51
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McGovern RE, Fernandes H, Khan AR, Power NP, Crowley PB. Protein camouflage in cytochrome c–calixarene complexes. Nat Chem 2012; 4:527-33. [DOI: 10.1038/nchem.1342] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 03/22/2012] [Indexed: 01/06/2023]
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52
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Biros S, Hof F. Supramolecular Approaches to Medicinal Chemistry. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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53
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Conley MP, Valero J, de Mendoza J. Guanidinium-Based Receptors for Oxoanions. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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54
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Battle CH, Jayawickramarajah J. Supramolecular Approaches for Inhibition of Protein-Protein and Protein-DNA Interactions. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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55
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Gordo S, Martos V, Vilaseca M, Menéndez M, de Mendoza J, Giralt E. On the role of flexibility in protein-ligand interactions: the example of p53 tetramerization domain. Chem Asian J 2011; 6:1463-9. [PMID: 21626703 DOI: 10.1002/asia.201000938] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The recognition of protein surfaces by designed ligands has become an attractive approach in drug discovery. However, the variable nature and irregular behavior of protein surfaces defy this new area of research. The easy to understand "lock-and-key" model is far from being the ideal paradigm in biomolecular interactions and, hence, any new finding on how proteins and ligands behave in recognition events paves a step of the way. Herein, we illustrate a clear example on how an increase in flexibility of both protein and ligand can result in an increase in the stability of the macromolecular complex. The biophysical study of the interaction between a designed flexible tetraguanidinium-calix[4]arene and the tetramerization domain of protein p53 (p53TD) and its natural mutant p53TD-R337H shows how the floppy mutant domain interacts more tightly with the ligand than the well-packed wild-type protein. Moreover, the flexible calixarene ligand interacts with higher affinity to both wild-type and mutated protein domains than a conformationally rigid calixarene analog previously reported. These findings underscore the crucial role of flexibility in molecular recognition processes, for both small ligands and large biomolecular surfaces.
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Affiliation(s)
- Susana Gordo
- Institute for Research in Biomedicine, Baldiri Reixac 10, 08028 Barcelona, Spain
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56
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Levy R, Sobolev V, Edelman M. First- and second-shell metal binding residues in human proteins are disproportionately associated with disease-related SNPs. Hum Mutat 2011; 32:1309-18. [DOI: 10.1002/humu.21573] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 07/06/2011] [Indexed: 11/10/2022]
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57
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Dyachenko A, Goldflam M, Vilaseca M, Giralt E. Molecular recognition at protein surface in solution and gas phase: Five VEGF peptidic ligands show inverse affinity when studied by NMR and CID-MS. Biopolymers 2011; 94:689-700. [PMID: 20564038 DOI: 10.1002/bip.21462] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein-protein interactions comprise of collection of molecular recognition events that take place at protein surfaces. A better understanding of the mechanism behind these interactions would provide deeper insight into the nature of many diseases, caused by the malfunction of protein networks, and contribute to design of molecules for efficient modulating of these interactions. One major factor in molecular recognition mechanism is interaction of reacting species with aqueous media. Thus, comparative study of noncovalent complex behavior in solution and gas phase can provide valuable information about the role of the solvent. Here examined interactions of vascular endothelial growth factor (VEGF) protein with five peptidic ligands of the same molecular weight but with different affinities. Interactions of VEGF with ligands in solution were studied by ITC and NMR, and K(D)s were determined. Gas phase stability was addressed using CID-MS approach. The energy transfer model was taken and adapted for the calculation of binding energy. Peptides were ranked on the basis of both solution and gas phase affinity to VEGF. The results indicate that the ranking of peptides in terms of affinity in solution is reversed compared with the gas phase ranking. This observation opens up a vast field for the future study of the system, and the determination and characterization of factors, responsible for the change of stability of noncovalent protein-ligand complexes upon complete or partial removal of the solvent.
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Affiliation(s)
- Andrey Dyachenko
- Institute for Research in Biomedicine, Parc Científic de Barcelona, Barcelona, Spain
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58
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Dutt S, Wilch C, Schrader T. Artificial synthetic receptors as regulators of protein activity. Chem Commun (Camb) 2011; 47:5376-83. [DOI: 10.1039/c0cc05812b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Superimposed snapshots of a MD simulation for the ternary complex between G6PD, a molecular clip and included NADP+ cofactor.
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Affiliation(s)
- Som Dutt
- Department of Chemistry
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | - Constanze Wilch
- Department of Chemistry
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | - Thomas Schrader
- Department of Chemistry
- University of Duisburg-Essen
- 45117 Essen
- Germany
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59
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Baldini L, Sansone F, Scaravelli F, Casnati A, Ungaro R. Proximal and distal N,C-linked tetra-peptidocalix[4]arenes as bifunctional receptors: synthesis, conformation and preliminary binding studies. Supramol Chem 2010. [DOI: 10.1080/10610278.2010.506548] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Laura Baldini
- a Dipartimento di Chimica Organica e Industriale , Università degli Studi di Parma , Parco Area delle Scienze 17/a, 43124 , Parma , Italy
| | - Francesco Sansone
- a Dipartimento di Chimica Organica e Industriale , Università degli Studi di Parma , Parco Area delle Scienze 17/a, 43124 , Parma , Italy
| | - Federico Scaravelli
- a Dipartimento di Chimica Organica e Industriale , Università degli Studi di Parma , Parco Area delle Scienze 17/a, 43124 , Parma , Italy
| | - Alessandro Casnati
- a Dipartimento di Chimica Organica e Industriale , Università degli Studi di Parma , Parco Area delle Scienze 17/a, 43124 , Parma , Italy
| | - Rocco Ungaro
- a Dipartimento di Chimica Organica e Industriale , Università degli Studi di Parma , Parco Area delle Scienze 17/a, 43124 , Parma , Italy
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60
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Maslon MM, Hupp TR. Drug discovery and mutant p53. Trends Cell Biol 2010; 20:542-55. [PMID: 20656489 DOI: 10.1016/j.tcb.2010.06.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/14/2010] [Accepted: 06/15/2010] [Indexed: 12/24/2022]
Abstract
Missense mutations in the p53 gene are commonly selected for in developing human cancer cells. These diverse mutations in p53 can inactivate its normal sequence-specific DNA-binding and transactivation function, but these mutations can also stabilize a mutant form of p53 with pro-oncogenic potential. Recent multi-disciplinary advances have demonstrated exciting and unexpected potential in therapeutically targeting the mutant p53 pathway, including: the development of biophysical models to explain how mutations inactivate p53 and strategies for refolding and reactivation of mutant p53, the ability of mutant p53 protein to escape MDM2-mediated degradation in human cancers, and the growing 'interactome' of mutant p53 that begins to explain how the mutant p53 protein can contribute to diverse oncogenic and pro-metastatic signaling. Our rapidly accumulating knowledge on mutant p53-signaling pathways will facilitate drug discovery programmes in the challenging area of protein-protein interactions and mutant protein conformational control.
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Affiliation(s)
- Magda M Maslon
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Cell Signalling Unit, Cancer Research UK p53 Signal Transduction Group, Edinburgh EH4 2XR, UK
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61
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Enhancement of transcriptional activity of mutant p53 tumor suppressor protein through stabilization of tetramer formation by calix[6]arene derivatives. Bioorg Med Chem Lett 2010; 20:4412-5. [PMID: 20605095 DOI: 10.1016/j.bmcl.2010.06.053] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 05/31/2010] [Accepted: 06/09/2010] [Indexed: 01/16/2023]
Abstract
Li-Fraumeni syndrome, a hereditary disorder characterized by familial clusters of early-onset multiple tumors, is caused by mutation of the TP53 gene, which encodes the p53 tumor suppressor protein. Mutation of Arg337 to histidine in the tetramerization domain of p53 is most frequently observed in Li-Fraumeni syndrome. This mutation is reported to destabilize the tetrameric structure of p53. We designed and synthesized calix[6]arene derivatives, which have six imidazole or pyrazole groups at the upper rim. In this study, we report, for the first time, the enhancement of the in vivo transcriptional activity of the most common Li-Fraumeni p53 mutant by imidazole-calix[6]arene through stabilization of the oligomer formation.
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62
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Uhlenheuer DA, Petkau K, Brunsveld L. Combining supramolecular chemistry with biology. Chem Soc Rev 2010; 39:2817-26. [PMID: 20461247 DOI: 10.1039/b820283b] [Citation(s) in RCA: 287] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Supramolecular chemistry has primarily found its inspiration in biological molecules, such as proteins and lipids, and their interactions. Currently the supramolecular assembly of designed compounds can be controlled to great extent. This provides the opportunity to combine these synthetic supramolecular elements with biomolecules for the study of biological phenomena. This tutorial review focuses on the possibilities of the marriage of synthetic supramolecular architectures and biological systems. It highlights that synthetic supramolecular elements are for example ideal platforms for the recognition and modulation of proteins and cells. The unique features of synthetic supramolecular systems with control over size, shape, valency, and interaction strength allow the generation of structures fitting the demands to approach the biological problems at hand. Supramolecular chemistry has come full circle, studying the biology and its molecules which initially inspired its conception.
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Affiliation(s)
- Dana A Uhlenheuer
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612AZ Eindhoven, The Netherlands
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63
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Joerger AC, Fersht AR. The tumor suppressor p53: from structures to drug discovery. Cold Spring Harb Perspect Biol 2010; 2:a000919. [PMID: 20516128 DOI: 10.1101/cshperspect.a000919] [Citation(s) in RCA: 233] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Even 30 years after its discovery, the tumor suppressor protein p53 is still somewhat of an enigma. p53's intimate and multifaceted role in the cell cycle is mirrored in its equally complex structural biology that is being unraveled only slowly. Here, we discuss key structural aspects of p53 function and its inactivation by oncogenic mutations. Concerted action of folded and intrinsically disordered domains of the highly dynamic p53 protein provides binding promiscuity and specificity, allowing p53 to process a myriad of cellular signals to maintain the integrity of the human genome. Importantly, progress in elucidating the structural biology of p53 and its partner proteins has opened various avenues for structure-guided rescue of p53 function in tumors. These emerging anticancer strategies include targeting mutant-specific lesions on the surface of destabilized cancer mutants with small molecules and selective inhibition of p53's degradative pathways.
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Affiliation(s)
- Andreas C Joerger
- MRC Centre for Protein Engineering, Hills Road, Cambridge, United Kingdom.
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64
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Dey A, Lane DP, Verma CS. Modulating the p53 pathway. Semin Cancer Biol 2010; 20:3-9. [DOI: 10.1016/j.semcancer.2010.02.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 02/23/2010] [Indexed: 12/21/2022]
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65
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RETRACTED: Carboxylated calixarenes bind strongly to CD69 and protect CD69+ killer cells from suicidal cell death induced by tumor cell surface ligands. Bioorg Med Chem 2010; 18:1434-40. [DOI: 10.1016/j.bmc.2010.01.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 01/06/2010] [Accepted: 01/07/2010] [Indexed: 12/28/2022]
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66
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Sansone F, Baldini L, Casnati A, Ungaro R. Calixarenes: from biomimetic receptors to multivalent ligands for biomolecular recognition. NEW J CHEM 2010. [DOI: 10.1039/c0nj00285b] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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67
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Gordo S, Giralt E. Knitting and untying the protein network: modulation of protein ensembles as a therapeutic strategy. Protein Sci 2009; 18:481-93. [PMID: 19241367 DOI: 10.1002/pro.43] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Proteins constitute the working machinery and structural support of all organisms. In performing a given function, they must adopt highly specific structures that can change with their level of activity, often through the direct or indirect action of other proteins. Indeed, proteins typically function within an ensemble, rather than individually. Hence, they must be sufficiently flexible to interact with each other and execute diverse tasks. The discovery that errors within these groups can ultimately cause disease has led to a paradigm shift in drug discovery, from an emphasis on single protein targets to a holistic approach whereby entire ensembles are targeted.
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Affiliation(s)
- Susana Gordo
- Institute for Research in Biomedicine, Parc Científic de Barcelona, Barcelona, Spain
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68
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Molecular recognition and self-assembly special feature: Calix[4]arene-based conical-shaped ligands for voltage-dependent potassium channels. Proc Natl Acad Sci U S A 2009; 106:10482-6. [PMID: 19435843 DOI: 10.1073/pnas.0813396106] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Potassium channels are among the core functional elements of life because they underpin essential cellular functions including excitability, homeostasis, and secretion. We present here a series of multivalent calix[4]arene ligands that bind to the surface of voltage-dependent potassium channels (K(v)1.x) in a reversible manner. Molecular modeling correctly predicts the best candidates with a conical C(4) symmetry for optimal binding, and the effects on channel function are assessed electrophysiologically. Reversible inhibition was observed, without noticeable damage of the oocytes, for tetraacylguanidinium or tetraarginine members of the series with small lower rim O-substituents. Apparent binding constants were in the low micromolar range and had Hill coefficients of 1, consistent with a single site of binding. Suppression of current amplitude was accompanied by a positive shift in the voltage dependence of gating and slowing of both voltage sensor motion and channel opening. These effects are in keeping with expectations for docking in the central pore and interaction with the pore domain "turret."
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69
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Martos V, Castreño P, Valero J, de Mendoza J. Binding to protein surfaces by supramolecular multivalent scaffolds. Curr Opin Chem Biol 2008; 12:698-706. [DOI: 10.1016/j.cbpa.2008.08.024] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Accepted: 08/18/2008] [Indexed: 11/26/2022]
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