Research Center; Korea Institute of Science and Technology (KIST); Department of Biological Chemistry; University of Science & Technology; Republic of Korea
| | - Piliang Hao
- School of Life Science and Technology; ShanghaiTech University; China
| | - Shao Q. Yao
- Department of Chemistry; National University of Singapore; Singapore
| | - Ke Ding
- School of Pharmacy; Jinan University; 601 Huangpu Avenue West Guangzhou 510632 China
| | - Zhengqiu Li
- School of Pharmacy; Jinan University; 601 Huangpu Avenue West Guangzhou 510632 China
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190
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Affiliation(s)
- Hope A. Flaxman
- Department of Chemistry and
Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Christina M. Woo
- Department of Chemistry and
Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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191
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Cheng K, Lee JS, Hao P, Yao SQ, Ding K, Li Z. Tetrazole-Based Probes for Integrated Phenotypic Screening, Affinity-Based Proteome Profiling, and Sensitive Detection of a Cancer Biomarker. Angew Chem Int Ed Engl 2017; 56:15044-15048. [PMID: 28967196 DOI: 10.1002/anie.201709584] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Indexed: 01/10/2023]
Abstract
Target-identification phenotypic screening has been a powerful approach in drug discovery; however, it is hindered by difficulties in identifying the underlying cellular targets. To address this challenge, we have combined phenotypic screening of a fully functionalized small-molecule library with competitive affinity-based proteome profiling to map and functionally characterize the targets of screening hits. Using this approach, we identified ANXA2, PDIA3/4, FLAD1, and NOS2 as primary cellular targets of two bioactive molecules that inhibit cancer cell proliferation. We further demonstrated that a panel of probes can label and/or image annexin A2 (a cancer biomarker) from different cancer cell lines, thus providing opportunities for potential cancer diagnosis and therapy.
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Affiliation(s)
- Ke Cheng
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Department of Biological Chemistry, University of Science & Technology, Republic of Korea
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore
| | - Ke Ding
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
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192
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He D, Xie X, Yang F, Zhang H, Su H, Ge Y, Song H, Chen PR. Quantitative and Comparative Profiling of Protease Substrates through a Genetically Encoded Multifunctional Photocrosslinker. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708151] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Dan He
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Xiao Xie
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Fan Yang
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Heng Zhang
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Haomiao Su
- College of Chemistry and Molecular Sciences; Wuhan University; Wuhan 430072 China
| | - Yun Ge
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Haiping Song
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Peng R. Chen
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
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193
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He D, Xie X, Yang F, Zhang H, Su H, Ge Y, Song H, Chen PR. Quantitative and Comparative Profiling of Protease Substrates through a Genetically Encoded Multifunctional Photocrosslinker. Angew Chem Int Ed Engl 2017; 56:14521-14525. [DOI: 10.1002/anie.201708151] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 09/14/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Dan He
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Xiao Xie
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Fan Yang
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Heng Zhang
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Haomiao Su
- College of Chemistry and Molecular Sciences; Wuhan University; Wuhan 430072 China
| | - Yun Ge
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Haiping Song
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Peng R. Chen
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
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194
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Gao T, Wang B, Shi L, Zhu X, Xiang Y, Anzai JI, Li G. Ultrasensitive Quantitation of Plasma Membrane Proteins via isRTA. Anal Chem 2017; 89:10776-10782. [PMID: 28930447 DOI: 10.1021/acs.analchem.7b02025] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Quantitation of plasma membrane proteins (PMPs) is fundamental and frequently performed daily in the lab. However, challenged by the inherent/interacting heterostructures and complex surroundings of the PMPs in lipid membrane, quantitative techniques for PMP often require complex treatments (e.g., labeling, isolation, purification, and determination), and the sensitivity is usually not satisfactory. To address this problem, we have proposed a novel method that enables quantitation of PMPs with extremely high sensitivity, in an easier-to-manipulate and more streamlined way. This method is based on the design of an in situ rolling cycling replication-templated amplification strategy (isRTA). In fact, two rounds of DNA cascade isothermal amplifications have been conducted. The first round of amplification can provide templates for the second round of amplification; thus, significant enhancement of quantitative signals can be achieved. In this way, PMPs are quantified with ultrahigh sensitivity; as few as 25 copies of PMPs can be detected per cell. Moreover, the advantages of isRTA have been demonstrated by simultaneous identification of several PMP biomarkers (MUC1, EpCAM, and HER2) that are expressed over a wide distribution range on breast cancer cells. The precise typing of breast cancer cell subsets is thus possible because of the "quantitative-to-qualitative" strategy. Therefore, the unprecedented sensitivity and high usability of the isRTA method may present significant prospects for delving into membrane proteins and their related biofunctions in many research fields.
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Affiliation(s)
- Tao Gao
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, P. R. China
| | - Bei Wang
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, P. R. China
| | - Liu Shi
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, P. R. China
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University , Shanghai 200444, P. R. China
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, P. R. China
| | - Jun-Ichi Anzai
- Graduate School of Pharmaceutical Sciences, Tohoku University , Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Genxi Li
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, P. R. China.,Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University , Shanghai 200444, P. R. China
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195
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Yang Y, Song H, He D, Zhang S, Dai S, Xie X, Lin S, Hao Z, Zheng H, Chen PR. Genetically encoded releasable photo-cross-linking strategies for studying protein–protein interactions in living cells. Nat Protoc 2017; 12:2147-2168. [DOI: 10.1038/nprot.2017.090] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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196
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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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197
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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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198
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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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199
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Lehmann J, Richers J, Pöthig A, Sieber SA. Synthesis of ramariolide natural products and discovery of their targets in mycobacteria. Chem Commun (Camb) 2017; 53:107-110. [PMID: 27847948 PMCID: PMC5322466 DOI: 10.1039/c6cc08365j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The total synthesis of ramariolides A–D and ABPP (photoprobe) derivatives have been synthesized for target identification in mycobacterial strains.
Ramariolides A–D are natural products with antibacterial activity. To exploit their cellular mechanism, we here devise the first total synthesis and prepare a photoprobe for target identification. Antibacterial testing against several pathogenic strains including Mycobacterium tuberculosis revealed the highest potency for ramariolide A. Chemical proteomics unraveled binding to essential proteins for amino acid anabolism.
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Affiliation(s)
- Johannes Lehmann
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany.
| | - Johannes Richers
- Catalysis Research Center (CRC), Technische Universität München, Ernst-Otto-Fischer Straße 1, 85747 Garching, Germany
| | - Alexander Pöthig
- Catalysis Research Center (CRC), Technische Universität München, Ernst-Otto-Fischer Straße 1, 85747 Garching, Germany
| | - Stephan A Sieber
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany.
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200
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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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