1
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Higbee PS, Dayhoff GW, Anbanandam A, Varma S, Daughdrill G. Structural Adaptation of Secondary p53 Binding Sites on MDM2 and MDMX. J Mol Biol 2024; 436:168626. [PMID: 38810774 DOI: 10.1016/j.jmb.2024.168626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/24/2024] [Accepted: 05/18/2024] [Indexed: 05/31/2024]
Abstract
The thermodynamics of secondary p53 binding sites on MDM2 and MDMX were evaluated using p53 peptides containing residues 16-29, 17-35, and 1-73. All the peptides had large, negative heat capacity (ΔCp), consistent with the burial of p53 residues F19, W23, and L26 in the primary binding sites of MDM2 and MDMX. MDMX has a higher affinity and more negative ΔCp than MDM2 for p5317-35, which is due to MDMX stabilization and not additional interactions with the secondary binding site. ΔCp measurements show binding to the secondary site is inhibited by the disordered tails of MDM2 for WT p53 but not a more helical mutant where proline 27 is changed to alanine. This result is supported by all-atom molecular dynamics simulations showing that p53 residues 30-35 turn away from the disordered tails of MDM2 in P27A17-35 and make direct contact with this region in p5317-35. Molecular dynamics simulations also suggest that an intramolecular methionine-aromatic motif found in both MDM2 and MDMX structurally adapts to support multiple p53 binding modes with the secondary site. ΔCp measurements also show that tighter binding of the P27A mutant to MDM2 and MDMX is due to increased helicity, which reduces the energetic penalty associated with coupled folding and binding. Our results will facilitate the design of selective p53 inhibitors for MDM2 and MDMX.
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Affiliation(s)
- Pirada Serena Higbee
- The Department of Molecular Biosciences, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Guy W Dayhoff
- The Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Asokan Anbanandam
- The Department of Molecular Biosciences, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Sameer Varma
- The Department of Molecular Biosciences, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA; The Department of Physics, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Gary Daughdrill
- The Department of Molecular Biosciences, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA.
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2
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Watanabe K, Zhao Q, Iwatsuki R, Fukui R, Ren W, Sugita Y, Nishida N. Deciphering the Multi-state Conformational Equilibrium of HDM2 in the Regulation of p53 Binding: Perspectives from Molecular Dynamics Simulation and NMR Analysis. J Am Chem Soc 2024; 146:9790-9800. [PMID: 38549219 DOI: 10.1021/jacs.3c14383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
HDM2 negatively regulates the activity of the tumor suppressor p53. Previous NMR studies have shown that apo-HDM2 interconverts between an "open" state in which the N-terminal "lid" is disordered and a "closed" state in which the lid covers the p53-binding site in the core region. Molecular dynamics (MD) simulation studies have been performed to elucidate the conformational dynamics of HDM2, but the direct relevance of the experimental and computational analyses is unclear. In addition, how the phosphorylation of S17 in the lid contributes to the inhibition of p53 binding remains controversial. Here, we used both NMR and MD simulations to investigate the conformational dynamics of apo-HDM2. The NMR analysis revealed that apo-HDM2 exists in a fast-exchanging equilibrium within two closed states, closed 1 and closed 2, in addition to a previously demonstrated slow-exchanging "open-closed" equilibrium. MD simulations visualized two characteristic closed states, where the spatial orientation of the key residues corresponds well to the chemical shift changes of the NMR spectra. Furthermore, the phosphorylation of S17 induced an equilibrium shift toward closed 1, thereby suppressing the binding of p53 to HDM2. This study reveals a multi-state equilibrium of apo-HDM2 and provides new insights into the regulation mechanism of HDM2-p53 interactions.
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Affiliation(s)
- Kazuki Watanabe
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Qingci Zhao
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Ryosuke Iwatsuki
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Ryota Fukui
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Weitong Ren
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Hirosawa 2-1, Wako 351-0918, Saitama, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Hirosawa 2-1, Wako 351-0918, Saitama, Japan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 6-7-1 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Hyogo, Japan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 6-7-1 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Hyogo, Japan
| | - Noritaka Nishida
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
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3
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Rizzuti B, Abian O, Velazquez-Campoy A, Neira JL. Conformational Stability of the N-Terminal Region of MDM2. Molecules 2023; 28:7578. [PMID: 38005300 PMCID: PMC10673428 DOI: 10.3390/molecules28227578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
MDM2 is an E3 ubiquitin ligase which is crucial for the degradation and inhibition of the key tumor-suppressor protein p53. In this work, we explored the stability and the conformational features of the N-terminal region of MDM2 (N-MDM2), through which it binds to the p53 protein as well as other protein partners. The isolated domain possessed a native-like conformational stability in a narrow pH range (7.0 to 10.0), as shown by intrinsic and 8-anilinonapthalene-1-sulfonic acid (ANS) fluorescence, far-UV circular dichroism (CD), and size exclusion chromatography (SEC). Guanidinium chloride (GdmCl) denaturation followed by intrinsic and ANS fluorescence, far-UV CD and SEC at physiological pH, and differential scanning calorimetry (DSC) and thermo-fluorescence experiments showed that (i) the conformational stability of isolated N-MDM2 was very low; and (ii) unfolding occurred through the presence of several intermediates. The presence of a hierarchy in the unfolding intermediates was also evidenced through DSC and by simulating the unfolding process with the help of computational techniques based on constraint network analysis (CNA). We propose that the low stability of this protein is related to its inherent flexibility and its ability to interact with several molecular partners through different routes.
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Affiliation(s)
- Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)—Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
| | - Olga Abian
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)—Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrián Velazquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)—Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - José L. Neira
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)—Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDIBE), Universidad Miguel Hernández, 03202 Elche, Spain
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4
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Wu J, Lu G, Wang X. MDM4 alternative splicing and implication in MDM4 targeted cancer therapies. Am J Cancer Res 2021; 11:5864-5880. [PMID: 35018230 PMCID: PMC8727814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/31/2021] [Indexed: 06/14/2023] Open
Abstract
The oncogenic MDM4, initially named MDMX, has been identified as a p53-interacting protein and a key upstream negative regulator of the tumor suppressor p53. Accumulating evidence indicates that MDM4 plays critical roles in the initiation and progression of multiple human cancers. MDM4 is frequently amplified and upregulated in human cancers, contributing to overgrowth and apoptosis inhibition by blocking the expression of downstream target genes of p53 pathway. Disruptors for MDM4-p53 interaction have been shown to restore the anti-tumor activity of p53 in cancer cells. MDM4 possesses multiple splicing isoforms whose expressions are driven by the presence of oncogenes in cancer cells. Some of the MDM4 splicing isoforms lack p53 binding domain and may exhibit p53-independent oncogenic functions. These features render MDM4 to be an attractive therapeutic target for cancer therapy. In the present review, we primarily focus on the detailed molecular structure of MDM4 splicing isoforms, candidate regulators for initiating MDM4 splicing, deregulation of MDM4 isoforms in cancer and potential therapy strategies by targeting splicing isoforms of MDM4.
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Affiliation(s)
- Jin Wu
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer CenterBuffalo, NY, USA
| | - Guanting Lu
- Department of Pathology, Key Laboratory of Tumor Molecular Research, People’s Hospital of Deyang City173 Tai Shan North Road, Deyang 618000, Sichuan, P. R. China
| | - Xinjiang Wang
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer CenterBuffalo, NY, USA
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5
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Li W, Peng X, Lang J, Xu C. Targeting Mouse Double Minute 2: Current Concepts in DNA Damage Repair and Therapeutic Approaches in Cancer. Front Pharmacol 2020; 11:631. [PMID: 32477121 PMCID: PMC7232544 DOI: 10.3389/fphar.2020.00631] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/21/2020] [Indexed: 01/14/2023] Open
Abstract
Defects in DNA damage repair may cause genome instability and cancer development. The tumor suppressor gene p53 regulates cell cycle arrest to allow time for DNA repair. The oncoprotein mouse double minute 2 (MDM2) promotes cell survival, proliferation, invasion, and therapeutic resistance in many types of cancer. The major role of MDM2 is to inhibit p53 activity and promote its degradation. In this review, we describe the influence of MDM2 on genomic instability, the role of MDM2 on releasing p53 and binding DNA repair proteins to inhibit repair, and the regulation network of MDM2 including its transcriptional modifications, protein stability, and localization following DNA damage in genome integrity maintenance and in MDM2-p53 axis control. We also discuss p53-dependent and p53 independent oncogenic function of MDM2 and the outcomes of clinical trials that have been used with clinical inhibitors targeting p53-MDM2 to treat certain cancers.
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Affiliation(s)
- Wen Li
- Cancer Clinical Research Center & Integrative Cancer Center, Sichuan Cancer Hospital & Institute Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xinhao Peng
- Cancer Clinical Research Center & Integrative Cancer Center, Sichuan Cancer Hospital & Institute Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.,Radiation Oncology Key Laboratory of Sichuan Province, Sichuan Cancer Hospital & Institute Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Jinyi Lang
- Cancer Clinical Research Center & Integrative Cancer Center, Sichuan Cancer Hospital & Institute Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.,Radiation Oncology Key Laboratory of Sichuan Province, Sichuan Cancer Hospital & Institute Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Chuan Xu
- Cancer Clinical Research Center & Integrative Cancer Center, Sichuan Cancer Hospital & Institute Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
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6
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Hitting on the move: Targeting intrinsically disordered protein states of the MDM2-p53 interaction. Eur J Med Chem 2019; 182:111588. [PMID: 31421630 DOI: 10.1016/j.ejmech.2019.111588] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/22/2019] [Accepted: 08/04/2019] [Indexed: 01/17/2023]
Abstract
Intrinsically disordered proteins are an emerging class of proteins without a folded structure and currently disorder-based drug targeting remains a challenge. p53 is the principal regulator of cell division and growth whereas MDM2 consists its main negative regulator. The MDM2-p53 recognition is a dynamic and multistage process that amongst other, employs the dissociation of a transient α-helical N-terminal ''lid'' segment of MDM2 from the proximity of the p53-complementary interface. Several small molecule inhibitors have been reported to inhibit the formation of the p53-MDM2 complex with the vast majority mimicking the p53 residues Phe19, Trp23 and Leu26. Recently, we have described the transit from the 3-point to 4-point pharmacophore model stabilizing this intrinsically disordered N-terminus by increasing the binding affinity by a factor of 3. Therefore, we performed a thorough SAR analysis, including chiral separation of key compound which was evaluated by FP and 2D NMR. Finally, p53-specific anti-cancer activity towards p53-wild-type cancer cells was observed for several representative compounds.
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7
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Neira JL, Díaz-García C, Prieto M, Coutinho A. The C-terminal SAM domain of p73 binds to the N terminus of MDM2. Biochim Biophys Acta Gen Subj 2019; 1863:760-770. [DOI: 10.1016/j.bbagen.2019.01.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/25/2019] [Accepted: 01/31/2019] [Indexed: 01/10/2023]
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8
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Levy R, Gregory E, Borcherds W, Daughdrill G. p53 Phosphomimetics Preserve Transient Secondary Structure but Reduce Binding to Mdm2 and MdmX. Biomolecules 2019; 9:biom9030083. [PMID: 30832340 PMCID: PMC6468375 DOI: 10.3390/biom9030083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 02/07/2023] Open
Abstract
The disordered p53 transactivation domain (p53TAD) contains specific levels of transient helical secondary structure that are necessary for its binding to the negative regulators, mouse double minute 2 (Mdm2) and MdmX. The interactions of p53 with Mdm2 and MdmX are also modulated by posttranslational modifications (PTMs) of p53TAD including phosphorylation at S15, T18 and S20 that inhibits p53-Mdm2 binding. It is unclear whether the levels of transient secondary structure in p53TAD are changed by phosphorylation or other PTMs. We used phosphomimetic mutants to determine if adding a negative charge at positions 15 and 18 has any effect on the transient secondary structure of p53TAD and protein-protein binding. Using a combination of biophysical and structural methods, we investigated the effects of single and multisite phosphomimetics on the transient secondary structure of p53TAD and its interaction with Mdm2, MdmX, and the KIX domain. The phosphomimetics reduced Mdm2 and MdmX binding affinity by 3–5-fold, but resulted in minimal changes in transient secondary structure, suggesting that the destabilizing effect of phosphorylation on the p53TAD-Mdm2 interaction is primarily electrostatic. Phosphomimetics had no effect on the p53-KIX interaction, suggesting that increased binding of phosphorylated p53 to KIX may be influenced by decreased competition with its negative regulators.
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Affiliation(s)
- Robin Levy
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA.
- Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL 33612, USA.
| | - Emily Gregory
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA.
- Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL 33612, USA.
| | - Wade Borcherds
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA.
- Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL 33612, USA.
| | - Gary Daughdrill
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA.
- Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL 33612, USA.
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9
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Chen J, Wang J, Pang L, Zhu W. Inhibiting mechanism of small molecule toward the p53-MDM2 interaction: A molecular dynamic exploration. Chem Biol Drug Des 2018; 92:1763-1777. [DOI: 10.1111/cbdd.13345] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/01/2018] [Accepted: 05/28/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Jianzhong Chen
- School of Science; Shandong Jiaotong University; Jinan China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center; Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Jinan Wang
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center; Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Laixue Pang
- School of Science; Shandong Jiaotong University; Jinan China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center; Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
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10
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Åberg E, Karlsson OA, Andersson E, Jemth P. Binding Kinetics of the Intrinsically Disordered p53 Family Transactivation Domains and MDM2. J Phys Chem B 2018; 122:6899-6905. [DOI: 10.1021/acs.jpcb.8b03876] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Emma Åberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - O. Andreas Karlsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
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11
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Chan JV, Ping Koh DX, Liu Y, Joseph TL, Lane DP, Verma CS, Tan YS. Role of the N-terminal lid in regulating the interaction of phosphorylated MDMX with p53. Oncotarget 2017; 8:112825-112840. [PMID: 29348869 PMCID: PMC5762554 DOI: 10.18632/oncotarget.22829] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/05/2017] [Indexed: 02/06/2023] Open
Abstract
Murine double minute 4 protein (MDMX) is crucial for the regulation of the tumor suppressor protein p53. Phosphorylation of the N-terminal domain of MDMX is thought to affect its binding with the transactivation domain of p53, thus playing a role in p53 regulation. In this study, the effects of MDMX phosphorylation on the binding of p53 were investigated using molecular dynamics simulations. It is shown that in addition to the previously proposed mechanism in which phosphorylated Y99 of MDMX inhibits p53 binding through steric clash with P27 of p53, the N-terminal lid of MDMX also appears to play an important role in regulating the phosphorylation-dependent interactions between MDMX and p53. In the proposed mechanism, phosphorylated Y99 aids in pulling the lid into the p53-binding pocket, thus inhibiting the binding between MDMX and p53. Rebinding of p53 appears to be facilitated by the subsequent phosphorylation of Y55, which draws the lid away from the binding pocket by electrostatic attraction of the lid's positively charged N-terminus. The ability to target these mechanisms for the proper regulation of p53 could have important implications for understanding cancer biology and for drug development.
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Affiliation(s)
- Jane Vin Chan
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore
| | - Dawn Xin Ping Koh
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore
| | - Yun Liu
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore
| | - Thomas L Joseph
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore
| | - David P Lane
- p53 Laboratory, Agency for Science, Technology and Research (ASTAR), Singapore
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore.,Department of Biological Sciences, National University of Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore
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12
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Kim D, Lee C, Lee S, Kim K, Han JJ, Cha E, Lim J, Cho Y, Hong S, Han K. The Mechanism of p53 Rescue by SUSP4. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201607819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Do‐Hyoung Kim
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Chewook Lee
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Si‐Hyung Lee
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Kyung‐Tae Kim
- Molecular Epidemology Branch Research Institute National Cancer Center 323 Ilsandong-gu, Goyang-si Gyeonggi-do 10408 Korea
| | - Joan J. Han
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- College of Human Medicine Michigan State University East Lansing MI 48824 USA
| | - Eun‐Ji Cha
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Ji‐Eun Lim
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Ye‐Jin Cho
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- Department of Bioinformatics University of Science and Technology 217, Gajeong-ro, Yuseong-gu Daejoen 34113 Korea
| | - Seung‐Hee Hong
- Division of Food Science and Culinary Art, Food and Nutrition Major Shinhan University 95 Hoam-ro, Uijeongbu-si Gyeonggi-do 11644 Korea
| | - Kyou‐Hoon Han
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- Department of Bioinformatics University of Science and Technology 217, Gajeong-ro, Yuseong-gu Daejoen 34113 Korea
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13
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Kim D, Lee C, Lee S, Kim K, Han JJ, Cha E, Lim J, Cho Y, Hong S, Han K. The Mechanism of p53 Rescue by SUSP4. Angew Chem Int Ed Engl 2016; 56:1278-1282. [DOI: 10.1002/anie.201607819] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/25/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Do‐Hyoung Kim
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Chewook Lee
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Si‐Hyung Lee
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Kyung‐Tae Kim
- Molecular Epidemology Branch Research Institute National Cancer Center 323 Ilsandong-gu, Goyang-si Gyeonggi-do 10408 Korea
| | - Joan J. Han
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- College of Human Medicine Michigan State University East Lansing MI 48824 USA
| | - Eun‐Ji Cha
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Ji‐Eun Lim
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Ye‐Jin Cho
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- Department of Bioinformatics University of Science and Technology 217, Gajeong-ro, Yuseong-gu Daejoen 34113 Korea
| | - Seung‐Hee Hong
- Division of Food Science and Culinary Art, Food and Nutrition Major Shinhan University 95 Hoam-ro, Uijeongbu-si Gyeonggi-do 11644 Korea
| | - Kyou‐Hoon Han
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- Department of Bioinformatics University of Science and Technology 217, Gajeong-ro, Yuseong-gu Daejoen 34113 Korea
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14
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Ciemny MP, Debinski A, Paczkowska M, Kolinski A, Kurcinski M, Kmiecik S. Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction. Sci Rep 2016; 6:37532. [PMID: 27905468 PMCID: PMC5131342 DOI: 10.1038/srep37532] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/27/2016] [Indexed: 12/27/2022] Open
Abstract
Protein-peptide interactions are often associated with large-scale conformational changes that are difficult to study either by classical molecular modeling or by experiment. Recently, we have developed the CABS-dock method for flexible protein-peptide docking that enables large-scale rearrangements of the protein chain. In this study, we use CABS-dock to investigate the binding of the p53-MDM2 complex, an element of the cell cycle regulation system crucial for anti-cancer drug design. Experimental data suggest that p53-MDM2 binding is affected by significant rearrangements of a lid region - the N-terminal highly flexible MDM2 fragment; however, the details are not clear. The large size of the highly flexible MDM2 fragments makes p53-MDM2 intractable for exhaustive binding dynamics studies using atomistic models. We performed extensive dynamics simulations using the CABS-dock method, including large-scale structural rearrangements of MDM2 flexible regions. Without a priori knowledge of the p53 peptide structure or its binding site, we obtained near-native models of the p53-MDM2 complex. The simulation results match well the experimental data and provide new insights into the possible role of the lid fragment in p53 binding. The presented case study demonstrates that CABS-dock methodology opens up new opportunities for protein-peptide docking with large-scale changes of the protein receptor structure.
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Affiliation(s)
- Maciej Pawel Ciemny
- University of Warsaw, Faculty of Chemistry, Warsaw 02-093, Poland
- University of Warsaw, Faculty of Physics, Warsaw, 02-093, Poland
| | | | - Marta Paczkowska
- University of Warsaw, Faculty of Chemistry, Warsaw 02-093, Poland
| | - Andrzej Kolinski
- University of Warsaw, Faculty of Chemistry, Warsaw 02-093, Poland
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15
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Zhang W, Zhong T, Chen Y. LC-MS/MS-based targeted proteomics quantitatively detects the interaction between p53 and MDM2 in breast cancer. J Proteomics 2016; 152:172-180. [PMID: 27826076 DOI: 10.1016/j.jprot.2016.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/19/2016] [Accepted: 11/01/2016] [Indexed: 12/31/2022]
Abstract
In breast cancer, p53 could be functionally compromised by interaction with several proteins. Among those proteins, MDM2 serves as a pivotal negative regulator and counteracts p53 activation. Thus, the ability to quantitatively and accurately monitor the changes in level of p53-MDM2 interaction with disease state can enable an improved understanding of this protein-protein interaction (PPI), provide a better insight into cancer development and allow the emergence of advanced treatments. However, rare studies have evaluated the quantitative extent of PPI including p53-MDM2 interaction so far. In this study, a LC-MS/MS-based targeted proteomics assay was developed and coupled with co-immunoprecipitation (Co-IP) for the quantification of p53-MDM2 complex. A p53 antibody with the epitope residing at 156-214 residues achieved the greatest IP efficiency. 321KPLDGEYFTLQIR333 (p53) and 327ENWLPEDK334 (MDM2) were selected as surrogate peptides in the targeted analysis. Stable isotope-labeled synthetic peptides were used as internal standards. An LOQ (limit of quantification) of 2ng/mL was obtained. Then, the assay was applied to quantitatively detect total p53, total MDM2 and p53-MDM2 in breast cells and tissue samples. Western blotting was performed for a comparison. Finally, a quantitative time-course analysis in MCF-7 cells with the treatment of nutlin-3 as a PPI inhibitor was also monitored. BIOLOGICAL SIGNIFICANCE Proteins do not function as single entities but rather as a team player that has to communicate. Protein-protein interaction (PPI), normally by means of non-covalent contact among binary or large protein complex, is essential for many cellular processes including cancer progression. Thus, the ability to quantitatively and accurately monitor the changes in level of PPI with disease state can enable an improved understanding of PPI, provide a better insight into cancer development and allow the emergence of advanced treatments. However, rare studies have evaluated the quantitative extent of PPI so far. The major issue of current available approaches is the trade-off between sensitivity and specificity. Thus, techniques with the ability to quantify PPIs with both high sensitivity (low false-negative rate) and high specificity (low false-positive rate) are eagerly desired. Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted proteomics has shown its potential to study biomolecules because of its high sensitivity, high selectivity and wide dynamic range. In this study, we made an effort to develop a LC-MS/MS-based targeted proteomics assay for the quantitative detection of p53-MDM2 interaction in breast cells and tissue samples.
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Affiliation(s)
- Wen Zhang
- School of Pharmacy, Nanjing Medical University, 818 Tian Yuan East Road, Nanjing 211166, China
| | - Ting Zhong
- School of Pharmacy, Nanjing Medical University, 818 Tian Yuan East Road, Nanjing 211166, China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, 818 Tian Yuan East Road, Nanjing 211166, China.
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16
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Zwier MC, Pratt AJ, Adelman JL, Kaus JW, Zuckerman DM, Chong LT. Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein-Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide. J Phys Chem Lett 2016; 7:3440-5. [PMID: 27532687 PMCID: PMC5008990 DOI: 10.1021/acs.jpclett.6b01502] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The characterization of protein binding processes - with all of the key conformational changes - has been a grand challenge in the field of biophysics. Here, we have used the weighted ensemble path sampling strategy to orchestrate molecular dynamics simulations, yielding atomistic views of protein-peptide binding pathways involving the MDM2 oncoprotein and an intrinsically disordered p53 peptide. A total of 182 independent, continuous binding pathways were generated, yielding a kon that is in good agreement with experiment. These pathways were generated in 15 days using 3500 cores of a supercomputer, substantially faster than would be possible with "brute force" simulations. Many of these pathways involve the anchoring of p53 residue F19 into the MDM2 binding cleft when forming the metastable encounter complex, indicating that F19 may be a kinetically important residue. Our study demonstrates that it is now practical to generate pathways and calculate rate constants for protein binding processes using atomistic simulation on typical computing resources.
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Affiliation(s)
- Matthew C. Zwier
- Department of Chemistry, Drake University, Des Moines, Iowa 50311, United States
| | - Adam J. Pratt
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Joshua L. Adelman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Joseph W. Kaus
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Daniel M. Zuckerman
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Lillian T. Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Institute of Biochemistry and Biotechnology, Martin-Luther Universität Halle-Wittenberg, Halle 06120, Germany
- Corresponding Author:
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17
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Marine JC, Jochemsen AG. MDMX (MDM4), a Promising Target for p53 Reactivation Therapy and Beyond. Cold Spring Harb Perspect Med 2016; 6:6/7/a026237. [PMID: 27371671 DOI: 10.1101/cshperspect.a026237] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The MDMX protein was identified as a p53-interacting protein with a strong similarity to MDM2. Like Mdm2, Mdmx expression is essential for curbing p53 activity during embryonic development, indicating nonredundant functions of Mdmx and Mdm2. There is now a large body of evidence indicating that cancers frequently up-regulate MDMX expression as a means to dampen p53 tumor-suppressor function. Importantly, MDMX also shows p53-independent oncogenic functions. These data make MDMX an attractive therapeutic target for cancer therapy. Here, we summarize the mechanisms used by cancer cells to increase MDMX expression and promising pharmacological strategies to target MDMX in cancer-in particular, the recent findings that antisense oligonucleotides (ASOs) can be used to efficiently modulate MDMX messenger RNA (mRNA) splicing.
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Affiliation(s)
- Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for the Biology of Disease, VIB, 3000 Leuven, Belgium Laboratory for Molecular Cancer Biology, Center of Human Genetics, KULeuven, 3000 Leuven, Belgium
| | - Aart G Jochemsen
- Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RA Leiden, The Netherlands
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18
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Bueren-Calabuig JA, Michel J. Impact of Ser17 Phosphorylation on the Conformational Dynamics of the Oncoprotein MDM2. Biochemistry 2016; 55:2500-9. [PMID: 27050388 DOI: 10.1021/acs.biochem.6b00127] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
MDM2 is an important oncoprotein that downregulates the activity of the tumor suppressor protein p53 via binding of its N-terminal domain to the p53 transactivation domain. The first 24 residues of the MDM2 N-terminal domain form an intrinsically disordered "lid" region that interconverts on a millisecond time scale between "open" and "closed" states in unliganded MDM2. While the former conformational state is expected to facilitate p53 binding, the latter competes in a pseudo-substrate manner with p53 for its binding site. Phosphorylation of serine 17 in the MDM2 lid region is thought to modulate the equilibrium between "open" and "closed" lid states, but contradictory findings on the favored lid conformational state upon phosphorylation have been reported. Here, the nature of the conformational states of MDM2 pSer17 and Ser17Asp variants was addressed by means of enhanced sampling molecular dynamics simulations. Detailed analyses of the computed lid conformational ensembles indicate that both lid variants stabilize a "closed" state, with respect to wild type. Nevertheless, the nature of the closed-state conformational ensembles differs significantly between the pSer17 and Ser17Asp variants. Thus, care should be applied in the interpretation of biochemical experiments that use phosphomimetic variants to model the effects of phosphorylation on the structure and dynamics of this disordered protein region.
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Affiliation(s)
- Juan A Bueren-Calabuig
- EaStCHEM School of Chemistry, The University of Edinburgh , Edinburgh, EH9 3FJ, United Kingdom
- Computational Biology, School of Life Sciences, School of Science and Engineering, University of Dundee , Dow Street, Dundee, DD1 5EH, United Kingdom
| | - Julien Michel
- EaStCHEM School of Chemistry, The University of Edinburgh , Edinburgh, EH9 3FJ, United Kingdom
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19
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Structural basis of how stress-induced MDMX phosphorylation activates p53. Oncogene 2016; 35:1919-25. [PMID: 26148237 PMCID: PMC5470632 DOI: 10.1038/onc.2015.255] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 05/04/2015] [Accepted: 05/10/2015] [Indexed: 02/06/2023]
Abstract
The tumor-suppressor protein p53 is tightly controlled in normal cells by its two negative regulators--the E3 ubiquitin ligase MDM2 and its homolog MDMX. Under stressed conditions such as DNA damage, p53 escapes MDM2- and MDMX-mediated functional inhibition and degradation, acting to prevent damaged cells from proliferating through induction of cell cycle arrest, DNA repair, senescence or apoptosis. Ample evidence suggests that stress signals induce phosphorylation of MDM2 and MDMX, leading to p53 activation. However, the structural basis of stress-induced p53 activation remains poorly understood because of the paucity of technical means to produce site-specifically phosphorylated MDM2 and MDMX proteins for biochemical and biophysical studies. Herein, we report total chemical synthesis, via native chemical ligation, and functional characterization of (24-108)MDMX and its Tyr99-phosphorylated analog with respect to their ability to interact with a panel of p53-derived peptide ligands and PMI, a p53-mimicking but more potent peptide antagonist of MDMX, using FP and surface plasmon resonance techniques. Phosphorylation of MDMX at Tyr99 weakens peptide binding by approximately two orders of magnitude. Comparative X-ray crystallographic analyses of MDMX and of pTyr99 MDMX in complex with PMI as well as modeling studies reveal that the phosphate group of pTyr99 imposes extensive steric clashes with the C-terminus of PMI or p53 peptide and induces a significant lateral shift of the peptide ligand, contributing to the dramatic decrease in the binding affinity of MDMX for p53. Because DNA damage activates c-Abl tyrosine kinase that phosphorylates MDMX at Tyr99, our findings afford a rare glimpse at the structural level of how stress-induced MDMX phosphorylation dislodges p53 from the inhibitory complex and activates it in response to DNA damage.
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20
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The E3 ubiquitin protein ligase MDM2 dictates all-trans retinoic acid-induced osteoblastic differentiation of osteosarcoma cells by modulating the degradation of RARα. Oncogene 2016; 35:4358-67. [DOI: 10.1038/onc.2015.503] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 11/30/2015] [Accepted: 12/04/2015] [Indexed: 12/15/2022]
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21
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Chen X, Lu W. Functional Interrogation of the N-Terminal Lid of MDMX in p53 Binding via Native Chemical Ligation. Chem Pharm Bull (Tokyo) 2016; 64:1004-8. [DOI: 10.1248/cpb.c15-00975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Xishan Chen
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute
| | - Weiyue Lu
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education
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22
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Shin JS, Ha JH, Lee DH, Ryu KS, Bae KH, Park BC, Park SG, Yi GS, Chi SW. Structural convergence of unstructured p53 family transactivation domains in MDM2 recognition. Cell Cycle 2015; 14:533-43. [PMID: 25591003 DOI: 10.1080/15384101.2014.998056] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The p53, p63, and p73 proteins belong to the p53 family of transcription factors, which play key roles in tumor suppression. Although the transactivation domains (TADs) of the p53 family are intrinsically disordered, these domains are commonly involved in the regulatory interactions with mouse double minute 2 (MDM2). In this study, we determined the solution structure of the p73TAD peptide in complex with MDM2 using NMR spectroscopy and biophysically characterized the interactions between the p53 family TAD peptides and MDM2. In combination with mutagenesis data, the complex structures revealed remarkably close mimicry of the MDM2 recognition mechanism among the p53 family TADs. Upon binding with MDM2, the intrinsically disordered p73TAD and p63TAD peptides adopt an amphipathic α-helical conformation, which is similar to the conformation of p53TAD, although the α-helical content induced by MDM2 binding varies. With isothermal titration calorimetry (ITC) and circular dichroism (CD) data, our biophysical characterization showed that p73TAD resembles p53TAD more closely than p63TAD in terms of helical stability, MDM2 binding affinity, and phosphorylation effects on MDM2 binding. Therefore, our structural information may be useful in establishing alternative anticancer strategies that exploit the activation of the p73 pathway against human tumors bearing p53 mutations.
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Affiliation(s)
- Jae-Sun Shin
- a Structural Biology & Nanopore Research Laboratory; Functional Genomics Research Center; KRIBB ; Daejeon , Republic of Korea
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23
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Pantelopulos GA, Mukherjee S, Voelz VA. Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics. Proteins 2015; 83:1665-76. [DOI: 10.1002/prot.24852] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 06/08/2015] [Accepted: 06/24/2015] [Indexed: 12/13/2022]
Affiliation(s)
| | - Sudipto Mukherjee
- Department of Chemistry; Temple University; Philadelphia Pennsylvania 19122
| | - Vincent A. Voelz
- Department of Chemistry; Temple University; Philadelphia Pennsylvania 19122
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24
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Bueren-Calabuig JA, Michel J. Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2. PLoS Comput Biol 2015; 11:e1004282. [PMID: 26046940 PMCID: PMC4457491 DOI: 10.1371/journal.pcbi.1004282] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 04/13/2015] [Indexed: 01/16/2023] Open
Abstract
Numerous biomolecular interactions involve unstructured protein regions, but how to exploit such interactions to enhance the affinity of a lead molecule in the context of rational drug design remains uncertain. Here clarification was sought for cases where interactions of different ligands with the same disordered protein region yield qualitatively different results. Specifically, conformational ensembles for the disordered lid region of the N-terminal domain of the oncoprotein MDM2 in the presence of different ligands were computed by means of a novel combination of accelerated molecular dynamics, umbrella sampling, and variational free energy profile methodologies. The resulting conformational ensembles for MDM2, free and bound to p53 TAD (17-29) peptide identify lid states compatible with previous NMR measurements. Remarkably, the MDM2 lid region is shown to adopt distinct conformational states in the presence of different small-molecule ligands. Detailed analyses of small-molecule bound ensembles reveal that the ca. 25-fold affinity improvement of the piperidinone family of inhibitors for MDM2 constructs that include the full lid correlates with interactions between ligand hydrophobic groups and the C-terminal lid region that is already partially ordered in apo MDM2. By contrast, Nutlin or benzodiazepinedione inhibitors, that bind with similar affinity to full lid and lid-truncated MDM2 constructs, interact additionally through their solubilizing groups with N-terminal lid residues that are more disordered in apo MDM2. Life as we know it depends on interactions between proteins. There is substantial evidence that many interactions between proteins involve very flexible protein regions. These disordered regions may undergo disorder/order transitions upon forming an interaction with another protein. Many successful approaches to medicinal chemistry are based on mimicking the interactions of biological molecules with man-made small molecules. However how drug-like small-molecules may modulate protein disorder is currently poorly understood, largely because it is difficult to measure in details this type of interaction with experimental methods. Here we have used computer simulations to resolve with great details the process by which different small-molecules modulate the flexibility of a disordered region of the protein MDM2. This protein is overexpressed in many cancers and small-molecules that recognize MDM2 have been developed over the last decade as possible novel anti-cancer agents. We show that the flexible MDM2 “lid” region adopts different conformational states in the presence of different small-molecules. Our results suggest why some classes of small-molecules form favorable interactions with the lid region, whereas others do not. These findings may prove crucial to develop new and more effective MDM2 inhibitors, and more generally to help drug designers target disordered proteins regions with small-molecules.
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Affiliation(s)
| | - Julien Michel
- EaStCHEM School of Chemistry, the University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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25
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Phosphomimetic mutation of the N-terminal lid of MDM2 enhances the polyubiquitination of p53 through stimulation of E2-ubiquitin thioester hydrolysis. J Mol Biol 2014; 427:1728-47. [PMID: 25543083 DOI: 10.1016/j.jmb.2014.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 12/18/2014] [Accepted: 12/19/2014] [Indexed: 11/24/2022]
Abstract
Mouse double minute 2 (MDM2) has a phosphorylation site within a lid motif at Ser17 whose phosphomimetic mutation to Asp17 stimulates MDM2-mediated polyubiquitination of p53. MDM2 lid deletion, but not Asp17 mutation, induced a blue shift in the λ(max) of intrinsic fluorescence derived from residues in the central domain including Trp235, Trp303, Trp323, and Trp329. This indicates that the Asp17 mutation does not alter the conformation of MDM2 surrounding the tryptophan residues. In addition, Phe235 mutation enhanced MDM2 binding to p53 but did not stimulate its ubiquitination function, thus uncoupling increases in p53 binding from its E3 ubiquitin ligase function. However, the Asp17 mutation in MDM2 stimulated its discharge of the UBCH5a-ubiquitin thioester adduct (UBCH5a is a ubiquitin-conjugating enzyme E2D 1 UBC4/5 homolog yeast). This stimulation of ubiquitin discharge from E2 was independent of the p53 substrate. There are now four known effects of the Asp17 mutation on MDM2: (i) it alters the conformation of the isolated N-terminus as defined by NMR; (ii) it induces increased thermostability of the isolated N-terminal domain; (iii) it stimulates the allosteric interaction of MDM2 with the DNA-binding domain of p53; and (iv) it stimulates a novel protein-protein interaction with the E2-ubiquitin complex in the absence of substrate p53 that, in turn, increases hydrolysis of the E2-ubiquitin thioester bond. These data also suggest a new strategy to disrupt MDM2 function by targeting the E2-ubiquitin discharge reaction.
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26
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Sim AYL, Joseph T, Lane DP, Verma C. Mechanism of Stapled Peptide Binding to MDM2: Possible Consequences for Peptide Design. J Chem Theory Comput 2014; 10:1753-61. [DOI: 10.1021/ct4009238] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Adelene Y. L. Sim
- Bioinformatics
Institute (A*STAR), 30
Biopolis Street #07-01, Matrix, Singapore 138671
| | - Thomas Joseph
- Bioinformatics
Institute (A*STAR), 30
Biopolis Street #07-01, Matrix, Singapore 138671
| | - David P. Lane
- p53
Laboratory (p53Lab, A*STAR), 8A Biomedical Grove, #06-06, Immunos, Singapore 138648
| | - Chandra Verma
- Bioinformatics
Institute (A*STAR), 30
Biopolis Street #07-01, Matrix, Singapore 138671
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551
- Department
of Biological Sciences, National University of Singapore, 14 Science
Drive 4, Singapore 117543
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27
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Nicholson J, Scherl A, Way L, Blackburn EA, Walkinshaw MD, Ball KL, Hupp TR. A systems wide mass spectrometric based linear motif screen to identify dominant in-vivo interacting proteins for the ubiquitin ligase MDM2. Cell Signal 2014; 26:1243-57. [PMID: 24583282 DOI: 10.1016/j.cellsig.2014.02.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 02/21/2014] [Indexed: 12/24/2022]
Abstract
Linear motifs mediate protein-protein interactions (PPI) that allow expansion of a target protein interactome at a systems level. This study uses a proteomics approach and linear motif sub-stratifications to expand on PPIs of MDM2. MDM2 is a multi-functional protein with over one hundred known binding partners not stratified by hierarchy or function. A new linear motif based on a MDM2 interaction consensus is used to select novel MDM2 interactors based on Nutlin-3 responsiveness in a cell-based proteomics screen. MDM2 binds a subset of peptide motifs corresponding to real proteins with a range of allosteric responses to MDM2 ligands. We validate cyclophilin B as a novel protein with a consensus MDM2 binding motif that is stabilised by Nutlin-3 in vivo, thus identifying one of the few known interactors of MDM2 that is stabilised by Nutlin-3. These data invoke two modes of peptide binding at the MDM2 N-terminus that rely on a consensus core motif to control the equilibrium between MDM2 binding proteins. This approach stratifies MDM2 interacting proteins based on the linear motif feature and provides a new biomarker assay to define clinically relevant Nutlin-3 responsive MDM2 interactors.
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Affiliation(s)
- Judith Nicholson
- Edinburgh Cancer Research Centre, Cell Signalling Unit, University of Edinburgh, EH4 2XR, United Kingdom; Department of Radiation Oncology and Biology, University of Oxford, OX3 7DQ, United Kingdom
| | - Alex Scherl
- Proteomics Core Facility, University of Geneva, Switzerland
| | - Luke Way
- Edinburgh Cancer Research Centre, Cell Signalling Unit, University of Edinburgh, EH4 2XR, United Kingdom
| | - Elizabeth A Blackburn
- Edinburgh Centre for Chemical Biology, University of Edinburgh, EH9 3JG, United Kingdom
| | - Malcolm D Walkinshaw
- Edinburgh Centre for Chemical Biology, University of Edinburgh, EH9 3JG, United Kingdom
| | - Kathryn L Ball
- Edinburgh Cancer Research Centre, Cell Signalling Unit, University of Edinburgh, EH4 2XR, United Kingdom
| | - Ted R Hupp
- Edinburgh Cancer Research Centre, Cell Signalling Unit, University of Edinburgh, EH4 2XR, United Kingdom.
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28
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Hernychova L, Man P, Verma C, Nicholson J, Sharma CA, Ruckova E, Teo JY, Ball K, Vojtesek B, Hupp TR. Identification of a second Nutlin-3 responsive interaction site in the N-terminal domain of MDM2 using hydrogen/deuterium exchange mass spectrometry. Proteomics 2014; 13:2512-25. [PMID: 23776060 DOI: 10.1002/pmic.201300029] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 05/01/2013] [Accepted: 05/13/2013] [Indexed: 11/07/2022]
Abstract
MDM2 is a multidomain protein that functions as an E3 ubiquitin ligase, transcription repressor, mRNA-binding protein, translation factor, and molecular chaperone. The small molecule Nutlin-3 has been engineered to bind to the N-terminal hydrophobic pocket domain of MDM2. This binding of Nutlin-3 has two consequences: (i) antagonistic effects through competitive disruption of the MDM2-p53 complex and (ii) agonist effects that allosterically stabilize MDM2 protein-protein interactions that increase p53 ubiquitination as well as nucleophosmin deoligomerization. We present a methodology using a hydrogen/deuterium (H/D) exchange platform that measures Nutlin-3 binding to the N-terminal domain of MDM2 (MDM2(1-126)) in order to begin to develop dynamic assays that evaluate MDM2 allostery. In order to localize the regions in MDM2 being suppressed by Nutlin-3, MDM2 was incubated with the ligand and H/D amide exchange was measured after pepsin digestion. One dynamic segment containing amino acids 55-60 exhibited slower deuterium exchange after Nutlin-3 binding, reflecting ligand binding within the hydrophobic pocket. However, another dominant suppression of H/D exchange was observed in a motif from amino acids 103-107 that reflects surface hydrophobic residues surrounding the hydrophobic pocket of MDM2. In order to explore the consequences of this latter Nutlin-3 interaction site on MDM2, the Y104G and L107G mutant series was constructed. The MDM2(Y104G) and MDM2(L107G) mutants were fully active in p53 binding. However, the authentic p53-derived peptide:MDM2(Y104G) complex exhibited partial resistance to Nutlin-3 inhibition, while the p53-mimetic 12.1 peptide:MDM2(Y104G) complex retained normal Nutlin-3 responsiveness. These data reveal the existence of a second functional Nutlin-3-binding site in a surface hydrophobic patch of MDM2, flanking the hydrophobic pocket. This reveals two modes of peptide binding by MDM2 and highlights the utility of H/D exchange as an assay for measuring allosteric effects in MDM2.
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Affiliation(s)
- Lenka Hernychova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
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29
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Bista M, Wolf S, Khoury K, Kowalska K, Huang Y, Wrona E, Arciniega M, Popowicz GM, Holak TA, Dömling A. Transient protein states in designing inhibitors of the MDM2-p53 interaction. Structure 2013; 21:2143-51. [PMID: 24207125 DOI: 10.1016/j.str.2013.09.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/10/2013] [Accepted: 09/13/2013] [Indexed: 11/28/2022]
Abstract
Reactivation of p53 by release of the functional protein from its inhibition by MDM2 provides an efficient, nongenotoxic approach to a wide variety of cancers. We present the cocrystal structures of two complexes of MDM2 with inhibitors based on 6-chloroindole scaffolds. Both molecules bound to a distinct conformational state of MDM2 with nM-μM affinities. In contrast to other structurally characterized antagonists, which mimic three amino acids of p53 (Phe19, Trp23, and Leu26), the compounds induced an additional hydrophobic pocket on the MDM2 surface and unveiled a four-point binding mode. The enlarged interaction interface of the inhibitors resulted in extension of small molecules binding toward the "lid" segment of MDM2 (residues 19-23)--a nascent element that interferes with p53 binding. As supported by protein engineering and molecular dynamics studies, employing these unstable elements of MDM2 provides an efficient and yet unexplored alternative in development of MDM2-p53 association inhibitors.
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Affiliation(s)
- Michal Bista
- Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany
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30
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Bhowmick P, Pancsa R, Guharoy M, Tompa P. Functional diversity and structural disorder in the human ubiquitination pathway. PLoS One 2013; 8:e65443. [PMID: 23734257 PMCID: PMC3667038 DOI: 10.1371/journal.pone.0065443] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/24/2013] [Indexed: 02/04/2023] Open
Abstract
The ubiquitin-proteasome system plays a central role in cellular regulation and protein quality control (PQC). The system is built as a pyramid of increasing complexity, with two E1 (ubiquitin activating), few dozen E2 (ubiquitin conjugating) and several hundred E3 (ubiquitin ligase) enzymes. By collecting and analyzing E3 sequences from the KEGG BRITE database and literature, we assembled a coherent dataset of 563 human E3s and analyzed their various physical features. We found an increase in structural disorder of the system with multiple disorder predictors (IUPred – E1: 5.97%, E2: 17.74%, E3: 20.03%). E3s that can bind E2 and substrate simultaneously (single subunit E3, ssE3) have significantly higher disorder (22.98%) than E3s in which E2 binding (multi RING-finger, mRF, 0.62%), scaffolding (6.01%) and substrate binding (adaptor/substrate recognition subunits, 17.33%) functions are separated. In ssE3s, the disorder was localized in the substrate/adaptor binding domains, whereas the E2-binding RING/HECT-domains were structured. To demonstrate the involvement of disorder in E3 function, we applied normal modes and molecular dynamics analyses to show how a disordered and highly flexible linker in human CBL (an E3 that acts as a regulator of several tyrosine kinase-mediated signalling pathways) facilitates long-range conformational changes bringing substrate and E2-binding domains towards each other and thus assisting in ubiquitin transfer. E3s with multiple interaction partners (as evidenced by data in STRING) also possess elevated levels of disorder (hubs, 22.90% vs. non-hubs, 18.36%). Furthermore, a search in PDB uncovered 21 distinct human E3 interactions, in 7 of which the disordered region of E3s undergoes induced folding (or mutual induced folding) in the presence of the partner. In conclusion, our data highlights the primary role of structural disorder in the functions of E3 ligases that manifests itself in the substrate/adaptor binding functions as well as the mechanism of ubiquitin transfer by long-range conformational transitions.
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Affiliation(s)
- Pallab Bhowmick
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Rita Pancsa
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Mainak Guharoy
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Tompa
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail:
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Wei SJ, Joseph T, Sim AYL, Yurlova L, Zolghadr K, Lane D, Verma C, Ghadessy F. In vitro selection of mutant HDM2 resistant to Nutlin inhibition. PLoS One 2013; 8:e62564. [PMID: 23653682 PMCID: PMC3641235 DOI: 10.1371/journal.pone.0062564] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/22/2013] [Indexed: 11/25/2022] Open
Abstract
HDM2 binds to the p53 tumour suppressor and targets it for proteosomal degradation. Presently in clinical trials, the small molecule Nutlin-3A competitively binds to HDM2 and abrogates its repressive function. Using a novel in vitro selection methodology, we simulated the emergence of resistance by evolving HDM2 mutants capable of binding p53 in the presence of Nutlin concentrations that inhibit the wild-type HDM2-p53 interaction. The in vitro phenotypes were recapitulated in ex vivo assays measuring both p53 transactivation function and the direct p53-HDM2 interaction in the presence of Nutlin. Mutations conferring drug resistance were not confined to the N-terminal p53/Nutlin–binding domain, and were additionally seen in the acidic, zinc finger and RING domains. Mechanistic insights gleaned from this broad spectrum of mutations will aid in future drug design and further our understanding of the complex p53-HDM2 interaction.
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Affiliation(s)
- Siau Jia Wei
- p53Lab, Agency for Science, Technology and Research, Singapore, Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singpore
| | - Thomas Joseph
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singpore
| | - Adelene Y. L. Sim
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singpore
| | | | | | - David Lane
- p53Lab, Agency for Science, Technology and Research, Singapore, Singapore
| | - Chandra Verma
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singpore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- * E-mail: (CV); sg (FG)
| | - Farid Ghadessy
- p53Lab, Agency for Science, Technology and Research, Singapore, Singapore
- * E-mail: (CV); sg (FG)
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Michelsen K, Jordan JB, Lewis J, Long AM, Yang E, Rew Y, Zhou J, Yakowec P, Schnier PD, Huang X, Poppe L. Ordering of the N-terminus of human MDM2 by small molecule inhibitors. J Am Chem Soc 2012; 134:17059-67. [PMID: 22991965 DOI: 10.1021/ja305839b] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Restoration of p53 function through the disruption of the MDM2-p53 protein complex is a promising strategy for the treatment of various types of cancer. Here, we present kinetic, thermodynamic, and structural rationale for the remarkable potency of a new class of MDM2 inhibitors, the piperidinones. While these compounds bind to the same site as previously reported for small molecule inhibitors, such as the Nutlins, data presented here demonstrate that the piperidinones also engage the N-terminal region (residues 10-16) of human MDM2, in particular, Val14 and Thr16. This portion of MDM2 is unstructured in both the apo form of the protein and in MDM2 complexes with p53 or Nutlin, but adopts a novel β-strand structure when complexed with the piperidinones. The ordering of the N-terminus upon binding of the piperidinones extends the current model of MDM2-p53 interaction and provides a new route to rational design of superior inhibitors.
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Affiliation(s)
- Klaus Michelsen
- Molecular Structure & Characterization, Amgen, Inc., Thousand Oaks, California 91320, USA
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Funston G, Goh W, Wei SJ, Tng QS, Brown C, Jiah Tong L, Verma C, Lane D, Ghadessy F. Binding of Translationally Controlled Tumour Protein to the N-terminal domain of HDM2 is inhibited by nutlin-3. PLoS One 2012; 7:e42642. [PMID: 22912717 PMCID: PMC3418249 DOI: 10.1371/journal.pone.0042642] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 07/10/2012] [Indexed: 11/18/2022] Open
Abstract
Translationally Controlled Tumour Protein (TCTP), a highly conserved protein present in all eukaryotic organisms, has a number of intracellular and extracellular functions including an anti-apoptotic role. TCTP was recently shown to interact with both p53 and HDM2, inhibiting auto-ubiquitination of the latter and thereby promoting p53 degradation. In this study, we further investigated the interaction between TCTP and HDM2, mapping the reciprocal binding sites of TCTP and HDM2. TCTP primarily interacts with the N-terminal, p53-binding region of HDM2 through its highly basic domain 2. Furthermore, we discovered that Nutlin-3, a small molecule known to promote apoptosis and cell cycle arrest by blocking binding between HDM2 and p53, has a similar inhibitory effect on the interaction of HDM2 and TCTP. This result may provide an additional explanation of how Nutlin-derived compounds currently in clinical trials function to promote apoptosis in cancer cells.
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Affiliation(s)
- Garth Funston
- School of Clinical Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom
| | | | | | | | | | - Loh Jiah Tong
- Bioinformatics Institute (A*STAR), Singapore, Singapore
| | - Chandra Verma
- Bioinformatics Institute (A*STAR), Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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Shan B, Li DW, Brüschweiler-Li L, Brüschweiler R. Competitive binding between dynamic p53 transactivation subdomains to human MDM2 protein: implications for regulating the p53·MDM2/MDMX interaction. J Biol Chem 2012; 287:30376-84. [PMID: 22807444 DOI: 10.1074/jbc.m112.369793] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The interaction between the transactivation domain of p53 (p53TAD) and the N-terminal domain of MDM2 and MDMX plays an essential role for cell function. Mutations in these proteins have been implicated in many forms of cancer. The intrinsically disordered p53TAD contains two subdomains, TAD1 and TAD2. Using NMR spectroscopy, site-directed mutagenesis, and molecular dynamics simulations, we demonstrate that TAD2 directly interacts with MDM2, adopting transient structures that bind to the same hydrophobic pocket of MDM2 as TAD1. Our data show that binding of TAD1 and TAD2 to MDM2 is competitive, which is further supported by the observation that the interaction of TAD2 with MDM2 can be blocked by the small molecule inhibitor nutlin-3. Our data further indicate that TAD2 interacts with MDMX in a fashion very similar to MDM2. Because TAD2 is known to have transcriptional activity, the interaction of TAD2 with MDM2/MDMX may play a direct role in the inhibition of p53 transactivation.
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Affiliation(s)
- Bing Shan
- Department of Chemistry and Biochemistry, The Florida State University, Tallahassee, FL 32306, USA
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Verkhivker GM. Simulating molecular mechanisms of the MDM2-mediated regulatory interactions: a conformational selection model of the MDM2 lid dynamics. PLoS One 2012; 7:e40897. [PMID: 22815859 PMCID: PMC3397965 DOI: 10.1371/journal.pone.0040897] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 06/14/2012] [Indexed: 12/20/2022] Open
Abstract
Diversity and complexity of MDM2 mechanisms govern its principal function as the cellular antagonist of the p53 tumor suppressor. Structural and biophysical studies have demonstrated that MDM2 binding could be regulated by the dynamics of a pseudo-substrate lid motif. However, these experiments and subsequent computational studies have produced conflicting mechanistic models of MDM2 function and dynamics. We propose a unifying conformational selection model that can reconcile experimental findings and reveal a fundamental role of the lid as a dynamic regulator of MDM2-mediated binding. In this work, structure, dynamics and energetics of apo-MDM2 are studied as a function of posttranslational modifications and length of the lid. We found that the dynamic equilibrium between "closed" and "semi-closed" lid forms may be a fundamental characteristic of MDM2 regulatory interactions, which can be modulated by phosphorylation, phosphomimetic mutation as well as by the lid size. Our results revealed that these factors may regulate p53-MDM2 binding by fine-tuning the thermodynamic equilibrium between preexisting conformational states of apo-MDM2. In agreement with NMR studies, the effect of phosphorylation on MDM2 interactions was more pronounced with the truncated lid variant that favored the thermodynamically dominant closed form. The phosphomimetic mutation S17D may alter the lid dynamics by shifting the thermodynamic equilibrium towards the ensemble of "semi-closed" conformations. The dominant "semi-closed" lid form and weakened dependence on the phosphorylation seen in simulations with the complete lid can provide a rationale for binding of small p53-based mimetics and inhibitors without a direct competition with the lid dynamics. The results suggested that a conformational selection model of preexisting MDM2 states may provide a robust theoretical framework for understanding MDM2 dynamics. Probing biological functions and mechanisms of MDM2 regulation would require further integration of computational and experimental studies and may help to guide drug design of novel anti-cancer therapeutics.
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Affiliation(s)
- Gennady M Verkhivker
- School of Computational Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America.
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36
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Zhan C, Zhao L, Wei X, Wu X, Chen X, Yuan W, Lu WY, Pazgier M, Lu W. An ultrahigh affinity d-peptide antagonist Of MDM2. J Med Chem 2012; 55:6237-41. [PMID: 22694121 DOI: 10.1021/jm3005465] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oncoprotein MDM2 negatively regulates the activity and stability of the p53 tumor suppressor and is an important molecular target for anticancer therapy. Aided by mirror image phage display and native chemical ligation, we have previously discovered several proteolysis-resistant duodecimal d-peptide antagonists of MDM2, termed (D)PMI-α, β, γ. The prototypic d-peptide inhibitor (D)PMI-α binds ((25-109))MDM2 at an affinity of 220 nM and kills tumor cells in vitro and inhibits tumor growth in vivo by reactivating the p53 pathway. Herein, we report the design of a superactive d-peptide antagonist of MDM2, termed (D)PMI-δ, of which the binding affinity for ((25-109))MDM2 has been improved over (D)PMI-α by 3 orders of magnitude (K(d) = 220 pM). X-ray crystallographic studies validate (D)PMI-δ as an exceedingly potent inhibitor of the p53-MDM2 interaction, promising to be a highly attractive lead drug candidate for anticancer therapeutic development.
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Affiliation(s)
- Changyou Zhan
- Institute of Human Virology & Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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37
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Zhan C, Varney K, Yuan W, Zhao L, Lu W. Interrogation of MDM2 phosphorylation in p53 activation using native chemical ligation: the functional role of Ser17 phosphorylation in MDM2 reexamined. J Am Chem Soc 2012; 134:6855-64. [PMID: 22444248 DOI: 10.1021/ja301255n] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The E3 ubiquitin ligase MDM2 functions as a crucial negative regulator of the p53 tumor suppressor protein by antagonizing p53 transactivation activity and targeting p53 for degradation. Cellular stress activates p53 by alleviating MDM2-mediated functional inhibition, even though the molecular mechanisms of stress-induced p53 activation still remain poorly understood. Two opposing models have been proposed to describe the functional and structural role in p53 activation of Ser17 phosphorylation in the N-terminal "lid" (residues 1-24) of MDM2. Using the native chemical ligation technique, we synthesized the p53-binding domain (1-109)MDM2 and its Ser17-phosphorylated analogue (1-109)MDM2 pS17 as well as (1-109)MDM2 S17D and (25-109)MDM2, and comparatively characterized their interactions with a panel of p53-derived peptide ligands using surface plasmon resonance, fluorescence polarization, and NMR and CD spectroscopic techniques. We found that the lid is partially structured in apo-MDM2 and occludes p53 peptide binding in a ligand size-dependent manner. Binding of (1-109)MDM2 by the (15-29)p53 peptide fully displaces the lid and renders it completely disordered in the peptide-protein complex. Importantly, neither Ser17 phosphorylation nor the phospho-mimetic mutation S17D has any functional impact on p53 peptide binding to MDM2. Although Ser17 phosphorylation or its mutation to Asp contributes marginally to the stability of the lid conformation in apo-MDM2, neither modification stabilizes apo-MDM2 globally or the displaced lid locally. Our findings demonstrate that Ser17 phosphorylation is functionally neutral with respect to p53 binding, suggesting that MDM2 phosphorylation at a single site is unlikely to play a dominant role in stress-induced p53 activation.
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Affiliation(s)
- Changyou Zhan
- Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, Maryland 21201, USA
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38
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Mancini F, Di Conza G, Moretti F. MDM4 (MDMX) and its Transcript Variants. Curr Genomics 2011; 10:42-50. [PMID: 19721810 PMCID: PMC2699833 DOI: 10.2174/138920209787581280] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 12/08/2008] [Accepted: 12/15/2008] [Indexed: 12/17/2022] Open
Abstract
MDM family proteins are crucial regulators of the oncosuppressor p53. Alterations of their gene status, mainly amplification events, have been frequently observed in human tumors.MDM4 is one of the two members of the MDM family. The human gene is located on chromosome 1 at q32-33 and codes for a protein of 490aa. In analogy to MDM2, besides the full-length mRNA several transcript variants of MDM4 have been identified. Almost all variants thus far described derive from a splicing process, both through canonical and aberrant splicing events. Some of these variants are expressed in normal tissues, others have been observed only in tumor samples. The presence of these variants may be considered a fine tuning of the function of the full-length protein, especially in normal cells. In tumor cells, some variants show oncogenic properties.This review summarizes all the different MDM4 splicing forms thus far described and their role in the regulation of the wild type protein function in normal and tumor cells. In addition, a description of the full-length protein structure with all known interacting proteins thus far identified and a comparison of the MDM4 variant structure with that of full-length protein are presented. Finally, a parallel between MDM4 and MDM2 variants is discussed.
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Affiliation(s)
- F Mancini
- National Council of Research, Institute of Neurobiology and Molecular Medicine, Roma
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39
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Abstract
p53 is a potent tumor suppressor with a crucial role in preventing uncontrolled cell proliferation and is therefore frequently deleted or mutated in cancer. For tumors with wild-type p53, its function can be overcome by overactive cellular antagonists, such as the ubiquitin ligase murine double minute clone 2 (MDM2). Restoring p53 activity by inhibiting MDM2 in such cancers can eradicate tumors. Consequently, the MDM2-p53 interaction has been extensively targeted for inhibition by small molecules. In recent years, MDM2-like protein (MDMX), another key downregulator of p53, has gained increasing importance as an additional target for drug development, in order to provide a complementary approach to MDM2 inhibition. In this review, we describe how detailed structural knowledge of the MDM2-p53 interface and, more recently, of the MDMX-p53 interaction have helped advance the development of inhibitors against the two targets. We present a summary of the functional biochemistry of MDM2, MDMX and p53 as well as their interactions and examine recent progress in the development of inhibitors of MDM2 and MDMX.
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40
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Riedinger C, Noble ME, Wright DJ, Mulks F, Hardcastle IR, Endicott JA, McDonnell JM. Understanding small-molecule binding to MDM2: insights into structural effects of isoindolinone inhibitors from NMR spectroscopy. Chem Biol Drug Des 2011; 77:301-8. [PMID: 21244642 DOI: 10.1111/j.1747-0285.2011.01091.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The interaction between murine double minute (MDM2) and p53 is a major target in anticancer drug design. Several potent compound series, including the nutlins and spirooxindoles, have previously been established as high-affinity antagonists of MDM2. In this paper, we describe the interaction of isoindolinone inhibitors with MDM2, as characterized by nuclear magnetic resonance spectroscopy. Isoindolinone inhibitors bind specifically to the MDM2 p53 binding site and exploit all sub-pockets used by p53, nutlins and spirooxindoles. Furthermore, isoindolinones bind with low micromolar to high nanomolar affinities, with the best compound approaching the potency of nutlin-3.
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Affiliation(s)
- Christiane Riedinger
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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41
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42
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Phillips A, Teunisse A, Lam S, Lodder K, Darley M, Emaduddin M, Wolf A, Richter J, de Lange J, Verlaan-de Vries M, Lenos K, Böhnke A, Bartel F, Blaydes JP, Jochemsen AG. HDMX-L is expressed from a functional p53-responsive promoter in the first intron of the HDMX gene and participates in an autoregulatory feedback loop to control p53 activity. J Biol Chem 2010; 285:29111-27. [PMID: 20659896 DOI: 10.1074/jbc.m110.129726] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The p53 regulatory network is critically involved in preventing the initiation of cancer. In unstressed cells, p53 is maintained at low levels and is largely inactive, mainly through the action of its two essential negative regulators, HDM2 and HDMX. p53 abundance and activity are up-regulated in response to various stresses, including DNA damage and oncogene activation. Active p53 initiates transcriptional and transcription-independent programs that result in cell cycle arrest, cellular senescence, or apoptosis. p53 also activates transcription of HDM2, which initially leads to the degradation of HDMX, creating a positive feedback loop to obtain maximal activation of p53. Subsequently, when stress-induced post-translational modifications start to decline, HDM2 becomes effective in targeting p53 for degradation, thus attenuating the p53 response. To date, no clear function for HDMX in this critical attenuation phase has been demonstrated experimentally. Like HDM2, the HDMX gene contains a promoter (P2) in its first intron that is potentially inducible by p53. We show that p53 activation in response to a plethora of p53-activating agents induces the transcription of a novel HDMX mRNA transcript from the HDMX-P2 promoter. This mRNA is more efficiently translated than that expressed from the constitutive HDMX-P1 promoter, and it encodes a long form of HDMX protein, HDMX-L. Importantly, we demonstrate that HDMX-L cooperates with HDM2 to promote the ubiquitination of p53 and that p53-induced HDMX transcription from the P2 promoter can play a key role in the attenuation phase of the p53 response, to effectively diminish p53 abundance as cells recover from stress.
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Affiliation(s)
- Anna Phillips
- Southampton Cancer Research UK Centre, University of Southampton School of Medicine, Southampton General Hospital, Southampton SO16 6YD, United Kingdom
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Poyurovsky MV, Katz C, Laptenko O, Beckerman R, Lokshin M, Ahn J, Byeon IJL, Gabizon R, Mattia M, Zupnick A, Brown LM, Friedler A, Prives C. The C terminus of p53 binds the N-terminal domain of MDM2. Nat Struct Mol Biol 2010; 17:982-9. [PMID: 20639885 PMCID: PMC2922928 DOI: 10.1038/nsmb.1872] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Accepted: 05/03/2010] [Indexed: 12/20/2022]
Abstract
The p53 tumor suppressor interacts with its negative regulator Mdm2 via the former’s N-terminal region and core domain. Yet the extreme p53 C-terminal region contains lysine residues ubiquitinated by Mdm2 and can bear post-translational modifications that inhibit Mdm2–p53 association. We show that, the Mdm2–p53 interaction is decreased upon deletion, mutation or acetylation of the p53 C-terminus. Mdm2 decreases the association of full-length but not C-terminally deleted p53 with a DNA target sequence in vitro and in cells. Further, using multiple approaches we demonstrate that a peptide from p53 C-terminus directly binds Mdm2 N-terminus in vitro. We also show that p300-acetylated p53 binds inefficiently to Mdm2 in vitro, and Nutlin-3 treatment induces C-terminal modification(s) of p53 in cells, explaining the low efficiency of Nutlin-3 in dissociating p53-MDM2 in vitro.
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Affiliation(s)
- Masha V Poyurovsky
- Department of Biological Sciences, Columbia University, New York, New York, USA
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44
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MDM4 binds ligands via a mechanism in which disordered regions become structured. FEBS Lett 2010; 584:3035-41. [PMID: 20515689 DOI: 10.1016/j.febslet.2010.05.058] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 05/25/2010] [Accepted: 05/26/2010] [Indexed: 11/23/2022]
Abstract
MDM2 and MDM4 are proteins involved in regulating the tumour suppressor p53. MDM2/4 and p53 interact through their N-terminal domains and disrupting this interaction is a potential anticancer strategy. The MDM2-p53 interaction is structurally and biophysically well characterised, whereas equivalent studies on MDM4 are hampered by aggregation of the protein. Here we present the NMR characterization of MDM4 (14-111) both free and in complexes with peptide and small-molecule ligands. MDM4 is more dynamic in its apo state than is MDM2, with parts of the protein being unstructured. These regions become structured upon binding of a ligand. MDM4 appears to bind its ligand through conformational selection and/or an induced fit mechanism; this might influence rational design of MDM4 inhibitors.
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45
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The Effects of Phosphomimetic Lid Mutation on the Thermostability of the N-terminal Domain of MDM2. J Mol Biol 2010; 398:414-28. [DOI: 10.1016/j.jmb.2010.03.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2010] [Revised: 03/11/2010] [Accepted: 03/11/2010] [Indexed: 12/21/2022]
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46
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Modulation of p53 binding to MDM2: computational studies reveal important roles of Tyr100. BMC Bioinformatics 2009; 10 Suppl 15:S6. [PMID: 19958516 PMCID: PMC2788357 DOI: 10.1186/1471-2105-10-s15-s6] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background The tumor suppressor protein p53 is regulated by the ubiquitin ligase MDM2 which down-regulates p53. In tumours with overexpressed MDM2, the p53-MDM2 interaction can be interrupted by a peptide or small molecule to stabilize p53 as a therapeutic strategy. Structural and biochemical/mutagenesis data show that p53 has 3 hydrophobic residues F19, W23 and L26 that embed into the ligand binding pocket of MDM2 which is highly plastic in nature and can modulate its size to accommodate a variety of ligands. This binding pocket is primarily dependent on the orientation of a particular residue, Y100. We have studied the role of the dynamics of Y100 in p53 recognition. Results Molecular dynamics simulations show that the Y100 side chain can be in "open" or "closed" states with only the former enabling complex formation. When both p53 and MDM2 are in near native conformations, complex formation is rapid and is driven by the formation of a hydrogen bond between W23 of p53 and L54 of MDM2 or by the embedding of F19 of p53 into MDM2. The transition of Y100 from "closed" to "open" can increase the size of the binding site. Interconversions between these two states can be induced by the N-terminal region of MDM2 or by the conformations of the p53 peptides. Conclusion Molecular dynamics simulations have revealed how the binding of p53 to MDM2 is modulated by the conformational mobility of Y100 which is the gatekeeper residue in MDM2. The mobility of this residue can be modulated by the conformations of p53 and the Nterminal lid region of MDM2.
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Carotti A, Macchiarulo A, Giacchè N, Pellicciari R. Targeting the conformational transitions of MDM2 and MDMX: Insights into key residues affecting p53 recognition. Proteins 2009; 77:524-35. [DOI: 10.1002/prot.22464] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Small-molecule inhibitors of MDM2 as new anticancer therapeutics. Semin Cancer Biol 2009; 20:10-8. [PMID: 19897042 DOI: 10.1016/j.semcancer.2009.10.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 10/29/2009] [Indexed: 11/23/2022]
Abstract
It has long been known that traditional anticancer radio- and chemotherapies in part work through direct or indirect activation of the p53 tumour suppressor pathway. However, many of these strategies are nonselective and genotoxic. The emerging understanding of the pathways that regulate p53 has led to the notion that it should be possible to activate the p53 pathway in ways that are inherently nongenotoxic. Important targets for pharmacological interference in this respect are MDM2 and MDMX, key negative regulators of p53. Genetic and pharmacologic studies suggest that blocking the physical interaction of these proteins with p53, or inhibiting the catalytic role of MDM2 in tagging p53 for proteasomal degradation, both of which lead to an increase in the transcriptional activity of p53, may indeed be an efficient and safe way to eradicate tumour cells that retain wild-type p53. Here we review the rationale for such strategies, as well as the current state in the discovery and development of drugs that reactivate p53 by inhibiting its inhibitors MDM2 and MDMX. The first compounds that have been shown in model systems to be able selectively to kill cancer cells in this way are now entering clinical trials and the promise of MDM2 inhibitors as a new therapeutic anticancer modality should therefore become clear in the not-too-distant future.
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Regulation of the E3 ubiquitin ligase activity of MDM2 by an N-terminal pseudo-substrate motif. J Chem Biol 2009; 2:113-29. [PMID: 19568783 DOI: 10.1007/s12154-009-0019-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 03/25/2009] [Indexed: 02/05/2023] Open
Abstract
The tumor suppressor p53 has evolved a MDM2-dependent feedback loop that promotes p53 protein degradation through the ubiquitin-proteasome system. MDM2 is an E3-RING containing ubiquitin ligase that catalyzes p53 ubiquitination by a dual-site mechanism requiring ligand occupation of its N-terminal hydrophobic pocket, which then stabilizes MDM2 binding to the ubiquitination signal in the DNA-binding domain of p53. A unique pseudo-substrate motif or "lid" in MDM2 is adjacent to its N-terminal hydrophobic pocket, and we have evaluated the effects of the flexible lid on the dual-site ubiquitination reaction mechanism catalyzed by MDM2. Deletion of this pseudo-substrate motif promotes MDM2 protein thermoinstability, indicating that the site can function as a positive regulatory element. Phospho-mimetic mutation in the pseudo-substrate motif at codon 17 (MDM2(S17D)) stabilizes the binding of MDM2 towards two distinct peptide docking sites within the p53 tetramer and enhances p53 ubiquitination. Molecular modeling orientates the phospho-mimetic pseudo-substrate motif in equilibrium over a charged surface patch on the MDM2 at Arg(97)/Lys(98), and mutation of these residues to the MDM4 equivalent reverses the activating effect of the phospho-mimetic mutation on MDM2 function. These data highlight the ability of the pseudo-substrate motif to regulate the allosteric interaction between the N-terminal hydrophobic pocket of MDM2 and its central acidic domain, which stimulates the E3 ubiquitin ligase function of MDM2. This model of MDM2 regulation implicates an as yet undefined lid-kinase as a component of pro-oncogenic pathways that stimulate the E3 ubiquitin ligase function of MDM2 in cells.
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Wade M, Wahl GM. Targeting Mdm2 and Mdmx in cancer therapy: better living through medicinal chemistry? Mol Cancer Res 2009; 7:1-11. [PMID: 19147532 DOI: 10.1158/1541-7786.mcr-08-0423] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Genomic and proteomic profiling of human tumor samples and tumor-derived cell lines are essential for the realization of personalized therapy in oncology. Identification of the changes required for tumor initiation or maintenance will likely provide new targets for small-molecule and biological therapeutics. For example, inactivation of the p53 tumor suppressor pathway occurs in most human cancers. Although this can be due to frank p53 gene mutation, almost half of all cancers retain the wild-type p53 allele, indicating that the pathway is disabled by other means. Alternate mechanisms include deletion or epigenetic inactivation of the p53-positive regulator arf, methylation of the p53 promoter, or elevated expression of the p53 regulators Mdm2 and Mdmx. This review discusses current models of p53 regulation by Mdm2 and Mdmx and presents the rationale for design of future Mdmx-specific therapeutics based on our knowledge of its structure and biological functions.
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Affiliation(s)
- Mark Wade
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
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