Articles | Volume 2, issue 1
https://doi.org/10.5194/mr-2-355-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Special issue:
https://doi.org/10.5194/mr-2-355-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
02 Jun 2021
Research article |
| 02 Jun 2021
| 02 Jun 2021
Small-molecule inhibitors of the PDZ domain of Dishevelled proteins interrupt Wnt signalling
Nestor Kamdem
Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
Yvette Roske
Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
Dmytro Kovalskyy
Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
ChemBio Ctr, Taras Shevchenko National University of Kyiv, 62 Volodymyrska, Kyiv 01033, Ukraine
Maxim O. Platonov
Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
ChemBio Ctr, Taras Shevchenko National University of Kyiv, 62 Volodymyrska, Kyiv 01033, Ukraine
Oleksii Balinskyi
Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
ChemBio Ctr, Taras Shevchenko National University of Kyiv, 62 Volodymyrska, Kyiv 01033, Ukraine
Annika Kreuchwig
Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
Jörn Saupe
Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
Liang Fang
Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
Anne Diehl
Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
Peter Schmieder
Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
Gerd Krause
Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
Jörg Rademann
Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
Institut für Pharmazie, Freie Universität Berlin, Königin-Luise-Straße 2 + 4, 14195 Berlin, Germany
Udo Heinemann
Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
Walter Birchmeier
Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
Hartmut Oschkinat
CORRESPONDING AUTHOR
Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
Related subject area
Field: Liquid-state NMR | Topic: Applications – biological macromolecules
NMR side-chain assignments of the Crimean–Congo hemorrhagic fever virus glycoprotein n cytosolic domain
Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR
Site-selective generation of lanthanoid binding sites on proteins using 4-fluoro-2,6-dicyanopyridine
Imatinib disassembles the regulatory core of Abelson kinase by binding to its ATP site and not by binding to its myristoyl pocket
Localising nuclear spins by pseudocontact shifts from a single tagging site
Localising individual atoms of tryptophan side chains in the metallo-β-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites
Fluorine NMR study of proline-rich sequences using fluoroprolines
Analysis of conformational exchange processes using methyl-TROSY-based Hahn echo measurements of quadruple-quantum relaxation
Anomalous amide proton chemical shifts as signatures of hydrogen bonding to aromatic sidechains
Rapid assessment of Watson–Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE imino 1H CEST
High-affinity tamoxifen analogues retain extensive positional disorder when bound to calmodulin
Structural polymorphism and substrate promiscuity of a ribosome-associated molecular chaperone
Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics
The long-standing relationship between paramagnetic NMR and iron–sulfur proteins: the mitoNEET example. An old method for new stories or the other way around?
Conformational features and ionization states of Lys side chains in a protein studied using the stereo-array isotope labeling (SAIL) method
Fragile protein folds: sequence and environmental factors affecting the equilibrium of two interconverting, stably folded protein conformations
Towards resolving the complex paramagnetic nuclear magnetic resonance (NMR) spectrum of small laccase: assignments of resonances to residue-specific nuclei
Phosphoserine for the generation of lanthanide-binding sites on proteins for paramagnetic nuclear magnetic resonance spectroscopy
Louis Brigandat, Maëlys Laux, Caroline Marteau, Laura Cole, Anja Böckmann, Lauriane Lecoq, Marie-Laure Fogeron, and Morgane Callon
Magn. Reson., 5, 95–101, https://doi.org/10.5194/mr-5-95-2024, https://doi.org/10.5194/mr-5-95-2024, 2024
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We used NMR to sequentially assign the side-chain resonances of the cytosolic domain of glycoprotein n of the Crimean–Congo hemorrhagic fever virus. The combination of cell-free protein synthesis with high-field NMR and artificial intelligence approaches facilitated a time- and effort-efficient approach. Our results will be harnessed to study the membrane-bound form of the domain and its interactions with virulence factors, which will ultimately help to understand their role in disease.
Sarah Kuschert, Martin Stroet, Yanni Ka-Yan Chin, Anne Claire Conibear, Xinying Jia, Thomas Lee, Christian Reinhard Otto Bartling, Kristian Strømgaard, Peter Güntert, Karl Johan Rosengren, Alan Edward Mark, and Mehdi Mobli
Magn. Reson., 4, 57–72, https://doi.org/10.5194/mr-4-57-2023, https://doi.org/10.5194/mr-4-57-2023, 2023
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The 20 genetically encoded amino acids provide the basis for most proteins and peptides that make up the machinery of life. This limited repertoire is vastly expanded by the introduction of non-canonical amino acids (ncAAs). Studying the structure of protein-containing ncAAs requires new computational representations that are compatible with existing modelling software. We have developed an online tool for this to aid future structural studies of this class of complex biopolymer.
Sreelakshmi Mekkattu Tharayil, Mithun C. Mahawaththa, Akiva Feintuch, Ansis Maleckis, Sven Ullrich, Richard Morewood, Michael J. Maxwell, Thomas Huber, Christoph Nitsche, Daniella Goldfarb, and Gottfried Otting
Magn. Reson., 3, 169–182, https://doi.org/10.5194/mr-3-169-2022, https://doi.org/10.5194/mr-3-169-2022, 2022
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Having shown that tagging a protein at a single site with different lanthanoid complexes delivers outstanding structural information at a selected site of a protein (such as active sites and ligand binding sites), we now present a simple way by which different lanthanoid complexes can be assembled on a highly solvent-exposed cysteine residue. Furthermore, the chemical assembly is selective for selenocysteine, if a selenocysteine residue can be introduced into the protein of interest.
Stephan Grzesiek, Johannes Paladini, Judith Habazettl, and Rajesh Sonti
Magn. Reson., 3, 91–99, https://doi.org/10.5194/mr-3-91-2022, https://doi.org/10.5194/mr-3-91-2022, 2022
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We show here that binding of the anticancer drug imatinib to the ATP site of Abelson kinase and not binding to its allosteric site coincides with the opening of the kinase regulatory core at nanomolar concentrations. This has implications for the understanding of Abelson’s kinase regulation and activity during medication as well as for the design of new Abelson kinase inhibitors.
Henry W. Orton, Elwy H. Abdelkader, Lydia Topping, Stephen J. Butler, and Gottfried Otting
Magn. Reson., 3, 65–76, https://doi.org/10.5194/mr-3-65-2022, https://doi.org/10.5194/mr-3-65-2022, 2022
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Installing a tag containing a paramagnetic metal ion on a protein can lead to large changes (pseudocontact shifts) in the resonances observed in NMR spectra. These are easily measured and contain valuable long-range structural information. The present work shows that a single tagging site furnished with different tags can be sufficient to localise atoms in proteins with high accuracy. In fact, this strategy works almost as well as the same number of tags distributed over multiple tagging sites.
Henry W. Orton, Iresha D. Herath, Ansis Maleckis, Shereen Jabar, Monika Szabo, Bim Graham, Colum Breen, Lydia Topping, Stephen J. Butler, and Gottfried Otting
Magn. Reson., 3, 1–13, https://doi.org/10.5194/mr-3-1-2022, https://doi.org/10.5194/mr-3-1-2022, 2022
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This paper explores a method for determining the solution structure of a solvent-exposed polypeptide segment (the L3 loop), which is next to the active site of the penicillin-degrading enzyme IMP-1. Tagging three different sites on the protein with paramagnetic metal ions allowed positioning of the L3 loop with atomic resolution. It was found that the method was more robust when omitting data obtained with different metal ions if obtained with the same tag at the same tagging site.
Davy Sinnaeve, Abir Ben Bouzayene, Emile Ottoy, Gert-Jan Hofman, Eva Erdmann, Bruno Linclau, Ilya Kuprov, José C. Martins, Vladimir Torbeev, and Bruno Kieffer
Magn. Reson., 2, 795–813, https://doi.org/10.5194/mr-2-795-2021, https://doi.org/10.5194/mr-2-795-2021, 2021
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Fluorine NMR was used to study the interaction between a proline-rich peptide and a SH3 domain using 4S- and 4R-fluorinated prolines whose potential as NMR probes has not been exploited yet. We present a comprehensive study addressing several aspects to be considered when using these residues as NMR probes, including relaxation and dynamics. We show that their conformational bias may be used to modulate the kinetics of protein binding to proline-rich motifs.
Christopher A. Waudby and John Christodoulou
Magn. Reson., 2, 777–793, https://doi.org/10.5194/mr-2-777-2021, https://doi.org/10.5194/mr-2-777-2021, 2021
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We describe a suite of experiments that exploit field-dependent relaxation measurements of four-spin transitions in methyl groups to characterise chemical exchange processes and which can be used as an alternative or complement to CPMG relaxation dispersion measurements. We show that these four-spin transitions benefit from the methyl TROSY effect and so provide a unique combination of slow intrinsic relaxation and high sensitivity to chemical exchange.
Kumaran Baskaran, Colin W. Wilburn, Jonathan R. Wedell, Leonardus M. I. Koharudin, Eldon L. Ulrich, Adam D. Schuyler, Hamid R. Eghbalnia, Angela M. Gronenborn, and Jeffrey C. Hoch
Magn. Reson., 2, 765–775, https://doi.org/10.5194/mr-2-765-2021, https://doi.org/10.5194/mr-2-765-2021, 2021
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The Biological Magnetic Resonance Data Bank (BMRB) has been used to identify overall trends, for example, the relationship between chemical shift and backbone conformation. The BMRB archive has grown so that statistical outliers are sufficiently numerous to afford insights into unusual or unique structural features in proteins. We analyze amide proton chemical shift outliers to gain insights into the occurrence of hydrogen bonds between an amide NH and the p-pi cloud of aromatic sidechains.
Bei Liu, Atul Rangadurai, Honglue Shi, and Hashim M. Al-Hashimi
Magn. Reson., 2, 715–731, https://doi.org/10.5194/mr-2-715-2021, https://doi.org/10.5194/mr-2-715-2021, 2021
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There is growing interest in mapping exchange dynamics between Watson–Crick and Hoogsteen conformations across different DNA contexts. However, current methods are ill-suited for measurements at a large scale because they require isotopically enriched samples. We report that Hoogsteen dynamics can be measured on unlabeled samples using 1H CEST experiments, which have higher throughput and lower cost relative to conventional methods and also provide new insights into Hoogsteen dynamics.
Lilia Milanesi, Clare R. Trevitt, Brian Whitehead, Andrea M. Hounslow, Salvador Tomas, Laszlo L. P. Hosszu, Christopher A. Hunter, and Jonathan P. Waltho
Magn. Reson., 2, 629–642, https://doi.org/10.5194/mr-2-629-2021, https://doi.org/10.5194/mr-2-629-2021, 2021
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The overall aim of the study is to provide a basis from which to improve the ability of tamoxifen family drugs to reduce the activity of a secondary target protein, calmodulin, during tumour development. The main conclusion is that the binding of a tamoxifen analogue is quite unlike that of other anti-calmodulin compounds in that two drug molecules bring the two domains of calmodulin into close proximity, but they are not fixed in orientation relative to the protein.
Chih-Ting Huang, Yei-Chen Lai, Szu-Yun Chen, Meng-Ru Ho, Yun-Wei Chiang, and Shang-Te Danny Hsu
Magn. Reson., 2, 375–386, https://doi.org/10.5194/mr-2-375-2021, https://doi.org/10.5194/mr-2-375-2021, 2021
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Trigger factor (TF) is a conserved bacterial molecular chaperone that exists in a monomer–dimer equilibrium in solution. It binds to the ribosome as a monomer to facilitate folding of nascent polypeptide chains. We showed that dimeric TF exhibits distinct domain dynamics and conformational polymorphism and that TF contains multiple substrate binding sites that are only accessible in its monomeric form. The equilibrium of TF in different oligomeric states may serve as a regulatory mechanism.
György Pintér, Katharina F. Hohmann, J. Tassilo Grün, Julia Wirmer-Bartoschek, Clemens Glaubitz, Boris Fürtig, and Harald Schwalbe
Magn. Reson., 2, 291–320, https://doi.org/10.5194/mr-2-291-2021, https://doi.org/10.5194/mr-2-291-2021, 2021
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The folding, refolding and misfolding of biomacromolecules including proteins, DNA and RNA is an important area of biophysical research to understand functional and disease states of a cell. NMR spectroscopy provides detailed insight, with both high time and atomic resolution. These experiments put stringent requirements on signal-to-noise for often irreversible folding reactions. The review describes methodological approaches and highlights key applications.
Francesca Camponeschi, Angelo Gallo, Mario Piccioli, and Lucia Banci
Magn. Reson., 2, 203–221, https://doi.org/10.5194/mr-2-203-2021, https://doi.org/10.5194/mr-2-203-2021, 2021
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The iron–sulfur cluster binding properties of human mitoNEET have been investigated by 1D and 2D 1H paramagnetic NMR spectroscopy. The NMR spectra of both oxidized and reduced mitoNEET are significantly different from those reported previously for other [Fe2S2] proteins. Our findings revealed the unique electronic properties of mitoNEET and suggests that the specific electronic structure of the cluster possibly drives the functional properties of different [Fe2S2] proteins.
Mitsuhiro Takeda, Yohei Miyanoiri, Tsutomu Terauchi, and Masatsune Kainosho
Magn. Reson., 2, 223–237, https://doi.org/10.5194/mr-2-223-2021, https://doi.org/10.5194/mr-2-223-2021, 2021
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Although both the hydrophobic aliphatic chain and hydrophilic ζ-amino group of the lysine side chain presumably contribute to the structures and functions of proteins, the dual nature of the lysine residue has not been fully understood yet, due to the lack of appropriate methods to acquire comprehensive information on its long consecutive methylene chain at the atomic scale. We describe herein a novel strategy to address the current situation using nuclear magnetic resonance spectroscopy.
Xingjian Xu, Igor Dikiy, Matthew R. Evans, Leandro P. Marcelino, and Kevin H. Gardner
Magn. Reson., 2, 63–76, https://doi.org/10.5194/mr-2-63-2021, https://doi.org/10.5194/mr-2-63-2021, 2021
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While most proteins adopt one conformation, several interconvert between two or more very different structures. Knowing how sequence changes and small-molecule binding can control this behavior is essential for both understanding biology and inspiring new “molecular switches” which can control cellular pathways. This work contributes by examining these topics in the ARNT protein, showing that features of both the folded and unfolded states contribute to the interconversion process.
Rubin Dasgupta, Karthick B. S. S. Gupta, Huub J. M. de Groot, and Marcellus Ubbink
Magn. Reson., 2, 15–23, https://doi.org/10.5194/mr-2-15-2021, https://doi.org/10.5194/mr-2-15-2021, 2021
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A method is demonstrated that can help in sequence-specific NMR signal assignment to nuclear spins near a strongly paramagnetic metal in an enzyme. A combination of paramagnetically tailored NMR experiments and second-shell mutagenesis was used to attribute previously observed chemical exchange processes in the active site of laccase to specific histidine ligands. The signals of nuclei close to the metal can be used as spies to unravel the role of motions in the catalytic process.
Sreelakshmi Mekkattu Tharayil, Mithun Chamikara Mahawaththa, Choy-Theng Loh, Ibidolapo Adekoya, and Gottfried Otting
Magn. Reson., 2, 1–13, https://doi.org/10.5194/mr-2-1-2021, https://doi.org/10.5194/mr-2-1-2021, 2021
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A new way is presented for creating lanthanide binding sites on proteins using site-specifically introduced phosphoserine residues. The paramagnetic effects of lanthanides generate long-range effects, which contain structural information and are readily measured by NMR spectroscopy. Excellent correlations between experimentally observed and back-calculated pseudocontact shifts attest to very good immobilization of the lanthanide ions relative to the proteins.
Cited articles
Behrens, J., von Kries, J. P., Kühl, M., Bruhn, L., Wedlich, D.,
Grosschedl, R., and Birchmeier, W.: Functional interaction of beta-catenin
with the transcription factor LEF-1, Nature, 382, 638–642, https://doi.org/10.1038/382638a0, 1996.
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig,
H., Shindyalov, I. N., and Bourne, P. E.: The protein data bank, Nucleic.
Acids Res., 28, 235–242, https://doi.org/10.1093/nar/28.1.235, 2000.
Bertini, I., Chevanace, S., Del Conte, R., Lalli, D., and Turano, P.: The
anti-apoptotic Bcl-x(L) protein, a new piece in the puzzle of cytochrome c
interactome, PLOS ONE, 6, e18329, https://doi.org/10.1371/journal.pone.0018329, 2001.
Boisguerin, P., Leben, R., Ay, B., Radziwill, G., Moelling, K., Dong, L., and
Volkmer-Engert, R.: An improved method for the synthesis of cellulose
membrane-bound peptides with free C termini is useful for PDZ domain binding
studies, Chem. Biol., 11, 449–459, https://doi.org/10.1016/j.chembiol.2004.03.010,
2004.
Bui, T. D., Beier, D. R., Jonssen, M., Smith, K., Dorrington, S. M.,
Kaklamanis, L., Kearney, L., Regan, R., Sussman, D. J., and Harris, A. L.:
cDNA cloning of a human dishevelled DVL-3 gene, mapping to 3q27, and
expression in humanbreast and colon carcinomas. Biochem. Biophys. Res.
Commun., 239, 510–516, https://doi.org/10.1006/bbrc.1997.7500, 1997.
Chandanamali, P., Antonio, M. F., Robert, C., Patrick, R., and Naoaki, F.:
Sequence and subtype specificity in the high-affinity interaction between
human frizzled and dishevelled proteins, Protein Sci., 18, 994–1002, https://doi.org/10.1002/pro.109, 2009.
Chen, V. B., Arendall III, W. B., Headd, J. J., and Keedy, D. A., Immormino, R. M., Karpral, G. J., Murray, L. W., Richardson, J. S., and Richardson, D. C.: MolProbity: all-atom structure validation for macromolecular crystallography, Acta Crystallogr. D, 66, 12–21, https://doi.org/10.1107/S0907444909042073, 2010.
Choi, J., Ma, S., Kim, H.-Y., Yun, J.-H., Heo, J.-N., Lee, W., Choi, K.-Y., and No, K.: Identification of small-molecule compounds targeting the
dishevelled PDZ domain by virtual screening and binding studies, Bioorg.
Med. Chem., 24, 3259–3266, https://doi.org/10.1016/j.bmc.2016.03.026, 2016.
Christensen, N. R., Čalyševa, J., Fernandes, E. F. A., Lüchow, S., Clemmensen, L. S., Haugaard‐Kedström, L. M., and Strømgaard, K.: PDZ Domains
as Drug Targets, Advanced Therapeutics, 2, 1800143, https://doi.org/10.1002/adtp.201800143, 2019.
Christensen, N. R., De Luca, M., Lever, M. B., Richner, M., Hansen, A. B.,
Noes-Holt, G., Jensen, K. L., Rathje, M., Jensen, D. B., Erlendsson, S.,
Bartling, C. R., Ammendrup-Johnsen, I., Pedersen, S. E., Schönauer, M.,
Nissen, K. B., Midtgaard, S. R., Teilum, K., Arleth, L., Sørensen, A. T.,
Bach, A., Strømgaard, K., Meehan, C. F., Vaegter, C. B., Gether, U., and
Madsen, K. L.: A high-affinity, bivalent PDZ domain inhibitor complexes
PICK1 to alleviate neuropathic pain, EMBO Mol. Med., 12, e11248, https://doi.org/10.15252/emmm.201911248, 2020.
Chuprina, A., Lukin, O., Demoiseaux, R., Buzko, A., and Shivanyuk, A.: Drug-
and lead-likeness, target class, and molecular diversity analysis of 7.9
million commercially available organic compounds provided by 29 suppliers,
J. Chem. Inf. Model., 50, 470–499, https://doi.org/10.1021/ci900464s, 2010.
Doyle, D. A., Lee, A., Lewis, J., Kim, E., Sheng, M., and MacKinnon, R.:
Crystal structures of a complexed and peptide-free membrane protein-binding
domain: Molecular basis of peptide recognition by PDZ, Cell, 85, 1067–1076,
https://doi.org/10.1016/s0092-8674(00)81307-0, 1996.
Emsley, P. and Cowtan, K.: Coot: model-building tools for molecular
graphics, Acta Crystallogr. D, 60, 2126–2132, https://doi.org/10.1107/S0907444904019158, 2004.
Fan, X., Quyang, N., Teng, H., and Yao, H.: Isolation and characterization of
spheroid cells from the HT29 colon cancer cell line, Int. J. Colorectal Dis.,
26, 1279–1285, https://doi.org/10.1007/s00384-011-1248-y, 2011.
Fang, L., Von Kries, J. P., and Birchmeier, W.: Identification of
small-molecule antagonists of the TCF/β-catenin protein complex, in
30 years of Wnt signalling, EMBO Conference, Egmond aan Zee, Netherlands, 27 June to 1 July 2012.
Fanning, A. S. and Anderson, J. M.: Protein-protein interactions: PDZ domain
networks, Curr. Biol., 6, 1385–1388, https://doi.org/10.1016/s0960-9822(96)00737-3,
1996.
Fritzmann, J., Morkel. M., Besser, D., Budczies, J., Kosel, F., Brembeck, F.
H., Stein, U., Fichtner, I., Schlag, P. M., and Birchmeier, W.: A colorectal
cancer expression profile that includes transforming growth factor beta
inhibitor BAMBI predicts metastatic potential, Gastroenterology, 137, 165–175, https://doi.org/10.1053/j.gastro.2009.03.041, 2009.
Fujii, N., You, L., Xu, Z., Uematsu, K., Shan, J., He, B., Mikami, I.,
Edmondson, L.R., Neale, G., Zheng, J., Guy, R. K., and Jablons, D. M.: An
antagonist of dishevelled protein-protein interaction suppresses β-catenin-dependent tumor cell growth, Cancer Res., 67, 573–579, https://doi.org/10.1158/0008-5472.CAN-06-2726, 2007.
Garrett, D. S., Seok, Y. J., Peterkofsky, A., and Gronenborn, A. M.:
Identification by NMR of the binding surface for the histidine-containing
phosphocarrier protein HPr on the N-terminal domain of enzyme I of the
Escherichia coli phosphotransferase system, Biochemistry, 36, 4393–4398, https://doi.org/10.1021/bi970221q, 1997.
Goddard, T. D. and Kneller, D. G.: SPARKY 3, University of California, San
Francisco, 2003.
Grandy, D., Shan, J., Zhang, X., Rao, S., Akunuru, S., Li, H., Zhang, Y.,
Alpatov, I., Zhang, X., Lang, R., Shi, De-Li., and Zheng, J.: Discovery and
characterization of a small molecule inhibitor of the PDZ domain of
dishevelled, J. Biol. Chem., 284, 16256–16263, https://doi.org/10.1074/jbc.M109.009647, 2009.
Hajduk, P. J., Sheppard, G., Nettesheim, D. G., Olejniczak, E. T., Shuker,
S. B., Meadows, R. P., Steinman, D. H., Carrera, G. M. Jr., Marcotte, P. A.,
Severin, J., Walter, K., Smith, H., Gubbins, E., Simmer, R., Holzman, T. F.,
Morgan, D. W., Davidsen, S. K., Summers, J. B., and Fesik, S. W.: Discovery
of Potent Nonpeptide Inhibitors of Stromelysin Using SAR by NMR, J. Am.
Chem. Soc., 119, 5818–5827, https://doi.org/10.1021/ja9702778, 1997.
Hammond, M. C, Harris, B. Z., Lim, W. A., and Bartlett, P. A.: β Strand
Peptidomimetics as Potent PDZ Domain Ligands, Chem. Biol., 13, 1247–1251, https://doi.org/10.1016/j.chembiol.2006.11.010, 2006.
Harris, B. Z., Lau, F. W., Fujii, N., Guy, R. K., and Lim, W. A.: Role of
electrostatic interactions in PDZ domain ligand recognition, Biochemistry, 42, 2797–2805, https://doi.org/10.1021/bi027061p, 2003.
Haugaard-Kedström, L. M., L. S., Clemmensen, V., Sereikaite, Z., Jin, E. F. A., Fernandes, B., Wind, F., Abalde-Gil, J., Daberger, M., Vistrup-Parry, D., Aguilar-Morante, R., Leblanc, A. L., Egea-Jimenez, M., Albrigtsen, K. E., Jensen, T. M. T., Jensen, Y., Ivarsson, R., Vincentelli, P., Hamerlik, J. H., Andersen, P., Zimmermann, W., Lee, and Strømgaard, K.: A High-Affinity
Peptide Ligand Targeting Syntenin Inhibits Glioblastoma, J. Med. Chem.,
64, 1423–1434, https://doi.org/10.1021/acs.jmedchem.0c00382, 2021.
Hegedüs, Z., Hóbor, F., Shoemark, D. K., Celis, S., Lian, L.-Y.,
Trinh, Ch. H., Sessions, R. B., Edwards, T. A., and Wilson, A. J.:
Identification of β-strand mediated protein–protein interaction
inhibitors using ligand-directed fragment ligation, Chem. Sci., 12, 2286–2293, https://doi.org/10.1039/d0sc05694d, 2021.
Hillier, B. J., Christopherson, K. S., Prehoda, K. E., Bredt, D. S., and Lim,
W. A.: Unexpected modes of PDZ domain scaffolding revealed by structure of
nNOS–syntrophin complex, Science, 284, 812–815, 1999.
Holland, J. D., Klaus, A., Garratt, A. N., and Birchmeier, W.: Wnt signaling
in stem and cancer stem cells, Curr. Opin. Cell Biol., 25, 254–264, https://doi.org/10.1016/j.ceb.2013.01.004, 2013.
Hori, K., Ajioky, K., Goda, N., Shindo, A., Tagagishi, M., Tenno, T., and
Hiroaki, H.: Discovery of Potent Dishevelled/Dvl Inhibitors Using Virtual
Screening Optimized With NMR-Based Docking Performance Index, Front.
Pharmacol., 9, 983, https://doi.org/10.3389/fphar.2018.00983, 2018.
Jain, A. K. and Dubes, R. C.: Algorithms for clustering data, Upper Saddle River, Prentice Hall, NJ, 320 pp., 1988.
Jho, E. H., Zhang, T., Domon, C., Joo, C.-K., Freund, J.-N., and Costantini,
F.: Wnt/beta-catenin/Tcf signaling induces the transcription of Axin2, a
negative regulator of the signaling pathway, Mol. Cell. Biol., 22, 1172–1183, https://doi.org/10.1128/mcb.22.4.1172-1183.2002, 2002.
Kanwar, S. S., Yu, Y., Nautyal, J., Patel, B. B., and Majumdar, A. P. N.: The
Wnt/beta-catenin pathway regulates growth and maintenance of colonospheres,
Mol. Cancer., 9, 212, https://doi.org/10.1186/1476-4598-9-212, 2010.
Kim, H. Y., Choi, S., Yoon, J. H., Lim, H. J., Lee, H., Choi, J., Ro, E. J.,
Heo, J. N., Lee, W., No, K. T., and Choi, K. Y.: Small molecule inhibitors of
the Dishevelled-CXXC5 interaction are new drug candidates for bone anabolic
osteoporosis therapy, EMBO Mol. Med., 8, 375–387, https://doi.org/10.15252/emmm.201505714, 2016.
Kishida, M., Koyama, S., Kishida, S., Matsubara, K., Nakashima, S., Higano, K., Takada, R., Takada, S., and Kikuchi, A.: Axin prevents Wnt-3a-induced accumulation of beta-catenin, Oncogene, 18, 979–985, https://doi.org/10.1038/sj.onc.1202388, 1999.
Klaus, A. and Birchmeier, W.: Wnt signalling and its impact on development
and cancer, Nat. Rev. Cancer, 8, 387–398, https://doi.org/10.1038/nrc2389, 2008.
Kurakin, A., Swistowski, A., Wu, S. C., and Bredesen, D. E.: The PDZ domain
as a complex adaptive system, PLOS ONE, 2, e953, https://doi.org/10.1371/journal.pone.0000953, 2007.
Lee, H. J., Wang, X. N., Shao, Y., and Zheng, J.: Identification
of tripeptides recognized by the PDZ domain of Dishevelled,
Bioorg. Med. Chem., 17, 1701–1708, https://doi.org/10.1016/j.bmc.2008.12.060, 2009a.
Lee, H. J., Wang, N. X., Shi, D. L., and Zheng, J. J.: Sulindac inhibits canonical Wnt signaling by blocking the PDZ domain of
the protein dishevelled, Angew. Chem. Int. Edit. Engl., 48, 6448–6452, https://doi.org/10.1002/anie.200902981, 2009b.
Lee, I., Choi, S., Yun, J. H., Seo, S. H., Choi, S., Choi, K. Y., and Lee,
W.: Crystal structure of the PDZ domain of mouse Dishevelled 1 and its
interaction with CXXC5, Biochem. Bioph. Res. Co., 485, 584–590, https://doi.org/10.1016/j.bbrc.2016.12.023, 2017.
Lewis, A., Segditsas, S., Deheragoda, M., Pollard, P., Jeffery, R., Nye, E.,
Lockstone, H., Davis, H., Clark,S., Stamp, G., Poulsom, R., Wright, N., and
Tomlinson, I.: Severe polyposis in Apc1322T mice is associated with
submaximal Wnt signalling and increased expression of the stem cell marker
Lgr5, Gut, 59, 1680–1686, https://doi.org/10.1136/gut.2009.193680, 2010.
Lipinski, C. A.: Drug-like properties and the causes of poor solubility and
poor permeability, J. Pharmacol. Tox. Met., 44, 235–249, https://doi.org/10.1016/s1056-8719(00)00107-6, 2000.
Lipinski, C. A., Lombardo, F., Dominy, B. W., and Feeney, P. J.: Experimental
and computational approaches to estimate solubility and permeability in drug
discovery and development settings, Adv. Drug Deliver. Rev., 23, 3–25, https://doi.org/10.1016/S0169-409X(96)00423-1, 1997.
Lv, P. C., Zhu, H. L., Li, H. Q., Sun, J., and Zho, Y.: Synthesis and
biological evaluation of pyrazole derivatives containing thiourea skeleton
as anticancer, Bioorg. Med. Chem., 18, 4606–4614, https://doi.org/10.1016/j.bmc.2010.05.034, 2010.
Madrzak, J., Fiedler, M. Johnson, C. M., Ewan, R., Knebel, A., Bienz, M., and Chin, J. W.: Ubiquitination of the Dishevelled DIX domain blocks its head-to-tail polymerization, Nat. Commun., 6, 6718, https://doi.org/10.1038/ncomms7718, 2015.
Malanchi, I., Peinado, H., Kassen, D., Hussenet, T., Metzger, D., Chambon,
P., Huber, M., Hohl, D., Cano, A., Birchmeier, W., and Huelsken, J.:
Cutaneous cancer stem cell maintenance is dependent on beta-catenin
signalling, Nature, 452, 650–653, https://doi.org/10.1038/nature06835, 2008.
Mathvink, R. J., Barritta, A. M., Candelore, M. R., Cascieri, M. A., Deng,
L., Tota, L., Strader, C. D., Wyvratt, M. J., Fosher, M. H., and Weber, A.
E.: Potent, elective human beta3 adrenergic receptor agonists containing a
substituted indoline-5-sulfonamide pharmacophore, Bioorg. Med. Chem. Lett.,
9, 1869–1874, https://doi.org/10.1016/s0960-894x(99)00277-2, 1999.
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni,
L. C., and Read, R. J.: Phaser crystallographic software, J. Appl. Crystallogr., 40, 658–674, https://doi.org/10.1107/S0021889807021206, 2007.
McMartin, C. and Bohacek, R. S.: Powerful, rapid computer algorithms for
structure-based drug design, J. Comput. Aid. Mol. Des., 11, 333–344,
https://doi.org/10.1023/a:1007907728892, 1997.
Mizutani, K., Miyamoto, S., Nagahata, T., Konishi, N., Emi, M., and Onda, M.:
Upregulation and overexpression of DVL1, the human counterpart of the
Drosophila Dishevelled gene, in prostate cancer, Tumori, 91, 546–551,
2005.
Molenaar, M., van de Wetering, M., Oosterwegegl, M., Peterson-Maduro, J.,
Godsave, S., Korinek, V., Roose, J., Destrée, O., and Clevers, H.: XTcf-3
transcription factor mediates β-catenin-induced axis formation in Xenopus embryos, Cell, 86, 391–399, https://doi.org/10.1016/s0092-8674(00)80112-9, 1996.
Mosmann, T.: Rapid colorimetric assay for cellular growth and survival:
application to proliferation and cytotoxicity assays, J. Immunol. Methods,
65, 55–63, https://doi.org/10.1016/0022-1759(83)90303-4, 1983.
Murshudov, G. N., Vagin, A. A., and Dodson, E. J.: Refinement of
macromolecular structures by the maximum-likelihood method, Acta Crystallogr. D, 53, 240–255, https://doi.org/10.1107/S0907444996012255, 1997.
O'Brien, P. M., Ortwine, D. F., Pavlovsky, A. G., Picard, J. A., Sliskovic,
D. R., Roth, B. D., Dyer, R. D., Johnson, L. L., Man, C. F., and Hallak, H.:
Structure-activity relationships and pharmacokinetic analysis for a series
of potent, systemically available biphenylsulfonamide matrix
metalloproteinase inhibitors, J. Med. Chem., 43, 156–166, https://doi.org/10.1021/jm9903141, 2000.
Osada, R., Funkhouser, T., Chazelle, D., and Dobkin, D.: Shape distributions,
ACM Transactions on Graphics, 21, 807–832, https://doi.org/10.1145/571647.571648,
2002
Pawson, T.: Dynamic control of signalling by modulator adaptor proteins.
Curr. Opin. Cell Biol., 19, 112 -116, https://doi.org/10.1016/j.ceb.2007.02.013, 2007.
Polakis, P.: Drugging Wnt signaling in cancer, EMBO J., 31, 2737–2746, https://doi.org/10.1038/emboj.2012.126, 2012.
Ponting, C. P., Phillips, C., Davies, K. E., and Blake, D. J.: PDZ domains:
targeting signalling molecules to submembranous sites, Bioassays, 19, 469–479, https://doi.org/10.1002/bies.950190606, 1997.
Puranik, P., Aakanksha, K., Tadas, S. V., Robert, D. B., Lalji, K. G., and
Vincent, C. O. N.: Potent anti-prostate cancer agents derived from a novel
androgen receptor down-regulating agent, Bioorgan. Med. Chem., 16, 3519–3529, https://doi.org/10.1016/j.bmc.2008.02.031, 2008.
Qin, Y., Feng, L., Fan, X., Zheng, L., Zhang, Y., Chang, L., and Li, T.:
Neuroprotective Effect of N-Cyclohexylethyl-[A/G]-[D/E]-X-V Peptides on
Ischemic Stroke by Blocking nNOS–CAPON Interaction, ACS Chem. Neurosci,
12, 244–255, https://doi.org/10.1021/acschemneuro.0c00739, 2021.
Riese, J., Yu, X., Munnerly, A., Eresh, L., Hsu, S.-C., Grosschedl, R., and
Bienz, M.: LEF-1, a nuclear factor coordinating signaling inputs from
wingless and decapentaplegic, Cell, 88, 777–787, https://doi.org/10.1016/s0092-8674(00)81924-8, 1997.
Rimbault, C., Maruthi, K., Breillat, C., Genuer, C., Crespillo, S.,
Puente-Muñoz, V., Chamma, I., Gauthereau, I., Antoine, S., Thibaut, C.,
Tai, F. W. J., Dartigues, B., Grillo-Bosch, D., Claverol, S., Poujol, C.,
Choquet, D., Mackereth, C. D., and Sainlos, M.: Engineering selective
competitors for the discrimination of highly conserved protein-protein
interaction modules, Nat. Commun., 10, 4521, https://doi.org/10.1038/s41467-019-12528-4, 2019.
Sack, U., Walther, W., Scudiero, D., Selby, M., Aumann, J., Lemos, C.,
Fichtner, I., Schlag, P. M., Shoemaker, R. H., and Stein, U.: S100A4-induced
cell motility and metastasis is restricted by the Wnt/β-catenin pathway
inhibitor calcimycin in colon cancer cells, Mol. Biol. Cell., 22, 3344–3354, https://doi.org/10.1091/mbc.E10-09-0739, 2011.
Sanner, M. F., Olson, A. J., and Spehner, J. C.: Reduced surface: an efficient
way to compute molecular surfaces, Biopolymers, 38, 305–320, https://doi.org/10.1002/(SICI)1097-0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y, 1996.
Saupe, J., Roske, Y., Schillinger, C., Kamdem, N., Radetzki, S., Diehl, A.,
Oschkinat, H., Krause, G., Heinemann, U., and Rademann, J.: Discovery,
structure-activity relationship studies, and crystal structure of
non-peptide inhibitors bound to the Shank3 PDZ domain, ChemMedChem, 6, 1411–1422, https://doi.org/10.1002/cmdc.201100094, 2011.
Schultz, J., Hoffmüller, U., Krause, G., Ashurts, J., Macias, M. J.,
Schmieder, P., Schneider-Mergener, J., and Oschkinat, H.: Specific
interactions between the syntrophin PDZ domain and voltage-gated sodium
channels, Nat. Struct. Biol., 5, 19–24, https://doi.org/10.1038/nsb0198-19, 1998.
Schwarz-Romond, T., Fiedler, M., Shibata, N., Butler, P. J. G., Kikuchi, A.,
Higuchi, Y., and Bienz, M.: The DIX domain of Dishevelled confers Wnt signaling
by dynamic polymerization, Nat. Struct. Mol. Biol., 14, 484–492, https://doi.org/10.1038/nsmb1247, 2007.
Shan, J., Shi, D. L., Wang, J., and Zheng, J.: Identification of a specific
inhibitor of the dishevelled PDZ domain, Biochemistry, 44, 15495–15503, https://doi.org/10.1021/bi0512602, 2005.
Shan, J., Zhang, X., Bao, J., Cassell, R., and Zheng, J. J.: Synthesis of
potent Dishevelled PDZ domain inhibitors guided by virtual screening and NMR
studies, Chem. Biol. Drug. Des., 79, 376–383, https://doi.org/10.1111/j.1747-0285.2011.01295.x, 2012.
Sheng, M. and Sala, C.: PDZ domains and the organization of supramolecular
complexes, Annu. Rev. Neurosci., 24, 1–29, https://doi.org/10.1146/annurev.neuro.24.1.1, 2001.
Shuker, S. B., Hajduk, P. J., Meadows, R. P., and Fesik, S. W.: Discovering
high-affinity ligands for proteins: SAR by NMR, Science, 274, 1531–1534,
https://doi.org/10.1126/science.274.5292.1531, 1996.
Sievers, F., Wilm, A., Dineen, D. G., Gibson, T. J., Karplus, K., Li, W.,
Lopez, R., McWilliam, H., Remmert, M., Söding, J., Thompson, J. D., and
Higgins, D. G.: Fast, Scalable generation of high-quality protein multiple
sequence alignments using Clustal Omega, Mol. Syst. Biol., 7, 539,
https://doi.org/10.1038/msb.2011.75, 2011.
Sineva, G. S. and Pospelov, V. A.: Inhibition of GSK3beta enhances both
adhesive and signalling activities of beta-catenin in mouse embryonic stem
cells, Biol. Cell, 102, 549–560, https://doi.org/10.1042/BC20100016, 2010.
Sleight, A. J., Boess, F. G., Bös, M., Levet-Trafit, B., Riemer, C., and
Bourson, A.: Characterization of Ro 04-6790 and Ro 63-0563: potent and
selective antagonists at human and rat 5-HT6 receptors, Brit. J. Pharmacol., 124, 556–562, https://doi.org/10.1038/sj.bjp.0701851, 1998.
Songyang, Z., Fanning, A. S., Fu, C., Xu, J., Marfatia, S. M., Chisti, A.
H., Crompton, A., Chan, A. C., Anderson, J. M., and Cantley, L. C.:
Recognition of unique carboxyl-terminals motifs by distinct PDZ domains,
Science, 275, 73–77, https://doi.org/10.1126/science.275.5296.73, 1997.
Tellew, J. E., Baska, R. A. F., Beyer, S. M., Carlson, K. E., Cornelius, L.
A., Fadnis, L., Gu, Z., Kunst, B. L., Kowala, M. C., Monshizadegan, H.,
Murugesan, N., Ryan, C. S., Valentine, M. T., Yang, Y., and Macor, J. E.:
Discovery of 4′-[(Imidazol-1-yl)methyl]biphenyl-2-sulfonamides as dual
endothelin/Angiotensin II receptor antagonists, Bioorg. Med. Chem.
Lett., 13, 1093–1096, https://doi.org/10.1016/s0960-894x(03)00018-0, 2003.
Uematsu, K., He, B., You, L., Xu, Z., McCormick, F., and Jablons, D. M.:
Activation of the Wnt pathway in non-small cell lung cancer: evidence of
dishevelled overexpression, Oncogene, 22, 7218–7221, https://doi.org/10.1038/sj.onc.1206817, 2003a.
Uematsu, K., Kanazawa, S., You, L., He, B., Xu, Z., Li, K., Peterlin, B. M.,
McCormick, F., and Jablons, D. M.: Wnt pathway activation inmesothelioma:
evidence of dishevelled overexpression and transcriptional activity of
β-catenin, Cancer Res., 63, 4547–4551, 2003b.
Vermeulen, L., De Sousa E Melo, F., van der Heijden, M., Cameron, K., de
Jong, J. H., Borovski, T., Tuynman, J. B., Todaro, M., Merz, C., Rodermond,
H., Sprick, M. R., Kemper, K., Richel, J. J., Stassi, G., and Medema, J. P.:
Wnt activity defines colon cancer stem cells and is regulated by the
microenvironment, Nat. Cell. Biol., 12, 468–476, https://doi.org/10.1038/ncb2048, 2010.
Wallingford, B. J. and Raymond, H.: The developmental biology of Dishevelled:
an enigmatic protein governing cell fate and cell polarity, Development,
132, 4421–4436, https://doi.org/10.1242/dev.02068, 2005.
Wang, C., Dai, J., Sun, Z., Shi, C., Cao, H., Chen, X., Gu, S., Li, Z.,
Qian, W., and Han, X.: Targeted inhibition of dishevelled PDZ domain via
NSC668036 depresses fibrotic process, Exp. Cell Res., 331, 115–122, https://doi.org/10.1016/j.yexcr.2014.10.023, 2015.
Weeraratna, A. T., Jiang, Y., Hostetter, G., Rosenblatt, K., Duray, P.,
Bittner, M., and Trent, J. M.: Wnt5a signalling directly affects cell
motility and invasion of metastic melanoma, Cancer Cell, 1, 279–288, https://doi.org/10.1016/s1535-6108(02)00045-4, 2002.
Wong, H. C., Mao, J., Nguyen, J. T., Srinivas, S., Zhang, W., Liu, B., Li, L.,
Wu, D., and Zheng, J.: Structural basis of the recognition of the dishevelled
DEP domain in the Wnt signalling pathway, Nat. Struct. Biol., 7, 1178–1184,
https://doi.org/10.1038/82047, 2000.
Wong, H. C., Bourdelas, A., Krauss, A., Lee, H. J., Shao, Y., Wu, D.,
Mlodzik, M., Shi, D. L., and Zheng, J.: Direct binding of the PDZ domain of
Dishevelled to a conserved internal sequence in the C-terminal region of
Frizzled, Mol. Cell, 12, 1251–1260, https://doi.org/10.1016/s1097-2765(03)00427-1,
2003.
Wu, C., Decker, E. R., Blok, N., Bui, H., Chen, Q., Raju, B., Bourgoyne, A.
R., Knowles, V., Biediger, R. J., Market, R. V., Lin, S., Dupre, B., Kogan,
T. P., Holland, G. W., Brock, T. A., and Dixon, R. A. F.: Endothelin
antagonists: substituted mesitylcarboxamides with high potency and
selectivity for ETA receptors, J. Med. Chem., 42, 4485–4499, https://doi.org/10.1021/jm9900063, 1999.
Zartler, E. R. and Shapiro, M. J.: Protein NMR-based screening in drug
discovery, Curr. Pharm. Design, 12, 3963–3972, https://doi.org/10.2174/138161206778743619, 2006.
Zartler, E. R., Hanson, J., Jones, B. E., Kline, A. D., Martin, G., Mo, H.,
Shapiro, M. J., Wang, R., Wu, H., and Yan, J.: RAMPED-UP NMR: multiplexed
NMR-based screening for drug discovery, J. Am. Chem. Soc., 125, 10941–10946, https://doi.org/10.1021/ja0348593, 2003.
Zhang, M. and Wang, W.: Organization of signalling complexes by PDZ-domain
scaffold proteins, Acc. Chem. Res., 36, 530–538, https://doi.org/10.1021/ar020210b,
2003.
Zhang, Y., Appleton, B. A., Wiesmann, C., Lau, T., Costa, M., Hannoush, R.
N., and Sidhu, S. S.: Inhibition of Wnt signaling by Dishevelled PDZ
peptides, Nat. Chem. Biol., 5, 217–219, https://doi.org/10.1038/nchembio.152, 2009.
Short summary
The Wnt signalling pathway plays a major role in prevention of cancer, whereby the protein Dishevelled connects from the transmembrane receptor Frizzled to downstream effectors via its PDZ domain. Here, cycles of chemical synthesis and structural biology are applied to develop PDZ ligands that block the Frizzled–Dishevelled interaction using NMR for screening, in ligand development, and for deriving structure–activity relationships. Cellular reporter assays demonstrate their efficacy.
The Wnt signalling pathway plays a major role in prevention of cancer, whereby the protein...
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