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Vickery HR, Virta JM, Konstantinidou M, Arkin MR. Development of a NanoBRET assay for evaluation of 14-3-3σ molecular glues. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100165. [PMID: 38797286 DOI: 10.1016/j.slasd.2024.100165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 05/08/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
We report the development of a 384-well formatted NanoBRET assay to characterize molecular glues of 14-3-3/client interactions in living cells. The seven isoforms of 14-3-3 are dimeric hub proteins with diverse roles including transcription factor regulation and signal transduction. 14-3-3 interacts with hundreds of client proteins to regulate their function and is therefore an ideal therapeutic target when client selectivity can be achieved. We have developed the NanoBRET system for three 14-3-3σ client proteins CRAF, TAZ, and estrogen receptor α (ERα), which represent three specific binding modes. We have measured stabilization of 14-3-3σ/client complexes by molecular glues with EC50 values between 100 nM and 1 μM in cells, which align with the EC50 values calculated by fluorescence anisotropy in vitro. Developing this NanoBRET system for the hub protein 14-3-3σ allows for a streamlined approach, bypassing multiple optimization steps in the assay development process for other 14-3-3σ clients. The NanoBRET system allows for an assessment of PPI stabilization in a more physiologically relevant, cell-based environment using full-length proteins. The method is applicable to diverse protein-protein interactions (PPIs) and offers a robust platform to explore libraries of compounds for both PPI stabilizers and inhibitors.
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Affiliation(s)
- Holly R Vickery
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, USA
| | - Johanna M Virta
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, USA
| | - Markella Konstantinidou
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, USA.
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Nadel CM, Wucherer K, Oehler A, Thwin AC, Basu K, Callahan MD, Southworth DR, Mordes DA, Craik CS, Gestwicki JE. Phosphorylation of a Cleaved Tau Proteoform at a Single Residue Inhibits Binding to the E3 Ubiquitin Ligase, CHIP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553575. [PMID: 37645969 PMCID: PMC10462110 DOI: 10.1101/2023.08.16.553575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Microtubule-associated protein tau (MAPT/tau) accumulates in a family of neurodegenerative diseases, including Alzheimer's disease (AD). In disease, tau is aberrantly modified by post-translational modifications (PTMs), including hyper-phosphorylation. However, it is often unclear which of these PTMs contribute to tau's accumulation or what mechanisms might be involved. To explore these questions, we focused on a cleaved proteoform of tau (tauC3), which selectively accumulates in AD and was recently shown to be degraded by its direct binding to the E3 ubiquitin ligase, CHIP. Here, we find that phosphorylation of tauC3 at a single residue, pS416, is sufficient to block its interaction with CHIP. A co-crystal structure of CHIP bound to the C-terminus of tauC3 revealed the mechanism of this clash and allowed design of a mutation (CHIPD134A) that partially restores binding and turnover of pS416 tauC3. We find that pS416 is produced by the known AD-associated kinase, MARK2/Par-1b, providing a potential link to disease. In further support of this idea, an antibody against pS416 co-localizes with tauC3 in degenerative neurons within the hippocampus of AD patients. Together, these studies suggest a discrete molecular mechanism for how phosphorylation at a specific site contributes to accumulation of an important tau proteoform.
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Affiliation(s)
- Cory M Nadel
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158
| | - Kristin Wucherer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
| | - Abby Oehler
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158
| | - Aye C Thwin
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, CA 94158
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158
| | - Koli Basu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
| | - Matthew D Callahan
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158
| | - Daniel R Southworth
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, CA 94158
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158
| | - Daniel A Mordes
- Department of Pathology, University of California San Francisco, San Francisco, CA 94158
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158
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Ng S, Brueckner AC, Bahmanjah S, Deng Q, Johnston JM, Ge L, Duggal R, Habulihaz B, Barlock B, Ha S, Sadruddin A, Yeo C, Strickland C, Peier A, Henry B, Sherer EC, Partridge AW. Discovery and Structure-Based Design of Macrocyclic Peptides Targeting STUB1. J Med Chem 2022; 65:9789-9801. [PMID: 35853179 DOI: 10.1021/acs.jmedchem.2c00406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent evidence suggests that deletion of STUB1─a pivotal negative regulator of interferon-γ sensing─may potentially clear malignant cells. However, current studies rely primarily on genetic approaches, as pharmacological inhibitors of STUB1 are lacking. Identifying a tool compound will be a step toward validating the target in a broader therapeutic sense. Herein, screening more than a billion macrocyclic peptides resulted in STUB1 binders, which were further optimized by a structure-enabled in silico design. The strategy to replace the macrocyclic peptides' hydrophilic and solvent-exposed region with a hydrophobic scaffold improved cellular permeability while maintaining the binding conformation. Further substitution of the permeability-limiting terminal aspartic acid with a tetrazole bioisostere retained the binding to a certain extent while improving permeability, suggesting a path forward. Although not optimal for cellular study, the current lead provides a valuable template for further development into selective tool compounds for STUB1 to enable target validation.
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Affiliation(s)
- Simon Ng
- Quantitative Biosciences, MSD, 8 Biomedical Grove, Singapore 138665
| | - Alexander C Brueckner
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Soheila Bahmanjah
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Qiaolin Deng
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Jennifer M Johnston
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Lan Ge
- Cell Sciences Innovation, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ruchia Duggal
- ADME Group 2, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Bahanu Habulihaz
- PPDM ADME Transporters & In Vitro Technology, Merck & Co., Inc., 126 East Lincoln Ave, Rahway, New Jersey 07065, United States
| | - Benjamin Barlock
- ADME Group 2, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Sookhee Ha
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ahmad Sadruddin
- Quantitative Biosciences, MSD, 8 Biomedical Grove, Singapore 138665
| | - Constance Yeo
- Quantitative Biosciences, MSD, 8 Biomedical Grove, Singapore 138665
| | - Corey Strickland
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Andrea Peier
- Screening & Compound Profiling, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Brian Henry
- Quantitative Biosciences, MSD, 8 Biomedical Grove, Singapore 138665
| | - Edward C Sherer
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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Umano A, Fang K, Qu Z, Scaglione JB, Altinok S, Treadway CJ, Wick ET, Paulakonis E, Karunanayake C, Chou S, Bardakjian TM, Gonzalez-Alegre P, Page RC, Schisler JC, Brown NG, Yan D, Scaglione KM. The molecular basis of spinocerebellar ataxia type 48 caused by a de novo mutation in the ubiquitin ligase CHIP. J Biol Chem 2022; 298:101899. [PMID: 35398354 PMCID: PMC9097460 DOI: 10.1016/j.jbc.2022.101899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 11/25/2022] Open
Abstract
The spinocerebellar ataxias (SCAs) are a class of incurable diseases characterized by degeneration of the cerebellum that results in movement disorder. Recently, a new heritable form of SCA, spinocerebellar ataxia type 48 (SCA48), was attributed to dominant mutations in STIP1 homology and U box-containing 1 (STUB1); however, little is known about how these mutations cause SCA48. STUB1 encodes for the protein C terminus of Hsc70 interacting protein (CHIP), an E3 ubiquitin ligase. CHIP is known to regulate proteostasis by recruiting chaperones via a N-terminal tetratricopeptide repeat domain and recruiting E2 ubiquitin-conjugating enzymes via a C-terminal U-box domain. These interactions allow CHIP to mediate the ubiquitination of chaperone-bound, misfolded proteins to promote their degradation via the proteasome. Here we have identified a novel, de novo mutation in STUB1 in a patient with SCA48 encoding for an A52G point mutation in the tetratricopeptide repeat domain of CHIP. Utilizing an array of biophysical, biochemical, and cellular assays, we demonstrate that the CHIPA52G point mutant retains E3-ligase activity but has decreased affinity for chaperones. We further show that this mutant decreases cellular fitness in response to certain cellular stressors and induces neurodegeneration in a transgenic Caenorhabditis elegans model of SCA48. Together, our data identify the A52G mutant as a cause of SCA48 and provide molecular insight into how mutations in STUB1 cause SCA48.
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Affiliation(s)
- A Umano
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - K Fang
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Z Qu
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - J B Scaglione
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - S Altinok
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - C J Treadway
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - E T Wick
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - E Paulakonis
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - C Karunanayake
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - S Chou
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - T M Bardakjian
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - P Gonzalez-Alegre
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - R C Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - J C Schisler
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - N G Brown
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - D Yan
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - K M Scaglione
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA; Department of Neurology, Duke University, Durham, North Carolina, USA; Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, North Carolina, USA.
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