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Golkowski M, Maly DJ, Ong SE. Proteomic Profiling of Protein Kinase Inhibitor Targets by Mass Spectrometry. Methods Mol Biol 2018; 1636:105-117. [PMID: 28730476 DOI: 10.1007/978-1-4939-7154-1_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Identifying cellular targets of bioactive small molecules from large-scale screening campaigns can be a significant bottleneck in developing novel therapeutics. Our rapid small-molecule target profiling protocol combines affinity enrichment and SILAC for proteomic identification of small molecule-protein interactions. Selective interactions are easily discernable from nonspecific protein binding by quantitative ratios. Using kinase inhibitors as an example, we provide an optimized protocol featuring on-bead protein digestion and single nano-flow liquid chromatographic-mass spectrometric (LC-MS) analyses, consequently increasing analytical throughput and sensitivity over gel-based sample preparation methods for rapid profiling of kinase inhibitor targets.
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Affiliation(s)
- Martin Golkowski
- Departments of Chemistry and Biochemistry, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195-7280, USA
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Shao-En Ong
- Departments of Chemistry and Biochemistry, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195-7280, USA.
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Kanoh N. Photo-cross-linked small-molecule affinity matrix as a tool for target identification of bioactive small molecules. Nat Prod Rep 2016; 33:709-18. [DOI: 10.1039/c5np00117j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review describes the status of the photo-cross-linked small-molecule affinity matrix while providing a useful tutorial for academic and industrial chemical biologists who are involved or interested in drug target identification.
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Affiliation(s)
- Naoki Kanoh
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
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3
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Shishido T, Hachisuka M, Ryuzaki K, Miura Y, Tanabe A, Tamura Y, Kusayanagi T, Takeuchi T, Kamisuki S, Sugawara F, Sahara H. EpsinR, a target for pyrenocine B, role in endogenous MHC-II-restricted antigen presentation. Eur J Immunol 2014; 44:3220-31. [DOI: 10.1002/eji.201444475] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 07/31/2014] [Accepted: 09/03/2014] [Indexed: 01/28/2023]
Affiliation(s)
- Tatsuya Shishido
- Laboratory of Biology; Azabu University School of Veterinary Medicine; Sagamihara Japan
| | - Masami Hachisuka
- Laboratory of Biology; Azabu University School of Veterinary Medicine; Sagamihara Japan
| | - Kai Ryuzaki
- Laboratory of Biology; Azabu University School of Veterinary Medicine; Sagamihara Japan
| | - Yuko Miura
- Laboratory of Biology; Azabu University School of Veterinary Medicine; Sagamihara Japan
| | - Atsushi Tanabe
- Laboratory of Biology; Azabu University School of Veterinary Medicine; Sagamihara Japan
| | - Yasuaki Tamura
- Department of Pathology; Sapporo Medical University School of Medicine; Sapporo Japan
| | - Tomoe Kusayanagi
- Genome and Drug Research Center; Tokyo University of Science; Chiba Japan
| | - Toshifumi Takeuchi
- Genome and Drug Research Center; Tokyo University of Science; Chiba Japan
| | - Shinji Kamisuki
- Genome and Drug Research Center; Tokyo University of Science; Chiba Japan
| | - Fumio Sugawara
- Genome and Drug Research Center; Tokyo University of Science; Chiba Japan
| | - Hiroeki Sahara
- Laboratory of Biology; Azabu University School of Veterinary Medicine; Sagamihara Japan
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Shimura S, Ishima M, Nakajima S, Fujii T, Himeno N, Ikeda K, Izaguirre-Carbonell J, Murata H, Takeuchi T, Kamisuki S, Suzuki T, Kuramochi K, Watashi K, Kobayashi S, Sugawara F. Total synthesis and anti-hepatitis C virus activity of MA026. J Am Chem Soc 2013; 135:18949-56. [PMID: 24251365 DOI: 10.1021/ja410145x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The first total synthesis of MA026 and the identification of its candidate target protein for anti-hepatitis C virus activity are presented. MA026, a novel lipocyclodepsipeptide isolated from the fermentation broth of Pseudomonas sp. RtIB026, consists of a cyclodepsipeptide, a chain peptide, and an N-terminal (R)-3-hydroxydecanoic acid. The first subunit, side chain 2, was prepared by coupling fatty acid moiety 4 with tripeptide 5. The key macrocyclization of the decadepsipeptide at L-Leu(10)-D-Gln(11) provided the second subunit, cyclodepsipeptide 3. Late-stage condensation of the two key subunits and final deprotection afforded MA026. This convergent, flexible, solution-phase synthesis will be invaluable in generating MA026 derivatives for future structure-activity relationship studies. An infectious hepatitis C virus (HCV) cell culture assay revealed that MA026 suppresses HCV infection into host hepatocytes by inhibiting the entry process in a dose-dependent manner. Phage display screening followed by surface plasmon resonance (SPR) binding analyses identified claudin-1, an HCV entry receptor, as a candidate target protein of MA026.
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Affiliation(s)
- Satomi Shimura
- Department of Applied Biological Science, Tokyo University of Sciences , Noda, Chiba 278-8510, Japan
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Pocci M, Alfei S, Castellaro S, Lucchesini F, Milanese M, Bertini V. Synthesis and evaluation of resins bearing substrate-like inhibitor functions for capturing copper amine oxidases. Polym J 2013. [DOI: 10.1038/pj.2013.38] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Brehm E, Breinbauer R. Investigation of the origin and synthetic application of the pseudodilution effect for Pd-catalyzed macrocyclisations in concentrated solutions with immobilized catalysts. Org Biomol Chem 2013; 11:4750-6. [DOI: 10.1039/c3ob41020j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Potyrailo R, Rajan K, Stoewe K, Takeuchi I, Chisholm B, Lam H. Combinatorial and high-throughput screening of materials libraries: review of state of the art. ACS COMBINATORIAL SCIENCE 2011; 13:579-633. [PMID: 21644562 DOI: 10.1021/co200007w] [Citation(s) in RCA: 363] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Rational materials design based on prior knowledge is attractive because it promises to avoid time-consuming synthesis and testing of numerous materials candidates. However with the increase of complexity of materials, the scientific ability for the rational materials design becomes progressively limited. As a result of this complexity, combinatorial and high-throughput (CHT) experimentation in materials science has been recognized as a new scientific approach to generate new knowledge. This review demonstrates the broad applicability of CHT experimentation technologies in discovery and optimization of new materials. We discuss general principles of CHT materials screening, followed by the detailed discussion of high-throughput materials characterization approaches, advances in data analysis/mining, and new materials developments facilitated by CHT experimentation. We critically analyze results of materials development in the areas most impacted by the CHT approaches, such as catalysis, electronic and functional materials, polymer-based industrial coatings, sensing materials, and biomaterials.
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Affiliation(s)
- Radislav Potyrailo
- Chemistry and Chemical Engineering, GE Global Research Center, Niskayuna, New York 12309, United States
| | - Krishna Rajan
- Department of Materials Science and Engineering and Institute for Combinatorial Discovery, Iowa State University, Ames, Iowa 50011, United States
| | - Klaus Stoewe
- Universität des Saarlandes, Technische Chemie, Campus C4.2, 66123, Saarbruecken, Germany
| | - Ichiro Takeuchi
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Bret Chisholm
- Center for Nanoscale Science and Engineering and Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Hubert Lam
- Chemistry and Chemical Engineering, GE Global Research Center, Niskayuna, New York 12309, United States
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Morohashi K, Sahara H, Watashi K, Iwabata K, Sunoki T, Kuramochi K, Takakusagi K, Miyashita H, Sato N, Tanabe A, Shimotohno K, Kobayashi S, Sakaguchi K, Sugawara F. Cyclosporin A associated helicase-like protein facilitates the association of hepatitis C virus RNA polymerase with its cellular cyclophilin B. PLoS One 2011; 6:e18285. [PMID: 21559518 PMCID: PMC3084704 DOI: 10.1371/journal.pone.0018285] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 03/02/2011] [Indexed: 01/07/2023] Open
Abstract
Background Cyclosporin A (CsA) is well known as an immunosuppressive drug useful for allogeneic transplantation. It has been reported that CsA inhibits hepatitis C virus (HCV) genome replication, which indicates that cellular targets of CsA regulate the viral replication. However, the regulation mechanisms of HCV replication governed by CsA target proteins have not been fully understood. Principal Findings Here we show a chemical biology approach that elucidates a novel mechanism of HCV replication. We developed a phage display screening to investigate compound-peptide interaction and identified a novel cellular target molecule of CsA. This protein, named CsA associated helicase-like protein (CAHL), possessed RNA-dependent ATPase activity that was negated by treatment with CsA. The downregulation of CAHL in the cells resulted in a decrease of HCV genome replication. CAHL formed a complex with HCV-derived RNA polymerase NS5B and host-derived cyclophilin B (CyPB), known as a cellular cofactor for HCV replication, to regulate NS5B-CyPB interaction. Conclusions We found a cellular factor, CAHL, as CsA associated helicase-like protein, which would form trimer complex with CyPB and NS5B of HCV. The strategy using a chemical compound and identifying its target molecule by our phage display analysis is useful to reveal a novel mechanism underlying cellular and viral physiology.
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Affiliation(s)
- Kengo Morohashi
- Genome and Drug Research Center, Tokyo University of Science, Noda, Chiba, Japan
| | - Hiroeki Sahara
- Laboratory of Biology, Azabu University School of Veterinary Medicine, Sagamihara, Kanagawa, Japan
- * E-mail:
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Kazuki Iwabata
- Genome and Drug Research Center, Tokyo University of Science, Noda, Chiba, Japan
| | - Takashi Sunoki
- Genome and Drug Research Center, Tokyo University of Science, Noda, Chiba, Japan
| | - Kouji Kuramochi
- Genome and Drug Research Center, Tokyo University of Science, Noda, Chiba, Japan
| | - Kaori Takakusagi
- Genome and Drug Research Center, Tokyo University of Science, Noda, Chiba, Japan
| | - Hiroki Miyashita
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Noriyuki Sato
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Atsushi Tanabe
- Laboratory of Biology, Azabu University School of Veterinary Medicine, Sagamihara, Kanagawa, Japan
| | | | - Susumu Kobayashi
- Genome and Drug Research Center, Tokyo University of Science, Noda, Chiba, Japan
| | - Kengo Sakaguchi
- Genome and Drug Research Center, Tokyo University of Science, Noda, Chiba, Japan
| | - Fumio Sugawara
- Genome and Drug Research Center, Tokyo University of Science, Noda, Chiba, Japan
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Kuramochi K, Miyano Y, Enomoto Y, Takeuchi R, Ishi K, Takakusagi Y, Saitoh T, Fukudome K, Manita D, Takeda Y, Kobayashi S, Sakaguchi K, Sugawara F. Identification of small molecule binding molecules by affinity purification using a specific ligand immobilized on PEGA resin. Bioconjug Chem 2009; 19:2417-26. [PMID: 19035789 DOI: 10.1021/bc8002716] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We investigated the application of resins used in solid-phase synthesis for affinity purification. A synthetic ligand for FK506-binding protein 12 (SLF) was immobilized on various resins, and the binding assays between the SLF-immobilized resins and FK506-binding protein 12 (FKBP12) were performed. Of the resins tested in this study, PEGA resin was the most effective for isolating FKBP12. This matrix enabled the isolation of FKBP12 from a cell lysate, and the identification of SLF-binding peptides from a phage cDNA library. We confirmed the interaction between SLF and these peptides using a cuvette type quartz crystal microbalance (QCM) apparatus. Our study suggests that PEGA resin has great potential as a tool not only for the purification and identification of small-molecule binding proteins but also for the selection of peptides that recognize target molecules.
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Affiliation(s)
- Kouji Kuramochi
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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10
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Kanoh N, Nakamura T, Honda K, Yamakoshi H, Iwabuchi Y, Osada H. Distribution of photo-cross-linked products from 3-aryl-3-trifluoromethyldiazirines and alcohols. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.04.031] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Leslie BJ, Hergenrother PJ. Identification of the cellular targets of bioactive small organic molecules using affinity reagents. Chem Soc Rev 2008; 37:1347-60. [PMID: 18568161 DOI: 10.1039/b702942j] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The elucidation of molecular targets of bioactive small organic molecules remains a significant challenge in modern biomedical research and drug discovery. This tutorial review summarizes strategies for the derivatization of bioactive small molecules and their use as affinity probes to identify cellular binding partners. Special emphasis is placed on logistical concerns as well as common problems encountered during such target identification experiments. The roadmap provided is a guide through the process of affinity probe selection, target identification, and downstream target validation.
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Affiliation(s)
- Benjamin J Leslie
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
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Aoki S, Morohashi K, Sunoki T, Kuramochi K, Kobayashi S, Sugawara F. Screening of paclitaxel-binding molecules from a library of random peptides displayed on T7 phage particles using paclitaxel-photoimmobilized resin. Bioconjug Chem 2007; 18:1981-6. [PMID: 17979224 DOI: 10.1021/bc700287v] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Paclitaxel (Taxol), an effective anticancer agent, is known to bind to tubulin and induce tubulin polymerization. Several other binding proteins of paclitaxel, such as Bcl-2, heat shock proteins, and NSC-1, have also been reported. Here, we describe a T7 phage-based display to screen for paclitaxel-binding molecules from a random peptide library using paclitaxel-photoimmobilized TentaGel resin. Specific phage particles that bind the paclitaxel-immobilized resin were obtained. Among them, two phage clones included the same consensus amino acid sequence (KACGRTRVTS). Analysis of the protein database using BLAST revealed that a portion of this sequence is conserved in the zinc finger domain of human NFX1. Binding affinity of paclitaxel against the partial recombinant protein of NFX1 (424aa-876aa) was confirmed by pull-down assays and surface plasmon resonance analyses.
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Affiliation(s)
- Sota Aoki
- Department of Applied Biological Science, Genome and Drug Research Center, and Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, Japan
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Kim DH, Lee HY, Kim H, Kim H, Lee YS, Park SB. Quantitative Evaluation of HiCore Resin for the Nonspecific Binding of Proteins by On-Bead Colorimetric Assay. ACTA ACUST UNITED AC 2006; 8:280-5. [PMID: 16676994 DOI: 10.1021/cc0501413] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Do-Hyun Kim
- School of Chemistry and School of Chemical and Biological Engineering, Seoul National University, Korea
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