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Rothenaigner I, Brenke JK, Schorpp K, Hadian K. Methods to Detect Small Molecule Inhibition of RING E3 Ligase Activity. Curr Protoc 2022; 2:e414. [PMID: 35435333 DOI: 10.1002/cpz1.414] [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] [Indexed: 06/14/2023]
Abstract
Protein ubiquitination is an essential post-translational modification that regulates a large number of cellular processes. This reaction is facilitated by the consecutive action of three central enzymes, i.e., E1 activating enzyme, E2 conjugating enzyme, and the E3 ligase. More than 600 E3 enzymes guarantee the specificity and selectivity of these reactions and thus represent an exciting, while highly underrepresented, class of drug targets. Specific methods can be employed to monitor their activity and thus query compound libraries for inhibitory small molecules. Here, we describe two protocols-one high-throughput and one low-throughput method-to detect E3 ligase activity and test small molecule modulation. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: AlphaScreen assay to measure TRAF6-Ubc13 interaction Basic Protocol 2: Gel-based in vitro ubiquitination assay (K63-linked chains).
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Affiliation(s)
- Ina Rothenaigner
- Cell Signaling and Chemical Biology, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jara Kerstin Brenke
- Cell Signaling and Chemical Biology, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Kenji Schorpp
- Cell Signaling and Chemical Biology, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Kamyar Hadian
- Cell Signaling and Chemical Biology, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, Neuherberg, Germany
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Kim YH, Kim M, Kim JE, Yoo M, Lee HK, Lee CO, Yoo M, Jung KY, Kim Y, Choi SU, Park CH. Novel brd4 inhibitors with a unique scaffold exhibit antitumor effects. Oncol Lett 2021; 21:473. [PMID: 33907583 PMCID: PMC8063330 DOI: 10.3892/ol.2021.12734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 01/18/2021] [Indexed: 01/01/2023] Open
Abstract
Since bromodomain containing 4 (brd4) has been considered as a prominent cancer target, numerous attempts have been made to develop potent brd4 bromodomain inhibitors. The present study provided a novel chemical scaffold which inhibited brd4 activity. Mid-throughput screening against brd4 bromodomain was performed using alpha-screen and homogeneous time-resolved fluorescence assays. Furthermore, cell cytotoxicity and xenograft assays were performed to examine if the compound was effective both in vitro and in vivo. As a result, it was revealed that compounds having naphthalene-1,4-dione scaffold inhibited the binding of bromodomain to acetylated histone. The compounds with naphthalene-1,4-dione had cytotoxic effects against the Ty82 cell line, a NUT midline carcinoma cell line, whose proliferation is dependent on brd4 activity. A10, one of the compounds with naphthalene-1,4-dione scaffold, also exhibited tumor growth inhibition effects in the xenograft assay. In addition, the compounds exhibited cytotoxic effects against gastric cancer cell lines which were resistant to I-BET-762, a BET bromodomain inhibitor. In conclusion, the novel scaffold to suppress brd4 activity was effective against cancer cells both in vitro and in vivo.
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Affiliation(s)
- Young Hun Kim
- Bio and Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Minsung Kim
- Bio and Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea.,School of Pharmacy, Sungkyunkwan University, Suwon, Kyunggi-do 16419, Republic of Korea
| | - Ji Eun Kim
- Bio and Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Miyoun Yoo
- Bio and Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Heung Kyoung Lee
- Bio and Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Chong Ock Lee
- Bio and Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Minjin Yoo
- Bio and Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea.,Department of Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Kwan-Young Jung
- Bio and Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea.,Department of Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Yeongrin Kim
- Bio and Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea.,Department of Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Sang Un Choi
- Bio and Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Chi Hoon Park
- Bio and Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea.,Department of Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
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Brenke JK, Popowicz GM, Schorpp K, Rothenaigner I, Roesner M, Meininger I, Kalinski C, Ringelstetter L, R'kyek O, Jürjens G, Vincendeau M, Plettenburg O, Sattler M, Krappmann D, Hadian K. Targeting TRAF6 E3 ligase activity with a small-molecule inhibitor combats autoimmunity. J Biol Chem 2018; 293:13191-13203. [PMID: 29950522 DOI: 10.1074/jbc.ra118.002649] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/15/2018] [Indexed: 12/29/2022] Open
Abstract
Constitutive NF-κB signaling represents a hallmark of chronic inflammation and autoimmune diseases. The E3 ligase TNF receptor-associated factor 6 (TRAF6) acts as a key regulator bridging innate immunity, pro-inflammatory cytokines, and antigen receptors to the canonical NF-κB pathway. Structural analysis and point mutations have unraveled the essential role of TRAF6 binding to the E2-conjugating enzyme ubiquitin-conjugating enzyme E2 N (Ubc13 or UBE2N) to generate Lys63-linked ubiquitin chains for inflammatory and immune signal propagation. Genetic mutations disrupting TRAF6-Ubc13 binding have been shown to reduce TRAF6 activity and, consequently, NF-κB activation. However, to date, no small-molecule modulator is available to inhibit the TRAF6-Ubc13 interaction and thereby counteract NF-κB signaling and associated diseases. Here, using a high-throughput small-molecule screening approach, we discovered an inhibitor of the TRAF6-Ubc13 interaction that reduces TRAF6-Ubc13 activity both in vitro and in cells. We found that this compound, C25-140, impedes NF-κB activation in various immune and inflammatory signaling pathways also in primary human and murine cells. Importantly, C25-140 ameliorated inflammation and improved disease outcomes of autoimmune psoriasis and rheumatoid arthritis in preclinical in vivo mouse models. Hence, the first-in-class TRAF6-Ubc13 inhibitor C25-140 expands the toolbox for studying the impact of the ubiquitin system on immune signaling and underscores the importance of TRAF6 E3 ligase activity in psoriasis and rheumatoid arthritis. We propose that inhibition of TRAF6 activity by small molecules represents a promising novel strategy for targeting autoimmune and chronic inflammatory diseases.
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Affiliation(s)
- Jara K Brenke
- From the Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology
| | - Grzegorz M Popowicz
- the Institute of Structural Biology.,the Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching 85747, Germany
| | - Kenji Schorpp
- From the Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology
| | - Ina Rothenaigner
- From the Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology
| | | | - Isabel Meininger
- the Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology
| | | | - Larissa Ringelstetter
- From the Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology
| | - Omar R'kyek
- the Institute of Medicinal Chemistry, and.,the Institute of Organic Chemistry, Leibnitz Universität Hannover, 30167 Hannover, Germany
| | - Gerrit Jürjens
- the Institute of Medicinal Chemistry, and.,the Institute of Organic Chemistry, Leibnitz Universität Hannover, 30167 Hannover, Germany
| | - Michelle Vincendeau
- the Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology.,the Institute of Virology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Oliver Plettenburg
- the Institute of Medicinal Chemistry, and.,the Institute of Organic Chemistry, Leibnitz Universität Hannover, 30167 Hannover, Germany
| | - Michael Sattler
- the Institute of Structural Biology.,the Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching 85747, Germany
| | - Daniel Krappmann
- the Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology
| | - Kamyar Hadian
- From the Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology,
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