1
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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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2
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Reddi RN, Rogel A, Gabizon R, Rawale DG, Harish B, Marom S, Tivon B, Arbel YS, Gurwicz N, Oren R, David K, Liu J, Duberstein S, Itkin M, Malitsky S, Barr H, Katz BZ, Herishanu Y, Shachar I, Shulman Z, London N. Sulfamate Acetamides as Self-Immolative Electrophiles for Covalent Ligand-Directed Release Chemistry. J Am Chem Soc 2023; 145:3346-3360. [PMID: 36738297 PMCID: PMC9936582 DOI: 10.1021/jacs.2c08853] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Indexed: 02/05/2023]
Abstract
Electrophiles for covalent inhibitors that are suitable for in vivo administration are rare. While acrylamides are prevalent in FDA-approved covalent drugs, chloroacetamides are considered too reactive for such purposes. We report sulfamate-based electrophiles that maintain chloroacetamide-like geometry with tunable reactivity. In the context of the BTK inhibitor ibrutinib, sulfamate analogues showed low reactivity with comparable potency in protein labeling, in vitro, and cellular kinase activity assays and were effective in a mouse model of CLL. In a second example, we converted a chloroacetamide Pin1 inhibitor to a potent and selective sulfamate acetamide with improved buffer stability. Finally, we show that sulfamate acetamides can be used for covalent ligand-directed release (CoLDR) chemistry, both for the generation of "turn-on" probes as well as for traceless ligand-directed site-specific labeling of proteins. Taken together, this chemistry represents a promising addition to the list of electrophiles suitable for in vivo covalent targeting.
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Affiliation(s)
- Rambabu N. Reddi
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Adi Rogel
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ronen Gabizon
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dattatraya Gautam Rawale
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Battu Harish
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shir Marom
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Barr Tivon
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yamit Shorer Arbel
- Sackler
Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel
| | - Neta Gurwicz
- Dept.
of Systems Immunology, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Roni Oren
- Department
of Veterinary Resources, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Keren David
- Dept.
of Systems Immunology, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Jingjing Liu
- Dept.
of Systems Immunology, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Shirly Duberstein
- Wohl
Institute for Drug Discovery of the Nancy and Stephen Grand Israel
National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maxim Itkin
- Life Sciences
Core Facilities, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Sergey Malitsky
- Life Sciences
Core Facilities, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Haim Barr
- Wohl
Institute for Drug Discovery of the Nancy and Stephen Grand Israel
National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ben-Zion Katz
- Sackler
Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel
- Department
of Hematology, Tel Aviv Sourasky Medical
Center, Tel Aviv 6423906, Israel
| | - Yair Herishanu
- Sackler
Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel
- Department
of Hematology, Tel Aviv Sourasky Medical
Center, Tel Aviv 6423906, Israel
| | - Idit Shachar
- Dept.
of Systems Immunology, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Ziv Shulman
- Dept.
of Systems Immunology, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Nir London
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
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3
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Structural Biology Inspired Development of a Series of Human Peroxisome Proliferator-Activated Receptor Gamma (PPARγ) Ligands: From Agonist to Antagonist. Int J Mol Sci 2023; 24:ijms24043940. [PMID: 36835351 PMCID: PMC9960108 DOI: 10.3390/ijms24043940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/11/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
Recent progress in the structural and molecular pharmacological understanding of the nuclear receptor, peroxisome proliferator-activated receptor gamma (hPPARγ)-a transcription factor with pleiotropic effects on biological responses-has enabled the investigation of various graded hPPARγ ligands (full agonist, partial agonist, and antagonist). Such ligands are useful tools to investigate the functions of hPPARγ in detail and are also candidate drugs for the treatment of hPPARγ-mediated diseases, such as metabolic syndrome and cancer. This review summarizes our medicinal chemistry research on the design, synthesis, and pharmacological evaluation of a covalent-binding and non-covalent-binding hPPARγ antagonist, both of which have been created based on our working hypothesis of the helix 12 (H12) holding induction/inhibition concept. X-ray crystallographic analyses of our representative antagonists complexed with an hPPARγ ligand binding domain (LBD) indicated the unique binding modes of hPPARγ LBD, which are quite different from the binding modes observed for hPPARγ agonists and partial agonists.
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4
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Sakamoto S, Hamachi I. Ligand‐Directed Chemistry for Protein Labeling for Affinity‐Based Protein Analysis. Isr J Chem 2023. [DOI: 10.1002/ijch.202200077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo-ku 615-8510 Kyoto Japan
- JST-ERATO Hamachi Innovative Molecular Technology for Neuroscience 615-8530 Kyoto Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo-ku 615-8510 Kyoto Japan
- JST-ERATO Hamachi Innovative Molecular Technology for Neuroscience 615-8530 Kyoto Japan
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5
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Fischer NH, Oliveira MT, Diness F. Chemical modification of proteins - challenges and trends at the start of the 2020s. Biomater Sci 2023; 11:719-748. [PMID: 36519403 DOI: 10.1039/d2bm01237e] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribosomally expressed proteins perform multiple, versatile, and specialized tasks throughout Nature. In modern times, chemically modified proteins, including improved hormones, enzymes, and antibody-drug-conjugates have become available and have found advanced industrial and pharmaceutical applications. Chemical modification of proteins is used to introduce new functionalities, improve stability or drugability. Undertaking chemical reactions with proteins without compromising their native function is still a core challenge as proteins are large conformation dependent multifunctional molecules. Methods for functionalization ideally should be chemo-selective, site-selective, and undertaken under biocompatible conditions in aqueous buffer to prevent denaturation of the protein. Here the present challenges in the field are discussed and methods for modification of the 20 encoded amino acids as well as the N-/C-termini and protein backbone are presented. For each amino acid, common and traditional modification methods are presented first, followed by more recent ones.
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Affiliation(s)
- Niklas Henrik Fischer
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Maria Teresa Oliveira
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Frederik Diness
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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6
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Miyamae Y. Insights into Dynamic Mechanism of Ligand Binding to Peroxisome Proliferator-Activated Receptor γ toward Potential Pharmacological Applications. Biol Pharm Bull 2021; 44:1185-1195. [PMID: 34471046 DOI: 10.1248/bpb.b21-00263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peroxisome proliferator-activated receptor γ (PPARγ) is a member of the nuclear receptor superfamily, which regulates the transcription of a variety of genes involved in lipid and glucose metabolism, inflammation, and cell proliferation. These functions correlate with the onset of type-2 diabetes, obesity, and immune disorders, which makes PPARγ a promising target for drug development. The majority of PPARγ functions are regulated by binding of small molecule ligands, which cause conformational changes of PPARγ followed by coregulator recruitment. The ligand-binding domain (LBD) of PPARγ contains a large Y-shaped cavity that can be occupied by various classes of compounds such as full agonists, partial agonists, natural lipids, and in some cases, a combination of multiple molecules. Several crystal structure studies have revealed the binding modes of these compounds in the LBD and insight into the resulting conformational changes. Notably, the apo form of the PPARγ LBD contains a highly mobile region that can be stabilized by ligand binding. Furthermore, recent biophysical investigations have shed light on the dynamic mechanism of how ligands induce conformational changes in PPARγ and result in functional output. This information may be useful for the design of new and repurposed structures of ligands that serve a different function from original compounds and more potent pharmacological effects with less undesirable clinical outcomes. This review provides an overview of the peculiar characteristics of the PPARγ LBD by examining a series of structural studies focused on the dynamic mechanism of binding and the potential applications of strategies for ligand screening and chemical labeling.
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Affiliation(s)
- Yusaku Miyamae
- Faculty of Life and Environmental Sciences, University of Tsukuba.,Alliance for Research on the Mediterranean and North Africa, University of Tsukuba
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7
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Kanamori S, Ohashi N, Ishida H, Yamamoto K, Itoh T. HNF4α Is a Covalent Bond-Forming Receptor. J Nutr Sci Vitaminol (Tokyo) 2021; 67:126-129. [PMID: 33952733 DOI: 10.3177/jnsv.67.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
HNF4α is a nuclear receptor whose ligands are fatty acids. HNF4α is a target molecule for drug discovery research and thus we tested its covalent binding ability to investigate the possible development of covalent modifiers of HNF4α. Oxidized polyunsaturated fatty acids (oxo-PUFAs) have moderate flexibility and possess a Michael acceptor that participates in conjugate addition reactions with nucleophilic amino acid residues. Thus, oxo-PUFAs were used as probes and their covalent binding abilities to HNF4α were verified. Several oxo-PUFAs, such as 4-oxoDHA, were shown to be covalent modifiers of HNF4α and therefore we concluded that HNF4α can form covalent bonds to ligands.
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8
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Wang Z, Zhang X, Zhang H, Tang Y, Pan H, Wang H, Ji T, Guo Y, Gao Q, Song T, Zhang Z. Discovery of a Fluorogenic Probe for In Situ Pyruvate Kinase M2 Isoform (PKM2) Labeling through Chemoselective S NAr with a Binding Site Lysine Residue. Anal Chem 2021; 93:9669-9676. [PMID: 34219457 DOI: 10.1021/acs.analchem.1c00208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The key challenge of developing reaction-based turn-on probes is to establish latent electrophilic fluorophores exhibiting high reactivity only upon binding to a specific protein(s). Herein, we identified such a fluorophore, 6-arylthioether-substituted 3-cyano-1-oxo-1H-phenalene-2-carboxylate, which chemoselectively labels binding site Cys or Lys residues. Based on this fluorophore, we developed the first reaction-based turn-on pyruvate kinase M2 isoform (PKM2) fluorescent probe AT-OPC1, which selectively labels PKM2 with the binding site Lys305. The latent electrophilic reactivity of the fluorophore endows the probe with precise detection of the expression of PKM2 in situ by means of both in-gel fluorescence imaging at the proteome level and real-time no-wash cell imaging approaches, which has the potential to be applied in cancer diagnoses.
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Affiliation(s)
- Ziqian Wang
- State Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xiaodong Zhang
- State Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Hong Zhang
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Yao Tang
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Hao Pan
- State Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Hang Wang
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Tong Ji
- State Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Yafei Guo
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Qishuang Gao
- State Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Ting Song
- State Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Zhichao Zhang
- State Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
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9
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Yoshikawa C, Ishida H, Ohashi N, Kojima H, Itoh T. Construction of 7-Diethylaminocoumarins Promoted by an Electron-Withdrawing Group. Chem Pharm Bull (Tokyo) 2021; 69:608-611. [PMID: 34193709 DOI: 10.1248/cpb.c21-00228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The coumarin skeleton has been a focus of attention for many years, and its fluorescence properties vary depending on the substituents. Fluorescent coumarin derivatives are useful tools for many strategies have been developed for their synthesis. Although 7-diethylaminocoumarin has excellent fluorescence properties, it is unstable. We have developed a facile strategy for the synthesis of 7-diethylaminocoumarin derivatives by increasing the electrophilicity of the ynone moiety to promote nucleophilic addition reactions and cyclization. The reaction tolerates a variety of substitutions at the 4-position.
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10
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Yoshikawa C, Ishida H, Ohashi N, Itoh T. Synthesis of a Coumarin-Based PPARγ Fluorescence Probe for Competitive Binding Assay. Int J Mol Sci 2021; 22:4034. [PMID: 33919837 PMCID: PMC8070791 DOI: 10.3390/ijms22084034] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/10/2021] [Accepted: 04/11/2021] [Indexed: 12/28/2022] Open
Abstract
Peroxisome proliferator-activated receptor γ (PPARγ) is a molecular target of metabolic syndrome and inflammatory disease. PPARγ is an important nuclear receptor and numerous PPARγ ligands were developed to date; thus, efficient assay methods are important. Here, we investigated the incorporation of 7-diethylamino coumarin into the PPARγ agonist rosiglitazone and used the compound in a binding assay for PPARγ. PPARγ-ligand-incorporated 7-methoxycoumarin, 1, showed weak fluorescence intensity in a previous report. We synthesized PPARγ-ligand-incorporating coumarin, 2, in this report, and it enhanced the fluorescence intensity. The PPARγ ligand 2 maintained the rosiglitazone activity. The obtained partial agonist 6 appeared to act through a novel mechanism. The fluorescence intensity of 2 and 6 increased by binding to the ligand binding domain (LBD) of PPARγ and the affinity of reported PPARγ ligands were evaluated using the probe.
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Affiliation(s)
| | | | | | - Toshimasa Itoh
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan; (C.Y.); (H.I.); (N.O.)
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11
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Reddi R, Resnick E, Rogel A, Rao BV, Gabizon R, Goldenberg K, Gurwicz N, Zaidman D, Plotnikov A, Barr H, Shulman Z, London N. Tunable Methacrylamides for Covalent Ligand Directed Release Chemistry. J Am Chem Soc 2021; 143:4979-4992. [PMID: 33761747 PMCID: PMC8041284 DOI: 10.1021/jacs.0c10644] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Indexed: 02/07/2023]
Abstract
Targeted covalent inhibitors are an important class of drugs and chemical probes. However, relatively few electrophiles meet the criteria for successful covalent inhibitor design. Here we describe α-substituted methacrylamides as a new class of electrophiles suitable for targeted covalent inhibitors. While typically α-substitutions inactivate acrylamides, we show that hetero α-substituted methacrylamides have higher thiol reactivity and undergo a conjugated addition-elimination reaction ultimately releasing the substituent. Their reactivity toward thiols is tunable and correlates with the pKa/pKb of the leaving group. In the context of the BTK inhibitor ibrutinib, these electrophiles showed lower intrinsic thiol reactivity than the unsubstituted ibrutinib acrylamide. This translated to comparable potency in protein labeling, in vitro kinase assays, and functional cellular assays, with improved selectivity. The conjugate addition-elimination reaction upon covalent binding to their target cysteine allows functionalizing α-substituted methacrylamides as turn-on probes. To demonstrate this, we prepared covalent ligand directed release (CoLDR) turn-on fluorescent probes for BTK, EGFR, and K-RasG12C. We further demonstrate a BTK CoLDR chemiluminescent probe that enabled a high-throughput screen for BTK inhibitors. Altogether we show that α-substituted methacrylamides represent a new and versatile addition to the toolbox of targeted covalent inhibitor design.
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Affiliation(s)
- Rambabu
N. Reddi
- Department
of Organic Chemistry, The Weizmann Institute
of Science, Rehovot, 7610001, Israel
| | - Efrat Resnick
- Department
of Organic Chemistry, The Weizmann Institute
of Science, Rehovot, 7610001, Israel
| | - Adi Rogel
- Department
of Organic Chemistry, The Weizmann Institute
of Science, Rehovot, 7610001, Israel
| | - Boddu Venkateswara Rao
- Department
of Organic Chemistry, The Weizmann Institute
of Science, Rehovot, 7610001, Israel
| | - Ronen Gabizon
- Department
of Organic Chemistry, The Weizmann Institute
of Science, Rehovot, 7610001, Israel
| | - Kim Goldenberg
- Department
of Organic Chemistry, The Weizmann Institute
of Science, Rehovot, 7610001, Israel
- Department
of Immunology, The Weizmann Institute of
Science, Rehovot, 7610001, Israel
| | - Neta Gurwicz
- Department
of Immunology, The Weizmann Institute of
Science, Rehovot, 7610001, Israel
| | - Daniel Zaidman
- Department
of Organic Chemistry, The Weizmann Institute
of Science, Rehovot, 7610001, Israel
| | - Alexander Plotnikov
- Wohl
Institute for Drug Discovery of the Nancy and Stephen Grand Israel
National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Haim Barr
- Wohl
Institute for Drug Discovery of the Nancy and Stephen Grand Israel
National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ziv Shulman
- Department
of Immunology, The Weizmann Institute of
Science, Rehovot, 7610001, Israel
| | - Nir London
- Department
of Organic Chemistry, The Weizmann Institute
of Science, Rehovot, 7610001, Israel
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12
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Huang HY, Fan SY, Chang EH, Lam CH, Lin YC, Lin XH, Gupta NK, Tan KT. Self-Immolative Difluorophenyl Ester Linker for Affinity-Based Fluorescence Turn-on Protein Detection. Anal Chem 2020; 92:15463-15471. [PMID: 33179902 DOI: 10.1021/acs.analchem.0c03178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Currently most fluorogenic probes are developed for the analysis of enzymes, where a bond breaking or rearrangement reaction is required to transform a nonfluorescent enzymatic substrate into a fluorescent product. However, this approach cannot be used for proteins that do not possess enzymatic activities. In this article, we show that fluorogenic probes with a self-immolative difluorophenyl ester linker can mimic the bond disassembly processes of fluorogenic enzyme substrates for the rapid analysis of nonenzymatic proteins. Although numerous self-immolative reagents have shown promising applications in sensors, drug delivery systems, and material chemistry, all of them are triggered by either enzymes or small reactive molecules. In our strategy, the probe binds to the protein via a specific protein-ligand interaction, inducing a chemical reaction between the self-immolative linker and an amino acid of the protein, thereby triggering a cascade reaction that leads to the activation and release of the fluorogenic reporter. In contrast, a phenyl ester linker without the difluoro substituent cannot be triggered to release the fluorogenic reporter. With this probe design, live-cell imaging of extracellular and intracellular endogenous tumor marker proteins can be achieved with high selectivity and sensitivity.
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Affiliation(s)
- Hsiang-Yun Huang
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Syuan-Yun Fan
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - En-Hao Chang
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Chak Hin Lam
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Yu-Chun Lin
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Xin-Hui Lin
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Nitesh K Gupta
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Kui-Thong Tan
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China.,Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan, Republic of China
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13
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Bianco G, Goodsell DS, Forli S. Selective and Effective: Current Progress in Computational Structure-Based Drug Discovery of Targeted Covalent Inhibitors. Trends Pharmacol Sci 2020; 41:1038-1049. [PMID: 33153778 PMCID: PMC7669701 DOI: 10.1016/j.tips.2020.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/28/2022]
Abstract
Targeted covalent inhibitors are currently showing great promise for systems that are normally difficult to target with small molecule therapies. This renewed interest has spurred the refinement of existing computational methods as well as the designof new ones, expanding the toolbox for discovery and optimization of selectiveand effective covalent inhibitors. Commonly applied approaches are covalentdocking methods that predict the conformation of the covalent complex with known residues. More recently, a new predictive method, reactive docking, was developed, building on the growing corpus of data generated by large proteomics experiments. This method was successfully used in several 'inverse drug discovery' programs that use high-throughput techniques to isolate effective compounds based on screening of entire compound libraries based on desired phenotypes.
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Affiliation(s)
- Giulia Bianco
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Research Collaboratory for Structure Bioinformatics Protein Data Bank, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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14
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Shiraiwa K, Cheng R, Nonaka H, Tamura T, Hamachi I. Chemical Tools for Endogenous Protein Labeling and Profiling. Cell Chem Biol 2020; 27:970-985. [DOI: 10.1016/j.chembiol.2020.06.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/29/2020] [Accepted: 06/25/2020] [Indexed: 12/31/2022]
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Preparation and Use of Turn-on Fluorescent Probe for Detection and Live Cell Imaging of Vitamin D Receptor as a Target Protein. STAR Protoc 2020; 1:100036. [PMID: 33111084 PMCID: PMC7580106 DOI: 10.1016/j.xpro.2020.100036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Turn-on fluorescent probe mediated by conjugate addition and cyclization (TCC probe) is a small molecule that reacts with a protein of interest in cells. TCC probe is applicable to various types of proteins by exchanging the ligand unit for target proteins. TCC probes are a potent tool for molecular imaging and chemical proteomics. This protocol describes the synthesis of a TCC probe via unstable intermediate and how to use this probe to visualize vitamin D receptor as a target protein. For complete details on the use and execution of this protocol, please refer to Kojima et al. (2020). Protocol to prepare a turn-on fluorescent probe for proteins Method for live cell imaging of a protein of interest Protocol can be used for chemical proteomics
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Yoshikawa C, Ishida H, Itoh T. Incorporation of a coumarin unit by nucleophilic addition reaction into a PPARγ ligand. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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