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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Fenton M, Borcherds W, Chen L, Anbanandam A, Levy R, Chen J, Daughdrill G. The MDMX Acidic Domain Uses Allovalency to Bind Both p53 and MDMX. J Mol Biol 2022; 434:167844. [PMID: 36181774 PMCID: PMC9644833 DOI: 10.1016/j.jmb.2022.167844] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/05/2022] [Accepted: 09/22/2022] [Indexed: 01/10/2023]
Abstract
Autoinhibition of p53 binding to MDMX requires two short-linear motifs (SLiMs) containing adjacent tryptophan (WW) and tryptophan-phenylalanine (WF) residues. NMR spectroscopy was used to show the WW and WF motifs directly compete for the p53 binding site on MDMX and circular dichroism spectroscopy was used to show the WW motif becomes helical when it is bound to the p53 binding domain (p53BD) of MDMX. Binding studies using isothermal titration calorimetry showed the WW motif is a stronger inhibitor of p53 binding than the WF motif when they are both tethered to p53BD by the natural disordered linker. We also investigated how the WW and WF motifs interact with the DNA binding domain (DBD) of p53. Both motifs bind independently to similar sites on DBD that overlap the DNA binding site. Taken together our work defines a model for complex formation between MDMX and p53 where a pair of disordered SLiMs bind overlapping sites on both proteins.
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Affiliation(s)
- Malissa Fenton
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, United States
| | - Wade Borcherds
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, United States
| | - Lihong Chen
- Molecular Oncology Department, Moffitt Cancer Center, Tampa, FL 33612, United States
| | - Asokan Anbanandam
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, United States
| | - Robin Levy
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, United States
| | - Jiandong Chen
- Molecular Oncology Department, Moffitt Cancer Center, Tampa, FL 33612, United States
| | - Gary Daughdrill
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, United States.
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3
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Cheng X, Chen R, Zhou T, Zhang B, Li Z, Gao M, Huang Y, Liu H, Su Z. Leveraging the multivalent p53 peptide-MdmX interaction to guide the improvement of small molecule inhibitors. Nat Commun 2022; 13:1087. [PMID: 35228542 PMCID: PMC8885691 DOI: 10.1038/s41467-022-28721-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/27/2022] [Indexed: 12/21/2022] Open
Abstract
Overexpressed Mdm2 and its 7homolog MdmX impair p53 activity in many cancers. Small molecules mimicking a p53 peptide can effectively inhibit Mdm2 but not MdmX. Here, we show a strategy for improving lead compounds for Mdm2 and MdmX inhibition based on the multivalency of the p53 peptide. Crystal structures of MdmX complexed with nutlin-3a, a strong Mdm2 inhibitor but a weak one for MdmX, reveal that nutlin-3a fits into the ligand binding pocket of MdmX mimicking the p53 peptide. However, due to distinct flexibility around the MdmX ligand binding pocket, the structures are missing many important intermolecular interactions that exist in the MdmX/p53 peptide and Mdm2/nultin-3a complexes. By targeting these flexible regions, we identify allosteric and additive fragments that enhance the binding affinity of nutlin-3a for MdmX, leading to potent Mdm2/MdmX inhibitors with anticancer activity. Our work provides a practical approach to drug design for signal transduction therapy. Peptide fragments derived from the interfaces of protein-protein interactions (PPIs) provide useful templates for designing small molecule PPI inhibitors. Here, the authors utilize the multivalency of an MdmX-binding p53 peptide to develop a weak inhibitor of MdmX into potent Mdm2/MdmX inhibitors.
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4
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Torner JM, Yang Y, Rooklin D, Zhang Y, Arora PS. Identification of Secondary Binding Sites on Protein Surfaces for Rational Elaboration of Synthetic Protein Mimics. ACS Chem Biol 2021; 16:1179-1183. [PMID: 34228913 DOI: 10.1021/acschembio.1c00418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Minimal mimics of protein conformations provide rationally designed ligands to modulate protein function. The advantage of minimal mimics is that they can be chemically synthesized and coaxed to be proteolytically resistant; a key disadvantage is that minimization of the protein binding epitope may be associated with loss of affinity and specificity. Several approaches to overcome this challenge may be envisioned, including deployment of covalent warheads and use of nonnatural residues to improve contacts with the binding surface. Herein, we describe our computational and experimental efforts to enhance the minimal protein mimics with fragments that can contact undiscovered binding pockets on Mdm2 and MdmX-two well-studied protein partners of p53.
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Affiliation(s)
- Justin M. Torner
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Yuwei Yang
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - David Rooklin
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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5
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Qin L, Liu H, Chen R, Zhou J, Cheng X, Chen Y, Huang Y, Su Z. Effect of the Flexible Regions of the Oncoprotein Mouse Double Minute X on Inhibitor Binding Affinity. Biochemistry 2017; 56:5943-5954. [DOI: 10.1021/acs.biochem.7b00903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Lingyun Qin
- Institute
of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Huili Liu
- National
Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics
and Mathematics, Chinese Academy of Science, Wuhan 430071, China
| | - Rong Chen
- Institute
of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Jingjing Zhou
- Institute
of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Xiyao Cheng
- Institute
of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Yao Chen
- Institute
of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Yongqi Huang
- Institute
of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Zhengding Su
- Institute
of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
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6
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Chen R, Zhou J, Qin L, Chen Y, Huang Y, Liu H, Su Z. A Fusion Protein of the p53 Transaction Domain and the p53-Binding Domain of the Oncoprotein MdmX as an Efficient System for High-Throughput Screening of MdmX Inhibitors. Biochemistry 2017; 56:3273-3282. [DOI: 10.1021/acs.biochem.7b00085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rong Chen
- Institute
of Biomedical and Pharmaceutical Sciences and Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Jingjing Zhou
- Institute
of Biomedical and Pharmaceutical Sciences and Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Lingyun Qin
- Institute
of Biomedical and Pharmaceutical Sciences and Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Yao Chen
- Institute
of Biomedical and Pharmaceutical Sciences and Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Yongqi Huang
- Institute
of Biomedical and Pharmaceutical Sciences and Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Huili Liu
- National
Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics
and Mathematics, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Zhengding Su
- Institute
of Biomedical and Pharmaceutical Sciences and Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, Hubei 430068, China
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7
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Optimal Affinity Enhancement by a Conserved Flexible Linker Controls p53 Mimicry in MdmX. Biophys J 2017; 112:2038-2042. [PMID: 28487147 DOI: 10.1016/j.bpj.2017.04.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/29/2017] [Accepted: 04/17/2017] [Indexed: 01/10/2023] Open
Abstract
MdmX contains an intramolecular binding motif that mimics the binding of the p53 tumor suppressor. This intramolecular binding motif is connected to the p53 binding domain of MdmX by a conserved flexible linker that is 85 residues long. The sequence of this flexible linker has an identity of 51% based on multiple protein sequence alignments of 52 MdmX homologs. We used polymer statistics to estimate a global KD value for p53 binding to MdmX in the presence of the flexible linker and the intramolecular binding motif by assuming the flexible linker behaves as a wormlike chain. The global KD estimated from the wormlike chain modeling was nearly identical to the value measured using isothermal titration calorimetry. According to our calculations and measurements, the intramolecular binding motif reduces the apparent affinity of p53 for MdmX by a factor of 400. This study promotes a more quantitative understanding of the role that flexible linkers play in intramolecular binding and provides valuable information to further studies of cellular inhibition of the p53/MdmX interaction.
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8
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Grace CR, Ban D, Min J, Mayasundari A, Min L, Finch KE, Griffiths L, Bharatham N, Bashford D, Kiplin Guy R, Dyer MA, Kriwacki RW. Monitoring Ligand-Induced Protein Ordering in Drug Discovery. J Mol Biol 2016; 428:1290-1303. [PMID: 26812210 DOI: 10.1016/j.jmb.2016.01.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/15/2016] [Accepted: 01/18/2016] [Indexed: 10/22/2022]
Abstract
While the gene for p53 is mutated in many human cancers causing loss of function, many others maintain a wild-type gene but exhibit reduced p53 tumor suppressor activity through overexpression of the negative regulators, Mdm2 and/or MdmX. For the latter mechanism of loss of function, the activity of endogenous p53 can be restored through inhibition of Mdm2 or MdmX with small molecules. We previously reported a series of compounds based upon the Nutlin-3 chemical scaffold that bind to both MdmX and Mdm2 [Vara, B. A. et al. (2014) Organocatalytic, diastereo- and enantioselective synthesis of nonsymmetric cis-stilbene diamines: A platform for the preparation of single-enantiomer cis-imidazolines for protein-protein inhibition. J. Org. Chem. 79, 6913-6938]. Here we present the first solution structures based on data from NMR spectroscopy for MdmX in complex with four of these compounds and compare them with the MdmX:p53 complex. A p53-derived peptide binds with high affinity (Kd value of 150nM) and causes the formation of an extensive network of hydrogen bonds within MdmX; this constitutes the induction of order within MdmX through ligand binding. In contrast, the compounds bind more weakly (Kd values from 600nM to 12μM) and induce an incomplete hydrogen bond network within MdmX. Despite relatively weak binding, the four compounds activated p53 and induced p21(Cip1) expression in retinoblastoma cell lines that overexpress MdmX, suggesting that they specifically target MdmX and/or Mdm2. Our results document structure-activity relationships for lead-like small molecules targeting MdmX and suggest a strategy for their further optimization in the future by using NMR spectroscopy to monitor small-molecule-induced protein order as manifested through hydrogen bond formation.
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Affiliation(s)
- Christy R Grace
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - David Ban
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Anand Mayasundari
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Lie Min
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Kristin E Finch
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Howard Hughes Medical Institute, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Lyra Griffiths
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Nagakumar Bharatham
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Donald Bashford
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - R Kiplin Guy
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Howard Hughes Medical Institute, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN 38105, USA.
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9
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Abstract
The p53 inhibitor MDMX is controlled by multiple stress signaling pathways. Using a proteolytic fragment release (PFR) assay, we detected an intramolecular interaction in MDMX that mechanistically mimics the interaction with p53, resulting in autoinhibition of MDMX. This mimicry is mediated by a hydrophobic peptide located in a long disordered central segment of MDMX that has sequence similarity to the p53 transactivation domain. NMR spectroscopy was used to show this hydrophobic peptide interacts with the N-terminal domain of MDMX in a structurally analogous manner to p53. Mutation of two critical tryptophan residues in the hydrophobic peptide disrupted the intramolecular interaction and increased p53 binding, providing further evidence for mechanistic mimicry. The PFR assay also revealed a second intramolecular interaction between the RING domain and central region that regulates MDMX nuclear import. These results establish the importance of intramolecular interactions in MDMX regulation, and validate a new assay for the study of intramolecular interactions in multidomain proteins with intrinsically disordered regions.
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10
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Bharatham N, Bharatham K, Shelat AA, Bashford D. Ligand binding mode prediction by docking: mdm2/mdmx inhibitors as a case study. J Chem Inf Model 2014; 54:648-59. [PMID: 24358984 DOI: 10.1021/ci4004656] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The p53-binding domains of Mdm2 and Mdmx, two negative regulators of the tumor suppressor p53, are validated targets for cancer therapeutics, but correct binding poses of some proven inhibitors, particularly the nutlins, have been difficult to obtain with standard docking procedures. Virtual screening pipelines typically draw from a database of compounds represented with 1D or 2D structural information from which one or more 3D conformations must be generated. These conformations are then passed to a docking algorithm that searches for optimal binding poses on the target protein. This work tests alternative pipelines using several commonly used conformation generation programs (LigPrep, ConfGen, MacroModel, and Corina/Rotate) and docking programs (GOLD, Glide, MOE-dock, and AutoDock Vina) for their ability to reproduce known poses for a series of Mdmx and/or Mdm2 inhibitors, including several nutlins. Most combinations of these programs using default settings fail to find correct poses for the nutlins but succeed for all other compounds. Docking success for the nutlin class requires either computationally intensive conformational exploration or an "anchoring" procedure that incorporates knowledge of the orientation of the central imidazoline ring.
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Affiliation(s)
- Nagakumar Bharatham
- Department of Structural Biology and ‡Department of Chemical Biology and Therapeutics, Saint Jude Children's Research Hospital , 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
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11
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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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12
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Wafer LN, Streicher WW, McCallum SA, Makhatadze GI. Thermodynamic and kinetic analysis of peptides derived from CapZ, NDR, p53, HDM2, and HDM4 binding to human S100B. Biochemistry 2012; 51:7189-201. [PMID: 22913742 PMCID: PMC3448795 DOI: 10.1021/bi300865g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
S100B is a member of the S100 subfamily of EF-hand proteins that has been implicated in malignant melanoma and neurodegenerative conditions such as Alzheimer's disease and Parkinson's disease. Calcium-induced conformational changes expose a hydrophobic binding cleft, facilitating interactions with a wide variety of nuclear, cytoplasmic, and extracellular target proteins. Previously, peptides derived from CapZ, p53, NDR, HDM2, and HDM4 have been shown to interact with S100B in a calcium-dependent manner. However, the thermodynamic and kinetic basis of these interactions remains largely unknown. To gain further insight, we screened these peptides against the S100B protein using isothermal titration calorimetry and nuclear magnetic resonance. All peptides were found to have binding affinities in the low micromolar to nanomolar range. Binding-induced changes in the line shapes of S100B backbone (1)H and (15)N resonances were monitored to obtain the dissociation constants and the kinetic binding parameters. The large microscopic K(on) rate constants observed in this study (≥1 × 10(7) M(-1) s(-1)) suggest that S100B utilizes a "fly casting mechanism" in the recognition of these peptide targets.
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Affiliation(s)
- Lucas N. Wafer
- Center for Biotechnology and Interdisciplinary Studies and Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, USA
| | | | - Scott A. McCallum
- Center for Biotechnology and Interdisciplinary Studies and Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, USA
| | - George I. Makhatadze
- Center for Biotechnology and Interdisciplinary Studies and Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, USA
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13
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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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14
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Macchiarulo A, Giacchè N, Carotti A, Moretti F, Pellicciari R. Expanding the horizon of chemotherapeutic targets: From MDM2 to MDMX (MDM4). MEDCHEMCOMM 2011. [DOI: 10.1039/c0md00238k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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