1
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Vijay A, Mukherjee A. Unraveling the folding-assisted unbinding mechanism of TCF with its binding partner β-catenin. Phys Chem Chem Phys 2024. [PMID: 38887991 DOI: 10.1039/d4cp01451k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
This study utilizes molecular dynamics simulations aided with multiple walker parallel bias metadynamics to investigate the TCF unbinding mechanism from the β-catenin interface. The results, consistent with experimental binding affinity calculations, unveil a folding-assisted unbinding mechanism.
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Affiliation(s)
- Amal Vijay
- Department of Chemistry, Indian Institute of Science Education and Research, Pune-411008, Maharashtra, India.
| | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research, Pune-411008, Maharashtra, India.
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2
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Zhang H, Liu C, Zhu D, Zhang Q, Li J. Medicinal Chemistry Strategies for the Development of Inhibitors Disrupting β-Catenin's Interactions with Its Nuclear Partners. J Med Chem 2023; 66:1-31. [PMID: 36583662 DOI: 10.1021/acs.jmedchem.2c01016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dysregulation of the Wnt/β-catenin signaling pathway is strongly associated with various aspects of cancer, including tumor initiation, proliferation, and metastasis as well as antitumor immunity, and presents a promising opportunity for cancer therapy. Wnt/β-catenin signaling activation increases nuclear dephosphorylated β-catenin levels, resulting in β-catenin binding to TCF and additional cotranscription factors, such as BCL9, CBP, and p300. Therefore, directly disrupting β-catenin's interactions with these nuclear partners holds promise for the effective and selective suppression of the aberrant activation of Wnt/β-catenin signaling. Herein, we summarize recent advances in biochemical techniques and medicinal chemistry strategies used to identify potent peptide-based and small-molecule inhibitors that directly disrupt β-catenin's interactions with its nuclear binding partners. We discuss the challenges involved in developing drug-like inhibitors that target the interactions of β-catenin and its nuclear binding partner into therapeutic agents.
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Affiliation(s)
- Hao Zhang
- School of Pharmacy, Fudan University, Shanghai 201203, China.,Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Chenglong Liu
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Di Zhu
- School of Pharmacy, Fudan University, Shanghai 201203, China.,Department of Pharmacology, School of Basic Medical Science, Fudan University, Shanghai 201100, China
| | - Qingwei Zhang
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Jianqi Li
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China
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3
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McCoy MA, Spicer D, Wells N, Hoogewijs K, Fiedler M, Baud MGJ. Biophysical Survey of Small-Molecule β-Catenin Inhibitors: A Cautionary Tale. J Med Chem 2022; 65:7246-7261. [PMID: 35581674 PMCID: PMC9150122 DOI: 10.1021/acs.jmedchem.2c00228] [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] [Indexed: 11/29/2022]
Abstract
![]()
The canonical Wingless-related
integration site signaling pathway
plays a critical role in human physiology, and its dysregulation can
lead to an array of diseases. β-Catenin is a multifunctional
protein within this pathway and an attractive yet challenging therapeutic
target, most notably in oncology. This has stimulated the search for
potent small-molecule inhibitors binding directly to the β-catenin
surface to inhibit its protein–protein interactions and downstream
signaling. Here, we provide an account of the claimed (and some putative)
small-molecule ligands of β-catenin from the literature. Through
in silico analysis, we show that most of these molecules contain promiscuous
chemical substructures notorious for interfering with screening assays.
Finally, and in line with this analysis, we demonstrate using orthogonal
biophysical techniques that none of the examined small molecules bind
at the surface of β-catenin. While shedding doubts on their
reported mode of action, this study also reaffirms β-catenin
as a prominent target in drug discovery.
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Affiliation(s)
- Michael A McCoy
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Dominique Spicer
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Neil Wells
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Kurt Hoogewijs
- National University of Ireland, University Road, Galway H91 TK33, Ireland
| | - Marc Fiedler
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Matthias G J Baud
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
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4
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Shi C, Yang EJ, Tao S, Ren G, Mou PK, Shim JS. Natural products targeting cancer cell dependency. J Antibiot (Tokyo) 2021; 74:677-686. [PMID: 34163025 DOI: 10.1038/s41429-021-00438-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
Precision cancer medicine is a tailored treatment approach for individual cancer patients with different genomic characteristics. Mutated or hyperactive oncogenes have served as main drug targets in current precision cancer medicine, while defective or inactivated tumor suppressors in general have not been considered as druggable targets. Synthetic lethality is one of very few approaches that enable to target defective tumor suppressors with pharmacological agents. Synthetic lethality exploits cancer cell dependency on a protein or pathway, which arises when the function of a tumor suppressor is defective. This approach has been proven to be effective in clinical settings since the successful clinical introduction of BRCA-PARP synthetic lethality for the treatment of breast and ovarian cancer with defective BRCA. Subsequently, large-scale screenings with RNAi, CRISPR/Cas9-sgRNAs, and chemical libraries have been applied to identify synthetic lethal partners of tumor suppressors. Natural products are an important source for the discovery of pharmacologically active small molecules. However, little effort has been made in the discovery of synthetic lethal small molecules from natural products. This review introduces recent advances in the discovery of natural products targeting cancer cell dependency and discusses potentials of natural products in the precision cancer medicine.
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Affiliation(s)
- Changxiang Shi
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Eun Ju Yang
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Shishi Tao
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Guowen Ren
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Pui Kei Mou
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Joong Sup Shim
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China. .,MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau SAR, China.
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5
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Blosser SL, Sawyer N, Maksimovic I, Ghosh B, Arora PS. Covalent and Noncovalent Targeting of the Tcf4/β-Catenin Strand Interface with β-Hairpin Mimics. ACS Chem Biol 2021; 16:1518-1525. [PMID: 34286954 DOI: 10.1021/acschembio.1c00389] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
β-Strands are a fundamental component of protein structure, and these extended peptide regions serve as binding epitopes for numerous protein-protein complexes. However, synthetic mimics that capture the conformation of these epitopes and inhibit selected protein-protein interactions are rare. Here we describe covalent and noncovalent β-hairpin mimics of an extended strand region mediating the Tcf4/β-catenin interaction. Our efforts afford a rationally designed lead for an underexplored region of β-catenin, which has been the subject of numerous ligand discovery campaigns.
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Affiliation(s)
- Sarah L. Blosser
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Igor Maksimovic
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Brahma Ghosh
- Discovery Chemistry, Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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6
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Smith BM, Rowling PJE, Dobson CM, Itzhaki LS. Parallel and Sequential Pathways of Molecular Recognition of a Tandem-Repeat Protein and Its Intrinsically Disordered Binding Partner. Biomolecules 2021; 11:827. [PMID: 34206070 PMCID: PMC8228192 DOI: 10.3390/biom11060827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023] Open
Abstract
The Wnt signalling pathway plays an important role in cell proliferation, differentiation, and fate decisions in embryonic development and the maintenance of adult tissues. The twelve armadillo (ARM) repeat-containing protein β-catenin acts as the signal transducer in this pathway. Here, we investigated the interaction between β-catenin and the intrinsically disordered transcription factor TCF7L2, comprising a very long nanomolar-affinity interface of approximately 4800 Å2 that spans ten of the twelve ARM repeats of β-catenin. First, a fluorescence reporter system for the interaction was engineered and used to determine the kinetic rate constants for the association and dissociation. The association kinetics of TCF7L2 and β-catenin were monophasic and rapid (7.3 ± 0.1 × 107 M-1·s-1), whereas dissociation was biphasic and slow (5.7 ± 0.4 × 10-4 s-1, 15.2 ± 2.8 × 10-4 s-1). This reporter system was then combined with site-directed mutagenesis to investigate the striking variability in the conformation adopted by TCF7L2 in the three different crystal structures of the TCF7L2-β-catenin complex. We found that the mutation had very little effect on the association kinetics, indicating that most interactions form after the rate-limiting barrier for association. Mutations of the N- and C-terminal subdomains of TCF7L2 that adopt relatively fixed conformations in the crystal structures had large effects on the dissociation kinetics, whereas the mutation of the labile sub-domain connecting them had negligible effect. These results point to a two-site avidity mechanism of binding with the linker region forming a "fuzzy" complex involving transient contacts that are not site-specific. Strikingly, the two mutations in the N-terminal subdomain that had the largest effects on the dissociation kinetics showed two additional phases, indicating partial flux through an alternative dissociation pathway that is inaccessible to the wild type. The results presented here provide insights into the kinetics of the molecular recognition of a long intrinsically disordered region with an elongated repeat-protein surface, a process found to involve parallel routes with sequential steps in each.
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Affiliation(s)
- Ben M. Smith
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK;
| | - Pamela J. E. Rowling
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK;
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK;
| | - Laura S. Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK;
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7
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Wang Z, Li Z, Ji H. Direct targeting of β-catenin in the Wnt signaling pathway: Current progress and perspectives. Med Res Rev 2021; 41:2109-2129. [PMID: 33475177 DOI: 10.1002/med.21787] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/30/2020] [Accepted: 01/05/2021] [Indexed: 12/28/2022]
Abstract
Aberrant activation of the Wnt/β-catenin signaling circuit is associated with cancer recurrence and relapse, cancer invasion and metastasis, and cancer immune evasion. Direct targeting of β-catenin, the central hub in this signaling pathway, is a promising strategy to suppress the hyperactive β-catenin signaling but has proven to be highly challenging. Substantial efforts have been made to discover compounds that bind with β-catenin, block β-catenin-mediated protein-protein interactions, and suppress β-catenin signaling. Herein, we characterize potential small-molecule binding sites in β-catenin, summarize bioactive small molecules that directly target β-catenin, and review structure-based inhibitor optimization, structure-activity relationship, and biological activities of reported inhibitors. This knowledge will benefit future inhibitor development and β-catenin-related drug discovery.
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Affiliation(s)
- Zhen Wang
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Zilu Li
- Department of Chemistry, University of South Florida, Tampa, Florida, USA
| | - Haitao Ji
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA.,Department of Chemistry, University of South Florida, Tampa, Florida, USA
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8
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Cui C, Zhou X, Zhang W, Qu Y, Ke X. Is β-Catenin a Druggable Target for Cancer Therapy? Trends Biochem Sci 2018; 43:623-634. [DOI: 10.1016/j.tibs.2018.06.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 06/02/2018] [Accepted: 06/03/2018] [Indexed: 01/09/2023]
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9
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Domingues MJ, Martinez-Sanz J, Papon L, Larue L, Mouawad L, Bonaventure J. Structure-based mutational analysis of ICAT residues mediating negative regulation of β-catenin co-transcriptional activity. PLoS One 2017; 12:e0172603. [PMID: 28273108 PMCID: PMC5342195 DOI: 10.1371/journal.pone.0172603] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 02/07/2017] [Indexed: 01/16/2023] Open
Abstract
ICAT (Inhibitor of β-CAtenin and TCF) is a small acidic protein that negatively regulates β-catenin co-transcriptional activity by competing with TCF/LEF factors in their binding to β-catenin superhelical core. In melanoma cells, ICAT competes with LEF1 to negatively regulate the M-MITF and NEDD9 target genes. The structure of ICAT consists of two domains: the 3-helix bundle N-terminal domain binds to β-catenin Armadillo (Arm) repeats 10–12 and the C-terminal tail binds to Arm repeats 5–9. To elucidate the structural mechanisms governing ICAT/β-catenin interactions in melanoma cells, three ICAT residues Y15, K19 and V22 in the N-terminal domain, contacting hydrophobic β-catenin residue F660, were mutated and interaction was assessed by immunoprecipitation. Despite the moderate hydrophobicity of the contact, its removal completely abolished the interaction. In the ICAT C-terminal tail consensus sequence, neutralization of the electrostatic interactions between residues D66, E75 and β-catenin residues K435, K312, coupled to deletion of the hydrophobic contact between F71 and β-catenin R386, markedly reduced, but failed to abolish the ICAT-mediated negative regulation of M-MITF and NEDD9 promoters. We conclude that in melanoma cells, anchoring of ICAT N-terminal domain to β-catenin through the hook made by residue F660, trapped in the pincers formed by ICAT residues Y15 and V22, is crucial for stabilizing the ICAT/β-catenin complex. This is a prerequisite for binding of the consensus peptide to Arm repeats 5–9 and competition with LEF1. Differences between ICAT and LEF1 in their affinity for β-catenin may rely on the absence in ICAT of hydrophilic residues between D66 and F71.
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Affiliation(s)
- Mélanie J. Domingues
- Institut Curie, PSL Research University, Bâtiment, Orsay, France
- University Paris-Sud, University Paris-Saclay, Orsay, France
- Inserm U1021, Normal and Pathological Development of Melanocytes, Orsay, France
- CNRS UMR 3347, Orsay, France
- Equipe Labellisée Ligue Contre le Cancer, Orsay, France
| | - Juan Martinez-Sanz
- Institut Curie, PSL Research University, Bâtiment, Orsay, France
- University Paris-Sud, University Paris-Saclay, Orsay, France
- Inserm, U1196, Chemistry, Modelling and Imaging for Biology, Orsay, France
- CNRS, UMR 9187, Orsay, France
| | - Laura Papon
- Institut Curie, PSL Research University, Bâtiment, Orsay, France
- University Paris-Sud, University Paris-Saclay, Orsay, France
- Inserm U1021, Normal and Pathological Development of Melanocytes, Orsay, France
- CNRS UMR 3347, Orsay, France
- Equipe Labellisée Ligue Contre le Cancer, Orsay, France
| | - Lionel Larue
- Institut Curie, PSL Research University, Bâtiment, Orsay, France
- University Paris-Sud, University Paris-Saclay, Orsay, France
- Inserm U1021, Normal and Pathological Development of Melanocytes, Orsay, France
- CNRS UMR 3347, Orsay, France
- Equipe Labellisée Ligue Contre le Cancer, Orsay, France
| | - Liliane Mouawad
- Institut Curie, PSL Research University, Bâtiment, Orsay, France
- University Paris-Sud, University Paris-Saclay, Orsay, France
- Inserm, U1196, Chemistry, Modelling and Imaging for Biology, Orsay, France
- CNRS, UMR 9187, Orsay, France
| | - Jacky Bonaventure
- Institut Curie, PSL Research University, Bâtiment, Orsay, France
- University Paris-Sud, University Paris-Saclay, Orsay, France
- Inserm U1021, Normal and Pathological Development of Melanocytes, Orsay, France
- CNRS UMR 3347, Orsay, France
- Equipe Labellisée Ligue Contre le Cancer, Orsay, France
- * E-mail:
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10
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Catrow JL, Zhang Y, Zhang M, Ji H. Discovery of Selective Small-Molecule Inhibitors for the β-Catenin/T-Cell Factor Protein-Protein Interaction through the Optimization of the Acyl Hydrazone Moiety. J Med Chem 2015; 58:4678-92. [PMID: 25985283 DOI: 10.1021/acs.jmedchem.5b00223] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Acyl hydrazone is an important functional group for the discovery of bioactive small molecules. This functional group is also recognized as a pan assay interference structure. In this study, a new small-molecule inhibitor for the β-catenin/Tcf protein-protein interaction (PPI), ZINC02092166, was identified through AlphaScreen and FP assays. This compound contains an acyl hydrazone group and exhibits higher inhibitory activities in cell-based assays than biochemical assays. Inhibitor optimization resulted in chemically stable derivatives that disrupt the β-catenin/Tcf PPI. The binding mode of new inhibitors was characterized by site-directed mutagenesis and structure-activity relationship studies. This series of inhibitors with a new scaffold exhibits dual selectivity for β-catenin/Tcf over β-catenin/cadherin and β-catenin/APC PPIs. One derivative of this series suppresses canonical Wnt signaling, downregulates the expression of Wnt target genes, and inhibits the growth of cancer cells. This compound represents a solid starting point for the development of potent and selective β-catenin/Tcf inhibitors.
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Affiliation(s)
- J Leon Catrow
- Department of Chemistry, Center for Cell and Genome Science, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Yongqiang Zhang
- Department of Chemistry, Center for Cell and Genome Science, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Min Zhang
- Department of Chemistry, Center for Cell and Genome Science, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Haitao Ji
- Department of Chemistry, Center for Cell and Genome Science, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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11
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Huang Z, Zhang M, Burton SD, Katsakhyan LN, Ji H. Targeting the Tcf4 G13ANDE17 binding site to selectively disrupt β-catenin/T-cell factor protein-protein interactions. ACS Chem Biol 2014; 9:193-201. [PMID: 24191653 DOI: 10.1021/cb400795x] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Selective disruption of protein-protein interactions by small molecules is important for probing the structure and dynamic aspects of cellular network. It can also provide new therapeutic targets. β-Catenin of the canonical Wnt signaling pathway uses the same positively charged groove to bind with T-cell factor (Tcf), cadherin, and adenomatous polysis coli (APC). The extravagant formation of β-catenin/Tcf interactions drives the initiation and progression of many cancers and fibroses, while β-catenin/cadherin and β-catenin/APC interactions are essential for cell-cell adhesion and β-catenin degradation. In this study, a selective binding site that can differentiate β-catenin/Tcf, β-catenin/cadherin, and β-catenin/APC interactions was identified by alanine scanning and biochemical assays. A new peptidomimetic strategy that incorporates SiteMap and multiple-copy simultaneous search was used to design selective small-molecule inhibitors for β-catenin/Tcf interactions. A potent inhibitor was discovered to bind with β-catenin and completely disrupt β-catenin/Tcf interactions. It also exhibits dual selectivity for β-catenin/Tcf over β-catenin/cadherin and β-catenin/APC interactions in both biochemical and cell-based assays. This study provides a proof of concept for designing selective inhibitors for β-catenin/Tcf interactions.
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Affiliation(s)
- Zheng Huang
- Department
of Chemistry,
Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112−0850, United States
| | - Min Zhang
- Department
of Chemistry,
Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112−0850, United States
| | - Shawn D. Burton
- Department
of Chemistry,
Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112−0850, United States
| | - Levon N. Katsakhyan
- Department
of Chemistry,
Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112−0850, United States
| | - Haitao Ji
- Department
of Chemistry,
Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112−0850, United States
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12
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Weiser K, Barton M, Gershoony D, DasGupta R, Cardozo T. HIV's Nef interacts with β-catenin of the Wnt signaling pathway in HEK293 cells. PLoS One 2013; 8:e77865. [PMID: 24130899 PMCID: PMC3795062 DOI: 10.1371/journal.pone.0077865] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 09/13/2013] [Indexed: 11/18/2022] Open
Abstract
The Wnt signaling pathway is implicated in major physiologic cellular functions, such as proliferation, migration, cell fate specification, maintenance of pluripotency and induction of tumorigenicity. Proliferation and migration are important responses of T-cells, which are major cellular targets of HIV infection. Using an informatics screen, we identified a previously unsuspected interaction between HIV’s Nef protein and β-catenin, a key component of the Wnt pathway. A segment in Nef contains identical amino acids at key positions and structurally mimics the β-catenin binding sites on endogenous β-catenin ligands. The interaction between Nef and β-catenin was confirmed in vitro and in a co-immunoprecipitation from HEK293 cells. Moreover, the introduction of Nef into HEK293 cells specifically inhibited a Wnt pathway reporter.
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Affiliation(s)
- Keren Weiser
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
| | - Meredith Barton
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
| | - Dafna Gershoony
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
| | - Ramanuj DasGupta
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
| | - Timothy Cardozo
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
- * E-mail:
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13
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Chandrasekhar S, Iyer LK, Panchal JP, Topp EM, Cannon JB, Ranade VV. Microarrays and microneedle arrays for delivery of peptides, proteins, vaccines and other applications. Expert Opin Drug Deliv 2013; 10:1155-70. [PMID: 23662940 DOI: 10.1517/17425247.2013.797405] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Peptide and protein microarray and microneedle array technology provides direct information on protein function and potential drug targets in drug discovery and delivery. Because of this unique ability, these arrays are well suited for protein profiling, drug target identification/validation and studies of protein interaction, biochemical activity, immune responses, clinical prognosis and diagnosis and for gene, protein and drug delivery. AREAS COVERED The aim of this review is to describe and summarize past and recent developments of microarrays in their construction, characterization and production and applications of microneedles in drug delivery. The scope and limitations of various technologies in this respect are discussed. EXPERT OPINION This article offers a review of microarray/microneedle technologies and possible future directions in targeting and in the delivery of pharmacologically active compounds for unmet needs in biopharmaceutical research. A better understanding of the production and use of microarrays and microneedles for delivery of peptides, proteins and vaccines is needed.
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Affiliation(s)
- Saradha Chandrasekhar
- Purdue University, Department of Industrial and Physical Pharmacy, West Lafayette, IN 47907, USA
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14
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Yu B, Huang Z, Zhang M, Dillard DR, Ji H. Rational design of small-molecule inhibitors for β-catenin/T-cell factor protein-protein interactions by bioisostere replacement. ACS Chem Biol 2013; 8:524-9. [PMID: 23272635 DOI: 10.1021/cb300564v] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A new hot spot-based design strategy using bioisostere replacement is reported to rationally design nonpeptidic small-molecule inhibitors for protein-protein interactions. This method is applied to design new potent inhibitors for β-catenin/T-cell factor (Tcf) interactions. Three hot spot regions of Tcf for binding to β-catenin were quantitatively evaluated; the key binding elements around K435 and K508 of β-catenin were derived; a bioisostere library was used to generate new fragments that can match the proposed critical binding elements. The most potent inhibitor, with a molecular weight of 230, has a Kd of 0.531 μM for binding to β-catenin and a Ki of 3.14 μM to completely disrupt β-catenin/Tcf interactions. The binding mode of the designed inhibitors was validated by the site-directed mutagenesis and structure-activity relationship (SAR) studies. This study provides a new approach to design new small-molecule inhibitors that bind to β-catenin and effectively disrupt β-catenin/Tcf interactions specific for canonical Wnt signaling.
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Affiliation(s)
- Binxun Yu
- Department of Chemistry, Center for
Cell and Genome
Science, University of Utah, Salt Lake
City, Utah 84112-0850, United States
| | - Zheng Huang
- Department of Chemistry, Center for
Cell and Genome
Science, University of Utah, Salt Lake
City, Utah 84112-0850, United States
| | - Min Zhang
- Department of Chemistry, Center for
Cell and Genome
Science, University of Utah, Salt Lake
City, Utah 84112-0850, United States
| | - Darren R. Dillard
- Department of Chemistry, Center for
Cell and Genome
Science, University of Utah, Salt Lake
City, Utah 84112-0850, United States
| | - Haitao Ji
- Department of Chemistry, Center for
Cell and Genome
Science, University of Utah, Salt Lake
City, Utah 84112-0850, United States
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15
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Zhang M, Huang Z, Yu B, Ji H. New homogeneous high-throughput assays for inhibitors of β-catenin/Tcf protein–protein interactions. Anal Biochem 2012; 424:57-63. [DOI: 10.1016/j.ab.2012.02.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Revised: 02/13/2012] [Accepted: 02/16/2012] [Indexed: 10/28/2022]
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16
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Volkmer R, Tapia V, Landgraf C. Synthetic peptide arrays for investigating protein interaction domains. FEBS Lett 2012; 586:2780-6. [PMID: 22576123 DOI: 10.1016/j.febslet.2012.04.028] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 04/16/2012] [Accepted: 04/17/2012] [Indexed: 11/28/2022]
Abstract
Synthetic peptide array technology was first developed in the early 1990s by Ronald Frank. Since then the technique has become a powerful tool for high throughput approaches in biology and biochemistry. Here, we focus on peptide arrays applied to investigate the binding specificity of protein interaction domains such as WW, SH3, and PDZ domains. We describe array-based methods used to reveal domain networks in yeast, and briefly review rules as well as ideas about the synthesis and application of peptide arrays. We also provide initial results of a study designed to investigate the nature and evolution of SH3 domain interaction networks in eukaryotes.
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Affiliation(s)
- Rudolf Volkmer
- Institut für Medizinische Immunologie Berlin, Molecular Libraries and Recognition Group, Charité-Universitätsmedizin Berlin, Hessische Str. 3-4, 10115 Berlin, Germany.
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17
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Mao Y, Lin N, Tian W, Han X, Han X, Huang Z, An J. Design, Synthesis, and Biological Evaluation of New Diaminoquinazolines as β-Catenin/Tcf4 Pathway Inhibitors. J Med Chem 2012; 55:1346-59. [DOI: 10.1021/jm201494a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yongjun Mao
- Department
of Pharmacology, State University of New York, Upstate Medical University, 750 East Adams Street,
Syracuse, New York 13210, United States
- Upstate
Cancer Research Institute, State University of New York, Upstate Medical University, 750 East Adams
Street, Syracuse, New York 13210, United States
| | - Nan Lin
- Department
of Pharmacology, State University of New York, Upstate Medical University, 750 East Adams Street,
Syracuse, New York 13210, United States
- Upstate
Cancer Research Institute, State University of New York, Upstate Medical University, 750 East Adams
Street, Syracuse, New York 13210, United States
| | - Wang Tian
- Department
of Pharmacology, State University of New York, Upstate Medical University, 750 East Adams Street,
Syracuse, New York 13210, United States
- Upstate
Cancer Research Institute, State University of New York, Upstate Medical University, 750 East Adams
Street, Syracuse, New York 13210, United States
| | - Xiaofeng Han
- Department
of Pharmacology, State University of New York, Upstate Medical University, 750 East Adams Street,
Syracuse, New York 13210, United States
- Upstate
Cancer Research Institute, State University of New York, Upstate Medical University, 750 East Adams
Street, Syracuse, New York 13210, United States
| | - Xiaobing Han
- Department
of Pharmacology, State University of New York, Upstate Medical University, 750 East Adams Street,
Syracuse, New York 13210, United States
- Upstate
Cancer Research Institute, State University of New York, Upstate Medical University, 750 East Adams
Street, Syracuse, New York 13210, United States
| | - Ziwei Huang
- Department
of Pharmacology, State University of New York, Upstate Medical University, 750 East Adams Street,
Syracuse, New York 13210, United States
- Upstate
Cancer Research Institute, State University of New York, Upstate Medical University, 750 East Adams
Street, Syracuse, New York 13210, United States
| | - Jing An
- Department
of Pharmacology, State University of New York, Upstate Medical University, 750 East Adams Street,
Syracuse, New York 13210, United States
- Upstate
Cancer Research Institute, State University of New York, Upstate Medical University, 750 East Adams
Street, Syracuse, New York 13210, United States
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18
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Tian W, Xu Y, Han X, Duggineni S, Han X, Huang Z, An J. Development of a Novel Fluorescence Polarization–Based Assay for Studying the β-Catenin/Tcf4 Interaction. ACTA ACUST UNITED AC 2011; 17:530-4. [DOI: 10.1177/1087057111429745] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Aberrant activation of the Wnt/β-catenin signaling pathway is associated with a wide range of human cancers. The interaction of β-catenin with T cell factor (Tcf) is a key step in activation of proliferative genes in this pathway. Interruption of this interaction would be a valuable strategy as a tumor therapy. In this study, we developed a novel fluorescein isothiocyanate (FITC)–labeled Tcf4-derived probe for identification of inhibitors of the β-catenin/Tcf4 interaction using a fluorescence polarization assay. This assay shows high potential for use in high-throughput screening for the discovery of inhibitors of the β-catenin/Tcf4 interaction.
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Affiliation(s)
- Wang Tian
- Department of Pharmacology, State University of New York, Upstate Medical University, Syracuse, NY, USA
- Upstate Cancer Research Institute, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | - Yan Xu
- Department of Pharmacology, State University of New York, Upstate Medical University, Syracuse, NY, USA
- Upstate Cancer Research Institute, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | - Xiaofeng Han
- Department of Pharmacology, State University of New York, Upstate Medical University, Syracuse, NY, USA
- Upstate Cancer Research Institute, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | - Srinivas Duggineni
- Department of Pharmacology, State University of New York, Upstate Medical University, Syracuse, NY, USA
- Upstate Cancer Research Institute, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | - Xiaobing Han
- Department of Pharmacology, State University of New York, Upstate Medical University, Syracuse, NY, USA
- Upstate Cancer Research Institute, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | - Ziwei Huang
- Department of Pharmacology, State University of New York, Upstate Medical University, Syracuse, NY, USA
- Upstate Cancer Research Institute, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | - Jing An
- Department of Pharmacology, State University of New York, Upstate Medical University, Syracuse, NY, USA
- Upstate Cancer Research Institute, State University of New York, Upstate Medical University, Syracuse, NY, USA
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19
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Burgess AW, Faux MC, Layton MJ, Ramsay RG. Wnt signaling and colon tumorigenesis--a view from the periphery. Exp Cell Res 2011; 317:2748-58. [PMID: 21884696 DOI: 10.1016/j.yexcr.2011.08.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 08/10/2011] [Accepted: 08/13/2011] [Indexed: 02/06/2023]
Abstract
In this brief overview we discuss the association between Wnt signaling and colon cell biology and tumorigenesis. Our current understanding of the role of Apc in the β-catenin destruction complex is compared with potential roles for Apc in cell adhesion and migration. The requirement for phosphorylation in the proteasomal-mediated degradation of β-catenin is contrasted with roles for phospho-β-catenin in the activation of transcription, cell adhesion and migration. The synergy between Myb and β-catenin regulation of transcription in crypt stem cells during Wnt signaling is discussed. Finally, potential effects of growth factor regulatory systems, Apc or truncated-Apc on crypt morphogenesis, stem cell localization and crypt fission are considered.
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Affiliation(s)
- Antony W Burgess
- Parkville Branch, Ludwig Institute for Cancer Research, Melbourne, 3050, Australia.
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20
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Volkmer R. Synthesis and application of peptide arrays: quo vadis SPOT technology. Chembiochem 2009; 10:1431-42. [PMID: 19437530 DOI: 10.1002/cbic.200900078] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Rudolf Volkmer
- Institut für Medizinische Immunologie, AG Molekulare Bibliotheken, Charité-Universitätsmedizin Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany.
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21
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The C. elegans SYS-1 protein is a bona fide beta-catenin. Dev Cell 2008; 14:751-61. [PMID: 18477457 DOI: 10.1016/j.devcel.2008.02.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Revised: 02/19/2008] [Accepted: 02/23/2008] [Indexed: 11/21/2022]
Abstract
C. elegans SYS-1 has key functional characteristics of a canonical beta-catenin, but no significant sequence similarity. Here, we report the SYS-1 crystal structure, both on its own and in a complex with POP-1, the C. elegans TCF homolog. The two structures possess signature features of canonical beta-catenin and the beta-catenin/TCF complex that could not be predicted by sequence. Most importantly, SYS-1 bears 12 armadillo repeats and the SYS-1/POP-1 interface is anchored by a conserved salt-bridge, the "charged button." We also modeled structures for three other C. elegans beta-catenins to predict the molecular basis of their distinct binding properties. Finally, we generated a phylogenetic tree, using the region of highest structural similarity between SYS-1 and beta-catenin, and found that SYS-1 clusters robustly within the beta-catenin clade. We conclude that the SYS-1 protein belongs to the beta-catenin family and suggest that additional divergent beta-catenins await discovery.
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22
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Large-scale analysis of protein-protein interactions using cellulose-bound peptide arrays. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008; 110:115-52. [PMID: 18418558 DOI: 10.1007/10_2008_096] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Peptide arrays for screening large numbers of peptide fragments and probing with large numbers of samples is discussed.
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23
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Ritco-Vonsovici M, Ababou A, Horton M. Molecular plasticity of beta-catenin: new insights from single-molecule measurements and MD simulation. Protein Sci 2007; 16:1984-98. [PMID: 17660262 PMCID: PMC2206973 DOI: 10.1110/ps.072773007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The multifunctional protein, beta-catenin, has essential roles in cell adhesion and, through the Wnt signaling pathway, in controlling cell differentiation, development, and generation of cancer. Could distinct molecular forms of beta-catenin underlie these two functions? Our single-molecule force spectroscopy of armadillo beta-catenin, with molecular dynamics (MD) simulation, suggests a model in which the cell generates various forms of beta-catenin, in equilibrium. We find beta-catenin and the transcriptional factor Tcf4 form two complexes with different affinities. Specific cellular response is achieved by the ligand binding to a particular matching preexisting conformer. Our MD simulation indicates that complexes derive from two conformers of the core region of the protein, whose preexisting molecular forms could arise from small variations in flexible regions of the beta-catenin main binding site. This mechanism for the generation of the various forms offers a route to tailoring future therapeutic strategies.
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Affiliation(s)
- Monica Ritco-Vonsovici
- London Centre for Nanotechnology and Department of Medicine, University College London, London WC1E 6JJ, United Kingdom
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24
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Hilpert K, Winkler DFH, Hancock REW. Cellulose-bound Peptide Arrays: Preparation and Applications. Biotechnol Genet Eng Rev 2007; 24:31-106. [DOI: 10.1080/02648725.2007.10648093] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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25
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Liu J, Xing Y, Hinds TR, Zheng J, Xu W. The third 20 amino acid repeat is the tightest binding site of APC for beta-catenin. J Mol Biol 2006; 360:133-44. [PMID: 16753179 DOI: 10.1016/j.jmb.2006.04.064] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Revised: 04/13/2006] [Accepted: 04/27/2006] [Indexed: 12/20/2022]
Abstract
Adenomatous polyposis coli (APC) plays a critical role in the Wnt signaling pathway by tightly regulating beta-catenin turnover and localization. The central region of APC is responsible for APC-beta-catenin interactions through its seven 20 amino acid (20aa) repeats and three 15 amino acid (15aa) repeats. Using isothermal titration calorimetry, we have determined the binding affinities of beta-catenin with an APC 15aa repeat fragment and each of the seven 20aa repeats in both phosphorylated and unphosphorylated states. Despite sequence homology, different beta-catenin binding repeats of APC have dramatically different binding affinities with beta-catenin and thus may play different biological roles. The third 20aa repeat is by far the tightest binding site for beta-catenin among all the repeats. The fact that most APC mutations associated with colon cancers have lost the third 20aa repeat underlines the importance of APC-beta-catenin interaction in Wnt signaling and human diseases. For every 20aa repeat, phosphorylation dramatically increases its binding affinity for beta-catenin, suggesting phosphorylation has a critical regulatory role in APC function. In addition, our CD and NMR studies demonstrate that the central region of APC is unstructured in the absence of beta-catenin and Axin, and suggest that beta-catenin may interact with each of the APC 15aa and 20aa repeats independently.
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Affiliation(s)
- Jing Liu
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
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26
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Choi HJ, Huber AH, Weis WI. Thermodynamics of beta-catenin-ligand interactions: the roles of the N- and C-terminal tails in modulating binding affinity. J Biol Chem 2005; 281:1027-38. [PMID: 16293619 DOI: 10.1074/jbc.m511338200] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
beta-Catenin is a structural component of adherens junctions, where it binds to the cytoplasmic domain of cadherin cell adhesion molecules. beta-Catenin is also a transcriptional coactivator in the Wnt signaling pathway, where it binds to Tcf/Lef family transcription factors. In the absence of a Wnt signal, nonjunctional beta-catenin is present in a multiprotein complex containing the proteins axin and adenomatous polyposis coli (APC), both of which bind directly to beta-catenin. The thermodynamics of beta-catenin binding to E-cadherin, Lef-1, APC, axin, and the transcriptional inhibitor ICAT have been determined by isothermal titration calorimetry. Most of the interactions showed large, unfavorable entropy changes, consistent with these ligands being natively unstructured in the absence of beta-catenin. Phosphorylation of serine residues present in a sequence motif common to cadherins and APC increased the affinity for beta-catenin 300-700-fold, and surface plasmon resonance measurements revealed that phosphorylation of E-cadherin both enhanced its on rate and decreased its off rate. The effects of the N- and C-terminal "tails" that flank the beta-catenin armadillo repeat domain on ligand binding have also been investigated using constructs lacking one or both tails. Contrary to earlier studies that employed less direct binding assays, the tails did not affect the affinity of beta-catenin for tight ligands such as E-cadherin, Lef-1, and phosphorylated APC. However, the beta-catenin C-terminal tail was found to decrease the affinity for the weaker ligands APC and axin, suggesting that this region may have a regulatory role in beta-catenin degradation.
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Affiliation(s)
- Hee-Jung Choi
- Department of Structural Biology, Stanford University School of Medicine, CA 94305-5126, USA
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