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Fersht AR. From covalent transition states in chemistry to noncovalent in biology: from β- to Φ-value analysis of protein folding. Q Rev Biophys 2024; 57:e4. [PMID: 38597675 DOI: 10.1017/s0033583523000045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Solving the mechanism of a chemical reaction requires determining the structures of all the ground states on the pathway and the elusive transition states linking them. 2024 is the centenary of Brønsted's landmark paper that introduced the β-value and structure-activity studies as the only experimental means to infer the structures of transition states. It involves making systematic small changes in the covalent structure of the reactants and analysing changes in activation and equilibrium-free energies. Protein engineering was introduced for an analogous procedure, Φ-value analysis, to analyse the noncovalent interactions in proteins central to biological chemistry. The methodology was developed first by analysing noncovalent interactions in transition states in enzyme catalysis. The mature procedure was then applied to study transition states in the pathway of protein folding - 'part (b) of the protein folding problem'. This review describes the development of Φ-value analysis of transition states and compares and contrasts the interpretation of β- and Φ-values and their limitations. Φ-analysis afforded the first description of transition states in protein folding at the level of individual residues. It revealed the nucleation-condensation folding mechanism of protein domains with the transition state as an expanded, distorted native structure, containing little fully formed secondary structure but many weak tertiary interactions. A spectrum of transition states with various degrees of structural polarisation was then uncovered that spanned from nucleation-condensation to the framework mechanism of fully formed secondary structure. Φ-analysis revealed how movement of the expanded transition state on an energy landscape accommodates the transition from framework to nucleation-condensation mechanisms with a malleability of structure as a unifying feature of folding mechanisms. Such movement follows the rubric of analysis of classical covalent chemical mechanisms that began with Brønsted. Φ-values are used to benchmark computer simulation, and Φ and simulation combine to describe folding pathways at atomic resolution.
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Affiliation(s)
- Alan R Fersht
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Gonville and Caius College, University of Cambridge, Cambridge, UK
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Biancalana M, Natan E, Lenardo MJ, Fersht AR. NF-κB Rel subunit exchange on a physiological timescale. Protein Sci 2021; 30:1818-1832. [PMID: 34089216 DOI: 10.1002/pro.4134] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/21/2022]
Abstract
The Rel proteins of the NF-κB complex comprise one of the most investigated transcription factor families, forming a variety of hetero- or homodimers. Nevertheless, very little is known about the fundamental kinetics of NF-κB complex assembly, or the inter-conversion potential of dimerised Rel subunits. Here, we examined an unexplored aspect of NF-κB dynamics, focusing on the dissociation and reassociation of the canonical p50 and p65 Rel subunits and their ability to form new hetero- or homodimers. We employed a soluble expression system to enable the facile production of NF-κB Rel subunits, and verified these proteins display canonical NF-κB nucleic acid binding properties. Using a combination of biophysical techniques, we demonstrated that, at physiological temperatures, homodimeric Rel complexes routinely exchange subunits with a half-life of less than 10 min. In contrast, we found a dramatic preference for the formation of the p50/p65 heterodimer, which demonstrated a kinetic stability of at least an order of magnitude greater than either homodimer. These results suggest that specific DNA targets of either the p50 or p65 homodimers can only be targeted when these subunits are expressed exclusively, or with the intervention of additional post-translational modifications. Together, this work implies a new model of how cells can modulate NF-κB activity by fine-tuning the relative proportions of the p50 and p65 proteins, as well as their time of expression. This work thus provides a new quantitative interpretation of Rel dimer distribution in the cell, particularly for those who are developing mathematical models of NF-κB activity.
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Affiliation(s)
- Matthew Biancalana
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.,Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alan R Fersht
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
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Fersht AR. AlphaFold - A Personal Perspective on the Impact of Machine Learning. J Mol Biol 2021; 433:167088. [PMID: 34087198 DOI: 10.1016/j.jmb.2021.167088] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 10/21/2022]
Abstract
I outline how over my career as a protein scientist Machine Learning has impacted my area of science and one of my pastimes, chess, where there are some interesting parallels. In 1968, modelling of three-dimensional structures was initiated based on a known structure as a template, the problem of the pathway of protein folding was posed and bets were taken in the emerging field of Machine Learning on whether computers could outplay humans at chess. Half a century later, Machine Learning has progressed from using computational power combined with human knowledge in solving problems to playing chess without human knowledge being used, where it has produced novel strategies. Protein structures are being solved by Machine Learning based on human-derived knowledge but without templates. There is much promise that programs like AlphaFold based on Machine Learning will be powerful tools for designing entirely novel protein folds and new activities. But, will they produce novel ideas on protein folding pathways and provide new insights into the principles that govern folds?
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Affiliation(s)
- Alan R Fersht
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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Bauer MR, Krämer A, Settanni G, Jones RN, Ni X, Khan Tareque R, Fersht AR, Spencer J, Joerger AC. Targeting Cavity-Creating p53 Cancer Mutations with Small-Molecule Stabilizers: the Y220X Paradigm. ACS Chem Biol 2020; 15:657-668. [PMID: 31990523 PMCID: PMC7307883 DOI: 10.1021/acschembio.9b00748] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have previously shown that the thermolabile, cavity-creating p53 cancer mutant Y220C can be reactivated by small-molecule stabilizers. In our ongoing efforts to unearth druggable variants of the p53 mutome, we have now analyzed the effects of other cancer-associated mutations at codon 220 on the structure, stability, and dynamics of the p53 DNA-binding domain (DBD). We found that the oncogenic Y220H, Y220N, and Y220S mutations are also highly destabilizing, suggesting that they are largely unfolded under physiological conditions. A high-resolution crystal structure of the Y220S mutant DBD revealed a mutation-induced surface crevice similar to that of Y220C, whereas the corresponding pocket's accessibility to small molecules was blocked in the structure of the Y220H mutant. Accordingly, a series of carbazole-based small molecules, designed for stabilizing the Y220C mutant, also bound to and stabilized the folded state of the Y220S mutant, albeit with varying affinities due to structural differences in the binding pocket of the two mutants. Some of the compounds also bound to and stabilized the Y220N mutant, but not the Y220H mutant. Our data validate the Y220S and Y220N mutants as druggable targets and provide a framework for the design of Y220S or Y220N-specific compounds as well as compounds with dual Y220C/Y220S specificity for use in personalized cancer therapy.
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Affiliation(s)
- Matthias R. Bauer
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Giovanni Settanni
- Physics Department, Johannes Gutenberg University, Staudingerweg 7, 55099 Mainz, Germany
| | - Rhiannon N. Jones
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex BN1 9QJ, United Kingdom
| | - Xiaomin Ni
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Raysa Khan Tareque
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex BN1 9QJ, United Kingdom
| | - Alan R. Fersht
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - John Spencer
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex BN1 9QJ, United Kingdom
| | - Andreas C. Joerger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
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Fersht AR, Gölitz P, Lehn JM. ChemBioChem@20-Some Reflections. Chembiochem 2020; 21:5-6. [PMID: 31769931 DOI: 10.1002/cbic.201900658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Looking back, looking forward: In 2000, ChemBioChem debuted. The chemistry of carbohydrates, nucleic acids, peptides, proteins, natural products and other small molecules had reached a level that allowed biological questions to be probed. Today, there is no end in sight to studying biological matter with chemical tools or making use of biological methods to produce chemicals.
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Affiliation(s)
- Alan R Fersht
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid Chemistry Division, University of Cambridge, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Peter Gölitz
- Wiley-VCH, Boschstrasse 12, 69469, Weinheim, Germany
| | - Jean-Marie Lehn
- Supramolecular Chemistry, Institut de Science et d'Ingenierie Supramoleculaires, 8 Allée Gaspard Monge, 67083, Strasbourg, France
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Baud MGJ, Bauer MR, Verduci L, Dingler FA, Patel KJ, Horil Roy D, Joerger AC, Fersht AR. Aminobenzothiazole derivatives stabilize the thermolabile p53 cancer mutant Y220C and show anticancer activity in p53-Y220C cell lines. Eur J Med Chem 2018; 152:101-114. [PMID: 29702446 PMCID: PMC5986712 DOI: 10.1016/j.ejmech.2018.04.035] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/15/2018] [Accepted: 04/17/2018] [Indexed: 12/22/2022]
Abstract
Many cancers have the tumor suppressor p53 inactivated by mutation, making reactivation of mutant p53 with small molecules a promising strategy for the development of novel anticancer therapeutics. The oncogenic p53 mutation Y220C, which accounts for approximately 100,000 cancer cases per year, creates an extended surface crevice in the DNA-binding domain, which destabilizes p53 and causes denaturation and aggregation. Here, we describe the structure-guided design of a novel class of small-molecule Y220C stabilizers and the challenging synthetic routes developed in the process. The synthesized chemical probe MB710, an aminobenzothiazole derivative, binds tightly to the Y220C pocket and stabilizes p53-Y220C in vitro. MB725, an ethylamide analogue of MB710, induced selective viability reduction in several p53-Y220C cancer cell lines while being well tolerated in control cell lines. Reduction of viability correlated with increased and selective transcription of p53 target genes such as BTG2, p21, PUMA, FAS, TNF, and TNFRSF10B, which promote apoptosis and cell cycle arrest, suggesting compound-mediated transcriptional activation of the Y220C mutant. Our data provide a framework for the development of a class of potent, non-toxic compounds for reactivating the Y220C mutant in anticancer therapy.
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Affiliation(s)
- Matthias G J Baud
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom; Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Matthias R Bauer
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom
| | - Lorena Verduci
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom
| | - Felix A Dingler
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom
| | - Ketan J Patel
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom
| | - Deeptee Horil Roy
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom
| | - Andreas C Joerger
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom; German Cancer Consortium (DKTK), German Cancer Center (DKFZ), 69120 Heidelberg, Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany
| | - Alan R Fersht
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom.
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Madan E, Parker TM, Bauer MR, Dhiman A, Pelham CJ, Nagane M, Kuppusamy ML, Holmes M, Holmes TR, Shaik K, Shee K, Kiparoidze S, Smith SD, Park YSA, Gomm JJ, Jones LJ, Tomás AR, Cunha AC, Selvendiran K, Hansen LA, Fersht AR, Hideg K, Gogna R, Kuppusamy P. The curcumin analog HO-3867 selectively kills cancer cells by converting mutant p53 protein to transcriptionally active wildtype p53. J Biol Chem 2018; 293:4262-4276. [PMID: 29382728 DOI: 10.1074/jbc.ra117.000950] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/10/2018] [Indexed: 01/13/2023] Open
Abstract
p53 is an important tumor-suppressor protein that is mutated in more than 50% of cancers. Strategies for restoring normal p53 function are complicated by the oncogenic properties of mutant p53 and have not met with clinical success. To counteract mutant p53 activity, a variety of drugs with the potential to reconvert mutant p53 to an active wildtype form have been developed. However, these drugs are associated with various negative effects such as cellular toxicity, nonspecific binding to other proteins, and inability to induce a wildtype p53 response in cancer tissue. Here, we report on the effects of a curcumin analog, HO-3867, on p53 activity in cancer cells from different origins. We found that HO-3867 covalently binds to mutant p53, initiates a wildtype p53-like anticancer genetic response, is exclusively cytotoxic toward cancer cells, and exhibits high anticancer efficacy in tumor models. In conclusion, HO-3867 is a p53 mutant-reactivating drug with high clinical anticancer potential.
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Affiliation(s)
- Esha Madan
- From the Champalimaud Research, Champalimaud Centre for the Unknown, 1400-038 Lisbon, Portugal.,the Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Gautam Buddha Nagar Section 125, Noida 201301, India
| | - Taylor M Parker
- the Department of Surgery, Simon Cancer Research Center, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Matthias R Bauer
- the Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Alisha Dhiman
- the Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907
| | - Christopher J Pelham
- the Department of Pharmacology and Physiology, Saint Louis University, St. Louis, Missouri 63104
| | - Masaki Nagane
- the Department of Biochemistry, School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5201, Japan
| | - M Lakshmi Kuppusamy
- the Department of Radiology and Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756
| | - Matti Holmes
- the Department of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178
| | - Thomas R Holmes
- the Department of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178
| | - Kranti Shaik
- the Department of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178
| | - Kevin Shee
- the Department of Radiology and Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756
| | | | - Sean D Smith
- the Department of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178
| | - Yu-Soon A Park
- the Department of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178
| | - Jennifer J Gomm
- the Centre for Tumour Biology, Barts Cancer Institute, Charterhouse Square, London, EC1M 6BQ, United Kingdom
| | - Louise J Jones
- the Centre for Tumour Biology, Barts Cancer Institute, Charterhouse Square, London, EC1M 6BQ, United Kingdom
| | - Ana R Tomás
- From the Champalimaud Research, Champalimaud Centre for the Unknown, 1400-038 Lisbon, Portugal
| | - Ana C Cunha
- From the Champalimaud Research, Champalimaud Centre for the Unknown, 1400-038 Lisbon, Portugal
| | - Karuppaiyah Selvendiran
- the Department of Obstetrics and Gynecology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, and
| | - Laura A Hansen
- the Department of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178
| | - Alan R Fersht
- the Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Kálmán Hideg
- the Institute of Organic and Medicinal Chemistry, Faculty of Sciences, University of Pécs, Pécs-H-7624, Hungary
| | - Rajan Gogna
- From the Champalimaud Research, Champalimaud Centre for the Unknown, 1400-038 Lisbon, Portugal, .,the Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Gautam Buddha Nagar Section 125, Noida 201301, India
| | - Periannan Kuppusamy
- the Department of Radiology and Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756,
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Synnott NC, Bauer MR, Madden S, Murray A, Klinger R, O'Donovan N, O'Connor D, Gallagher WM, Crown J, Fersht AR, Duffy MJ. Mutant p53 as a therapeutic target for the treatment of triple-negative breast cancer: Preclinical investigation with the anti-p53 drug, PK11007. Cancer Lett 2017; 414:99-106. [PMID: 29069577 DOI: 10.1016/j.canlet.2017.09.053] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 01/01/2023]
Abstract
The identification of a targeted therapy for patients with triple-negative breast cancer (TNBC) is one of the most urgent needs in breast cancer therapeutics. The p53 gene is mutated in approximately 80% of patients with TNBC, and is a potential therapeutic target for patients with this form of breast cancer. The 2-sulfonylpyrimidine compound, PK11007, preferentially decreases viability in p53-compromised cancer cell lines. We investigated PK11007 as a potential new treatment for TNBC. IC50 values for inhibition of proliferation in a panel of 17 breast cell lines by PK11007 ranged from 2.3 to 42.2 μM. There were significantly lower IC50 values for TNBC than for non-TNBC cell lines (p = 0.03) and for p53-mutated cell lines compared with p53 WT cells (p = 0.003). Response to PK11007 however, was independent of the estrogen receptor (ER) or HER2 status of the cell lines. In addition to inhibiting cell proliferation, PK11007 induced apoptosis in p53 mutant cell lines. Using RNAseq and gene ontology analysis, we found that PK11007 altered the expression of genes enriched in pathways involved in regulated cell death, regulation of apoptosis, signal transduction, protein refolding and locomotion. The observations that PK11007 inhibited cell proliferation, induced apoptosis and altered genes involved in cell death are all consistent with the ability of PK11007 to reactivate mutant p53. Based on our data, we conclude that targeting mutant p53 with PK11007 is a potential approach for treating p53-mutated breast cancer, including the subgroup with TN disease.
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Affiliation(s)
- Naoise C Synnott
- UCD School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Matthias R Bauer
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Stephen Madden
- Population Health Sciences, Department of Psychology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Alyson Murray
- UCD School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Rut Klinger
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Norma O'Donovan
- National Institute for Cellular Biotechnology (NICB), Dublin City University, Dublin, Ireland
| | - Darran O'Connor
- Department of Molecular & Cellular Therapeutics, Royal College of Surgeons Ireland, Dublin, Ireland
| | - William M Gallagher
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - John Crown
- Department of Medical Oncology, St Vincent's University Hospital, Dublin 4, Ireland
| | - Alan R Fersht
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Michael J Duffy
- UCD School of Medicine, University College Dublin, Dublin 4, Ireland; UCD Clinical Research Centre, St. Vincent's University Hospital, Dublin 4, Ireland.
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Synnott NC, Bauer MR, Madden SF, Murray AM, Klinger R, O'Donovan N, O'Connor D, Gallagher WM, Crown J, Fersht AR, Duffy MJ. Targeting mutant p53 with PK11007: A new approach for the treatment of patients with triple-negative breast cancer? J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.e14099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e14099 Background:The identification of a targeted therapy for patients with triple-negative breast cancer (TNBC) is one of the most urgent needs in breast cancer therapeutics. Since the p53 gene is mutated in approximately 80% of TNBC patients, it is a potential therapeutic target for this form of breast cancer. PK11007 is a 2-sulfonypyrimidine that stabilizes and reactivates mutant p53 (Bauer et al, PNAS 2016). The compound recently was reported to preferentially decrease viability in p53-compromised cancer cells. The aim of this investigation was to evaluate PK11007 as a potential new treatment for TNBC. Methods: Cell viability was determined using the MTT assay. Apoptosis was detected using Annexin V Apoptosis Detection Kit. Migration was determined by Transwell migration assay. Knockdowns of p53 protein were carried out using predesigned Flexitube sequences (Qiagen). Results: IC50 values for inhibition of proliferation by PK11007 in the panel of 17 breast cell lines ranged from 2.3 to 42.2 μM. There were significantly lower IC50values for TNBC than for non-TNBC cell lines (p = 0.03) and for p53-mutated cell lines compared with p53 WT cells (p = 0.003). Response to PK11007 however, was independent of ER or HER2 status of the cells. In addition, PK11007 induced apoptosis and inhibited migration in p53 mutant cell lines. Using RNAseq and gene ontogeny analysis, we found that PK11007 altered the expression of genes enriched in pathways involved in regulated cell death, regulation of apoptosis, signal transduction, protein refolding and locomotion. To establish if PK11007 acts by targeting mutant p53, we used siRNA to knockdown p53 in 3 p53-mutated TNBC cell lines. Reduction in p53 protein levels resulted in a significant decrease in the growth inhibitory effects of PK11007, in all 3 cell lines investigated, suggesting that PK11007 mediates growth inhibition via p53. The observations that PK11007 inhibited cell growth, induced apoptosis, blocked cell migration and altered genes involved in cell death, are all consistent with the ability of PK11007 to activate mutant p53. Conclusions: Based on our data, we conclude that targeting mutant p53 with PK11007 is a potential approach for treating p53-mutated TNBC.
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Affiliation(s)
- Naoise C Synnott
- Education and Research Centre, St. Vincent's University Hospital, Dublin, Ireland
| | - Matthias R Bauer
- Medical Research Council Lab of Molecular Biology, Cambridge, United Kingdom
| | - Stephen F. Madden
- Population Health Sciences, Department of Psychology, Royal College of Surgeons, Dublin, Ireland
| | - Alyson M. Murray
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Rut Klinger
- University College Dublin School of Biomolecular and Biomedical Science, Dublin, Ireland
| | - Norma O'Donovan
- Molecular Therapeutics for Cancer Ireland, National Institute for Cellular Biotechnology, Dublin City University, Dublin, Ireland
| | - Darran O'Connor
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - William M. Gallagher
- University College Dublin School of Biomolecular and Biomedical Science, Dublin, Ireland
| | - John Crown
- Irish Cooperative Oncology Research Group, Dublin, Ireland
| | - Alan R Fersht
- Medical Research Council Lab of Molecular Biology, Cambridge, United Kingdom
| | - Michael J. Duffy
- Clinical Research Centre, St.Vincent's University Hospital and School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
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Baretić D, Pollard HK, Fisher DI, Johnson CM, Santhanam B, Truman CM, Kouba T, Fersht AR, Phillips C, Williams RL. Structures of closed and open conformations of dimeric human ATM. Sci Adv 2017; 3:e1700933. [PMID: 28508083 PMCID: PMC5425235 DOI: 10.1126/sciadv.1700933] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/19/2017] [Indexed: 05/31/2023]
Abstract
ATM (ataxia-telangiectasia mutated) is a phosphatidylinositol 3-kinase-related protein kinase (PIKK) best known for its role in DNA damage response. ATM also functions in oxidative stress response, insulin signaling, and neurogenesis. Our electron cryomicroscopy (cryo-EM) suggests that human ATM is in a dynamic equilibrium between closed and open dimers. In the closed state, the PIKK regulatory domain blocks the peptide substrate-binding site, suggesting that this conformation may represent an inactive or basally active enzyme. The active site is held in this closed conformation by interaction with a long helical hairpin in the TRD3 (tetratricopeptide repeats domain 3) domain of the symmetry-related molecule. The open dimer has two protomers with only a limited contact interface, and it lacks the intermolecular interactions that block the peptide-binding site in the closed dimer. This suggests that the open conformation may be more active. The ATM structure shows the detailed topology of the regulator-interacting N-terminal helical solenoid. The ATM conformational dynamics shown by the structures represent an important step in understanding the enzyme regulation.
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Affiliation(s)
- Domagoj Baretić
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Hannah K. Pollard
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, Cambridge CB4 0WG, UK
| | - David I. Fisher
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, Cambridge CB4 0WG, UK
| | | | - Balaji Santhanam
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Caroline M. Truman
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, Cambridge CB4 0WG, UK
| | - Tomas Kouba
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Alan R. Fersht
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Christopher Phillips
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, Cambridge CB4 0WG, UK
| | - Roger L. Williams
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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11
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Martin TG, Bharat TAM, Joerger AC, Bai XC, Praetorius F, Fersht AR, Dietz H, Scheres SHW. Design of a molecular support for cryo-EM structure determination. Proc Natl Acad Sci U S A 2016; 113:E7456-E7463. [PMID: 27821763 PMCID: PMC5127339 DOI: 10.1073/pnas.1612720113] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite the recent rapid progress in cryo-electron microscopy (cryo-EM), there still exist ample opportunities for improvement in sample preparation. Macromolecular complexes may disassociate or adopt nonrandom orientations against the extended air-water interface that exists for a short time before the sample is frozen. We designed a hollow support structure using 3D DNA origami to protect complexes from the detrimental effects of cryo-EM sample preparation. For a first proof-of-principle, we concentrated on the transcription factor p53, which binds to specific DNA sequences on double-stranded DNA. The support structures spontaneously form monolayers of preoriented particles in a thin film of water, and offer advantages in particle picking and sorting. By controlling the position of the binding sequence on a single helix that spans the hollow support structure, we also sought to control the orientation of individual p53 complexes. Although the latter did not yet yield the desired results, the support structures did provide partial information about the relative orientations of individual p53 complexes. We used this information to calculate a tomographic 3D reconstruction, and refined this structure to a final resolution of ∼15 Å. This structure settles an ongoing debate about the symmetry of the p53 tetramer bound to DNA.
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Affiliation(s)
- Thomas G Martin
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Tanmay A M Bharat
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Andreas C Joerger
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
- German Cancer Consortium (DKTK), Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany
| | - Xiao-Chen Bai
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Florian Praetorius
- Physik Department, Walter Schottky Institute, Technische Universität München, 85748 Garching near Munich, Germany
| | - Alan R Fersht
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Hendrik Dietz
- Physik Department, Walter Schottky Institute, Technische Universität München, 85748 Garching near Munich, Germany
| | - Sjors H W Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom;
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12
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Joerger AC, Bauer MR, Wilcken R, Baud MGJ, Harbrecht H, Exner TE, Boeckler FM, Spencer J, Fersht AR. Exploiting Transient Protein States for the Design of Small-Molecule Stabilizers of Mutant p53. Structure 2016; 23:2246-2255. [PMID: 26636255 PMCID: PMC4671956 DOI: 10.1016/j.str.2015.10.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/30/2015] [Accepted: 10/04/2015] [Indexed: 12/01/2022]
Abstract
The destabilizing p53 cancer mutation Y220C creates an extended crevice on the surface of the protein that can be targeted by small-molecule stabilizers. Here, we identify different classes of small molecules that bind to this crevice and determine their binding modes by X-ray crystallography. These structures reveal two major conformational states of the pocket and a cryptic, transiently open hydrophobic subpocket that is modulated by Cys220. In one instance, specifically targeting this transient protein state by a pyrrole moiety resulted in a 40-fold increase in binding affinity. Molecular dynamics simulations showed that both open and closed states of this subsite were populated at comparable frequencies along the trajectories. Our data extend the framework for the design of high-affinity Y220C mutant binders for use in personalized anticancer therapy and, more generally, highlight the importance of implementing protein dynamics and hydration patterns in the drug-discovery process.
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Affiliation(s)
- Andreas C Joerger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Matthias R Bauer
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Rainer Wilcken
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Matthias G J Baud
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Hannes Harbrecht
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Thomas E Exner
- Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Frank M Boeckler
- Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - John Spencer
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex BN1 9QJ, UK
| | - Alan R Fersht
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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13
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Bromley D, Bauer MR, Fersht AR, Daggett V. An in silico algorithm for identifying stabilizing pockets in proteins: test case, the Y220C mutant of the p53 tumor suppressor protein. Protein Eng Des Sel 2016; 29:377-90. [PMID: 27503952 PMCID: PMC5001139 DOI: 10.1093/protein/gzw035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 04/23/2016] [Accepted: 04/23/2016] [Indexed: 11/14/2022] Open
Abstract
The p53 tumor suppressor protein performs a critical role in stimulating apoptosis and cell cycle arrest in response to oncogenic stress. The function of p53 can be compromised by mutation, leading to increased risk of cancer; approximately 50% of cancers are associated with mutations in the p53 gene, the majority of which are in the core DNA-binding domain. The Y220C mutation of p53, for example, destabilizes the core domain by 4 kcal/mol, leading to rapid denaturation and aggregation. The associated loss of tumor suppressor functionality is associated with approximately 75 000 new cancer cases every year. Destabilized p53 mutants can be 'rescued' and their function restored; binding of a small molecule into a pocket on the surface of mutant p53 can stabilize its wild-type structure and restore its function. Here, we describe an in silico algorithm for identifying potential rescue pockets, including the algorithm's integration with the Dynameomics molecular dynamics data warehouse and the DIVE visual analytics engine. We discuss the results of the application of the method to the Y220C p53 mutant, entailing finding a putative rescue pocket through MD simulations followed by an in silico search for stabilizing ligands that dock into the putative rescue pocket. The top three compounds from this search were tested experimentally and one of them bound in the pocket, as shown by nuclear magnetic resonance, and weakly stabilized the mutant.
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Affiliation(s)
- Dennis Bromley
- Division of Biomedical and Health Informatics, Department of Biomedical Informatics and Medical Education, University of Washington, Box SLU-BIME 358047, 850 Republican St, Building C, Seattle, WA 98109-4714, USA
| | - Matthias R Bauer
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alan R Fersht
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Valerie Daggett
- Division of Biomedical and Health Informatics, Department of Biomedical Informatics and Medical Education, University of Washington, Box SLU-BIME 358047, 850 Republican St, Building C, Seattle, WA 98109-4714, USA Department of Bioengineering, University of Washington, Box 355013, Seattle, WA 98195-5013, USA
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14
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Bauer MR, Jones RN, Baud MGJ, Wilcken R, Boeckler FM, Fersht AR, Joerger AC, Spencer J. Harnessing Fluorine-Sulfur Contacts and Multipolar Interactions for the Design of p53 Mutant Y220C Rescue Drugs. ACS Chem Biol 2016; 11:2265-74. [PMID: 27267810 PMCID: PMC4994063 DOI: 10.1021/acschembio.6b00315] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Many oncogenic mutants
of the tumor suppressor p53 are conformationally unstable, including
the frequently occurring Y220C mutant. We have previously developed
several small-molecule stabilizers of this mutant. One of these molecules,
PhiKan083, 1-(9-ethyl-9H-carbazole-3-yl)-N-methylmethanamine,
binds to a mutation-induced surface crevice with a KD = 150 μM, thereby increasing the melting temperature
of the protein and slowing its rate of aggregation. Incorporation
of fluorine atoms into small molecule ligands can substantially improve
binding affinity to their protein targets. We have, therefore, harnessed
fluorine–protein interactions to improve the affinity of this
ligand. Step-wise introduction of fluorines at the carbazole ethyl
anchor, which is deeply buried within the binding site in the Y220C–PhiKan083
complex, led to a 5-fold increase in affinity for a 2,2,2-trifluoroethyl
anchor (ligand efficiency of 0.3 kcal mol–1 atom–1). High-resolution crystal structures of the Y220C–ligand
complexes combined with quantum chemical calculations revealed favorable
interactions of the fluorines with protein backbone carbonyl groups
(Leu145 and Trp146) and the sulfur of Cys220 at the mutation site.
Affinity gains were, however, only achieved upon trifluorination,
despite favorable interactions of the mono- and difluorinated anchors
with the binding pocket, indicating a trade-off between energetically
favorable protein–fluorine interactions and increased desolvation
penalties. Taken together, the optimized carbazole scaffold provides
a promising starting point for the development of high-affinity ligands
to reactivate the tumor suppressor function of the p53 mutant Y220C
in cancer cells.
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Affiliation(s)
- Matthias R. Bauer
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge
Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Rhiannon N. Jones
- Department
of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex BN1 9QJ, United Kingdom
| | - Matthias G. J. Baud
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge
Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Rainer Wilcken
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge
Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Frank M. Boeckler
- Molecular Design and Pharmaceutical Biophysics,
Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Alan R. Fersht
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge
Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Andreas C. Joerger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge
Biomedical Campus, Cambridge CB2 0QH, United Kingdom
- Department
of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex BN1 9QJ, United Kingdom
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe-University and Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str.
9, 60438 Frankfurt
am Main, Germany
| | - John Spencer
- Department
of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex BN1 9QJ, United Kingdom
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15
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Affiliation(s)
- Andreas C. Joerger
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany;
| | - Alan R. Fersht
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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16
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Wilcken R, Zimmermann MO, Bauer MR, Rutherford TJ, Fersht AR, Joerger AC, Boeckler FM. Experimental and Theoretical Evaluation of the Ethynyl Moiety as a Halogen Bioisostere. ACS Chem Biol 2015; 10:2725-32. [PMID: 26378745 PMCID: PMC4836799 DOI: 10.1021/acschembio.5b00515] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
![]()
Bioisosteric replacements
are widely used in medicinal chemistry
to improve physicochemical and ADME properties of molecules while
retaining or improving affinity. Here, using the p53 cancer mutant
Y220C as a test case, we investigate both computationally and experimentally
whether an ethynyl moiety is a suitable bioisostere to replace iodine
in ligands that form halogen bonds with the protein backbone. This
bioisosteric transformation is synthetically feasible via Sonogashira
cross-coupling. In our test case of a particularly strong halogen
bond, replacement of the iodine with an ethynyl group resulted in
a 13-fold affinity loss. High-resolution crystal structures of the
two analogues in complex with the p53-Y220C mutant enabled us to correlate
the different affinities with particular features of the binding site
and subtle changes in ligand binding mode. In addition, using QM calculations
and analyzing the PDB, we provide general guidelines for identifying
cases where such a transformation is likely to improve ligand recognition.
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Affiliation(s)
- Rainer Wilcken
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Markus O. Zimmermann
- Molecular
Design and Pharmaceutical Biophysics, Department of Pharmaceutical
and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Sand 1, 72076 Tübingen, Germany
| | - Matthias R. Bauer
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Trevor J. Rutherford
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Alan R. Fersht
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Andreas C. Joerger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Frank M. Boeckler
- Molecular
Design and Pharmaceutical Biophysics, Department of Pharmaceutical
and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Sand 1, 72076 Tübingen, Germany
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17
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Nasedkin A, Marcellini M, Religa TL, Freund SM, Menzel A, Fersht AR, Jemth P, van der Spoel D, Davidsson J. Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation. PLoS One 2015; 10:e0125662. [PMID: 25946337 PMCID: PMC4422743 DOI: 10.1371/journal.pone.0125662] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/11/2015] [Indexed: 12/30/2022] Open
Abstract
The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution.
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Affiliation(s)
- Alexandr Nasedkin
- Department of Chemistry-Ångström laboratory, Uppsala University, Box 523, SE-75110 Uppsala, Sweden
| | - Moreno Marcellini
- Uppsala Center for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden
| | - Tomasz L. Religa
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Stefan M. Freund
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | | | - Alan R. Fersht
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - David van der Spoel
- Uppsala Center for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden
| | - Jan Davidsson
- Department of Chemistry-Ångström laboratory, Uppsala University, Box 523, SE-75110 Uppsala, Sweden
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18
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Liu X, Wilcken R, Joerger AC, Chuckowree IS, Amin J, Spencer J, Fersht AR. Small molecule induced reactivation of mutant p53 in cancer cells. Nucleic Acids Res 2013; 41:6034-44. [PMID: 23630318 PMCID: PMC3695503 DOI: 10.1093/nar/gkt305] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The p53 cancer mutant Y220C is an excellent paradigm for rescuing the function of conformationally unstable p53 mutants because it has a unique surface crevice that can be targeted by small-molecule stabilizers. Here, we have identified a compound, PK7088, which is active in vitro: PK7088 bound to the mutant with a dissociation constant of 140 μM and raised its melting temperature, and we have determined the binding mode of a close structural analogue by X-ray crystallography. We showed that PK7088 is biologically active in cancer cells carrying the Y220C mutant by a battery of tests. PK7088 increased the amount of folded mutant protein with wild-type conformation, as monitored by immunofluorescence, and restored its transcriptional functions. It induced p53-Y220C-dependent growth inhibition, cell-cycle arrest and apoptosis. Most notably, PK7088 increased the expression levels of p21 and the proapoptotic NOXA protein. PK7088 worked synergistically with Nutlin-3 on up-regulating p21 expression, whereas Nutlin-3 on its own had no effect, consistent with its mechanism of action. PK7088 also restored non-transcriptional apoptotic functions of p53 by triggering nuclear export of BAX to the mitochondria. We suggest a set of criteria for assigning activation of p53.
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Affiliation(s)
- Xiangrui Liu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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19
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Herzog G, Joerger AC, Shmueli MD, Fersht AR, Gazit E, Segal D. Evaluating Drosophila p53 as a model system for studying cancer mutations. J Biol Chem 2012; 287:44330-7. [PMID: 23135266 DOI: 10.1074/jbc.m112.417980] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The transcription factor p53 is a key tumor suppressor protein. In about half of human cancers, p53 is inactivated directly through mutation in its sequence-specific DNA-binding domain. Drosophila p53 (Dmp53) has similar apoptotic functions as its human homolog and is therefore an attractive model system for studying cancer pathways. To probe the structure and function of Dmp53, we studied the effect of point mutations, corresponding to cancer hot spot mutations in human p53 (Hp53), on the stability and DNA binding affinity of the full-length protein. Despite low sequence conservation, the Hp53 and Dmp53 proteins had a similar melting temperature and generally showed a similar energetic and functional response to cancer-associated mutations. We also found a correlation between the thermodynamic stability of the mutant proteins and their rate of aggregation. The effects of the mutations were rationalized based on homology modeling of the Dmp53 DNA-binding domain, suggesting that the drastically different effects of a cancer mutation in the loop-sheet-helix motif (R282W in Hp53 and R268W in Dmp53) on stability and DNA binding affinity of the two proteins are related to conformational differences in the L1 loop adjacent to the mutation site. On the basis of these data, we discuss the advantages and limitations of using Dmp53 as a model system for studying p53 function and testing p53 rescue drugs.
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Affiliation(s)
- Gal Herzog
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
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20
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Abstract
Most proteins have not evolved for maximal thermal stability. Some are only marginally stable, as for example, the DNA-binding domains of p53 and its homologs, whose kinetic and thermodynamic stabilities are strongly correlated. Here, we applied high-throughput methods using a real-time PCR thermocycler to study the stability of several full-length orthologs and paralogs of the p53 family of transcription factors, which have diverse functions, ranging from tumour suppression to control of developmental processes. From isothermal denaturation fluorimetry and differential scanning fluorimetry, we found that full-length proteins showed the same correlation between kinetic and thermodynamic stability as their isolated DNA-binding domains. The stabilities of the full-length p53 orthologs were marginal and correlated with the temperature of their organism, paralleling the stability of the isolated DNA-binding domains. Additionally, the paralogs p63 and p73 were significantly more stable and long-lived than p53. The short half-life of p53 orthologs and the greater persistence of the paralogs may be biologically relevant.
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Affiliation(s)
- Tobias Brandt
- MRC Centre for Protein Engineering, Cambridge, United Kingdom
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Joel L. Kaar
- MRC Centre for Protein Engineering, Cambridge, United Kingdom
| | - Alan R. Fersht
- MRC Centre for Protein Engineering, Cambridge, United Kingdom
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Dmitry B. Veprintsev
- MRC Centre for Protein Engineering, Cambridge, United Kingdom
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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21
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Pagel K, Natan E, Hall Z, Fersht AR, Robinson CV. Intrinsically disordered p53 and its complexes populate compact conformations in the gas phase. Angew Chem Int Ed Engl 2012; 52:361-5. [PMID: 22777995 DOI: 10.1002/anie.201203047] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 05/16/2012] [Indexed: 11/11/2022]
Abstract
Spontaneous shrinking: the intrinsically disordered tumor suppressor protein p53 was analyzed by using a combination of ion mobility mass spectrometry and molecular dynamics simulations. Structured p53 subdomains retain their overall topology upon transfer into the gas phase. When intrinsically disordered segments are introduced into the protein sequence, however, the complex spontaneously collapses in the gas phase to a compact conformation.
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Affiliation(s)
- Kevin Pagel
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, UK
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22
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Pagel K, Natan E, Hall Z, Fersht AR, Robinson CV. Intrinsically Disordered p53 and Its Complexes Populate Compact Conformations in the Gas Phase. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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23
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Wilcken R, Liu X, Zimmermann MO, Rutherford TJ, Fersht AR, Joerger AC, Boeckler FM. Halogen-enriched fragment libraries as leads for drug rescue of mutant p53. J Am Chem Soc 2012; 134:6810-8. [PMID: 22439615 PMCID: PMC3789257 DOI: 10.1021/ja301056a] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Indexed: 12/14/2022]
Abstract
The destabilizing p53 cancer mutation Y220C creates a druggable surface crevice. We developed a strategy exploiting halogen bonding for lead discovery to stabilize the mutant with small molecules. We designed halogen-enriched fragment libraries (HEFLibs) as starting points to complement classical approaches. From screening of HEFLibs and subsequent structure-guided design, we developed substituted 2-(aminomethyl)-4-ethynyl-6-iodophenols as p53-Y220C stabilizers. Crystal structures of their complexes highlight two key features: (i) a central scaffold with a robust binding mode anchored by halogen bonding of an iodine with a main-chain carbonyl and (ii) an acetylene linker, enabling the targeting of an additional subsite in the crevice. The best binders showed induction of apoptosis in a human cancer cell line with homozygous Y220C mutation. Our structural and biophysical data suggest a more widespread applicability of HEFLibs in drug discovery.
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Affiliation(s)
- Rainer Wilcken
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard-Karls-University
Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
- MRC
Laboratory
of Molecular Biology, Hills Road, Cambridge CB2 0QH,
United Kingdom
| | - Xiangrui Liu
- MRC
Laboratory
of Molecular Biology, Hills Road, Cambridge CB2 0QH,
United Kingdom
| | - Markus O. Zimmermann
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard-Karls-University
Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
| | - Trevor J. Rutherford
- MRC
Laboratory
of Molecular Biology, Hills Road, Cambridge CB2 0QH,
United Kingdom
| | - Alan R. Fersht
- MRC
Laboratory
of Molecular Biology, Hills Road, Cambridge CB2 0QH,
United Kingdom
| | - Andreas C. Joerger
- MRC
Laboratory
of Molecular Biology, Hills Road, Cambridge CB2 0QH,
United Kingdom
| | - Frank M. Boeckler
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard-Karls-University
Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
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24
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Lum JK, Neuweiler H, Fersht AR. Long-range modulation of chain motions within the intrinsically disordered transactivation domain of tumor suppressor p53. J Am Chem Soc 2012; 134:1617-22. [PMID: 22176582 PMCID: PMC3265989 DOI: 10.1021/ja2078619] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tumor suppressor p53 is a hub protein with a multitude of binding partners, many of which target its intrinsically disordered N-terminal domain, p53-TAD. Partners, such as the N-terminal domain of MDM2, induce formation of local structure and leave the remainder of the domain apparently disordered. We investigated segmental chain motions in p53-TAD using fluorescence quenching of an extrinsic label by tryptophan in combination with fluorescence correlation spectroscopy (PET-FCS). We studied the loop closure kinetics of four consecutive segments within p53-TAD and their response to protein binding and phosphorylation. The kinetics was multiexponential, showing that the conformational ensemble of the domain deviates from random coil, in agreement with previous findings from NMR spectroscopy. Phosphorylations or binding of MDM2 changed the pattern of intrachain kinetics. Unexpectedly, we found that upon binding and phosphorylation chain motions were altered not only within the targeted segments but also in remote regions. Long-range interactions can be induced in an intrinsically disordered domain by partner proteins that induce apparently only local structure or by post-translational modification.
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Affiliation(s)
- Jenifer K Lum
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
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25
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Korzhnev DM, Vernon RM, Religa TL, Hansen AL, Baker D, Fersht AR, Kay LE. Nonnative interactions in the FF domain folding pathway from an atomic resolution structure of a sparsely populated intermediate: an NMR relaxation dispersion study. J Am Chem Soc 2011; 133:10974-82. [PMID: 21639149 DOI: 10.1021/ja203686t] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Several all-helical single-domain proteins have been shown to fold rapidly (microsecond time scale) to a compact intermediate state and subsequently rearrange more slowly to the native conformation. An understanding of this process has been hindered by difficulties in experimental studies of intermediates in cases where they are both low-populated and only transiently formed. One such example is provided by the on-pathway folding intermediate of the small four-helix bundle FF domain from HYPA/FBP11 that is populated at several percent with a millisecond lifetime at room temperature. Here we have studied the L24A mutant that has been shown previously to form nonnative interactions in the folding transition state. A suite of Carr-Purcell-Meiboom-Gill relaxation dispersion NMR experiments have been used to measure backbone chemical shifts and amide bond vector orientations of the invisible folding intermediate that form the input restraints in calculations of atomic resolution models of its structure. Despite the fact that the intermediate structure has many features that are similar to that of the native state, a set of nonnative contacts is observed that is even more extensive than noted previously for the wild-type (WT) folding intermediate. Such nonnative interactions, which must be broken prior to adoption of the native conformation, explain why the transition from the intermediate state to the native conformer (millisecond time scale) is significantly slower than from the unfolded ensemble to the intermediate and why the L24A mutant folds more slowly than the WT.
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Affiliation(s)
- Dmitry M Korzhnev
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
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26
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Radford IH, Fersht AR, Settanni G. Combination of Markov state models and kinetic networks for the analysis of molecular dynamics simulations of peptide folding. J Phys Chem B 2011; 115:7459-71. [PMID: 21553833 PMCID: PMC3106446 DOI: 10.1021/jp112158w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Atomistic molecular dynamics simulations of the TZ1 beta-hairpin peptide have been carried out using an implicit model for the solvent. The trajectories have been analyzed using a Markov state model defined on the projections along two significant observables and a kinetic network approach. The Markov state model allowed for an unbiased identification of the metastable states of the system, and provided the basis for commitment probability calculations performed on the kinetic network. The kinetic network analysis served to extract the main transition state for folding of the peptide and to validate the results from the Markov state analysis. The combination of the two techniques allowed for a consistent and concise characterization of the dynamics of the peptide. The slowest relaxation process identified is the exchange between variably folded and denatured species, and the second slowest process is the exchange between two different subsets of the denatured state which could not be otherwise identified by simple inspection of the projected trajectory. The third slowest process is the exchange between a fully native and a partially folded intermediate state characterized by a native turn with a proximal backbone H-bond, and frayed side-chain packing and termini. The transition state for the main folding reaction is similar to the intermediate state, although a more native like side-chain packing is observed.
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27
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Paleček E, Ostatná V, Černocká H, Joerger AC, Fersht AR. Electrocatalytic Monitoring of Metal Binding and Mutation-Induced Conformational Changes in p53 at Picomole Level. J Am Chem Soc 2011; 133:7190-6. [DOI: 10.1021/ja201006s] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Emil Paleček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Veronika Ostatná
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Hana Černocká
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | | | - Alan R. Fersht
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, U.K
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28
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Kaar JL, Basse N, Joerger AC, Stephens E, Rutherford TJ, Fersht AR. Stabilization of mutant p53 via alkylation of cysteines and effects on DNA binding. Protein Sci 2011; 19:2267-78. [PMID: 20878668 DOI: 10.1002/pro.507] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Oncogenic mutations inactivate the tumor suppressor p53 by lowering its stability or by weakening its binding to DNA. Alkylating agents that reactivate mutant p53 are currently being explored for cancer therapy. We have discovered ligands containing an α,β-unsaturated double bond, characteristic of Michael acceptors, that bind covalently to generic cysteine sites in the p53 core domain. They raised the melting temperature of the core domain of wild-type p53 and the hotspot mutants R175H, Y220C, G245S, R249S, and R282 by up to 3°C. Analysis of the relative reactivity of the cysteines in p53 by mass spectrometry found that C124 and C141 react first, followed by C135, C182, and C277, and eventually C176 and C275. Post-translational modifications of cysteines are known to be involved in regulation of other transcription factors. Modification of C277, which sits on the DNA-binding surface, may, for example, play a role in regulating p53 activity in cells in response to environmental cues. We found that the modifications progressively reduced DNA-binding activity of full-length p53. In light of these results, it is likely that the anticancer activity of the alkylating drugs works via a nontranscriptional activity of p53.
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Affiliation(s)
- Joel L Kaar
- Medical Research Council Centre for Protein Engineering, Cambridge CB2 0QH, United Kingdom
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29
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Arbely E, Neuweiler H, Sharpe TD, Johnson CM, Fersht AR. The human peripheral subunit-binding domain folds rapidly while overcoming repulsive Coulomb forces. Protein Sci 2011; 19:1704-13. [PMID: 20662005 DOI: 10.1002/pro.453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Peripheral subunit binding domains (PSBDs) are integral parts of large multienzyme complexes involved in carbohydrate metabolism. PSBDs facilitate shuttling of prosthetic groups between different catalytic subunits. Their protein surface is characterized by a high density of positive charges required for binding to subunits within the complex. Here, we investigated folding thermodynamics and kinetics of the human PSBD (HSBD) using circular dichroism and tryptophan fluorescence experiments. HSBD was only marginally stable under physiological solvent conditions but folded within microseconds via a barrier-limited apparent two-state transition, analogous to its bacterial homologues. The high positive surface-charge density of HSBD leads to repulsive Coulomb forces that modulate protein stability and folding kinetics, and appear to even induce native-state movement. The electrostatic strain was alleviated at high solution-ionic-strength by Debye-Hückel screening. Differences in ionic-strength dependent characteristics among PSBD homologues could be explained by differences in their surface charge distributions. The findings highlight the trade-off between protein function and stability during protein evolution.
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Affiliation(s)
- Eyal Arbely
- Medical Research Council Centre for Protein Engineering, Cambridge, United Kingdom
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30
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Konuma T, Kimura T, Matsumoto S, Goto Y, Fujisawa T, Fersht AR, Takahashi S. Time-Resolved Small-Angle X-ray Scattering Study of the Folding Dynamics of Barnase. J Mol Biol 2011; 405:1284-94. [DOI: 10.1016/j.jmb.2010.11.052] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 11/24/2010] [Accepted: 11/25/2010] [Indexed: 12/01/2022]
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31
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McCully ME, Beck DAC, Fersht AR, Daggett V. Refolding the engrailed homeodomain: structural basis for the accumulation of a folding intermediate. Biophys J 2010; 99:1628-36. [PMID: 20816076 DOI: 10.1016/j.bpj.2010.06.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 06/14/2010] [Accepted: 06/22/2010] [Indexed: 11/15/2022] Open
Abstract
The ultrafast folding pathway of the engrailed homeodomain has been exceptionally well characterized by experiment and simulation. Helices II and III of the three-helix bundle protein form the native helix-turn-helix motif as an on-pathway intermediate within a few microseconds. The slow step is then the proper docking of the helices in approximately 15 mus. However, there is still the unexplained puzzle of why helix docking is relatively slow, which is part of the more general question as to why rearrangements of intermediates occur slowly. To address this problem, we performed 46 all-atom molecular dynamics refolding simulations in explicit water, for a total of 15 micros of simulation time. The simulations started from an intermediate state structure that was generated in an unfolding simulation at 498 K and was then quenched to folding-permissive temperatures. The protein refolded successfully in only one of the 46 simulations, and in that case the refolding pathway mirrored the unfolding pathway at high temperature. In the 45 simulations in which the protein did not fully fold, nonnative salt bridges trapped the protein, which explains why the protein folds relatively slowly from the intermediate state.
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Affiliation(s)
- Michelle E McCully
- Biomolecular Structure and Design Program, Department of Bioengineering, University of Washington, Seattle, Washington, USA
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32
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Rajagopalan S, Huang F, Fersht AR. Single-Molecule characterization of oligomerization kinetics and equilibria of the tumor suppressor p53. Nucleic Acids Res 2010; 39:2294-303. [PMID: 21097469 PMCID: PMC3064802 DOI: 10.1093/nar/gkq800] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The state of oligomerization of the tumor suppressor p53 is an important factor in its various biological functions. It has a well-defined tetramerization domain, and the protein exists as monomers, dimers and tetramers in equilibrium. The dissociation constants between oligomeric forms are so low that they are at the limits of measurement by conventional methods in vitro. Here, we have used the high sensitivity of single-molecule methods to measure the equilibria and kinetics of oligomerization of full-length p53 and its isolated tetramerization domain, p53tet, at physiological temperature, pH and ionic strength using fluorescence correlation spectroscopy (FCS) in vitro. The dissociation constant at 37°C for tetramers dissociating into dimers for full-length p53 was 50 ± 7 nM, and the corresponding value for dimers into monomers was 0.55 ± 0.08 nM. The half-lives for the two processes were 20 and 50 min, respectively. The equivalent quantities for p53tet were 150 ± 10 nM, 1.0 ± 0.14 nM, 2.5 ± 0.4 min and 13 ± 2 min. The data suggest that unligated p53 in unstressed cells should be predominantly dimeric. Single-molecule FCS is a useful procedure for measuring dissociation equilibria, kinetics and aggregation at extreme sensitivity.
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33
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Briseño-Roa L, Timperley CM, Griffiths AD, Fersht AR. Phosphotriesterase variants with high methylphosphonatase activity and strong negative trade-off against phosphotriesters. Protein Eng Des Sel 2010; 24:151-9. [PMID: 21037279 DOI: 10.1093/protein/gzq076] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The most lethal organophosphorus nerve agents (NA), like sarin, soman, agent-VX and Russian-VX, share a methylphosphonate moiety. Pseudomonas diminuta phosphotriesterase (PTE) catalyses the hydrolysis of methylphosphonate NA analogues with a catalytic efficiency orders of magnitude lower than that towards the pesticide paraoxon. With a view to obtaining PTE variants that more readily accept methylphosphonate NA, ~75,000 PTE variants of the substrate-binding residues Gly-60, Ile-106, Leu-303 and Ser-308 were screened with fluorogenic analogues of the NA Russian-VX and cyclosarin. Seven new PTE variants were isolated, purified and their k(cat)/K(M) determined against five phosphotriesters and five methylphosphonate analogues of sarin, cyclosarin, soman, agent-VX and Russian-VX. The novel PTE variants exhibited as much as a 10-fold increase in activity towards the methylphosphonate compounds--many reaching a k(cat)/K(M) of 10⁶ M⁻¹ s⁻¹--and as much as a 29,000-fold decrease in their phosphotriesterase activity. The mutations found in two of the variants, SS0.5 (G60V/I106L/S308G) and SS4.5 (G60V/I106A/S308G), were modelled into a high-resolution structure of PTE-wild type and docked with analogues of cyclosarin and Russian-VX using Autodock 4.2. The kinetic data and docking simulations suggest that the increase in activity towards the methylphosphonates and the loss of function against the phosphotriesters were due to an alteration of the shape and hydrophobicity of the binding pocket that hinders the productive binding of non-chiral racemic phosphotriesters, yet allows the binding of the highly asymmetric methylphosphonates.
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Affiliation(s)
- Luis Briseño-Roa
- MRC Centre for Protein Engineering, Hills Road, Cambridge CB20QH, UK.
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34
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Arbely E, Rutherford TJ, Neuweiler H, Sharpe TD, Ferguson N, Fersht AR. Carboxyl pKa Values and Acid Denaturation of BBL. J Mol Biol 2010; 403:313-27. [DOI: 10.1016/j.jmb.2010.08.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 08/16/2010] [Accepted: 08/27/2010] [Indexed: 11/28/2022]
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35
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Korzhnev DM, Religa TL, Banachewicz W, Fersht AR, Kay LE. A Transient and Low-Populated Protein-Folding Intermediate at Atomic Resolution. Science 2010; 329:1312-6. [DOI: 10.1126/science.1191723] [Citation(s) in RCA: 250] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Proteins can sample conformational states that are critical for function but are seldom detected directly because of their low occupancies and short lifetimes. In this work, we used chemical shifts and bond-vector orientation constraints obtained from nuclear magnetic resonance relaxation dispersion spectroscopy, in concert with a chemical shift–based method for structure elucidation, to determine an atomic-resolution structure of an “invisible” folding intermediate of a small protein module: the FF domain. The structure reveals non-native elements preventing formation of the native conformation in the carboxyl-terminal part of the protein. This is consistent with the kinetics of folding in which a well-structured intermediate forms rapidly and then rearranges slowly to the native state. The approach introduces a general strategy for structure determination of low-populated and transiently formed protein states.
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36
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Briseño-Roa L, Oliynyk Z, Timperley CM, Griffiths AD, Fersht AR. Highest paraoxonase turnover rate found in a bacterial phosphotriesterase variant. Protein Eng Des Sel 2010; 24:209-11. [PMID: 20650962 DOI: 10.1093/protein/gzq046] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The bacterial phosphotriesterase (PTE) catalyses the hydrolysis of the man-made pesticide paraoxon with a diffusion-limited efficiency. Here we describe the selection and characterisation of PTE variant SS0.2 that possesses the highest paraoxonase turnover number so far described (k(cat) = 31,000 s⁻¹). The PTE-SS0.2 was selected from a library of binding-site mutants using a novel screening method that combines partial lysis of bacterial colonies and fluorogenic probes.
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Affiliation(s)
- Luis Briseño-Roa
- MRC Centre for Protein Engineering, Hills Road, Cambridge CB20QH, UK.
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37
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van Dieck J, Lum JK, Teufel DP, Fersht AR. S100 proteins interact with the N-terminal domain of MDM2. FEBS Lett 2010; 584:3269-74. [PMID: 20591429 DOI: 10.1016/j.febslet.2010.06.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 06/01/2010] [Accepted: 06/14/2010] [Indexed: 01/16/2023]
Abstract
S100 proteins interact with the transactivation domain and the C-terminus of p53. Further, S100B has been shown to interact with MDM2, a central negative regulator of p53. Here, we show that S100B bound directly to the folded N-terminal domain of MDM2 (residues 2-125) by size exclusion chromatography and surface plasmon resonance experiments. This interaction with MDM2 (2-125) is a general feature of S100 proteins; S100A1, S100A2, S100A4 and S100A6 also interact with MDM2 (2-125). These interactions with S100 proteins do not result in a ternary complex with MDM2 (2-125) and p53. Instead, we observe the ability of a subset of S100 proteins to disrupt the extent of MDM2-mediated p53 ubiquitylation in vitro.
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Affiliation(s)
- Jan van Dieck
- MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK
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38
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Rajagopalan S, Andreeva A, Rutherford TJ, Fersht AR. Mapping the physical and functional interactions between the tumor suppressors p53 and BRCA2. Proc Natl Acad Sci U S A 2010; 107:8587-92. [PMID: 20421506 PMCID: PMC2889359 DOI: 10.1073/pnas.1003689107] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
p53 maintains genome integrity either by regulating the transcription of genes involved in cell cycle, apoptosis, and DNA repair or by interacting with partner proteins. Here we provide evidence for a direct physical interaction between the tumor suppressors p53 and BRCA2. We found that the transactivation domain of p53 made specific interactions with the C-terminal oligonucleotide/oligosaccharide-binding-fold domains of BRCA2 (BRCA2(CTD)). A second distinct site situated on the p53 DNA-binding domain, bound to a region containing BRC repeats of BRCA2 (BRCA2([BRC1-8])) and may contribute synergistically for high affinity association of intact full-length proteins. Overexpression of BRCA2 and BRCA2(CTD) suppressed the transcriptional activity of p53 with a concomitant reduction in the expression of p53-target genes such as Bax and p21. Consequently, p53-mediated apoptosis was significantly attenuated by BRCA2. The observed physical association of p53 and BRCA2 may have important functional implications in the p53 transactivation-independent suppression of homologous recombination and suggests a possible interregulatory role for both proteins in apoptosis and DNA repair.
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Affiliation(s)
| | - Antonina Andreeva
- Laboratory of Molecular Biology, Medical Research Council Centre, Hills Road, Cambridge, CB2 0QH, United Kingdom
| | - Trevor J. Rutherford
- Laboratory of Molecular Biology, Medical Research Council Centre, Hills Road, Cambridge, CB2 0QH, United Kingdom
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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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40
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van Dieck J, Brandt T, Teufel DP, Veprintsev DB, Joerger AC, Fersht AR. Molecular basis of S100 proteins interacting with the p53 homologs p63 and p73. Oncogene 2010; 29:2024-35. [PMID: 20140014 DOI: 10.1038/onc.2009.490] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
S100 proteins modulate p53 activity by interacting with its tetramerization (p53TET, residues 325-355) and transactivation (residues 1-57) domains. In this study, we characterized biophysically the binding of S100A1, S100A2, S100A4, S100A6 and S100B to homologous domains of p63 and p73 in vitro by fluorescence anisotropy, analytical ultracentrifugation and analytical gel filtration. We found that S100A1, S100A2, S100A4, S100A6 and S100B proteins bound different p63 and p73 tetramerization domain variants and naturally occurring isoforms with varying affinities in a calcium-dependent manner. Additional interactions were observed with peptides derived from the p63 and p73 N-terminal transactivation domains. Importantly, S100 proteins bound p63 and p73 with different affinities in their different oligomeric states, similarly to the differential modes of binding to p53. On the basis of our data, we hypothesize that S100 proteins regulate the oligomerization state of all three p53 family members and their isoforms, with a potential physiological relevance in developmental and disease-related processes. The regulation of the p53 family by S100 is complicated and depends on the target preference of each individual S100 protein, the concentration of the proteins and calcium, as well as the splicing variation of p63 or p73. Our results outlining the complexity of the interaction should be considered when studying the functional effects of S100 proteins in their biological context.
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Affiliation(s)
- J van Dieck
- MRC Centre for Protein Engineering, Hills Road, Cambridge, UK
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41
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Abstract
The SAP domain from the Saccharomyces cerevisiae THO1 protein contains a hydrophobic core and just two α-helices. It could provide a system for studying protein folding that bridges the gap between studies on isolated helices and those on larger protein domains. We have engineered the SAP domain for protein folding studies by inserting a tryptophan residue into the hydrophobic core (L31W) and solved its structure. The helical regions had a backbone root mean-squared deviation of 0.9 Å from those of wild type. The mutation L31W destabilised wild type by 0.8 ± 0.1 kcal mol−1. The mutant folded in a reversible, apparent two-state manner with a microscopic folding rate constant of around 3700 s−1 and is suitable for extended studies of folding.
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42
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Basse N, Kaar JL, Settanni G, Joerger AC, Rutherford TJ, Fersht AR. Toward the Rational Design of p53-Stabilizing Drugs: Probing the Surface of the Oncogenic Y220C Mutant. ACTA ACUST UNITED AC 2010; 17:46-56. [DOI: 10.1016/j.chembiol.2009.12.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Revised: 11/27/2009] [Accepted: 12/14/2009] [Indexed: 01/13/2023]
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43
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Abstract
Currently, around 11 million people are living with a tumour that contains an inactivating mutation of TP53 (the human gene that encodes p53) and another 11 million have tumours in which the p53 pathway is partially abrogated through the inactivation of other signalling or effector components. The p53 pathway is therefore a prime target for new cancer drug development, and several original approaches to drug discovery that could have wide applications to drug development are being used. In one approach, molecules that activate p53 by blocking protein-protein interactions with MDM2 are in early clinical development. Remarkable progress has also been made in the development of p53-binding molecules that can rescue the function of certain p53 mutants. Finally, cell-based assays are being used to discover compounds that exploit the p53 pathway by either seeking targets and compounds that show synthetic lethality with TP53 mutations or by looking for non-genotoxic activators of the p53 response.
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44
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Fersht AR. Abstract IA-8: p53: From structure to drug discovery. Cancer Res 2009. [DOI: 10.1158/0008-5472.fbcr09-ia-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The ability to produce quantities of stable p53 and the use of new biophysical methods are giving novel insights into the oligomerization of p53 and how this may be important in its regulation. We have discovered that the association and dissociation of p53 is extremely slow and can take more time than the half-life of p53 in the cell. The rate of association equilibria can be catalyzed by the binding to DNA and proteins and also be regulated by the binding to proteins, such as members of the S100 family, for example. I will discuss these phenomena and the latest developments in rescuing unstable oncogenic mutants of p53 by lead compounds for novel anti-cancer drugs.
Citation Information: Cancer Res 2009;69(23 Suppl):IA-8.
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45
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Abstract
p53 maintains genome integrity by initiating the transcription of genes involved in cell-cycle arrest, senescence, apoptosis and DNA repair. The activity of p53 is regulated by both post-translational modifications and protein–protein interactions. p53 that has been phosphorylated at S366, S378 and T387 binds 14-3-3 proteins in vitro. Here, we show that these sites are potential 14-3-3 binding sites in vivo. Epsilon (ε) and gamma (γ) isoforms required phosphorylation at either of these sites for efficient interaction with p53, while for sigma (σ) and tau (τ) these sites are dispensable. Further, σ and τ bound more weakly to p53 C-terminal phosphopeptides than did ε and γ. However, the four isoforms bound tightly to di-phosphorylated p53 C-terminal peptides than did the mono-phosphorylated counterparts. Interestingly, all the isoforms studied transcriptionally activated wild-type p53. σ and τ stabilized p53 levels in cells, while ε and γ stimulated p53-DNA binding activity in vitro. Overall, the results suggest that structurally and functionally similar 14-3-3 isoforms may exert their regulatory potential on p53 through different mechanisms. We discuss the isoform-specific roles of 14-3-3 in p53 stabilization and activation of specific-DNA binding.
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46
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Abstract
The core domain of the tumor suppressor p53 has low thermodynamic stability, and many oncogenic mutations cause it to denature rapidly at body temperature. We made a series of core domain mutants that are significantly less or more stable than wild type to investigate effects of stability on the transcriptional activity and levels of native full-length p53 in H1299 mammalian cells. The levels of transcriptionally inactive native protein with inactivating mutations in the N-terminal transactivation domain correlated strongly with stability. The levels of transcriptionally active proteins, however, depended on both their stability and the transcriptional activity that leads to the feedback loop of proteolytic degradation via transcription of E3 ligases. A very highly stabilized quadruple mutant and an even more stable hexamutant were more active than wild-type p53 in terms of Bax transcription and apoptotic activity, and reached higher levels than wild type in cells. The increased activity did not result from increased overall stability but was due to a single known suppressor mutation, N239Y. It is possible that the low intrinsic stability of p53 is a means of keeping its level low in the cell by spontaneous denaturation, by a route additional to that of proteolytic degradation via E3 ligase pathways. Denatured p53 does accumulate in cells, and there are pathways for the proteolysis of denatured proteins.
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Affiliation(s)
- Kian Hoe Khoo
- From the Medical Research Council Centre for Protein Engineering, Cambridge CB2 0QH, United Kingdom
| | - Sebastian Mayer
- From the Medical Research Council Centre for Protein Engineering, Cambridge CB2 0QH, United Kingdom
| | - Alan R. Fersht
- From the Medical Research Council Centre for Protein Engineering, Cambridge CB2 0QH, United Kingdom
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47
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Abstract
The tumor suppressor protein p53 is a transcription factor that plays a key role in the prevention of cancer development. In response to oncogenic or other stresses, the p53 protein is activated and regulates the expression of a variety of target genes, resulting in cell cycle arrest, senescence, or apoptosis. Mutation of the p53 gene is the most common genetic alteration in human cancer, affecting more than 50% of human tumors. Most of these mutations inactivate the DNA-binding domain of the protein. In this chapter, we describe the structure of the wild-type p53 protein and present structural and functional data that provide the molecular basis for understanding the effects of common cancer mutations. Further, we assess novel therapeutic strategies that aim to rescue the function of p53 cancer mutants.
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Affiliation(s)
- Andreas C Joerger
- MRC Centre for Protein Engineering, Cambridge CB2 2QH, United Kingdom
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48
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Wong TS, Rajagopalan S, Freund SM, Rutherford TJ, Andreeva A, Townsley FM, Petrovich M, Fersht AR. Biophysical characterizations of human mitochondrial transcription factor A and its binding to tumor suppressor p53. Nucleic Acids Res 2009; 37:6765-83. [PMID: 19755502 PMCID: PMC2777442 DOI: 10.1093/nar/gkp750] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Human mitochondrial transcription factor A (TFAM) is a multi-functional protein, involved in different aspects of maintaining mitochondrial genome integrity. In this report, we characterized TFAM and its interaction with tumor suppressor p53 using various biophysical methods. DNA-free TFAM is a thermally unstable protein that is in equilibrium between monomers and dimers. Self-association of TFAM is modulated by its basic C-terminal tail. The DNA-binding ability of TFAM is mainly contributed by its first HMG-box, while the second HMG-box has low-DNA-binding capability. We also obtained backbone resonance assignments from the NMR spectra of both HMG-boxes of TFAM. TFAM binds primarily to the N-terminal transactivation domain of p53, with a Kd of 1.95 ± 0.19 μM. The C-terminal regulatory domain of p53 provides a secondary binding site for TFAM. The TFAM–p53-binding interface involves both TAD1 and TAD2 sub-domains of p53. Helices α1 and α2 of the HMG-box constitute the main p53-binding region. Since both TFAM and p53 binds preferentially to distorted DNA, the TFAM–p53 interaction is implicated in DNA damage and repair. In addition, the DNA-binding mechanism of TFAM and biological relevance of the TFAM–p53 interaction are discussed.
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Affiliation(s)
- Tuck Seng Wong
- MRC Centre for Protein Engineering, Medical Research Council, Hills Road, Cambridge CB2 0QH, UK
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49
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Rajagopalan S, Andreeva A, Teufel DP, Freund SM, Fersht AR. Interaction between the transactivation domain of p53 and PC4 exemplifies acidic activation domains as single-stranded DNA mimics. J Biol Chem 2009; 284:21728-37. [PMID: 19525231 PMCID: PMC2755895 DOI: 10.1074/jbc.m109.006429] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 06/11/2009] [Indexed: 12/03/2022] Open
Abstract
The tumor suppressor p53 regulates cell cycle arrest and apoptosis by transactivating several genes that are critical for these processes. The transcriptional activity of p53 is often regulated by post-translational modifications and its interactions with various transcriptional coactivators. Here we report a physical interaction between the N-terminal transactivation domain (TAD) of p53 and the C-terminal DNA-binding domain of positive cofactor 4 (PC4(CTD)). Using NMR spectroscopy, we showed that residues 35-57 (TAD2) interact with PC4. (15)N,(1)H HSQC and fluorescence competition experiments indicated that TAD binds to the DNA-binding site of PC4. Hepta-phosphorylation of the TAD peptide increased its binding affinity. Computer modeling of the p53N-PC4 complex revealed several important interactions that are reminiscent of those in the single-stranded DNA-PC4 complex. The ubiquitous nature of the acidic transactivation domain of p53 in mediating interactions with several transcription cofactors is also manifested as a DNA mimetic.
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Affiliation(s)
| | - Antonina Andreeva
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
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50
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Di Re M, Sembongi H, He J, Reyes A, Yasukawa T, Martinsson P, Bailey LJ, Goffart S, Boyd-Kirkup JD, Wong TS, Fersht AR, Spelbrink JN, Holt IJ. The accessory subunit of mitochondrial DNA polymerase gamma determines the DNA content of mitochondrial nucleoids in human cultured cells. Nucleic Acids Res 2009; 37:5701-13. [PMID: 19625489 PMCID: PMC2761280 DOI: 10.1093/nar/gkp614] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The accessory subunit of mitochondrial DNA polymerase gamma, POLGbeta, functions as a processivity factor in vitro. Here we show POLGbeta has additional roles in mitochondrial DNA metabolism. Mitochondrial DNA is arranged in nucleoprotein complexes, or nucleoids, which often contain multiple copies of the mitochondrial genome. Gene-silencing of POLGbeta increased nucleoid numbers, whereas over-expression of POLGbeta reduced the number and increased the size of mitochondrial nucleoids. Both increased and decreased expression of POLGbeta altered nucleoid structure and precipitated a marked decrease in 7S DNA molecules, which form short displacement-loops on mitochondrial DNA. Recombinant POLGbeta preferentially bound to plasmids with a short displacement-loop, in contrast to POLGalpha. These findings support the view that the mitochondrial D-loop acts as a protein recruitment centre, and suggest POLGbeta is a key factor in the organization of mitochondrial DNA in multigenomic nucleoprotein complexes.
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Affiliation(s)
- M Di Re
- MRC-Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
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