1
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Gui T, Fleming C, Manzato C, Bourgeois B, Sirati N, Heuer J, Papadionysiou I, Montfort DIV, Gijzen MV, Smits LMM, Burgering BMT, Madl T, Schuijers J. Targeted perturbation of signaling-driven condensates. Mol Cell 2023; 83:4141-4157.e11. [PMID: 37977121 DOI: 10.1016/j.molcel.2023.10.023] [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] [Received: 07/28/2023] [Revised: 09/27/2023] [Accepted: 10/17/2023] [Indexed: 11/19/2023]
Abstract
Biomolecular condensates have emerged as a major organizational principle in the cell. However, the formation, maintenance, and dissolution of condensates are still poorly understood. Transcriptional machinery partitions into biomolecular condensates at key cell identity genes to activate these. Here, we report a specific perturbation of WNT-activated β-catenin condensates that disrupts oncogenic signaling. We use a live-cell condensate imaging method in human cancer cells to discover FOXO and TCF-derived peptides that specifically inhibit β-catenin condensate formation on DNA, perturb nuclear β-catenin condensates in cells, and inhibit β-catenin-driven transcriptional activation and colorectal cancer cell growth. We show that these peptides compete with homotypic intermolecular interactions that normally drive condensate formation. Using this framework, we derive short peptides that specifically perturb condensates and transcriptional activation of YAP and TAZ in the Hippo pathway. We propose a "monomer saturation" model in which short interacting peptides can be used to specifically inhibit condensate-associated transcription in disease.
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Affiliation(s)
- Tianshu Gui
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands; Oncode Institute, 3721 AL Utrecht, the Netherlands
| | - Cassio Fleming
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Caterina Manzato
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Benjamin Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Nafiseh Sirati
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Jasper Heuer
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Ioanna Papadionysiou
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Daniel I van Montfort
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Merel van Gijzen
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Lydia M M Smits
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Boudewijn M T Burgering
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands; Oncode Institute, 3721 AL Utrecht, the Netherlands
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria
| | - Jurian Schuijers
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands; Oncode Institute, 3721 AL Utrecht, the Netherlands.
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2
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Fujita M, Tsuchiya K, Kurohara T, Fukuhara K, Misawa T, Demizu Y. In silico optimization of peptides that inhibit Wnt/β-catenin signaling. Bioorg Med Chem 2023; 84:117264. [PMID: 37003158 DOI: 10.1016/j.bmc.2023.117264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023]
Abstract
The Wnt/β-catenin signaling pathway causes transcriptional activation through the interaction between β-catenin and T cell-specific transcription factor (TCF) and regulates a wide variety of cellular responses, including proliferation, differentiation and cell motility. Excessive transcriptional activation of the Wnt/β-catenin pathway is implicated in developing or exacerbating various cancers. We have recently reported that liver receptor homolog-1 (LRH-1)-derived peptides inhibit the β-catenin/TCF interaction. In addition, we developed a cell-penetrating peptide (CPP)-conjugated LRH-1-derived peptide that inhibits the growth of colon cancer cells and specifically inhibits the Wnt/β-catenin pathway. Nonetheless, the inhibitory activity of the CPP-conjugated LRH-1-derived peptide was unsatisfactory (ca. 20 μM), and improving the bioactivity of peptide inhibitors is required for their in vivo applications. In this study, we optimized the LRH-1-derived peptide using in silico design to enhance its activity further. The newly designed peptides showed binding affinity toward β-catenin comparable to the parent peptide. In addition, the CPP-conjugated stapled peptide, Penetratin-st6, showed excellent inhibition (ca. 5 μM). Thus, the combination of in silico design by MOE and MD calculations has revealed that logical molecular design of PPI inhibitory peptides targeting β-catenin is possible. This method can be also applied to the rational design of peptide-based inhibitors targeting other proteins.
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Affiliation(s)
- Minami Fujita
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan
| | - Keisuke Tsuchiya
- Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan; Graduate School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan.
| | - Takashi Kurohara
- Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan
| | - Kiyoshi Fukuhara
- Graduate School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Takashi Misawa
- Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan
| | - Yosuke Demizu
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan; Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan.
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3
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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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4
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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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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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Wendt M, Bellavita R, Gerber A, Efrém NL, van Ramshorst T, Pearce NM, Davey PRJ, Everard I, Vazquez-Chantada M, Chiarparin E, Grieco P, Hennig S, Grossmann TN. Bicyclic β-Sheet Mimetics that Target the Transcriptional Coactivator β-Catenin and Inhibit Wnt Signaling. Angew Chem Int Ed Engl 2021; 60:13937-13944. [PMID: 33783110 PMCID: PMC8252567 DOI: 10.1002/anie.202102082] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Indexed: 12/29/2022]
Abstract
Protein complexes are defined by the three-dimensional structure of participating binding partners. Knowledge about these structures can facilitate the design of peptidomimetics which have been applied for example, as inhibitors of protein-protein interactions (PPIs). Even though β-sheets participate widely in PPIs, they have only rarely served as the basis for peptidomimetic PPI inhibitors, in particular when addressing intracellular targets. Here, we present the structure-based design of β-sheet mimetics targeting the intracellular protein β-catenin, a central component of the Wnt signaling pathway. Based on a protein binding partner of β-catenin, a macrocyclic peptide was designed and its crystal structure in complex with β-catenin obtained. Using this structure, we designed a library of bicyclic β-sheet mimetics employing a late-stage diversification strategy. Several mimetics were identified that compete with transcription factor binding to β-catenin and inhibit Wnt signaling in cells. The presented design strategy can support the development of inhibitors for other β-sheet-mediated PPIs.
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Affiliation(s)
- Mathias Wendt
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Rosa Bellavita
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Alan Gerber
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Nina-Louisa Efrém
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Thirza van Ramshorst
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Nicholas M Pearce
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Paul R J Davey
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Isabel Everard
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | | | - Paolo Grieco
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Sven Hennig
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
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7
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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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8
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Wendt M, Bellavita R, Gerber A, Efrém N, Ramshorst T, Pearce NM, Davey PRJ, Everard I, Vazquez‐Chantada M, Chiarparin E, Grieco P, Hennig S, Grossmann TN. Bicyclic β‐Sheet Mimetics that Target the Transcriptional Coactivator β‐Catenin and Inhibit Wnt Signaling. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Mathias Wendt
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Rosa Bellavita
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
- Department of Pharmacy University of Naples Federico II Naples Italy
| | - Alan Gerber
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Nina‐Louisa Efrém
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Thirza Ramshorst
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Nicholas M. Pearce
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | | | - Isabel Everard
- Mechanistic Biology and Profiling Discovery Sciences, R&D AstraZeneca Cambridge UK
| | | | | | - Paolo Grieco
- Department of Pharmacy University of Naples Federico II Naples Italy
| | - Sven Hennig
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Tom N. Grossmann
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
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9
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Judy E, Kishore N. Discrepancies in Thermodynamic Information Obtained from Calorimetry and Spectroscopy in Ligand Binding Reactions: Implications on Correct Analysis in Systems of Biological Importance. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Eva Judy
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai – 400 076, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai – 400 076, India
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10
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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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11
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Kessler D, Mayer M, Zahn SK, Zeeb M, Wöhrle S, Bergner A, Bruchhaus J, Ciftci T, Dahmann G, Dettling M, Döbel S, Fuchs JE, Geist L, Hela W, Kofink C, Kousek R, Moser F, Puchner T, Rumpel K, Scharnweber M, Werni P, Wolkerstorfer B, Breitsprecher D, Baaske P, Pearson M, McConnell DB, Böttcher J. Getting a Grip on the Undrugged: Targeting β-Catenin with Fragment-Based Methods. ChemMedChem 2021; 16:1420-1424. [PMID: 33275320 PMCID: PMC8247886 DOI: 10.1002/cmdc.202000839] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Indexed: 12/20/2022]
Abstract
Aberrant WNT pathway activation, leading to nuclear accumulation of β‐catenin, is a key oncogenic driver event. Mutations in the tumor suppressor gene APC lead to impaired proteasomal degradation of β‐catenin and subsequent nuclear translocation. Restoring cellular degradation of β‐catenin represents a potential therapeutic strategy. Here, we report the fragment‐based discovery of a small molecule binder to β‐catenin, including the structural elucidation of the binding mode by X‐ray crystallography. The difficulty in drugging β‐catenin was confirmed as the primary screening campaigns identified only few and very weak hits. Iterative virtual and NMR screening techniques were required to discover a compound with sufficient potency to be able to obtain an X‐ray co‐crystal structure. The binding site is located between armadillo repeats two and three, adjacent to the BCL9 and TCF4 binding sites. Genetic studies show that it is unlikely to be useful for the development of protein–protein interaction inhibitors but structural information and established assays provide a solid basis for a prospective optimization towards β‐catenin proteolysis targeting chimeras (PROTACs) as alternative modality.
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Affiliation(s)
- Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Stephan K Zahn
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Markus Zeeb
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach, Germany
| | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Andreas Bergner
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Jens Bruchhaus
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Tuncay Ciftci
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach, Germany
| | - Georg Dahmann
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach, Germany
| | - Maike Dettling
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Sandra Döbel
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Julian E Fuchs
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Leonhard Geist
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Wolfgang Hela
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Christiane Kofink
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Roland Kousek
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Franziska Moser
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach, Germany
| | - Teresa Puchner
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | | | - Patrick Werni
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | | | - Dennis Breitsprecher
- NanoTemper Technologies GmbH, Floessergasse 4, 81369, Muenchen, Germany.,Leica Microsystems AG, Max Schmidheiny-Strasse 201, 9435, Heerbrugg, Switzerland
| | - Philipp Baaske
- NanoTemper Technologies GmbH, Floessergasse 4, 81369, Muenchen, Germany
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Darryl B McConnell
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
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12
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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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13
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Modeling disordered protein interactions from biophysical principles. PLoS Comput Biol 2017; 13:e1005485. [PMID: 28394890 PMCID: PMC5402988 DOI: 10.1371/journal.pcbi.1005485] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 04/24/2017] [Accepted: 03/29/2017] [Indexed: 12/12/2022] Open
Abstract
Disordered protein-protein interactions (PPIs), those involving a folded protein and an intrinsically disordered protein (IDP), are prevalent in the cell, including important signaling and regulatory pathways. IDPs do not adopt a single dominant structure in isolation but often become ordered upon binding. To aid understanding of the molecular mechanisms of disordered PPIs, it is crucial to obtain the tertiary structure of the PPIs. However, experimental methods have difficulty in solving disordered PPIs and existing protein-protein and protein-peptide docking methods are not able to model them. Here we present a novel computational method, IDP-LZerD, which models the conformation of a disordered PPI by considering the biophysical binding mechanism of an IDP to a structured protein, whereby a local segment of the IDP initiates the interaction and subsequently the remaining IDP regions explore and coalesce around the initial binding site. On a dataset of 22 disordered PPIs with IDPs up to 69 amino acids, successful predictions were made for 21 bound and 18 unbound receptors. The successful modeling provides additional support for biophysical principles. Moreover, the new technique significantly expands the capability of protein structure modeling and provides crucial insights into the molecular mechanisms of disordered PPIs. A substantial fraction of the proteins encoded in genomes are intrinsically disordered proteins (IDPs), which lack a single stable structure in the native state. IDPs serve many functions including mediating protein-protein interactions (PPIs). Such disordered PPIs are prevalent in important regulatory pathways, including many interactions of the tumor suppressor protein p53. To elucidate the molecular mechanisms of disordered PPIs, obtaining tertiary structure information is essential; however, they are difficult to study with experimental techniques and existing computational protein-protein and protein-peptide modeling methods are unable to model disordered PPIs. Here we present a novel computational method for modeling the structure of disordered PPIs, which is the first of this sort. The method, IDP-LZerD, is designed to follow a known biophysical picture of the mechanism of how IDPs interact with structured proteins. IDP-LZerD successfully modeled the majority of disordered PPIs tested. This technique opens up new possibilities for structural studies of IDPs and their interactions.
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14
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Arai S, Shibazaki C, Adachi M, Honjo E, Tamada T, Maeda Y, Tahara T, Kato T, Miyazaki H, Blaber M, Kuroki R. An insight into the thermodynamic characteristics of human thrombopoietin complexation with TN1 antibody. Protein Sci 2016; 25:1786-96. [PMID: 27419667 PMCID: PMC5029525 DOI: 10.1002/pro.2985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 11/10/2022]
Abstract
Human thrombopoietin (hTPO) primarily stimulates megakaryocytopoiesis and platelet production and is neutralized by the mouse TN1 antibody. The thermodynamic characteristics of TN1 antibody-hTPO complexation were analyzed by isothermal titration calorimetry (ITC) using an antigen-binding fragment (Fab) derived from the TN1 antibody (TN1-Fab). To clarify the mechanism by which hTPO is recognized by TN1-Fab the conformation of free TN1-Fab was determined to a resolution of 2.0 Å using X-ray crystallography and compared with the hTPO-bound form of TN1-Fab determined by a previous study. This structural comparison revealed that the conformation of TN1-Fab does not substantially change after hTPO binding and a set of 15 water molecules is released from the antigen-binding site (paratope) of TN1-Fab upon hTPO complexation. Interestingly, the heat capacity change (ΔCp) measured by ITC (-1.52 ± 0.05 kJ mol(-1) K(-1) ) differed significantly from calculations based upon the X-ray structure data of the hTPO-bound and unbound forms of TN1-Fab (-1.02 ∼ 0.25 kJ mol(-1) K(-1) ) suggesting that hTPO undergoes an induced-fit conformational change combined with significant desolvation upon TN1-Fab binding. The results shed light on the structural biology associated with neutralizing antibody recognition.
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Affiliation(s)
- Shigeki Arai
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki, 319-1106, Japan.
| | - Chie Shibazaki
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki, 319-1106, Japan
| | - Motoyasu Adachi
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki, 319-1106, Japan
| | - Eijiro Honjo
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki, 319-1106, Japan
| | - Taro Tamada
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki, 319-1106, Japan
| | - Yoshitake Maeda
- Kyowa Hakko Kirin Co. Ltd, 3-6-6 Asahi-Cho, Machida, Tokyo, 194-8533, Japan
| | - Tomoyuki Tahara
- Kyowa Hakko Kirin Co. Ltd, 3-6-6 Asahi-Cho, Machida, Tokyo, 194-8533, Japan
| | - Takashi Kato
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-8480, Japan
| | - Hiroshi Miyazaki
- Department of Innovative Drug Discovery and Development, Japan Agency for Medical Research and Development, 1-5-5 Nihonbashi-muromachi, Chuo, Tokyo, 103-0022, Japan
| | - Michael Blaber
- College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, Florida, 32306-4300, USA
| | - Ryota Kuroki
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki, 319-1106, Japan
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15
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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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16
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Geist L, Henen MA, Haiderer S, Schwarz TC, Kurzbach D, Zawadzka-Kazimierczuk A, Saxena S, Zerko S, Koźmiński W, Hinderberger D, Konrat R. Protonation-dependent conformational variability of intrinsically disordered proteins. Protein Sci 2014; 22:1196-205. [PMID: 23821606 DOI: 10.1002/pro.2304] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/20/2013] [Accepted: 06/21/2013] [Indexed: 11/11/2022]
Abstract
Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity and undergo rearrangements of the time-averaged conformational ensemble on changes of environmental conditions (e.g., in ionic strength, pH, molecular crowding). In contrast to stably folded proteins, IDPs often form compact conformations at acidic pH. The biological relevance of this process was, for example, demonstrated by nuclear magnetic resonance studies of the aggregation prone (low pH) state of α-synuclein. In this study, we report a large-scale analysis of the pH dependence of disordered proteins using the recently developed meta-structure approach. The meta-structure analysis of a large set of IDPs revealed a significant tendency of IDPs to form α-helical secondary structure elements and to preferentially fold into more compact structures under acidic conditions. The predictive validity of this novel approach was demonstrated with applications to the tumor-suppressor BASP1 and the transcription factor Tcf4.
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Affiliation(s)
- Leonhard Geist
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria
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17
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Jamieson C, Sharma M, Henderson BR. Targeting the β-catenin nuclear transport pathway in cancer. Semin Cancer Biol 2014; 27:20-9. [PMID: 24820952 DOI: 10.1016/j.semcancer.2014.04.012] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 04/29/2014] [Indexed: 12/20/2022]
Abstract
The nuclear localization of specific proteins is critical for cellular processes such as cell division, and in recent years perturbation of the nuclear transport cycle of key proteins has been linked to cancer. In particular, specific gene mutations can alter nuclear transport of tumor suppressing and oncogenic proteins, leading to cell transformation or cancer progression. This review will focus on one such factor, β-catenin, a key mediator of the canonical wnt signaling pathway. In response to a wnt stimulus or specific gene mutations, β-catenin is stabilized and translocates to the nucleus where it binds TCF/LEF-1 transcription factors to transactivate genes that drive tumor formation. Moreover, the nuclear import and accumulation of β-catenin correlates with clinical tumor grade. Recent evidence suggests that the primary nuclear transport route of β-catenin is independent of the classical Ran/importin import machinery, and that β-catenin directly contacts the nuclear pore complex to self-regulate its own entry into the nucleus. Here we propose that the β-catenin nuclear import pathway may provide an opportunity for identification of specific drug targets and inhibition of β-catenin nuclear function, much like the current screening of drugs that block binding of β-catenin to LEF-1/TCFs. Here we will discuss the diverse mechanisms regulating nuclear localization of β-catenin and their potential as targets for anticancer agent development.
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Affiliation(s)
- Cara Jamieson
- Westmead Institute for Cancer Research, The University of Sydney, Westmead Millennium Institute at Westmead Hospital, Westmead, NSW 2145, Australia
| | - Manisha Sharma
- Westmead Institute for Cancer Research, The University of Sydney, Westmead Millennium Institute at Westmead Hospital, Westmead, NSW 2145, Australia
| | - Beric R Henderson
- Westmead Institute for Cancer Research, The University of Sydney, Westmead Millennium Institute at Westmead Hospital, Westmead, NSW 2145, Australia.
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18
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Chodaparambil JV, Pate KT, Hepler MRD, Tsai BP, Muthurajan UM, Luger K, Waterman ML, Weis WI. Molecular functions of the TLE tetramerization domain in Wnt target gene repression. EMBO J 2014; 33:719-31. [PMID: 24596249 DOI: 10.1002/embj.201387188] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Wnt signaling activates target genes by promoting association of the co-activator β-catenin with TCF/LEF transcription factors. In the absence of β-catenin, target genes are silenced by TCF-mediated recruitment of TLE/Groucho proteins, but the molecular basis for TLE/TCF-dependent repression is unclear. We describe the unusual three-dimensional structure of the N-terminal Q domain of TLE1 that mediates tetramerization and binds to TCFs. We find that differences in repression potential of TCF/LEFs correlates with their affinities for TLE-Q, rather than direct competition between β-catenin and TLE for TCFs as part of an activation-repression switch. Structure-based mutation of the TLE tetramer interface shows that dimers cannot mediate repression, even though they bind to TCFs with the same affinity as tetramers. Furthermore, the TLE Q tetramer, not the dimer, binds to chromatin, specifically to K20 methylated histone H4 tails, suggesting that the TCF/TLE tetramer complex promotes structural transitions of chromatin to mediate repression.
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Affiliation(s)
- Jayanth V Chodaparambil
- Departments of Structural Biology and Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
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19
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de la Roche M, Ibrahim AEK, Mieszczanek J, Bienz M. LEF1 and B9L shield β-catenin from inactivation by Axin, desensitizing colorectal cancer cells to tankyrase inhibitors. Cancer Res 2014; 74:1495-505. [PMID: 24419084 PMCID: PMC3947273 DOI: 10.1158/0008-5472.can-13-2682] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Hyperactive β-catenin drives colorectal cancer, yet inhibiting its activity remains a formidable challenge. Interest is mounting in tankyrase inhibitors (TNKSi), which destabilize β-catenin through stabilizing Axin. Here, we confirm that TNKSi inhibit Wnt-induced transcription, similarly to carnosate, which reduces the transcriptional activity of β-catenin by blocking its binding to BCL9, and attenuates intestinal tumors in Apc(Min) mice. By contrast, β-catenin's activity is unresponsive to TNKSi in colorectal cancer cells and in cells after prolonged Wnt stimulation. This TNKSi insensitivity is conferred by β-catenin's association with LEF1 and BCL9-2/B9L, which accumulate during Wnt stimulation, thereby providing a feed-forward loop that converts transient into chronic β-catenin signaling. This limits the therapeutic value of TNKSi in colorectal carcinomas, most of which express high LEF1 levels. Our study provides proof-of-concept that the successful inhibition of oncogenic β-catenin in colorectal cancer requires the targeting of its interaction with LEF1 and/or BCL9/B9L, as exemplified by carnosate.
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Affiliation(s)
- Marc de la Roche
- corresponding authors Phone +44 1223 267 093, +44 1223 746 851 Fax +44 1223 268 305 ,
| | - Ashraf E. K. Ibrahim
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Juliusz Mieszczanek
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Mariann Bienz
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
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20
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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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21
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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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22
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Features of protein-protein interactions that translate into potent inhibitors: topology, surface area and affinity. Expert Rev Mol Med 2012; 14:e16. [PMID: 22831787 DOI: 10.1017/erm.2012.10] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-protein interactions (PPIs) control the assembly of multi-protein complexes and, thus, these contacts have enormous potential as drug targets. However, the field has produced a mix of both exciting success stories and frustrating challenges. Here, we review known examples and explore how the physical features of a PPI, such as its affinity, hotspots, off-rates, buried surface area and topology, might influence the chances of success in finding inhibitors. This analysis suggests that concise, tight binding PPIs are most amenable to inhibition. However, it is also clear that emerging technical methods are expanding the repertoire of 'druggable' protein contacts and increasing the odds against difficult targets. In particular, natural product-like compound libraries, high throughput screens specifically designed for PPIs and approaches that favour discovery of allosteric inhibitors appear to be attractive routes. The first group of PPI inhibitors has entered clinical trials, further motivating the need to understand the challenges and opportunities in pursuing these types of targets.
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23
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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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24
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Tian W, Han X, Yan M, Xu Y, Duggineni S, Lin N, Luo G, Li YM, Han X, Huang Z, An J. Structure-based discovery of a novel inhibitor targeting the β-catenin/Tcf4 interaction. Biochemistry 2012; 51:724-31. [PMID: 22224445 DOI: 10.1021/bi201428h] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Overactivation or overexpression of β-catenin in the Wnt (wingless) signaling pathway plays an important role in tumorigenesis. Interaction of β-catenin with T-cell factor (Tcf) DNA binding proteins is a key step in the activation of the proliferative genes in response to upstream signals of this Wnt/β-catenin pathway. Recently, we identified a new small molecule inhibitor, named BC21 (C(32)H(36)Cl(2)Cu(2)N(2)O(2)), which effectively inhibits the binding of β-catenin with Tcf4-derived peptide and suppresses β-catenin/Tcf4 driven reporter gene activity. This inhibitor decreases the viability of β-catenin overexpressing HCT116 colon cancer cells that harbor the β-catenin mutation, and more significantly, it inhibits the clonogenic activity of these cells. Down-regulation of c-Myc and cyclin D1 expression, the two important effectors of the Wnt/β-catenin signaling, is confirmed by treating HCT116 cells with BC21. This compound represents a new and modifiable potential anticancer candidate that targets β-catenin/Tcf-4 interaction.
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Affiliation(s)
- Wang Tian
- Department of Pharmacology, State University of New York, Upstate Medical University, Syracuse, New York 13210, United States
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25
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Sun J, Weis WI. Biochemical and structural characterization of β-catenin interactions with nonphosphorylated and CK2-phosphorylated Lef-1. J Mol Biol 2010; 405:519-30. [PMID: 21075118 DOI: 10.1016/j.jmb.2010.11.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 11/01/2010] [Accepted: 11/02/2010] [Indexed: 12/22/2022]
Abstract
In the Wnt/β-catenin signaling pathway, β-catenin activates target genes through its interactions with the T-cell factor/lymphoid enhancer-binding factor (TCF/Lef) family of transcription factors. The crystal structures of complexes between the β-catenin armadillo domain and the Lef-1 N-terminal domain show that the overall conformation and many of the interactions are similar to other published structures of TCFs bound to β-catenin. However, a second salt bridge in other TCF-β-catenin structures is absent in the structure of β-catenin-Lef-1 complex, indicating that this feature is not obligatory for β-catenin binding. Casein kinase II (CK2) has been shown to act as a positive regulator of Wnt signaling, and Lef-1 is a substrate of CK2. In vitro phosphorylation of purified Lef-1 was used to examine the effect of CK2 on the interaction of Lef-1 with β-catenin. Mass spectrometry data show that CK2 phosphorylation of Lef-1 N-terminal domain results in a single phosphorylation site at Ser40. Isothermal titration calorimetry revealed that β-catenin binds to nonphosphorylated or CK2-phosphorylated Lef-1 with the same affinity, which is consistent with the absence of phospho-Ser40 interactions in the crystal structure of phosphorylated Lef-1 N-terminal domain bound to β-catenin. These data indicate that the effect of CK2 on the Wnt/β-catenin pathway does not appear to be at the level of the Lef-1-β-catenin interaction.
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Affiliation(s)
- Jinglucy Sun
- Department of Structural Biology, Stanford University School of Medicine,Stanford, CA 94305-5126, USA
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26
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Kitazoe M, Futami J, Nishikawa M, Yamada H, Maeda Y. Polyethylenimine-cationized β-catenin protein transduction activates the Wnt canonical signaling pathway more effectively than cationic lipid-based transduction. Biotechnol J 2010; 5:385-92. [DOI: 10.1002/biot.200900132] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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27
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Choi YS, Hur J, Lee HK, Jeong S. The RNA aptamer disrupts protein-protein interaction between beta-catenin and nuclear factor-kappaB p50 and regulates the expression of C-reactive protein. FEBS Lett 2009; 583:1415-21. [PMID: 19358846 DOI: 10.1016/j.febslet.2009.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Revised: 03/30/2009] [Accepted: 04/01/2009] [Indexed: 10/20/2022]
Abstract
Transcription is activated by signal-induced protein-protein interaction between transcription factors on regulatory elements positioned near their target genes. Here, we tested the utility of the beta-catenin binding RNA aptamer as a tool for studying protein-protein interaction within transcription complex and for modulating expression of a target gene. The RNA aptamer bound Armadillo repeats of beta-catenin and was effective in disrupting protein-protein interaction between beta-catenin and nuclear factor-kappaB (NF-kappaB) p50. In addition, the RNA aptamer effectively reduced tumor necrosis factor-alpha induced transcription from the promoter of C-reactive protein regulated by beta-catenin and NF-kappaB p50. Taken together, beta-catenin binding RNA aptamer was an effective regulator of beta-catenin and NF-kappaB p50 mediated transcription.
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Affiliation(s)
- Yong Seok Choi
- National Research Laboratory for RNA Cell Biology, BK21 Graduate Program for RNA Biology and Department of Molecular Biology, Dankook University, 126, Yongin-si, Gyeonggi-do 448-701, Republic of Korea
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28
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Tompa P, Fuxreiter M, Oldfield CJ, Simon I, Dunker AK, Uversky VN. Close encounters of the third kind: disordered domains and the interactions of proteins. Bioessays 2009; 31:328-35. [DOI: 10.1002/bies.200800151] [Citation(s) in RCA: 200] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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29
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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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30
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Baminger B, Ludwiczek ML, Kontaxis G, Knapp S, Konrat R. Protein-protein interaction site mapping using NMR-detected mutational scanning. JOURNAL OF BIOMOLECULAR NMR 2007; 38:133-7. [PMID: 17447011 DOI: 10.1007/s10858-007-9154-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 03/12/2007] [Indexed: 05/15/2023]
Abstract
We demonstrate a novel NMR method for the mapping of protein-protein interaction sites. In our approach protein-protein binding sites are mapped by competition binding experiments using indirect NMR reporter technology and Ala positional scanning. The methodology provides high sensitivity, ease of implementation and high-throughput capabilities. The feasibility of the technique is demonstrated with an application to the beta-Catenin/Tcf4 complex.
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Affiliation(s)
- Bettina Baminger
- Department of Biomolecular Structural Chemistry, Max F. Perutz Laboratories, University of Vienna, Vienna, 1030, Austria
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31
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Abstract
Aberrant activation of the Wnt pathway is implicated in driving the formation of various human cancers, particularly those of the digestive tract. Inhibition of aberrant Wnt pathway activity in cancer cell lines efficiently blocks their growth, highlighting the great potential of therapeutics designed to achieve this in cancer patients. Here we provide an overview of the promise and pitfalls of current drug development strategies striving to inhibit the Wnt pathway and present new opportunities for therapeutic intervention.
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Affiliation(s)
- Nick Barker
- Hubrecht laboratory, Netherlands Institute for Developmental Biology, Uppsalalaan 8 3584CT, Utrecht, The Netherlands.
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32
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Theisen H, Syed A, Nguyen BT, Lukacsovich T, Purcell J, Srivastava GP, Iron D, Gaudenz K, Nie Q, Wan FY, Waterman ML, Marsh JL. Wingless directly represses DPP morphogen expression via an armadillo/TCF/Brinker complex. PLoS One 2007; 2:e142. [PMID: 17206277 PMCID: PMC1764032 DOI: 10.1371/journal.pone.0000142] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Accepted: 12/08/2006] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Spatially restricted morphogen expression drives many patterning and regeneration processes, but how is the pattern of morphogen expression established and maintained? Patterning of Drosophila leg imaginal discs requires expression of the DPP morphogen dorsally and the wingless (WG) morphogen ventrally. We have shown that these mutually exclusive patterns of expression are controlled by a self-organizing system of feedback loops that involve WG and DPP, but whether the feedback is direct or indirect is not known. METHODS/FINDINGS By analyzing expression patterns of regulatory DNA driving reporter genes in different genetic backgrounds, we identify a key component of this system by showing that WG directly represses transcription of the dpp gene in the ventral leg disc. Repression of dpp requires a tri-partite complex of the WG mediators armadillo (ARM) and dTCF, and the co-repressor Brinker, (BRK), wherein ARM.dTCF and BRK bind to independent sites within the dpp locus. CONCLUSIONS/SIGNIFICANCE Many examples of dTCF repression in the absence of WNT signaling have been described, but few examples of signal-driven repression requiring both ARM and dTCF binding have been reported. Thus, our findings represent a new mode of WG mediated repression and demonstrate that direct regulation between morphogen signaling pathways can contribute to a robust self-organizing system capable of dynamically maintaining territories of morphogen expression.
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Affiliation(s)
- Heidi Theisen
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Developmental Biology Center, University of California Irvine, Irvine, California, United States of America
| | - Adeela Syed
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Developmental Biology Center, University of California Irvine, Irvine, California, United States of America
| | - Baochi T. Nguyen
- Department of Mathematics, University of California Irvine, Irvine, California, United States of America
| | - Tamas Lukacsovich
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Developmental Biology Center, University of California Irvine, Irvine, California, United States of America
| | - Judith Purcell
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Developmental Biology Center, University of California Irvine, Irvine, California, United States of America
| | - Gyan Prakash Srivastava
- Developmental Biology Center, University of California Irvine, Irvine, California, United States of America
| | - David Iron
- Department of Mathematics, University of California Irvine, Irvine, California, United States of America
| | - Karin Gaudenz
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Developmental Biology Center, University of California Irvine, Irvine, California, United States of America
| | - Qing Nie
- Department of Mathematics, University of California Irvine, Irvine, California, United States of America
| | - Frederic Y.M. Wan
- Department of Mathematics, University of California Irvine, Irvine, California, United States of America
| | - Marian L. Waterman
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, United States of America
| | - J. Lawrence Marsh
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Developmental Biology Center, University of California Irvine, Irvine, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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33
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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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34
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Minezaki Y, Homma K, Kinjo AR, Nishikawa K. Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation. J Mol Biol 2006; 359:1137-49. [PMID: 16697407 DOI: 10.1016/j.jmb.2006.04.016] [Citation(s) in RCA: 193] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2006] [Revised: 04/04/2006] [Accepted: 04/05/2006] [Indexed: 12/11/2022]
Abstract
Human transcriptional regulation factors, such as activators, repressors, and enhancer-binding factors are quite different from their prokaryotic counterparts in two respects: the average sequence in human is more than twice as long as that in prokaryotes, while the fraction of sequence aligned to domains of known structure is 31% in human transcription factors (TFs), less than half of that in bacterial TFs (72%). Intrinsically disordered (ID) regions were identified by a disorder-prediction program, and were found to be in good agreement with available experimental data. Analysis of 401 human TFs with experimental evidence from the Swiss-Prot database showed that as high as 49% of the entire sequence of human TFs is occupied by ID regions. More than half of the human TFs consist of a small DNA binding domain (DBD) and long ID regions frequently sandwiching unassigned regions. The remaining TFs have structural domains in addition to DBDs and ID regions. Experimental studies, particularly those with NMR, revealed that the transactivation domains in unbound TFs are usually unstructured, but become structured upon binding to their partners. The sequences of human and mouse TF orthologues are 90.5% identical despite a high incidence of ID regions, probably reflecting important functional roles played by ID regions. In general ID regions occupy a high fraction in TFs of eukaryotes, but not in prokaryotes. Implications of this dichotomy are discussed in connection with their functional roles in transcriptional regulation and evolution.
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Affiliation(s)
- Yoshiaki Minezaki
- Laboratory of Gene-Product Informatics, Center For Information Biology & DNA Data Bank of Japan, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
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35
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Meher AK, Bal NC, Chary KVR, Arora A. Mycobacterium tuberculosis H37Rv ESAT-6-CFP-10 complex formation confers thermodynamic and biochemical stability. FEBS J 2006; 273:1445-62. [PMID: 16689931 DOI: 10.1111/j.1742-4658.2006.05166.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The 6-kDa early secretory antigenic target (ESAT-6) and culture filtrate protein-10 (CFP-10), expressed from the region of deletion-1 (RD1) of Mycobacterium tuberculosis H37Rv, are known to play a key role in virulence. In this study, we explored the thermodynamic and biochemical changes associated with the formation of the 1 : 1 heterodimeric complex between ESAT-6 and CFP-10. Using isothermal titration calorimetry (ITC), we precisely determined the association constant and free energy change for formation of the complex to be 2 x 10(7) M(-1) and -9.95 kcal.mol(-1), respectively. Strikingly, the thermal unfolding of the ESAT-6-CFP-10 heterodimeric complex was completely reversible, with a T(m) of 53.4 degrees C and DeltaH of 69 kcal.mol(-1). Mixing of ESAT-6 and CFP-10 at any temperature below the T(m) of the complex led to induction of helical conformation, suggesting molecular recognition between specific segments of unfolded ESAT-6 and CFP-10. Enhanced biochemical stability of the complex was indicated by protection of ESAT-6 and an N-terminal fragment of CFP-10 from proteolysis with trypsin. However, the flexible C-terminal of CFP-10 in the complex, which has been shown to be responsible for binding to macrophages and monocytes, was cleaved by trypsin. In the presence of phospholipid membranes, ESAT-6, but not CFP-10 and the complex, showed an increase in alpha-helical content and enhanced thermal stability. Overall, complex formation resulted in structural changes, enhanced thermodynamic and biochemical stability, and loss of binding to phospholipid membranes. These features of complex formation probably determine the physiological role of ESAT-6, CFP-10 and/or the complex in vivo. The ITC and thermal unfolding approach described in this study can readily be applied to characterization of the 11 other pairs of ESAT-6 family proteins and for screening ESAT-6 and CFP-10 mutants.
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Affiliation(s)
- Akshaya K Meher
- Molecular and Structural Biology, Central Drug Research Institute, Lucknow, India
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36
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Trosset JY, Dalvit C, Knapp S, Fasolini M, Veronesi M, Mantegani S, Gianellini LM, Catana C, Sundström M, Stouten PFW, Moll JK. Inhibition of protein–protein interactions: The discovery of druglike β‐catenin inhibitors by combining virtual and biophysical screening. Proteins 2006; 64:60-7. [PMID: 16568448 DOI: 10.1002/prot.20955] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The interaction between beta-catenin and Tcf family members is crucial for the Wnt signal transduction pathway, which is commonly mutated in cancer. This interaction extends over a very large surface area (4800 A(2)), and inhibiting such interactions using low molecular weight inhibitors is a challenge. However, protein surfaces frequently contain "hot spots," small patches that are the main mediators of binding affinity. By making tight interactions with a hot spot, a small molecule can compete with a protein. The Tcf3/Tcf4-binding surface on beta-catenin contains a well-defined hot spot around residues K435 and R469. A 17,700 compounds subset of the Pharmacia corporate collection was docked to this hot spot with the QXP program; 22 of the best scoring compounds were put into a biophysical (NMR and ITC) screening funnel, where specific binding to beta-catenin, competition with Tcf4 and finally binding constants were determined. This process led to the discovery of three druglike, low molecular weight Tcf4-competitive compounds with the tightest binder having a K(D) of 450 nM. Our approach can be used in several situations (e.g., when selecting compounds from external collections, when no biochemical functional assay is available, or when no HTS is envisioned), and it may be generally applicable to the identification of inhibitors of protein-protein interactions.
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Affiliation(s)
- Jean-Yves Trosset
- Department of Chemistry, Nerviano Medical Sciences, Nerviano, MI, Italy.
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37
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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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38
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Lee SK, Park MW, Yang EG, Yu J, Jeong S. An RNA aptamer that binds to the beta-catenin interaction domain of TCF-1 protein. Biochem Biophys Res Commun 2005; 327:294-9. [PMID: 15629461 DOI: 10.1016/j.bbrc.2004.12.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2004] [Indexed: 11/25/2022]
Abstract
The architectural transcription factor TCF-1 interacts directly with beta-catenin and activates transcription of various target genes that are important for early development and carcinogenesis. We selected an RNA aptamer that specifically bound to the beta-catenin-interacting N-terminal motif of TCF-1. Structural analysis revealed that it formed a stem-loop structure that was responsible for binding TCF-1 and contained a pair of internal loops. The RNA aptamer interfered with the binding of TCF-1 to beta-catenin and also inhibited the formation of TCF-1/beta-catenin complexes. Disruption of TCF-1/beta-catenin complexes could alter the transcriptional activity of TCF-1. Taken together our observations show that a rationally designed RNA aptamer can disrupt protein-protein interactions required for the formation of an active transcription complex.
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Affiliation(s)
- Su Kyung Lee
- Department of Molecular Biology, Institute of Nanosensor and Biotechnology, Dankook University, Seoul 140-714, Republic of Korea
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39
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Gail R, Frank R, Wittinghofer A. Systematic Peptide Array-based Delineation of the Differential β-Catenin Interaction with Tcf4, E-Cadherin, and Adenomatous Polyposis Coli. J Biol Chem 2005; 280:7107-17. [PMID: 15591320 DOI: 10.1074/jbc.m410215200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Nuclear accumulation of the complex between beta-catenin and proteins of the T-cell factor (Tcf) family is a hallmark of many cancers. Targeting this interaction for drug development is complicated by the fact that E-cadherin and adenomatous polyposis coli (APC) bind to overlapping sites on beta-catenin. Inhibiting their interactions might actually promote tumor growth. To identify selective beta-catenin binding hot spots of Tcf4, E-cadherin, and APC, array technology with peptides of up to 53 amino acids length was used. Interactions were monitored by a quantitative fluorescent readout, which was shown to represent a monitor of true equilibrium binding constants. We identified minimal binding motifs in the beta-catenin ligands and showed that most of the 15-mer and 20-mer repeats of APC did not interact, at least when non-phosphorylated, and defined a consensus binding motif also present in APC. We confirmed previously found hot spots and identified new ones. The method allowed us to locate a hydrophobic pocket that was relevant for the Tcf, but not the E-cadherin interaction, and would thus constitute an ideal drug target site.
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Affiliation(s)
- Robert Gail
- Abteilung strukturelle Biologie, Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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40
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Fuxreiter M, Simon I, Friedrich P, Tompa P. Preformed structural elements feature in partner recognition by intrinsically unstructured proteins. J Mol Biol 2004; 338:1015-26. [PMID: 15111064 DOI: 10.1016/j.jmb.2004.03.017] [Citation(s) in RCA: 422] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Revised: 03/02/2004] [Accepted: 03/02/2004] [Indexed: 12/25/2022]
Abstract
Intrinsically unstructured proteins (IUPs) are devoid of extensive structural order but often display signs of local and limited residual structure. To explain their effective functioning, we reasoned that such residual structure can be crucial in their interactions with their structured partner(s) in a way that preformed structural elements presage their final conformational state. To check this assumption, a database of 24 IUPs with known 3D structures in the bound state has been assembled and the distribution of secondary structure elements and backbone torsion angles have been analysed. The high proportion of residues in coil conformation and with phi, psi angles in the disallowed regions of the Ramachandran map compared to the reference set of globular proteins shows that IUPs are not fully ordered even in their bound form. To probe the effect of partner proteins on IUP folding, inherent conformational preferences of IUP sequences have been assessed by secondary structure predictions using the GOR, ALB and PROF algorithms. The accuracy of predicting secondary structure elements of IUPs is similar to that of their partner proteins and is significantly higher than the corresponding values for random sequences. We propose that strong conformational preferences mark regions in IUPs (mostly helices), which correspond to their final structural state, while regions with weak conformational preferences represent flexible linkers between them. In our interpretation, preformed elements could serve as initial contact points, the binding of which facilitates the reeling of the flexible regions onto the template. This finding implies that IUPs draw a functional advantage from preformed structural elements, as they enable their facile, kinetically and energetically less demanding, interaction with their physiological partner.
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Affiliation(s)
- Monika Fuxreiter
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
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41
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Junutula JR, Schonteich E, Wilson GM, Peden AA, Scheller RH, Prekeris R. Molecular characterization of Rab11 interactions with members of the family of Rab11-interacting proteins. J Biol Chem 2004; 279:33430-7. [PMID: 15173169 DOI: 10.1074/jbc.m404633200] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The Rab11 subfamily of GTPases plays an important role in vesicle trafficking from endosomes to the plasma membrane. At least six Rab11 effectors (family of Rab11-interacting proteins (FIPs)) have been shown to interact with Rab11 and are hypothesized to regulate various membrane trafficking pathways such as transferrin recycling, cytokinesis, and epidermal growth factor trafficking. In this study, we characterized interactions of FIPs with the Rab11 GTPase using isothermal titration calorimetric studies and mutational analysis. Our data suggest that FIPs cannot differentiate between GTP-bound Rab11a and Rab11b in vitro (50-100 nm affinity) and in vivo. We also show that, although FIPs interact with the GDP-bound form of Rab11 in vitro, the binding affinity (>1000 nm) is not sufficient for FIP and GDP-bound Rab11 interactions to occur in vivo. Mutational analysis revealed that both the conserved hydrophobic patch and Tyr628 are important for the GTP-dependent binding of Rab11 to FIPs. The entropy and enthalpy analyses suggest that binding to Rab11a/b may induce conformational changes in FIPs.
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42
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Beckett D. Functional Switches in Transcription Regulation; Molecular Mimicry and Plasticity in Protein−Protein Interactions. Biochemistry 2004; 43:7983-91. [PMID: 15209493 DOI: 10.1021/bi049890b] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The pairwise interactions in which a protein participates can dictate the functional properties of the protein. Indeed, there are many biological regulatory processes in which protein function is orchestrated via exchange of one protein partner for another. Several transcription regulatory proteins that participate in functional switching have been identified and extensively studied. In the examination of the structural basis of the switch for four of these proteins, a common theme of mutually exclusive protein-protein interactions emerges. The ability of these proteins to utilize the same surface to form alternative interactions reflects a second characteristic of these systems of molecular mimicry. Finally, in two of the systems, plasticity in adoption of secondary structure is integral to the formation of alternative protein-protein interactions. Regulation of formation of the alternative parings occurs by a range of mechanisms. In the simplest systems, the outcome of the switch reflects the relative probability of encounter of one partner versus another. Alternatively, more complex mechanisms include regulation of protein availability and compartmentalization of protein partners.
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Affiliation(s)
- Dorothy Beckett
- Department of Chemistry and Biochemistry, College of Life Sciences, University of Maryland, College Park, Maryland 20742, USA.
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43
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Lepourcelet M, Chen YNP, France DS, Wang H, Crews P, Petersen F, Bruseo C, Wood AW, Shivdasani RA. Small-molecule antagonists of the oncogenic Tcf/beta-catenin protein complex. Cancer Cell 2004; 5:91-102. [PMID: 14749129 DOI: 10.1016/s1535-6108(03)00334-9] [Citation(s) in RCA: 505] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Key molecular lesions in colorectal and other cancers cause beta-catenin-dependent transactivation of T cell factor (Tcf)-dependent genes. Disruption of this signal represents an opportunity for rational cancer therapy. To identify compounds that inhibit association between Tcf4 and beta-catenin, we screened libraries of natural compounds in a high-throughput assay for immunoenzymatic detection of the protein-protein interaction. Selected compounds disrupt Tcf/beta-catenin complexes in several independent in vitro assays and potently antagonize cellular effects of beta-catenin-dependent activities, including reporter gene activation, c-myc or cyclin D1 expression, cell proliferation, and duplication of the Xenopus embryonic dorsal axis. These compounds thus meet predicted criteria for disrupting Tcf/beta-catenin complexes and define a general standard to establish mechanism-based activity of small molecule inhibitors of this pathogenic protein-protein interaction.
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Affiliation(s)
- Maina Lepourcelet
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
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44
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Fasolini M, Wu X, Flocco M, Trosset JY, Oppermann U, Knapp S. Hot spots in Tcf4 for the interaction with beta-catenin. J Biol Chem 2003; 278:21092-8. [PMID: 12657632 DOI: 10.1074/jbc.m301781200] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The interaction of beta-catenin with T-cell factor (Tcf) 4 plays a central role in the Wnt signaling pathway and has been discussed as a possible site of intervention for the development of anti-cancer drugs. In this study, we performed Ala-scanning mutagenesis of all Tcf4 residues in the Tcf-beta-catenin interface and studied the binding energetics of these mutants using isothermal titration calorimetry. Binding of Tcf4 was found to be highly cooperative. Single site mutations of most Tcf4 residues resulted in a significant reduction in binding enthalpies but in similar binding constants as compared with wild type Tcf4. Interestingly, this was also true for residues that are disordered in the reported crystal structures. The mutation D16A caused the largest reduction in binding constant (50-fold) accompanied by a large unfavorable enthalpy change (DeltaDeltaHobs) of +8 kcal/mol at 25 degrees C. In contrast, the mutation of the Tcf residues Glu24 and Glu28, which have been proposed as an interaction hot spot due to their location in a field of strong positive electrostatic potential on the beta-catenin surface (charge button), resulted only in a significant reduction of binding enthalpies, which were largely compensated for by unfavorable entropic contributions to the binding. Other mutations that significantly reduced Tcf binding constants were D11A and alanine mutations of the hydrophobic residues Leu41, Val44, and Leu48. The measured thermodynamic data are discussed with the available structural information of Tcf-beta-catenin crystal structures and allow us to propose possible sites for development of Tcf antagonists.
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Affiliation(s)
- Marina Fasolini
- Pharmacia Corporation Discovery Research Oncology, Department of Chemistry, Viale Pasteur 10, 20014 Nerviano, Italy
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45
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Abstract
We have assembled references of 700 articles published in 2001 that describe work performed using commercially available optical biosensors. To illustrate the technology's diversity, the citation list is divided into reviews, methods and specific applications, as well as instrument type. We noted marked improvements in the utilization of biosensors and the presentation of kinetic data over previous years. These advances reflect a maturing of the technology, which has become a standard method for characterizing biomolecular interactions.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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46
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Daniels DL, Weis WI. ICAT inhibits beta-catenin binding to Tcf/Lef-family transcription factors and the general coactivator p300 using independent structural modules. Mol Cell 2002; 10:573-84. [PMID: 12408825 DOI: 10.1016/s1097-2765(02)00631-7] [Citation(s) in RCA: 147] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the canonical Wnt signaling pathway, beta-catenin activates target genes through its interactions with Tcf/Lef-family transcription factors and additional transcriptional coactivators. The crystal structure of ICAT, an inhibitor of beta-catenin-mediated transcription, bound to the armadillo repeat domain of beta-catenin, has been determined. ICAT contains an N-terminal helilical domain that binds to repeats 11 and 12 of beta-catenin, and an extended C-terminal region that binds to repeats 5-10 in a manner similar to that of Tcfs and other beta-catenin ligands. Full-length ICAT dissociates complexes of beta-catenin, Lef-1, and the transcriptional coactivator p300, whereas the helical domain alone selectively blocks binding to p300. The C-terminal armadillo repeats of beta-catenin may be an attractive target for compounds designed to disrupt aberrant beta-catenin-mediated transcription associated with various cancers.
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Affiliation(s)
- Danette L Daniels
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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47
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Hegde SS, Dam TK, Brewer CF, Blanchard JS. Thermodynamics of aminoglycoside and acyl-coenzyme A binding to the Salmonella enterica AAC(6')-Iy aminoglycoside N-acetyltransferase. Biochemistry 2002; 41:7519-27. [PMID: 12044186 DOI: 10.1021/bi020190l] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Kinetic and mechanistic studies on the chromosomally encoded aminoglycoside 6'-N-acetyltransferase, AAC(6')-Iy, of Salmonella enterica that confers resistance toward aminoglycosides have been previously reported [Magnet et al. (2001) Biochemistry 40, 3700-3709]. In the present study, equilibrium binding and the thermodynamic parameters of binding of aminoglycosides and acyl-coenzyme A derivatives to AAC(6')-Iy and of two mutants, C109A and the C109A/C70A double mutant, have been studied using fluorescence spectroscopy and isothermal titration calorimetry (ITC). Association constants for different aminoglycosides varied greatly (4 x 10(4)-150 x 10(4)) while the association constants of several acyl-coenzyme A derivatives were similar (3.2 x 10(4)-4.5 x 10(4)). The association constants and van't Hoff enthalpy changes derived from intrinsic protein fluorescence changes were in agreement with independently measured values from isothermal titration calorimetry studies. Binding of both aminoglycosides and acyl-coenzyme A derivatives is strongly enthalpically driven and revealed opposing negative entropy changes, resulting in enthalpy-entropy compensation. The acetyltransferase exhibited a temperature-dependent binding of tobramycin with a negative heat capacity value of 410 cal mol(-1) K(-1). Isothermal titration studies of acetyl-coenzyme A and tobramycin binding to mutant forms of the enzyme indicated that completely conserved C109 does not play any direct role in the binding of either of the substrates, while C70 is directly involved in aminoglycoside binding. These results are discussed and compared with previous steady-state kinetic studies of the enzyme.
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Affiliation(s)
- Subray S Hegde
- Departments of Biochemistry and Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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48
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Cooper A, Johnson CM, Lakey JH, Nöllmann M. Heat does not come in different colours: entropy-enthalpy compensation, free energy windows, quantum confinement, pressure perturbation calorimetry, solvation and the multiple causes of heat capacity effects in biomolecular interactions. Biophys Chem 2001; 93:215-30. [PMID: 11804727 DOI: 10.1016/s0301-4622(01)00222-8] [Citation(s) in RCA: 262] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Modern techniques in microcalorimetry allow us to measure directly the heat changes and associated thermodynamics for biomolecular processes in aqueous solution at reasonable concentrations. All these processes involve changes in solvation/hydration, and it is natural to assume that the heats for these processes should reflect, in some way, such changes in solvation. However, the interpretation of data is still somewhat ambiguous, since different non-covalent interactions may have similar thermodynamic signatures, and analysis is frustrated by large entropy-enthalpy compensation effects. Changes in heat capacity (Delta C(p)) have been related to changes in hydrophobic hydration and non-polar accessible surface areas, but more recent empirical and theoretical work has shown how this need not always be the case. Entropy-enthalpy compensation is a natural consequence of finite Delta C(p) values and, more generally, can arise as a result of quantum confinement effects, multiple weak interactions, and limited free energy windows, giving rise to thermodynamic homeostasis that may be of evolutionary and functional advantage. The new technique of pressure perturbation calorimetry (PPC) has enormous potential here as a means of probing solvation-related volumetric changes in biomolecules at modest pressures, as illustrated with preliminary data for a simple protein-inhibitor complex.
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Affiliation(s)
- A Cooper
- Department of Chemistry, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, Scotland, UK.
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49
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Spink KE, Fridman SG, Weis WI. Molecular mechanisms of beta-catenin recognition by adenomatous polyposis coli revealed by the structure of an APC-beta-catenin complex. EMBO J 2001; 20:6203-12. [PMID: 11707392 PMCID: PMC125720 DOI: 10.1093/emboj/20.22.6203] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The adenomatous polyposis coli (APC) tumor suppressor protein plays a critical role in regulating cellular levels of the oncogene product beta-catenin. APC binds to beta-catenin through a series of homologous 15 and 20 amino acid repeats. We have determined the crystal structure of a 15 amino acid beta-catenin binding repeat from APC bound to the armadillo repeat region of beta-catenin. Although it lacks significant sequence homology, the N-terminal half of the repeat binds in a manner similar to portions of E-cadherin and XTcf3, but the remaining interactions are unique to APC. We discuss the implications of this new structure for the design of therapeutics, and present evidence from structural, biochemical and sequence data, which suggest that the 20 amino acid repeats can adopt two modes of binding to beta-catenin.
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Affiliation(s)
- Katharine Eklof Spink
- Departments of Structural Biology and of Molecular and Cellular Physiology and Program in Cancer Biology, Stanford University School of Medicine, 299 Campus Dr. West Stanford, CA 94305, USA Corresponding author e-mail:
| | - Sofiya G. Fridman
- Departments of Structural Biology and of Molecular and Cellular Physiology and Program in Cancer Biology, Stanford University School of Medicine, 299 Campus Dr. West Stanford, CA 94305, USA Corresponding author e-mail:
| | - William I. Weis
- Departments of Structural Biology and of Molecular and Cellular Physiology and Program in Cancer Biology, Stanford University School of Medicine, 299 Campus Dr. West Stanford, CA 94305, USA Corresponding author e-mail:
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50
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Leavitt S, Freire E. Direct measurement of protein binding energetics by isothermal titration calorimetry. Curr Opin Struct Biol 2001; 11:560-6. [PMID: 11785756 DOI: 10.1016/s0959-440x(00)00248-7] [Citation(s) in RCA: 471] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Of all the techniques that are currently available to measure binding, isothermal titration calorimetry is the only one capable of measuring not only the magnitude of the binding affinity but also the magnitude of the two thermodynamic terms that define the binding affinity: the enthalpy (AH) and entropy (AS) changes. Recent advances in instrumentation have facilitated the development of experimental designs that permit the direct measurement of arbitrarily high binding affinities, the coupling of binding to protonation/deprotonation processes and the analysis of binding thermodynamics in terms of structural parameters. Because isothermal titration calorimetry has the capability to measure different energetic contributions to the binding affinity, it provides a unique bridge between computational and experimental analysis. As such, it is increasingly becoming an essential tool in molecular design.
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Affiliation(s)
- S Leavitt
- Department of Biology and Biocalorimetry Center, The Johns Hopkins University, Baltimore, MD 21218, USA
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