1
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Zhuo L, Guo M, Zhang S, Wu J, Wang M, Shen Y, Peng X, Wang Z, Jiang W, Huang W. Structure-activity relationship study of 1,6-naphthyridinone derivatives as selective type II AXL inhibitors with potent antitumor efficacy. Eur J Med Chem 2024; 265:116090. [PMID: 38169272 DOI: 10.1016/j.ejmech.2023.116090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/08/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
The role of AXL in various oncogenic processes has made it an attractive target for cancer therapy. Currently, kinase selectivity profiles, especially circumventing MET inhibition, remain a scientific issue of great interest in the discovery of selective type II AXL inhibitors. Starting from a dual MET/AXL-targeted lead structure from our previous work, we optimized a 1,6-naphthyridinone series using molecular modeling-assisted compound design to improve AXL potency and selectivity over MET, resulting in the potent and selective type II AXL-targeted compound 25c. This showed excellent AXL inhibitory activity (IC50 = 1.1 nM) and 343-fold selectivity over the highly homologous kinase MET in biochemical assays. Moreover, compound 25c significantly inhibited AXL-driven cell proliferation, dose-dependently suppressed 4T1 cell migration and invasion, and induced apoptosis. Compound 25c also showed noticeable antitumor efficacy in a BaF3/TEL-AXL xenograft model at well-tolerated doses. Overall, this study presented a potent and selective type II AXL-targeted lead compound for further drug discovery.
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Affiliation(s)
- Linsheng Zhuo
- Postdoctoral Station for Basic Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China; School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Mengqin Guo
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Siyi Zhang
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Junbo Wu
- Department of Colorectal Surgery, Hengyang Central Hospital, Hengyang, Hunan, 421001, China
| | - Mingshu Wang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Yang Shen
- Postdoctoral Station for Basic Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Xue Peng
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Zhen Wang
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Weifan Jiang
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Wei Huang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, China.
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2
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Meyer C, McCoy M, Li L, Posner B, Westover KD. LIMS-Kinase provides sensitive and generalizable label-free in vitro measurement of kinase activity using mass spectrometry. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101599. [PMID: 38213501 PMCID: PMC10783653 DOI: 10.1016/j.xcrp.2023.101599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Measurements of kinase activity are important for kinase-directed drug development, analysis of inhibitor structure and function, and understanding mechanisms of drug resistance. Sensitive, accurate, and miniaturized assay methods are crucial for these investigations. Here, we describe a label-free, high-throughput mass spectrometry-based assay for studying individual kinase enzymology and drug discovery in a purified system, with a focus on validated drug targets as benchmarks. We demonstrate that this approach can be adapted to many known kinase substrates and highlight the benefits of using mass spectrometry to measure kinase activity in vitro, including increased sensitivity. We speculate that this approach to measuring kinase activity will be generally applicable across most of the kinome, enabling research on understudied kinases and kinase drug discovery.
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Affiliation(s)
- Cynthia Meyer
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
- Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Melissa McCoy
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Lianbo Li
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
- Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Bruce Posner
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Kenneth D. Westover
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
- Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
- X (formerly Twitter): @KENWESTOVER
- Lead contact
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3
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Wardman JF, Sim L, Liu J, Howard TA, Geissner A, Danby PM, Boraston AB, Wakarchuk WW, Withers SG. A high-throughput screening platform for enzymes active on mucin-type O-glycoproteins. Nat Chem Biol 2023; 19:1246-1255. [PMID: 37592157 DOI: 10.1038/s41589-023-01405-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/12/2023] [Indexed: 08/19/2023]
Abstract
Mucin-type O-glycosylation is a post-translational modification present at the interface between cells where it has important roles in cellular communication. However, deciphering the function of O-glycoproteins and O-glycans can be challenging, especially as few enzymes are available for their assembly or selective degradation. Here, to address this deficiency, we developed a genetically encoded screening methodology for the discovery and engineering of the diverse classes of enzymes that act on O-glycoproteins. The method uses Escherichia coli that have been engineered to produce an O-glycosylated fluorescence resonance energy transfer probe that can be used to screen for O-glycopeptidase activity. Subsequent cleavage of the substrate by O-glycopeptidases provides a read-out of the glycosylation state of the probe, allowing the method to also be used to assay glycosidases and glycosyltransferases. We further show the potential of this methodology in the first ultrahigh-throughput-directed evolution of an O-glycopeptidase.
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Affiliation(s)
- Jacob F Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Lyann Sim
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer Liu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Teresa A Howard
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andreas Geissner
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Phillip M Danby
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alisdair B Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Warren W Wakarchuk
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
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4
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Li S, Si H, Song X, Lei C, He X, Wang J, Liu Y, Zhou Y, Song JG, Peng L, Tang X, Chan S, Ren X, Tu Z, Li Z, Wang Z, Zhang Z, Ding K. Discovery of Hexahydrofuro[3,2- b]furans as New Kinase-Selective and Orally Bioavailable JAK3 Inhibitors for the Treatment of Leukemia Harboring a JAK3 Activating Mutant. J Med Chem 2022; 65:10674-10690. [PMID: 35860875 DOI: 10.1021/acs.jmedchem.2c00922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Janus kinase 3 (JAK3) is a potential target for the treatment of hematological malignancies. Herein, we report the discovery of a series of new orally bioavailable irreversible JAK3 kinase inhibitors. The representative compound 12n potently inhibited JAK3 kinase activity with an IC50 value of 1.2 nM and was more than 900-fold selective over JAK1, JAK2, and Tyk2. Cell-based assays revealed that 12n significantly suppressed phosphorylation of JAK3 and the downstream effectors STAT3/5 and also robustly restrained proliferation of BaF3 cells transfected with JAK3M511I activating mutation and human leukemia U937 cells harboring JAK3M511I with IC50 values of 22.9 and 20.2 nM, respectively. More importantly, 12n showed reasonable pharmacokinetic (PK) properties, and oral administration of 12n at a dose of 50 mg/kg twice daily led to tumor regression in a U937 cell inoculated xenograft mouse model. Thus, 12n represents a promising lead compound for further optimization to discover new therapeutic agents for hematological malignancies.
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Affiliation(s)
- Shan Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Hongfei Si
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Xiaojuan Song
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, #190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou 510530, China
| | - Chong Lei
- State Key Laboratory of Bioorganic Chemistry and Natural Products, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Lingling Road, Shanghai 200032, China
| | - Xiaoqiang He
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Jie Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Yiling Liu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Yang Zhou
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Jian-Guo Song
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Lijie Peng
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Xia Tang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Shingpan Chan
- Guangzhou Lixin Pharmaceuticals, Guangzhou 510530, China
| | - Xiaomei Ren
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Zhengchao Tu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, #190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou 510530, China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Zhen Wang
- State Key Laboratory of Bioorganic Chemistry and Natural Products, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Lingling Road, Shanghai 200032, China
| | - Zhang Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China.,State Key Laboratory of Bioorganic Chemistry and Natural Products, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Lingling Road, Shanghai 200032, China.,The First Affiliated Hospital (Huaqiao Hospital), Jinan University, #601 Huangpu Avenue West, Guangzhou 510632, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
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5
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Mei LC, Zhuo LS, Xu HC, Huang W, Hao GF, Yang GF. Conformational adjustment overcomes multiple drug-resistance mutants of tropomyosin receptor kinase. Eur J Med Chem 2022; 237:114406. [PMID: 35486994 DOI: 10.1016/j.ejmech.2022.114406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 12/01/2022]
Abstract
Mutation-induced resistance to targeted drug treatment poses a serious threat to successful chemotherapy. Multiple mutations underlying drug resistance remain a largely unsolved scientific issue. Tropomyosin receptor kinases (TRKs) are promising therapeutic targets for several malignant human cancers, but they have become less effective due to multiple resistance mutations. Thus, TRKs are representative cases to explore the problem of multiple resistance mutations. Here, we proposed a conformational adjustment strategy of drug design to overcome multiple resistance mutations in cancer treatments. A representative inhibitor, TIY-7, exhibited remarkable inhibitory activity against five TRK mutants, showing an IC50 value of 1.1 nM against the most severe mutant TRKA-G595R. Moreover, it displayed superior tumor growth inhibitory activity compared with the clinically used drug selitrectinib. These results validated our strategy to design a new inhibitor structure to overcome multiple resistance mutations.
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Affiliation(s)
- Long-Can Mei
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Lin-Sheng Zhuo
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Hong-Chuang Xu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Wei Huang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, China.
| | - Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, China.
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, China.
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6
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Scheele RA, Lindenburg LH, Petek M, Schober M, Dalby KN, Hollfelder F. Droplet-based screening of phosphate transfer catalysis reveals how epistasis shapes MAP kinase interactions with substrates. Nat Commun 2022; 13:844. [PMID: 35149678 PMCID: PMC8837617 DOI: 10.1038/s41467-022-28396-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 01/10/2022] [Indexed: 11/20/2022] Open
Abstract
The combination of ultrahigh-throughput screening and sequencing informs on function and intragenic epistasis within combinatorial protein mutant libraries. Establishing a droplet-based, in vitro compartmentalised approach for robust expression and screening of protein kinase cascades (>107 variants/day) allowed us to dissect the intrinsic molecular features of the MKK-ERK signalling pathway, without interference from endogenous cellular components. In a six-residue combinatorial library of the MKK1 docking domain, we identified 29,563 sequence permutations that allow MKK1 to efficiently phosphorylate and activate its downstream target kinase ERK2. A flexibly placed hydrophobic sequence motif emerges which is defined by higher order epistatic interactions between six residues, suggesting synergy that enables high connectivity in the sequence landscape. Through positive epistasis, MKK1 maintains function during mutagenesis, establishing the importance of co-dependent residues in mammalian protein kinase-substrate interactions, and creating a scenario for the evolution of diverse human signalling networks. Here, the authors use a droplet-based screen for phosphate transfer catalysis, testing variants of the human protein kinase MKK1 for its ability to activate its downstream target ERK2. Data reveal a flexible motif in the MKK1 docking domain that promotes efficient activation of ERK2, and suggest epistasis between the residues within that sequence.
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Affiliation(s)
- Remkes A Scheele
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | | | - Maya Petek
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.,Faculty of Medicine, University of Maribor, SI-2000, Maribor, Slovenia
| | - Markus Schober
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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7
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Nisiewicz MK, Kowalczyk A, Gajda A, Kasprzak A, Bamburowicz-Klimkowska M, Grudzinski IP, Nowicka AM. Enzymatic cleavage of specific dipeptide conjugated with ferrocene as a flexible ultra-sensitive and fast voltammetric assay of matrix metalloproteinase-9 considered a prognostic cancer biomarker in plasma samples. Biosens Bioelectron 2022; 195:113653. [PMID: 34563889 DOI: 10.1016/j.bios.2021.113653] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/02/2021] [Accepted: 09/16/2021] [Indexed: 11/18/2022]
Abstract
Studies over the last decade have shown that matrix metalloproteinases (MMPs) play a key role in the growth and metastasis of cancer. This zinc-dependent family of endopeptidases is crucial for the degradation of extracellular matrix (ECM), as well as serves as important ECM transducers which have been recognized as early biomarkers for both cancer diagnosis and treatment. In this study, we designed a new type of voltammetric biosensor, composed of a glycine-methionine dipeptide conjugated covalently to ferrocene (Gly-Met-Fc), for fast and ultrasensitive detection of the active form of MMP-9 in plasma samples. The detection was based on specific enzymatic cleavage of the Gly-Met peptide bond, which was monitored by voltammetry and gravimetry measurements. The ferrocene units act as voltammetric visualizers for the detection process. The cysteamine layer directly anchored to the gold surface ensured that the packing density of Gly-Met-Fc in the receptor layer was appropriate for the sensitive detection of MMP-9 in its active form. The developed biosensor was characterized by the widest analytical range (2.0·10-6 - 5.0 μg⋅mL-1) and low detection limit (0.04 pg⋅mL-1). Another valuable feature of the proposed biosensor is that it can be applied directly to the plasma samples without any additional preparation step and thus speeds up the analysis.
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Affiliation(s)
- Monika K Nisiewicz
- Faculty of Chemistry, University of Warsaw, Pasteura Str. 1, PL 02-093, Warsaw, Poland; Faculty of Chemistry, Warsaw University of Technology, Noakowskiego Str. 3, PL 00-664, Warsaw, Poland
| | - Agata Kowalczyk
- Faculty of Chemistry, University of Warsaw, Pasteura Str. 1, PL 02-093, Warsaw, Poland
| | - Aleksandra Gajda
- Faculty of Chemistry, University of Warsaw, Pasteura Str. 1, PL 02-093, Warsaw, Poland
| | - Artur Kasprzak
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego Str. 3, PL 00-664, Warsaw, Poland
| | | | - Ireneusz P Grudzinski
- Faculty of Pharmacy, Medical University of Warsaw, Banacha Str. 1, PL-02-097, Warsaw, Poland
| | - Anna M Nowicka
- Faculty of Chemistry, University of Warsaw, Pasteura Str. 1, PL 02-093, Warsaw, Poland.
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8
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Zhuo LS, Wang MS, Wu FX, Xu HC, Gong Y, Yu ZC, Tian YG, Pang C, Hao GF, Huang W, Yang GF. Discovery of Next-Generation Tropomyosin Receptor Kinase Inhibitors for Combating Multiple Resistance Associated with Protein Mutation. J Med Chem 2021; 64:15503-15514. [PMID: 34668694 DOI: 10.1021/acs.jmedchem.1c01539] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Tropomyosin receptor kinase (TRK) inhibition is an effective therapeutic approach for treatment of a variety of cancers. Despite the use of first-generation TRK inhibitor (TRKI) larotrectinib (1) resulting in significant therapeutic response in patients, acquired resistance develops invariably. The emergence of secondary mutations occurring at the solvent-front, xDFG, and gatekeeper regions of TRK represents a common mechanism for acquired resistance. However, xDFG mutations remain insensitive to second-generation macrocyclic TRKIs selitrectinib (3) and repotrectinib (4) designed to overcome the resistance mediated by solvent-front and gatekeeper mutations. Here, we report the structure-based drug design and discovery of a next-generation TRKI. The structure-activity relationship studies culminated in the identification of a promising drug candidate 8 that showed excellent in vitro potency on a panel of TRK mutants, especially TRKAG667C in the xDFG motif, and improved in vivo efficacy than 1 and 3 in TRK wild-type and mutant fusion-driven tumor xenograft models, respectively.
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Affiliation(s)
- Lin-Sheng Zhuo
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Ming-Shu Wang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Feng-Xu Wu
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, School of Pharmaceutical Sciences, Hubei University of Medicine, Hubei 442000, P. R. China
| | - Hong-Chuang Xu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Yi Gong
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Zhi-Cheng Yu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Yan-Guang Tian
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Chao Pang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Wei Huang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
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9
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Huang YMM. Multiscale computational study of ligand binding pathways: Case of p38 MAP kinase and its inhibitors. Biophys J 2021; 120:3881-3892. [PMID: 34453922 PMCID: PMC8511166 DOI: 10.1016/j.bpj.2021.08.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 06/07/2021] [Accepted: 08/20/2021] [Indexed: 01/09/2023] Open
Abstract
Protein kinases are one of the most important drug targets in the past 10 years. Understanding the inhibitor association processes will profoundly impact new binder designs with preferred binding kinetics. However, after more than a decade of effort, a complete atomistic-level study of kinase inhibitor binding pathways is still lacking. As all kinases share a similar scaffold, we used p38 kinase as a model system to investigate the conformational dynamics and free energy transition of inhibitor binding toward kinases. Two major kinase conformations, Asp-Phe-Gly (DFG)-in and DFG-out, and three types of inhibitors, type I, II, and III, were thoroughly investigated in this work. We performed Brownian dynamics simulations and up to 340 μs Gaussian-accelerated molecular dynamics simulations to capture the inhibitor binding paths and a series of conformational transitions of the p38 kinase from its apo to inhibitor-bound form. Eighteen successful binding trajectories, including all types of inhibitors, are reported herein. Our simulations suggest a mechanism of inhibitor recruitment, a faster ligand association step to a pre-existing DFG-in/DFG-out p38 protein, followed by a slower molecular rearrangement step to adjust the protein-ligand conformation followed by a shift in the energy landscape to reach the final bound state. The ligand association processes also reflect the energetic favor of type I and type II/III inhibitor binding through ATP and allosteric channels, respectively. These different binding routes are directly responsible for the fast (type I binders) and slow (type II/III binders) kinetics of different types of p38 inhibitors. Our findings also echo the recent study of p38 inhibitor dissociation, implying that ligand unbinding could undergo a reverse path of binding, and both processes share similar metastates. This study deepens the understanding of molecular and energetic features of kinase inhibitor-binding processes and will inspire future drug development from a kinetic point of view.
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Affiliation(s)
- Yu-Ming M Huang
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan.
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10
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Chen Y, Sabatini BL. The Kinase Specificity of Protein Kinase Inhibitor Peptide. Front Pharmacol 2021; 12:632815. [PMID: 33584320 PMCID: PMC7878667 DOI: 10.3389/fphar.2021.632815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/04/2021] [Indexed: 11/13/2022] Open
Abstract
G-protein-coupled-receptor (GPCR) signaling is exquisitely controlled to achieve spatial and temporal specificity. The endogenous protein kinase inhibitor peptide (PKI) confines the spatial and temporal spread of the activity of protein kinase A (PKA), which integrates inputs from three major types of GPCRs. Despite its wide usage as a pharmaceutical inhibitor of PKA, it was unclear whether PKI only inhibits PKA activity. Here, the effects of PKI on 55 mouse kinases were tested in in vitro assays. We found that in addition to inhibiting PKA activity, both PKI (6-22) amide and full-length PKIα facilitated the activation of multiple isoforms of protein kinase C (PKC), albeit at much higher concentrations than necessary to inhibit PKA. Thus, our results call for appropriate interpretation of experimental results using PKI as a pharmaceutical agent. Furthermore, our study lays the foundation to explore the potential functions of PKI in regulating PKC activity and in coordinating PKC and PKA activities.
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Affiliation(s)
- Yao Chen
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, United States.,Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, United States
| | - Bernardo L Sabatini
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, United States
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11
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Thomas C, Nothaft H, Yadav R, Fodor C, Alemka A, Oni O, Bell M, Rada B, Szymanski CM. Characterization of ecotin homologs from Campylobacter rectus and Campylobacter showae. PLoS One 2020; 15:e0244031. [PMID: 33378351 PMCID: PMC7773321 DOI: 10.1371/journal.pone.0244031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/01/2020] [Indexed: 12/18/2022] Open
Abstract
Ecotin, first described in Escherichia coli, is a potent
inhibitor of a broad range of serine proteases including those typically
released by the innate immune system such as neutrophil elastase (NE). Here we
describe the identification of ecotin orthologs in various
Campylobacter species, including Campylobacter
rectus and Campylobacter showae residing in the
oral cavity and implicated in the development and progression of periodontal
disease in humans. To investigate the function of these ecotins in
vitro, the orthologs from C.
rectus and C. showae were
recombinantly expressed and purified from E.
coli. Using CmeA degradation/protection assays,
fluorescence resonance energy transfer and NE activity assays, we found that
ecotins from C. rectus and C.
showae inhibit NE, factor Xa and trypsin, but not the
Campylobacter jejuni serine protease HtrA or its ortholog
in E. coli, DegP. To further evaluate ecotin
function in vivo, an E. coli
ecotin-deficient mutant was complemented with the C.
rectus and C. showae
homologs. Using a neutrophil killing assay, we demonstrate that the low survival
rate of the E. coli ecotin-deficient mutant
can be rescued upon expression of ecotins from C.
rectus and C. showae. In
addition, the C. rectus and
C. showae ecotins partially compensate for
loss of N-glycosylation and increased protease susceptibility in the related
pathogen, Campylobacter jejuni, thus implicating a similar role
for these proteins in the native host to cope with the protease-rich environment
of the oral cavity.
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Affiliation(s)
- Cody Thomas
- Department of Microbiology and Complex Carbohydrate Research Center,
University of Georgia, Athens, Georgia, United States of
America
| | - Harald Nothaft
- Department of Biological Sciences, University of Alberta, Edmonton,
Alberta, Canada
| | - Ruchi Yadav
- Department of Infectious Diseases, University of Georgia, Athens,
Georgia, United States of America
| | - Christopher Fodor
- Department of Biological Sciences, University of Alberta, Edmonton,
Alberta, Canada
| | - Abofu Alemka
- Department of Biological Sciences, University of Alberta, Edmonton,
Alberta, Canada
| | - Oluwadamilola Oni
- Department of Infectious Diseases, University of Georgia, Athens,
Georgia, United States of America
| | - Michael Bell
- Department of Infectious Diseases, University of Georgia, Athens,
Georgia, United States of America
| | - Balázs Rada
- Department of Infectious Diseases, University of Georgia, Athens,
Georgia, United States of America
| | - Christine M. Szymanski
- Department of Microbiology and Complex Carbohydrate Research Center,
University of Georgia, Athens, Georgia, United States of
America
- Department of Biological Sciences, University of Alberta, Edmonton,
Alberta, Canada
- * E-mail:
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12
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Kim D, Kim YS, Kim CS, Lee NK. Method for the Rapid Screening of Drug Candidates Using Single‐Protein Tracking in a Living Cell. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Dong‐Kyun Kim
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology, 77, Cheongam‐ro, Nam‐gu, Pohang‐si Gyeongsangbuk‐do 37673 Republic of Korea
| | - Young Sook Kim
- Herbal Medicine Research Division Korea Institute of Oriental Medicine, 1672, Yuseong‐daero, Yuseong‐gu Daejeon 34054 Republic of Korea
| | - Chan Sik Kim
- Clinical Medicine Division Korea Institute of Oriental Medicine, 1672, Yuseong‐daero, Yuseong‐gu Daejeon 34054 Republic of Korea
| | - Nam Ki Lee
- Department of Chemistry Seoul National University, 1, Gwanak‐ro, Gwanak‐gu Seoul 08826 Republic of Korea
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13
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Design, synthesis, and Structure–Activity Relationships (SAR) of 3-vinylindazole derivatives as new selective tropomyosin receptor kinases (Trk) inhibitors. Eur J Med Chem 2020; 203:112552. [DOI: 10.1016/j.ejmech.2020.112552] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/07/2020] [Accepted: 06/07/2020] [Indexed: 11/20/2022]
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14
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How to make an undruggable enzyme druggable: lessons from ras proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020. [PMID: 32951811 DOI: 10.1016/bs.apcsb.2020.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Significant advances have been made toward discovering allosteric inhibitors for challenging drug targets such as the Ras family of membrane-associated signaling proteins. Malfunction of Ras proteins due to somatic mutations is associated with up to a quarter of all human cancers. Computational techniques have played critical roles in identifying and characterizing allosteric ligand-binding sites on these proteins, and to screen ligand libraries against those sites. These efforts, combined with a wide range of biophysical, structural, biochemical and cell biological experiments, are beginning to yield promising inhibitors to treat malignancies associated with mutated Ras proteins. In this chapter, we discuss some of these developments and how the lessons learned from Ras might be applied to similar other challenging drug targets.
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15
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Lee CS, Oh DE, Kim TH. Label-free assay of protein kinase A activity and inhibition in cancer cell using electrochemically-prepared AuNP/rGO nanohybrid electrode modified with C-Kemptide. Talanta 2020; 215:120899. [DOI: 10.1016/j.talanta.2020.120899] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 12/01/2022]
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16
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Wang L, Saarela J, Poque S, Valkonen JP. Development of FRET-based high-throughput screening for viral RNase III inhibitors. MOLECULAR PLANT PATHOLOGY 2020; 21:961-974. [PMID: 32436305 PMCID: PMC7280029 DOI: 10.1111/mpp.12942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/09/2020] [Accepted: 03/16/2020] [Indexed: 06/11/2023]
Abstract
The class 1 ribonuclease III (RNase III) encoded by Sweet potato chlorotic stunt virus (CSR3) suppresses RNA silencing in plant cells and thereby counters the host antiviral response by cleaving host small interfering RNAs, which are indispensable components of the plant RNA interference (RNAi) pathway. The synergy between sweet potato chlorotic stunt virus and sweet potato feathery mottle virus can reduce crop yields by 90%. Inhibitors of CSR3 might prove efficacious to counter this viral threat, yet no screen has been carried out to identify such inhibitors. Here, we report a novel high-throughput screening (HTS) assay based on fluorescence resonance energy transfer (FRET) for identifying inhibitors of CSR3. For monitoring CSR3 activity via HTS, we used a small interfering RNA substrate that was labelled with a FRET-compatible dye. The optimized HTS assay yielded 109 potential inhibitors of CSR3 out of 6,620 compounds tested from different small-molecule libraries. The three best inhibitor candidates were validated with a dose-response assay. In addition, a parallel screen of the selected candidates was carried out for a similar class 1 RNase III enzyme from Escherichia coli (EcR3), and this screen yielded a different set of inhibitors. Thus, our results show that the CSR3 and EcR3 enzymes were inhibited by distinct types of molecules, indicating that this HTS assay could be widely applied in drug discovery of class 1 RNase III enzymes.
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Affiliation(s)
- Linping Wang
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
| | - Jani Saarela
- Institute for Molecular Medicine FinlandUniversity of HelsinkiHelsinkiFinland
| | - Sylvain Poque
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
| | - Jari P.T. Valkonen
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
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17
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Li Y, Sun S, Tian X, Qiu JG, Jiang B, Wang LJ, Zhang CY. Dephosphorylation-directed tricyclic DNA amplification cascades for sensitive detection of protein tyrosine phosphatase. Chem Commun (Camb) 2020; 56:11581-11584. [DOI: 10.1039/d0cc04714g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A new fluorescence method is developed for the sensitive detection of protein tyrosine phosphatase based on dephosphorylation-directed tricyclic DNA amplification cascades.
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Affiliation(s)
- Yueying Li
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Shuli Sun
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Xiaorui Tian
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Jian-Ge Qiu
- Academy of Medical Sciences
- Zhengzhou University
- Zhengzhou 450000
- China
| | - BingHua Jiang
- Academy of Medical Sciences
- Zhengzhou University
- Zhengzhou 450000
- China
| | - Li-juan Wang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chun-yang Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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18
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Somogyi M, Szimler T, Baksa A, Végh BM, Bakos T, Paréj K, Ádám C, Zsigmond Á, Megyeri M, Flachner B, Sajó R, Gráczer É, Závodszky P, Hajdú I, Beinrohr L. A versatile modular vector set for optimizing protein expression among bacterial, yeast, insect and mammalian hosts. PLoS One 2019; 14:e0227110. [PMID: 31887188 PMCID: PMC6936851 DOI: 10.1371/journal.pone.0227110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/12/2019] [Indexed: 12/28/2022] Open
Abstract
We have developed a unified, versatile vector set for expression of recombinant proteins, fit for use in any bacterial, yeast, insect or mammalian cell host. The advantage of this system is its versatility at the vector level, achieved by the introduction of a novel expression cassette. This cassette contains a unified multi-cloning site, affinity tags, protease cleavable linkers, an optional secretion signal, and common restriction endonuclease sites at key positions. This way, genes of interest and all elements of the cassette can be switched freely among the vectors, using restriction digestion and ligation without the need of polymerase chain reaction (PCR). This vector set allows rapid protein expression screening of various hosts and affinity tags. The reason behind this approach was that it is difficult to predict which expression host and which affinity tag will lead to functional expression. The new system is based on four optimized and frequently used expression systems (Escherichia coli pET, the yeast Pichia pastoris, pVL and pIEx for Spodoptera frugiperda insect cells and pLEXm based mammalian systems), which were modified as described above. The resulting vector set was named pONE series. We have successfully applied the pONE vector set for expression of the following human proteins: the tumour suppressor RASSF1A and the protein kinases Aurora A and LIMK1. Finally, we used it to express the large multidomain protein, Rho-associated protein kinase 2 (ROCK2, 164 kDa) and demonstrated that the yeast Pichia pastoris reproducibly expresses the large ROCK2 kinase with identical activity to the insect cell produced counterpart. To our knowledge this is among the largest proteins ever expressed in yeast. This demonstrates that the cost-effective yeast system can match and replace the industry-standard insect cell expression system even for large and complex mammalian proteins. These experiments demonstrate the applicability of our pONE vector set.
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Affiliation(s)
- Márk Somogyi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Pázmány Péter sétány, Budapest, Hungary
| | - Tamás Szimler
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Pázmány Péter sétány, Budapest, Hungary
| | - Attila Baksa
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Pázmány Péter sétány, Budapest, Hungary
| | - Barbara M. Végh
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Pázmány Péter sétány, Budapest, Hungary
| | - Tamás Bakos
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Pázmány Péter sétány, Budapest, Hungary
| | - Katalin Paréj
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Pázmány Péter sétány, Budapest, Hungary
| | - Csaba Ádám
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Pázmány Péter sétány, Budapest, Hungary
| | - Áron Zsigmond
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Pázmány Péter sétány, Budapest, Hungary
| | - Márton Megyeri
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Pázmány Péter sétány, Budapest, Hungary
| | - Beáta Flachner
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Pázmány Péter sétány, Budapest, Hungary
| | - Ráchel Sajó
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Pázmány Péter sétány, Budapest, Hungary
| | - Éva Gráczer
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Pázmány Péter sétány, Budapest, Hungary
| | - Péter Závodszky
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Pázmány Péter sétány, Budapest, Hungary
| | - István Hajdú
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Pázmány Péter sétány, Budapest, Hungary
- * E-mail: (LB); (IH)
| | - László Beinrohr
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Pázmány Péter sétány, Budapest, Hungary
- * E-mail: (LB); (IH)
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19
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Wang L, Hu C, Wang A, Chen C, Wu J, Jiang Z, Zou F, Yu K, Wu H, Liu J, Wang W, Wang Z, Wang B, Qi Z, Liu Q, Wang W, Li L, Ge J, Liu J, Liu Q. Discovery of a novel and highly selective CDK9 kinase inhibitor (JSH-009) with potent antitumor efficacy in preclinical acute myeloid leukemia models. Invest New Drugs 2019; 38:1272-1281. [PMID: 31872348 DOI: 10.1007/s10637-019-00868-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/11/2019] [Indexed: 11/29/2022]
Abstract
Acute myeloid leukemia (AML) is reported to be vulnerable to transcription disruption due to transcriptional addiction. Cyclin-dependent kinase 9 (CDK9), which regulates transcriptional elongation, has attracted extensive attention as a drug target. Although several inhibitors, such as alvocidib and dinaciclib, have shown potent therapeutic effects in clinical trials on AML, the lack of high selectivity for CDK9 and other CDKs has limited their optimal clinical efficacy. Therefore, developing highly selective CDK9 inhibitors is still imperative for the efficacy and safety profile in treating AML. Here, we report a novel highly selective CDK9 inhibitor, JSH-009, which exhibited high potency against CDK9 and displayed great selectivity over 468 kinases/mutants. It also demonstrates impressive in vitro and in vivo antileukemic efficacy in preclinical models of AML, which makes JSH-009 a useful pharmacological tool for elucidating CDK9-mediated transcription and a novel therapeutic candidate for AML.
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Affiliation(s)
- Li Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui, 230031, People's Republic of China
- University of Science and Technology of China, Hefei, Anhui, 230036, People's Republic of China
| | - Chen Hu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui, 230031, People's Republic of China
- University of Science and Technology of China, Hefei, Anhui, 230036, People's Republic of China
| | - Aoli Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui, 230031, People's Republic of China
- Precision Medicine Research Laboratory of Anhui Province, Hefei, Anhui, 230088, People's Republic of China
| | - Cheng Chen
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui, 230031, People's Republic of China
- University of Science and Technology of China, Hefei, Anhui, 230036, People's Republic of China
| | - Jiaxin Wu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui, 230031, People's Republic of China
- University of Science and Technology of China, Hefei, Anhui, 230036, People's Republic of China
| | - Zongru Jiang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui, 230031, People's Republic of China
- University of Science and Technology of China, Hefei, Anhui, 230036, People's Republic of China
| | - Fengming Zou
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui, 230031, People's Republic of China
- Precision Medicine Research Laboratory of Anhui Province, Hefei, Anhui, 230088, People's Republic of China
| | - Kailin Yu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui, 230031, People's Republic of China
- Precision Medicine Research Laboratory of Anhui Province, Hefei, Anhui, 230088, People's Republic of China
| | - Hong Wu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui, 230031, People's Republic of China
- Precision Medicine Research Laboratory of Anhui Province, Hefei, Anhui, 230088, People's Republic of China
| | - Juan Liu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui, 230031, People's Republic of China
- University of Science and Technology of China, Hefei, Anhui, 230036, People's Republic of China
| | - Wenliang Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui, 230031, People's Republic of China
- University of Science and Technology of China, Hefei, Anhui, 230036, People's Republic of China
| | - Zuowei Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui, 230031, People's Republic of China
- University of Science and Technology of China, Hefei, Anhui, 230036, People's Republic of China
| | - Beilei Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui, 230031, People's Republic of China
- University of Science and Technology of China, Hefei, Anhui, 230036, People's Republic of China
| | - Ziping Qi
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui, 230031, People's Republic of China
- Precision Medicine Research Laboratory of Anhui Province, Hefei, Anhui, 230088, People's Republic of China
| | - Qingwang Liu
- Precision Medicine Research Laboratory of Anhui Province, Hefei, Anhui, 230088, People's Republic of China
- Precision Targeted Therapy Discovery Center, Institute of Technology Innovation, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230088, People's Republic of China
| | - Wenchao Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui, 230031, People's Republic of China
- Precision Medicine Research Laboratory of Anhui Province, Hefei, Anhui, 230088, People's Republic of China
- Precision Targeted Therapy Discovery Center, Institute of Technology Innovation, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230088, People's Republic of China
| | - Lili Li
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, People's Republic of China
| | - Jian Ge
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, People's Republic of China.
| | - Jing Liu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui, 230031, People's Republic of China.
- Precision Medicine Research Laboratory of Anhui Province, Hefei, Anhui, 230088, People's Republic of China.
- Precision Targeted Therapy Discovery Center, Institute of Technology Innovation, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230088, People's Republic of China.
| | - Qingsong Liu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui, 230031, People's Republic of China.
- University of Science and Technology of China, Hefei, Anhui, 230036, People's Republic of China.
- Precision Medicine Research Laboratory of Anhui Province, Hefei, Anhui, 230088, People's Republic of China.
- Precision Targeted Therapy Discovery Center, Institute of Technology Innovation, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230088, People's Republic of China.
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, People's Republic of China.
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20
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Patel RK, Weir MC, Shen K, Snyder D, Cooper VS, Smithgall TE. Expression of myeloid Src-family kinases is associated with poor prognosis in AML and influences Flt3-ITD kinase inhibitor acquired resistance. PLoS One 2019; 14:e0225887. [PMID: 31790499 PMCID: PMC6886798 DOI: 10.1371/journal.pone.0225887] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 11/14/2019] [Indexed: 01/08/2023] Open
Abstract
Unregulated protein-tyrosine kinase signaling is a common feature of AML, often involving mutations in Flt3 and overexpression of myeloid Src-family kinases (Hck, Fgr, Lyn). Here we show that high-level expression of these Src kinases predicts poor survival in a large cohort of AML patients. To test the therapeutic benefit of Flt3 and Src-family kinase inhibition, we used the pyrrolopyrimidine kinase inhibitor A-419259. This compound potently inhibits Hck, Fgr, and Lyn as well as Flt3 bearing an activating internal tandem duplication (ITD). Flt3-ITD expression sensitized human TF-1 myeloid cells to growth arrest by A-419259, supporting direct action on the Flt3-ITD kinase domain. Cells transformed with the Flt3-ITD mutants D835Y and F691L were resistant to A-419259, while co-expression of Hck or Fgr restored inhibitor sensitivity to Flt3-ITD D835Y. Conversely, Hck and Fgr mutants with engineered A-419259 resistance mutations decreased sensitivity of TF-1/Flt3-ITD cells. To investigate de novo resistance mechanisms, A-419259-resistant Flt3-ITD+ AML cell populations were derived via long-term dose escalation. Whole exome sequencing identified a distinct Flt3-ITD kinase domain mutation (N676S/T) among all A-419259 target kinases in each of six independent resistant cell populations. These studies show that Hck and Fgr expression influences inhibitor sensitivity and the pathway to acquired resistance in Flt3-ITD+ AML.
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MESH Headings
- Amino Acid Substitution
- Cell Line, Tumor
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Gene Expression Regulation, Developmental/drug effects
- Gene Expression Regulation, Leukemic/drug effects
- Humans
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/enzymology
- Leukemia, Myeloid, Acute/genetics
- Mutation, Missense
- Prognosis
- Protein Kinase Inhibitors/pharmacology
- Proto-Oncogene Proteins/biosynthesis
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins c-hck/biosynthesis
- Proto-Oncogene Proteins c-hck/genetics
- Pyrimidines/pharmacology
- Pyrroles/pharmacology
- Exome Sequencing
- fms-Like Tyrosine Kinase 3/antagonists & inhibitors
- fms-Like Tyrosine Kinase 3/genetics
- fms-Like Tyrosine Kinase 3/metabolism
- src-Family Kinases/biosynthesis
- src-Family Kinases/genetics
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Affiliation(s)
- Ravi K. Patel
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Mark C. Weir
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Kexin Shen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Daniel Snyder
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Vaughn S. Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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21
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Cui S, Wang Y, Wang Y, Tang X, Ren X, Zhang L, Xu Y, Zhang Z, Zhang ZM, Lu X, Ding K. Design, synthesis and biological evaluation of 3-(imidazo[1,2-a]pyrazin-3-ylethynyl)-2-methylbenzamides as potent and selective pan-tropomyosin receptor kinase (TRK) inhibitors. Eur J Med Chem 2019; 179:470-482. [DOI: 10.1016/j.ejmech.2019.06.064] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/21/2019] [Accepted: 06/21/2019] [Indexed: 01/14/2023]
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22
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Discovery of Small-Molecule Selective mTORC1 Inhibitors via Direct Inhibition of Glucose Transporters. Cell Chem Biol 2019; 26:1203-1213.e13. [PMID: 31231029 DOI: 10.1016/j.chembiol.2019.05.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/12/2019] [Accepted: 05/22/2019] [Indexed: 12/30/2022]
Abstract
The mechanistic target of rapamycin (mTOR) is a central regulator of cellular metabolic processes. Dysregulation of this kinase complex can result in a variety of human diseases. Rapamycin and its analogs target mTORC1 directly; however, chronic treatment in certain cell types and in vivo results in the inhibition of both mTORC1 and mTORC2. We have developed a high-throughput cell-based screen for the detection of phosphorylated forms of the mTORC1 (4E-BP1, S6K1) and mTORC2 (Akt) substrates and have identified and characterized a chemical scaffold that demonstrates a profile consistent with the selective inhibition of mTORC1. Stable isotope labeling of amino acids in cell culture-based proteomic target identification revealed that class I glucose transporters were the primary target for these compounds yielding potent inhibition of glucose uptake and, as a result, selective inhibition of mTORC1. The link between the glucose uptake and selective mTORC1 inhibition are discussed in the context of a yet-to-be discovered glucose sensor.
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23
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Quinolone antibiotic derivatives as new selective Axl kinase inhibitors. Eur J Med Chem 2019; 166:318-327. [DOI: 10.1016/j.ejmech.2019.01.065] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/27/2019] [Accepted: 01/27/2019] [Indexed: 12/25/2022]
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24
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Kempa EE, Hollywood KA, Smith CA, Barran PE. High throughput screening of complex biological samples with mass spectrometry – from bulk measurements to single cell analysis. Analyst 2019; 144:872-891. [DOI: 10.1039/c8an01448e] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We review the state of the art in HTS using mass spectrometry with minimal sample preparation from complex biological matrices. We focus on industrial and biotechnological applications.
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Affiliation(s)
- Emily E. Kempa
- Michael Barber Centre for Collaborative Mass Spectrometry
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester
- UK
| | - Katherine A. Hollywood
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM)
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester M1 7DN
- UK
| | - Clive A. Smith
- Sphere Fluidics Limited
- The Jonas-Webb Building
- Babraham Research Campus
- Cambridge
- UK
| | - Perdita E. Barran
- Michael Barber Centre for Collaborative Mass Spectrometry
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester
- UK
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25
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Díaz Galicia ME, Aldehaiman A, Hong S, Arold ST, Grünberg R. Methods for the recombinant expression of active tyrosine kinase domains: Guidelines and pitfalls. Methods Enzymol 2019; 621:131-152. [DOI: 10.1016/bs.mie.2019.02.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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26
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Xun Q, Zhang Z, Luo J, Tong L, Huang M, Wang Z, Zou J, Liu Y, Xu Y, Xie H, Tu ZC, Lu X, Ding K. Design, Synthesis, and Structure–Activity Relationship Study of 2-Oxo-3,4-dihydropyrimido[4,5-d]pyrimidines as New Colony Stimulating Factor 1 Receptor (CSF1R) Kinase Inhibitors. J Med Chem 2018; 61:2353-2371. [PMID: 29499108 DOI: 10.1021/acs.jmedchem.7b01612] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Qiuju Xun
- State Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Zhang Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Jinfeng Luo
- State Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Linjiang Tong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zu-Chong-Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Minhao Huang
- State Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Zhen Wang
- State Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Jian Zou
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yingqiang Liu
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zu-Chong-Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- School of Life Sciences, Shanghai University, No. 99 Shangda Road, Shanghai 200444, China
| | - Yong Xu
- State Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Hua Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zu-Chong-Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Zheng-Chao Tu
- State Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Xiaoyun Lu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- State Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- Guangzhou City Key Laboratory of Precision Chemical Drug Development, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People’s Republic of China, Guangzhou 510632, China
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27
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Molecular dynamics and integrated pharmacophore-based identification of dual [Formula: see text] inhibitors. Mol Divers 2017; 22:95-112. [PMID: 29138965 DOI: 10.1007/s11030-017-9794-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 10/24/2017] [Indexed: 12/14/2022]
Abstract
Despite increase in the understanding of the pathogenesis of rheumatoid arthritis (RA), it remains a tough challenge. The advent of kinases involved in key intracellular pathways in pathogenesis of RA may provide a new phase of drug discovery for RA. The present study is aimed to identify dual JAK3/[Formula: see text] inhibitors by developing an optimum pharmacophore model integrating the information revealed by ligand-based pharmacophore models and structure-based pharmacophore models (SBPMs). For JAK3 inhibitors, the addition of an aromatic ring feature and for [Formula: see text] the addition of a hydrophobic feature proposed by SBPMs lead to five-point pharmacophore (i.e., AADHR.54 (JAK3)) and six-point pharmacophore (i.e., AAAHRR.45 ([Formula: see text])). The obtained pharmacophores were validated and used for virtual screening and then for docking-based screening. Molecules were further evaluated for ADME properties, and their docked protein complexes were subjected to MM-GBSA energy calculations and molecular dynamic simulations. The top two hit compounds with novel scaffolds 2-oxo-1,2-dihydroquinoline and benzo[d]oxazole showed inhibitory activity for JAK3 and [Formula: see text].
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28
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Luzi NM, Lyons CE, Peterson DL, Ellis KC. Characterization of PKACα enzyme kinetics and inhibition in an HPLC assay with a chromophoric substrate. Anal Biochem 2017; 532:45-52. [PMID: 28595966 PMCID: PMC5889107 DOI: 10.1016/j.ab.2017.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 05/30/2017] [Accepted: 06/02/2017] [Indexed: 11/16/2022]
Abstract
Here we describe a convenient, inexpensive, and non-hazardous method for the measurement of the kinase activity of the catalytic subunit of cAMP-dependent protein kinase (PKACα). The assay is based on the separation of a substrate peptide labeled with a strong chromophore from the phosphorylated product peptide by high-performance liquid chromatograph (HPLC) and quantification of the product ratiometrically at a wavelength in the visual spectrum (Vis). The utility and reliability of the HPLC-Vis assay were demonstrated by characterizing the kinetic parameters (KM, Vmax) of the new Rh-MAB-Kemptide substrate, a commercially prepared TAMRA-Kemptide substrate, and ATP as well as the potency (IC50, Ki) of the known PKACα inhibitors H89 and PKI(5-24). The advantages of this assay are that it is convenient and inexpensive, uses readily synthesized or commercially available substrates that are shelf-stable, uses a common piece of laboratory equipment, and does not require any hazardous materials such as radioactive γ-32P-ATP. The assay format is also highly flexible and could be adapted for the testing of many different kinases by changing the peptide substrate sequence.
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Affiliation(s)
- Nicole M Luzi
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298-0540, United States
| | - Charles E Lyons
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298-0035, United States
| | - Darrell L Peterson
- Institute for Structural Biology, Drug Discovery, and Development, Virginia Commonwealth University, Richmond, VA 23219-1540, United States; Department of Biochemistry and Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298-0614, United States
| | - Keith C Ellis
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298-0540, United States; Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298-0035, United States; Institute for Structural Biology, Drug Discovery, and Development, Virginia Commonwealth University, Richmond, VA 23219-1540, United States.
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29
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De Simone A, Fiori J, Naldi M, D’Urzo A, Tumiatti V, Milelli A, Andrisano V. Application of an ESI-QTOF method for the detailed characterization of GSK-3β inhibitors. J Pharm Biomed Anal 2017; 144:159-166. [DOI: 10.1016/j.jpba.2017.02.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/30/2017] [Accepted: 02/18/2017] [Indexed: 10/20/2022]
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30
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Oxindole-based SYK and JAK3 dual inhibitors for rheumatoid arthritis: designing, synthesis and biological evaluation. Future Med Chem 2017; 9:1193-1211. [DOI: 10.4155/fmc-2017-0037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: Autoimmune disorders have complex pathophysiology and focus is laid on the development of multitargeted agents. Two well-established kinases: SYK and JAK3, were considered to design dual inhibitors as potential therapeutics using various molecular-modeling approaches. Mehodology: Pharmacophore models for SYK and JAK3 were generated using oxindole-based inhibitors. Furthermore, an in-house database was designed that was screened against the best selected models. The obtained hits were employed for docking analysis and subjected to MM-GBSA analysis and molecular dynamic simulation. Results: Top five oxindole derivatives were synthesized and evaluated for in vitro SYK and JAK3 activity. The most active compound 4a was evaluated for in vivo antiarthritic activity. It showed significant anti-arthritic activity. Conclusion: Thus, the designed inhibitors resulted in potential therapeutic agents for rheumatoid arthritis.
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31
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Jeong EM, Lee MY, Lee JH, Lee BH, Oh KS. A Dual Readout Assay Based on Fluorescence Polarization and Time-Resolved Fluorescence Resonance Energy Transfer to Screen for RSK1 Inhibitors. Biol Pharm Bull 2017; 39:547-55. [PMID: 27040627 DOI: 10.1248/bpb.b15-00808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A dual readout assay based on fluorescence polarization (FP) and time-resolved fluorescence resonance energy transfer (TR-FRET) exhibits many advantages over single assay technology in terms of screening quality and efficiency. In this study, we developed a dual readout assay combining FP and TR-FRET to identify ribosomal S6 kinase 1 (RSK1) inhibitors. This dual readout assay can monitor both FP and TR-FRET signals from a single RSK1 kinase reaction by using the immobilized metal affinity for phosphochemical (IMAP)-based assay. The Z' value and signal to background (S/B) ratio were 0.85 and 4.0 using FP, and 0.79 and 10.6 using TR-FRET, which led to performance of a pilot library screening against the drug repositioning set consisting of 2320 compounds with a reasonable reproducibility. From this screening, we identified 16 compounds showing greater than 50% inhibition against RSK1 for both FP and TR-FRET; 6 compounds with greater than 50% inhibition only for FP; and 4 compounds with greater than 50% inhibition only for TR-FRET. In a cell-based functional assay to validate the hit compounds, 10 compounds identified only in a single assay had little effect on the RSK-mediated phosphorylation of liver kinase B1, whereas 5 compounds showing greater than 80% inhibition for both FP and TR-FRET reduced the phosphorylation of liver kinase B1. These results demonstrate that the dual readout assay can be used to identify hit compounds by subsequently monitoring both FP and TR-FRET signals from one RSK1 reaction.
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Affiliation(s)
- Eun-mi Jeong
- Bio-Organic Science Division, Korea Research Institute of Chemical Technology
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32
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Kaur M, Silakari O. Ligand-based and e-pharmacophore modeling, 3D-QSAR and hierarchical virtual screening to identify dual inhibitors of spleen tyrosine kinase (Syk) and janus kinase 3 (JAK3). J Biomol Struct Dyn 2016; 35:3043-3060. [PMID: 27678281 DOI: 10.1080/07391102.2016.1240108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The clinical efficacy of multiple kinase inhibitors has caught the interest of Pharmaceutical and Biotech researchers to develop potential drugs with multi-kinase inhibitory activity for complex diseases. In the present work, we attempted to identify dual inhibitors of spleen tyrosine kinase (Syk) and janus kinase 3 (JAK3), keys players in immune signaling, by developing ideal pharmacophores integrating Ligand-based pharmacophore models (LBPMs) and Structure-based pharmacophore models (SBPMs), thereby projecting the optimum pharmacophoric required for inhibition of both the kinases. The four point LBPM; ADPR.14 suggested the presence of one hydrogen bond acceptor, one hydrogen bond donor, one positive ionizable, and one ring aromatic feature for Syk inhibitory activity and AADH.54 proposed the necessity of two hydrogen bond acceptor, one hydrogen bond donor, and one hydrophobic feature for JAK3 inhibitory activity. To our interest, SBPMs identified additional ring aromatic features required for inhibition of both the kinases. For Syk inhibitory activity, the hydrogen bond acceptor feature indicated by LBPM was devoid of forming hydrogen bonding interaction with the hinge region amino acid residue (Ala451). Thus merging the information revealed by both LBPMs and SBPMs, ideal pharmacophore models i.e. ADPRR.14 (Syk) and AADHR.54 (JAK3) were generated. These models after rigorous statistical validation were used for screening of Asinex database. The systematic virtual screening protocol, including pharmacophore and docking-based screening, ADME property, and MM-GBSA energy calculations, retrieved final 10 hits as dual inhibitors of Syk and JAK3. Final 10 hits thus obtained can aid in the development of potential therapeutic agents for autoimmune disorders. Also the top two hits were evaluated against both the enzymes.
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Affiliation(s)
- Maninder Kaur
- a Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research , Punjabi University , Patiala , Punjab 147002 , India
| | - Om Silakari
- a Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research , Punjabi University , Patiala , Punjab 147002 , India
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33
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Al-Ghabkari A, Deng JT, McDonald PC, Dedhar S, Alshehri M, Walsh MP, MacDonald JA. A novel inhibitory effect of oxazol-5-one compounds on ROCKII signaling in human coronary artery vascular smooth muscle cells. Sci Rep 2016; 6:32118. [PMID: 27573465 PMCID: PMC5004178 DOI: 10.1038/srep32118] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/02/2016] [Indexed: 12/27/2022] Open
Abstract
The selectivity of (4Z)-2-(4-chloro-3-nitrophenyl)-4-(pyridin-3-ylmethylidene)-1,3-oxazol-5-one (DI) for zipper-interacting protein kinase (ZIPK) was previously described by in silico computational modeling, screening a large panel of kinases, and determining the inhibition efficacy. Our assessment of DI revealed another target, the Rho-associated coiled-coil-containing protein kinase 2 (ROCKII). In vitro studies showed DI to be a competitive inhibitor of ROCKII (Ki, 132 nM with respect to ATP). This finding was supported by in silico molecular surface docking of DI with the ROCKII ATP-binding pocket. Time course analysis of myosin regulatory light chain (LC20) phosphorylation catalyzed by ROCKII in vitro revealed a significant decrease upon treatment with DI. ROCKII signaling was investigated in situ in human coronary artery vascular smooth muscle cells (CASMCs). ROCKII down-regulation using siRNA revealed several potential substrates involved in smooth muscle contraction (e.g., LC20, Par-4, MYPT1) and actin cytoskeletal dynamics (cofilin). The application of DI to CASMCs attenuated LC20, Par-4, LIMK, and cofilin phosphorylations. Notably, cofilin phosphorylation was not significantly decreased with a novel ZIPK selective inhibitor (HS-38). In addition, CASMCs treated with DI underwent cytoskeletal changes that were associated with diminution of cofilin phosphorylation. We conclude that DI is not selective for ZIPK and is a potent inhibitor of ROCKII.
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Affiliation(s)
- Abdulhameed Al-Ghabkari
- Department of Biochemistry &Molecular Biology, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Jing-Ti Deng
- Department of Biochemistry &Molecular Biology, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Paul C McDonald
- Department of Integrative Oncology, BC Cancer Research Centre, 675 West 10th Ave, Vancouver, BC, V5Z 1L3, Canada
| | - Shoukat Dedhar
- Department of Integrative Oncology, BC Cancer Research Centre, 675 West 10th Ave, Vancouver, BC, V5Z 1L3, Canada
| | - Mana Alshehri
- Department of Biochemistry &Molecular Biology, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Michael P Walsh
- Department of Biochemistry &Molecular Biology, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Justin A MacDonald
- Department of Biochemistry &Molecular Biology, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
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34
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Tan L, Zhang Z, Gao D, Luo J, Tu ZC, Li Z, Peng L, Ren X, Ding K. 4-Oxo-1,4-dihydroquinoline-3-carboxamide Derivatives as New Axl Kinase Inhibitors. J Med Chem 2016; 59:6807-25. [PMID: 27379978 DOI: 10.1021/acs.jmedchem.6b00608] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Li Tan
- State
Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Zhang Zhang
- State
Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
- School
of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Donglin Gao
- State
Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jinfeng Luo
- State
Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Zheng-Chao Tu
- State
Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Zhengqiu Li
- School
of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Lijie Peng
- School
of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xiaomei Ren
- State
Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
- School
of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- State
Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
- School
of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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35
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Kornienko O, Lacson R, Kunapuli P, Schneeweis J, Hoffman I, Smith T, Alberts M, Inglese J, Strulovici B. Miniaturization of Whole Live Cell-Based GPCR Assays Using Microdispensing and Detection Systems. ACTA ACUST UNITED AC 2016; 9:186-95. [PMID: 15140380 DOI: 10.1177/1087057103260070] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cell-based β-lactamase reporter gene assays designed to measure the functional responses of G-protein-coupled receptors (GPCRs) were miniaturized to less than 2 μL total assay volume in a 3456-well microplate. Studies were done to evaluate both receptor agonists and antagonists. The pharmacology of agonists and antagonists for target GPCRs originally developed in a 96-well format was recapitulated in a 3456-well microplate format without compromising data quality or EC50/IC50 precision. These assays were employed in high-throughput screening campaigns, allowing the testing of more than 150,000 compounds in 8 h. The instrumentation used and practical aspects of the assay development are discussed.
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MESH Headings
- Animals
- Biological Assay/instrumentation
- Biological Assay/methods
- Combinatorial Chemistry Techniques
- Cricetinae
- Dose-Response Relationship, Drug
- Drug Evaluation, Preclinical/instrumentation
- Drug Evaluation, Preclinical/methods
- Genes, Reporter
- Humans
- Inhibitory Concentration 50
- Nanotechnology/methods
- Receptors, G-Protein-Coupled/agonists
- Receptors, G-Protein-Coupled/antagonists & inhibitors
- Receptors, Neurotensin/drug effects
- Receptors, Neurotensin/genetics
- Receptors, Oxytocin/agonists
- Receptors, Oxytocin/antagonists & inhibitors
- Receptors, Oxytocin/genetics
- Reproducibility of Results
- Spectrometry, Fluorescence
- beta-Lactamases/genetics
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Affiliation(s)
- Oleg Kornienko
- Merck Research Laboratories, Department of Automated Biotechnology, North Wales, PA 19454, USA.
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36
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Arfeen M, Bhagat S, Patel R, Prasad S, Roy I, Chakraborti AK, Bharatam PV. Design, synthesis and biological evaluation of 5-benzylidene-2-iminothiazolidin-4-ones as selective GSK-3β inhibitors. Eur J Med Chem 2016; 121:727-736. [PMID: 27423119 DOI: 10.1016/j.ejmech.2016.04.075] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/26/2016] [Accepted: 04/28/2016] [Indexed: 01/16/2023]
Abstract
In this work, iminothiazolidin-4-one derivatives were explored as selective GSK-3β inhibitors. Molecular docking analysis was carried to design a series of compounds, which were synthesized using substituted thiourea, 2-bromoacetophenones and benzaldehydes. Out of the twenty five compounds synthesized during this work, the in vitro evaluation against GSK-3 led to the identification of nine compounds with activity in lower nano-molar range (2-85 nM). Further, in vitro evaluation against CDK-2 showed five compounds to be selective towards GSK-3.
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Affiliation(s)
- Minhajul Arfeen
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, 160062, Punjab, India
| | - Shweta Bhagat
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, 160062, Punjab, India
| | - Rahul Patel
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, 160062, Punjab, India
| | - Shivcharan Prasad
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, 160062, Punjab, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, 160062, Punjab, India
| | - Asit K Chakraborti
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, 160062, Punjab, India
| | - Prasad V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, 160062, Punjab, India.
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37
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Direct determination of GSK-3β activity and inhibition by UHPLC-UV–vis diode arrays detector (DAD). J Pharm Biomed Anal 2016; 124:104-111. [DOI: 10.1016/j.jpba.2016.02.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/15/2016] [Accepted: 02/20/2016] [Indexed: 01/09/2023]
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Phosphorylation regulates proteolytic efficiency of TEV protease detected by a 5(6)-carboxyfluorescein-pyrene based fluorescent sensor. Talanta 2016; 150:340-5. [DOI: 10.1016/j.talanta.2015.12.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/01/2015] [Accepted: 12/10/2015] [Indexed: 12/21/2022]
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Wu J, Liu S, Fan Z, Zhang L, Tian Y, Yang R. A novel and selective inhibitor of PKC ζ potently inhibits human breast cancer metastasis in vitro and in mice. Tumour Biol 2016; 37:8391-401. [DOI: 10.1007/s13277-015-4744-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/27/2015] [Indexed: 12/16/2022] Open
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Nguyen PD, Cong VT, Baek C, Min J. Fabrication of peptide stabilized fluorescent gold nanocluster/graphene oxide nanocomplex and its application in turn-on detection of metalloproteinase-9. Biosens Bioelectron 2015; 89:666-672. [PMID: 26725932 DOI: 10.1016/j.bios.2015.12.031] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 11/30/2015] [Accepted: 12/14/2015] [Indexed: 01/14/2023]
Abstract
This study introduces the double-ligands stabilizing gold nanoclusters and the fabrication of gold nanocluster/graphene nanocomplex as a "turn-on" fluorescent probe for the detection of cancer-related enzyme matrix metalloproteinase-9. A facile, one-step approach was developed for the synthesis of fluorescent gold nanoclusters using peptides and mercaptoundecanoic acid as co-templating ligands. The peptide was designed to possess a metalloproteinase-9 cleavage site and to act not only as a stabilizer but also as a targeting ligand for the enzyme detection. The prepared gold nanoclusters show an intense red fluorescence with a broad adsorption spectrum. In the presence of the enzyme, due to the excellent quenching properties and the negligible background of graphene oxide, the developed peptide-gold nanocluster/graphene nanocomplex yielded an intense "turn-on" fluorescent response, which strongly correlated with the enzyme concentration. The limit of detection of the nanocomplex was 0.15nM. The sensor was successfully applied for "turn-on" detection of metalloproteinase-9 secreted from human breast adenocarcinoma MCF-7 cells with high sensitivity, selectivity, significant improvement in terms of detection time and simplicity.
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Affiliation(s)
- Phuong-Diem Nguyen
- School of Integrative Engineering, Chung-Ang University, Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Vu Thanh Cong
- School of Integrative Engineering, Chung-Ang University, Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Changyoon Baek
- School of Integrative Engineering, Chung-Ang University, Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Junhong Min
- School of Integrative Engineering, Chung-Ang University, Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea.
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Group I Paks as therapeutic targets in NF2-deficient meningioma. Oncotarget 2015; 6:1981-94. [PMID: 25596744 PMCID: PMC4385830 DOI: 10.18632/oncotarget.2810] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/24/2014] [Indexed: 11/25/2022] Open
Abstract
Neurofibromatosis type 2 (NF2) is an autosomal dominant disorder characterized by the development of multiple tumors in the central nervous system, most notably schwannomas and meningiomas. Mutational inactivation of NF2 is found in 40-60% of sporadic meningiomas, but the molecular mechanisms underlying malignant changes of meningioma cells remain unclear. Because group I p21-activated kinases (Paks) bind to and are inhibited by the NF2-encoded protein Merlin, we assessed the signaling and anti-tumor effects of three group-I specific Pak inhibitors - Frax597, 716 and 1036 - in NF2-/- meningiomas in vitro and in an orthotopic mouse model. We found that these Pak inhibitors suppressed the proliferation and motility of both benign (Ben-Men1) and malignant (KT21-MG1) meningiomas cells. In addition, we found a strong reduction in phosphorylation of Mek and S6, and decreased cyclin D1 expression in both cell lines after treatment with Pak inhibitors. Using intracranial xenografts of luciferase-expressing KT21-MG1 cells, we found that treated mice showed significant tumor suppression for all three Pak inhibitors. Similar effects were observed in Ben-Men1 cells. Tumors dissected from treated animals exhibited an increase in apoptosis without notable change in proliferation. Collectively, these results suggest that Pak inhibitors might be useful agents in treating NF2-deficient meningiomas.
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Leoni A, Locatelli A, Morigi R, Rambaldi M. 2-Indolinone a versatile scaffold for treatment of cancer: a patent review (2008-2014). Expert Opin Ther Pat 2015; 26:149-73. [PMID: 26561198 DOI: 10.1517/13543776.2016.1118059] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION 2-Indolinone is a well-known aromatic heterocyclic organic compound. A lot of work has been done on this bicyclic structure by academic and company researchers to synthesize compounds directed to a plethora of molecular targets in order to discover new drug leads. This review presents up-to-date information in the field of cancer therapy research based on this small building block. AREAS COVERED The present review gives an account of the recent patent literature (2008-2014) describing the discovery of 2-indolinone derivatives with selected therapeutic activities. In this period, a large amount of patents were published on this topic. We have limited the analysis to 37 patents on 2-indolinone derivatives having potential clinical application as chemotherapeutic agents. In this review, the therapeutic applications of 2-indolinone derivatives for the treatment of cancer reported in international patents have been discussed. EXPERT OPINION 2-Indolinone is the scaffold of the compounds considered from a medicinal chemistry perspective. Many of them have been developed and marketed for therapeutic use. In cancer chemotherapy, progress has been made in designing selective 2-indolinone derivatives. Some of them show preclinical efficacy. However, 2-indolinone has not exhausted all of its potential in the development of new compounds for clinical applications and remains a great tool for future research.
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Affiliation(s)
- Alberto Leoni
- a Dipartimento di Farmacia e Biotecnologie , Università degli Studi di Bologna , Bologna , Italy
| | - Alessandra Locatelli
- a Dipartimento di Farmacia e Biotecnologie , Università degli Studi di Bologna , Bologna , Italy
| | - Rita Morigi
- a Dipartimento di Farmacia e Biotecnologie , Università degli Studi di Bologna , Bologna , Italy
| | - Mirella Rambaldi
- a Dipartimento di Farmacia e Biotecnologie , Università degli Studi di Bologna , Bologna , Italy
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Strom TA, Durdagi S, Ersoz SS, Salmas RE, Supuran CT, Barron AR. Fullerene-based inhibitors of HIV-1 protease. J Pept Sci 2015; 21:862-70. [DOI: 10.1002/psc.2828] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/07/2015] [Accepted: 09/14/2015] [Indexed: 11/08/2022]
Affiliation(s)
- T. Amanda Strom
- Department of Chemistry; Rice University; Houston TX 77005 USA
| | - Serdar Durdagi
- Department of Biophysics, School of Medicine; Bahcesehir University; Istanbul Turkey
- Department of Biological Sciences, Institute for Biocomplexity and Informatics; University of Calgary; Calgary Alberta Canada
| | | | | | - Claudiu T. Supuran
- Laboratorio di Chimica Bioinorganica; Università degli Studi di Firenze; Rm. 188, Via della Lastruccia 3 I-50019 Sesto Fiorentino (Firenze) Italy
| | - Andrew R. Barron
- Department of Chemistry; Rice University; Houston TX 77005 USA
- Department of Materials Science and Nanoengineering; Rice University; Houston TX 77005 USA
- Institute of Life Sciences; Swansea University; Singleton Park Swansea SA2 8PP Wales UK
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44
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Ma H, Howitz KT, Horiuchi KY, Wang Y. Histone Methyltransferase Activity Assays. EPIGENETICS FOR DRUG DISCOVERY 2015. [DOI: 10.1039/9781782628484-00267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Histone methyltransferases (HMTs) methylate either the lysine or arginine residues on histones and other proteins and play a crucial role in epigenetic regulation. Over 70 HMTs are encoded by the human genome, and many have been implicated in the aetiology of cancer, inflammatory diseases, neurodegenerative diseases and other conditions. There are currently about a dozen HMT activity assays available, and many of these assay formats are applicable to other epigenetic factors, such as histone acetyltransferases, histone deacetylases, and histone and DNA demethylases. Many factors need to be considered in selecting an HMT assay for drug discovery studies, including cost, adaptability to high-throughput screening, and rates of false positives and false negatives. This chapter describes the mechanisms of the major assay platforms available for HMT screening and profiling and presents the advantages and limitations associated with each.
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Affiliation(s)
- Haiching Ma
- Reaction Biology Corporation One Great Valley Parkway, Suite 2 Malvern PA 19355 USA
| | - Konrad T. Howitz
- Reaction Biology Corporation One Great Valley Parkway, Suite 2 Malvern PA 19355 USA
| | - Kurumi Y. Horiuchi
- Reaction Biology Corporation One Great Valley Parkway, Suite 2 Malvern PA 19355 USA
| | - Yuren Wang
- Reaction Biology Corporation One Great Valley Parkway, Suite 2 Malvern PA 19355 USA
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Beck JR, Zhou X, Casey GR, Stains CI. Design and evaluation of a real-time activity probe for focal adhesion kinase. Anal Chim Acta 2015; 897:62-8. [PMID: 26515006 DOI: 10.1016/j.aca.2015.09.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/11/2015] [Accepted: 09/15/2015] [Indexed: 12/22/2022]
Abstract
Focal adhesion kinase (FAK) has been identified as a potential therapeutic target for the treatment of metastatic cancers. Herein we describe the design, synthesis and optimization of a direct activity sensor for FAK and its application to screening FAK inhibitors. We find that the position of the sensing moiety, a phosphorylation-sensitive sulfonamido-oxine fluorophore, can dramatically influence the performance of peptide sensors for FAK. Real-time fluorescence activity assays using an optimized sensor construct, termed FAKtide-S2, are highly reproducible (Z' = 0.91) and are capable of detecting as little as 1 nM recombinant FAK. Utilizing this robust assay format, we define conditions for the screening of FAK inhibitors and demonstrate the utility of this platform using a set of well-characterized small molecule kinase inhibitors. Additionally, we provide the selectivity profile of FAKtide-S2 among a panel of closely related enzymes, identifying conditions for selectively monitoring FAK activity in the presence of off-target enzymes. In the long term, the chemosensor platform described in this work can be used to identify novel FAK inhibitor scaffolds and potentially assess the efficacy of FAK inhibitors in disease models.
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Affiliation(s)
- Jon R Beck
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588, United States
| | - Xinqi Zhou
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588, United States
| | - Garrett R Casey
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588, United States
| | - Cliff I Stains
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588, United States.
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Zn(II)-Coordinated Quantum Dot-FRET Nanosensors for the Detection of Protein Kinase Activity. SENSORS 2015. [PMID: 26213934 PMCID: PMC4570303 DOI: 10.3390/s150817977] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We report a simple detection of protein kinase activity using Zn(II)-mediated fluorescent resonance energy transfer (FRET) between quantum dots (QDs) and dye-tethered peptides. With neither complex chemical ligands nor surface modification of QDs, Zn(II) was the only metal ion that enabled the phosphorylated peptides to be strongly attached on the carboxyl groups of the QD surface via metal coordination, thus leading to a significant FRET efficiency. As a result, protein kinase activity in intermixed solution was efficiently detected by QD-FRET via Zn(II) coordination, especially when the peptide substrate was combined with affinity-based purification. We also found that mono- and di-phosphorylation in the peptide substrate could be discriminated by the Zn(II)-mediated QD-FRET. Our approach is expected to find applications for studying physiological function and signal transduction with respect to protein kinase activity.
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Lee JY, Kim JS, Park JC, Nam YS. Protein-quantum dot nanohybrids for bioanalytical applications. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2015; 8:178-90. [DOI: 10.1002/wnan.1345] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 02/26/2015] [Accepted: 03/07/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Jeong Yu Lee
- Institute of Biomedical Engineering; Department of Engineering Science, University of Oxford; Oxford UK
| | - Jee Seon Kim
- Department of Materials Science and Engineering; Korea Advanced Institute of Science and Technology; Daejeon Republic of Korea
| | - Jae Chul Park
- Department of Materials Science and Engineering; Korea Advanced Institute of Science and Technology; Daejeon Republic of Korea
| | - Yoon Sung Nam
- Department of Materials Science and Engineering; Korea Advanced Institute of Science and Technology; Daejeon Republic of Korea
- KAIST Institute for NanoCentury (KINC CNiT); Korea Advanced Institute of Science and Technology; Daejeon Republic of Korea
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48
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Moroco JA, Baumgartner MP, Rust HL, Choi HG, Hur W, Gray NS, Camacho CJ, Smithgall TE. A Discovery Strategy for Selective Inhibitors of c-Src in Complex with the Focal Adhesion Kinase SH3/SH2-binding Region. Chem Biol Drug Des 2014; 86:144-55. [PMID: 25376742 DOI: 10.1111/cbdd.12473] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 09/29/2014] [Accepted: 10/29/2014] [Indexed: 11/30/2022]
Abstract
The c-Src tyrosine kinase co-operates with the focal adhesion kinase to regulate cell adhesion and motility. Focal adhesion kinase engages the regulatory SH3 and SH2 domains of c-Src, resulting in localized kinase activation that contributes to tumor cell metastasis. Using assay conditions where c-Src kinase activity required binding to a tyrosine phosphopeptide based on the focal adhesion kinase SH3-SH2 docking sequence, we screened a kinase-biased library for selective inhibitors of the Src/focal adhesion kinase peptide complex versus c-Src alone. This approach identified an aminopyrimidinyl carbamate compound, WH-4-124-2, with nanomolar inhibitory potency and fivefold selectivity for c-Src when bound to the phospho-focal adhesion kinase peptide. Molecular docking studies indicate that WH-4-124-2 may preferentially inhibit the 'DFG-out' conformation of the kinase active site. These findings suggest that interaction of c-Src with focal adhesion kinase induces a unique kinase domain conformation amenable to selective inhibition.
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Affiliation(s)
- Jamie A Moroco
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA
| | - Matthew P Baumgartner
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - Heather L Rust
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA
| | - Hwan Geun Choi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , 250 Longwood Avenue, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, 250 Longwood Avenue, Boston, MA, 02115, USA
| | - Wooyoung Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , 250 Longwood Avenue, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, 250 Longwood Avenue, Boston, MA, 02115, USA
| | - Nathanael S Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , 250 Longwood Avenue, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, 250 Longwood Avenue, Boston, MA, 02115, USA
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA
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Vetter ML, Zhang Z, Liu S, Wang J, Cho H, Zhang J, Zhang W, Gray NS, Yang PL. Fluorescent visualization of Src by using dasatinib-BODIPY. Chembiochem 2014; 15:1317-24. [PMID: 24828915 DOI: 10.1002/cbic.201402010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Indexed: 12/12/2022]
Abstract
Many biological experiments are not compatible with the use of immunofluorescence, genetically encoded fluorescent tags, or FRET-based reporters. Conjugation of existing kinase inhibitors to cell-permeable fluorophores can provide a generalized approach to develop fluorescent probes of intracellular kinases. Here, we report the development of a small molecule probe of Src through conjugation of BODIPY to two well-established dual Src-Abl kinase inhibitors, dasatinib and saracatinib. We show that this approach is not successful for saracatinib but that dasatinib-BODIPY largely retains the biological activity of its parent compound and can be used to monitor the presence of Src kinase in individual cells by flow cytometry. It can also be used to track the localization of Src by fixed and live-cell fluorescence microscopy. This strategy could enable generation of additional kinase-specific probes useful in systems not amenable to genetic manipulation or could be used together with fluorescent proteins to enable a multiplexed assay readout.
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Affiliation(s)
- Michael L Vetter
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 (USA)
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50
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Considerations for the design and reporting of enzyme assays in high-throughput screening applications. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.pisc.2013.12.001] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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