1
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Mihalič F, Arcila D, Pettersson ME, Farkhondehkish P, Andersson E, Andersson L, Betancur-R R, Jemth P. Conservation of Affinity Rather Than Sequence Underlies a Dynamic Evolution of the Motif-Mediated p53/MDM2 Interaction in Ray-Finned Fishes. Mol Biol Evol 2024; 41:msae018. [PMID: 38301272 PMCID: PMC10901556 DOI: 10.1093/molbev/msae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/12/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
The transcription factor and cell cycle regulator p53 is marked for degradation by the ubiquitin ligase MDM2. The interaction between these 2 proteins is mediated by a conserved binding motif in the disordered p53 transactivation domain (p53TAD) and the folded SWIB domain in MDM2. The conserved motif in p53TAD from zebrafish displays a 20-fold weaker interaction with MDM2, compared to the interaction in human and chicken. To investigate this apparent difference, we tracked the molecular evolution of the p53TAD/MDM2 interaction among ray-finned fishes (Actinopterygii), the largest vertebrate clade. Intriguingly, phylogenetic analyses, ancestral sequence reconstructions, and binding experiments showed that different loss-of-affinity changes in the canonical binding motif within p53TAD have occurred repeatedly and convergently in different fish lineages, resulting in relatively low extant affinities (KD = 0.5 to 5 μM). However, for 11 different fish p53TAD/MDM2 interactions, nonconserved regions flanking the canonical motif increased the affinity 4- to 73-fold to be on par with the human interaction. Our findings suggest that compensating changes at conserved and nonconserved positions within the motif, as well as in flanking regions of low conservation, underlie a stabilizing selection of "functional affinity" in the p53TAD/MDM2 interaction. Such interplay complicates bioinformatic prediction of binding and calls for experimental validation. Motif-mediated protein-protein interactions involving short binding motifs and folded interaction domains are very common across multicellular life. It is likely that the evolution of affinity in motif-mediated interactions often involves an interplay between specific interactions made by conserved motif residues and nonspecific interactions by nonconserved disordered regions.
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Affiliation(s)
- Filip Mihalič
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala SE-75123, Sweden
| | - Dahiana Arcila
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Mats E Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala SE-75123, Sweden
| | - Pouria Farkhondehkish
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala SE-75123, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala SE-75123, Sweden
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala SE-75123, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77483, USA
| | - Ricardo Betancur-R
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala SE-75123, Sweden
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3
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Oyedele AQK, Adelusi TI, Ogunlana AT, Ayoola MA, Adeyemi RO, Babalola MO, Ayorinde JB, Isong JA, Ajasa TO, Boyenle ID. Promising disruptors of p53-MDM2 dimerization from some medicinal plant phytochemicals: a molecular modeling study. J Biomol Struct Dyn 2023; 41:5817-5826. [PMID: 35822492 DOI: 10.1080/07391102.2022.2097313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/28/2022] [Indexed: 01/18/2023]
Abstract
Cancer is a major global health issue that has a high mortality rate. p53, which functions as a tumor suppressor, is critical in preventing tumor development by regulating the cell cycle and inducing apoptosis in damaged cells. However, the tumor suppressor function of p53 is effectively inhibited by its direct interaction with the hydrophobic cleft of MDM2 protein via multiple mechanisms As a result, restoring p53 activity by blocking the p53-MDM2 protein-protein interaction has been proposed as a compelling therapeutic strategy for cancer treatment. The use of molecular docking and phytochemical screening procedures are appraised to inhibit MDM2's hydrophobic cleft and disrupt the p53-MDM2 interaction. For this purpose, a library of 51 bioactive compounds from 10 medicinal plants was compiled and subjected to structure-based virtual screening. Out of these, only 3 compounds (Atalantoflavone, Cudraxanthone 1, and Ursolic acid) emerged as promising inhibitors of MDM2-p53 based on their binding affinities (-9.1 kcal/mol, -8.8 kcal/mol, and -8.8 kcal/mol respectively) when compared to the standard (-8.8 kcal/mol). Moreover, these compounds showed better pharmacokinetic and drug-like profiling than the standard inhibitor (Chromonotriazolopyrimidine 1). Finally, the 100 ns MD simulation analysis confirmed no significant perturbation in the conformational dynamics of the simulated binary complexes when compared to the standard. In particular, Ursolic acid was found to satisfy the molecular enumeration the most compared to the other inhibitors. Our overall molecular modeling finding shows why these compounds may emerge as potent arsenals for cancer therapeutics. Nonetheless, extensive experimental and clinical research is needed to augment their use in clinics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdul-Quddus Kehinde Oyedele
- Computational Biology, Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
- Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research (NIMR), Lagos, Nigeria
| | - Temitope Isaac Adelusi
- Computational Biology, Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
| | - Abdeen Tunde Ogunlana
- Computational Biology, Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
| | - Mojeed Ashiru Ayoola
- Department of Chemical Sciences, Biochemistry Unit, College of Natural and Applied Science, Fountain University, Osogbo, Nigeria
| | - Rofiat Oluwabusola Adeyemi
- Computational Biology, Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
| | | | - James Babatunde Ayorinde
- Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research (NIMR), Lagos, Nigeria
| | - Josiah Ayoola Isong
- Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research (NIMR), Lagos, Nigeria
| | - Toheeb Olakunle Ajasa
- Computational Biology, Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
| | - Ibrahim Damilare Boyenle
- Computational Biology, Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
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4
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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5
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Kowalczyk D, Nakasone MA, Smith BO, Huang DT. Bivalent binding of p14ARF to MDM2 RING and acidic domains inhibits E3 ligase function. Life Sci Alliance 2022; 5:e202201472. [PMID: 35944929 PMCID: PMC9366199 DOI: 10.26508/lsa.202201472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 12/29/2022] Open
Abstract
ARF tumor suppressor protein is a key regulator of the MDM2-p53 signaling axis. ARF interferes with MDM2-mediated ubiquitination and degradation of p53 by sequestering MDM2 in the nucleolus and preventing MDM2-p53 interaction and nuclear export of p53. Moreover, ARF also directly inhibits MDM2 ubiquitin ligase (E3) activity, but the mechanism remains elusive. Here, we apply nuclear magnetic resonance and biochemical analyses to uncover the mechanism of ARF-mediated inhibition of MDM2 E3 activity. We show that MDM2 acidic and zinc finger domains (AD-ZnF) form a weak intramolecular interaction with the RING domain, where the binding site overlaps with the E2∼ubiquitin binding surface and thereby partially reduces MDM2 E3 activity. Binding of human N-terminal 32 residues of p14ARF to the acidic domain of MDM2 strengthens the AD-ZnF-RING domain interaction. Furthermore, the N-terminal RxFxV motifs of p14ARF participate directly in the MDM2 RING domain interaction. This bivalent binding mode of p14ARF to MDM2 acidic and RING domains restricts E2∼ubiquitin recruitment and massively hinders MDM2 E3 activity. These findings elucidate the mechanism by which ARF inhibits MDM2 E3 activity.
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Affiliation(s)
| | | | - Brian O Smith
- Institute of Molecular Cell and System Biology, University of Glasgow, Glasgow, UK
| | - Danny T Huang
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
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6
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Song Q, Liu XQ, Rainey JK. 1H, 15N and 13C backbone resonance assignments of the acidic domain of the human MDMX protein. Biomol NMR Assign 2022; 16:171-178. [PMID: 35359247 DOI: 10.1007/s12104-022-10081-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
The human MDMX protein, also known as MDM4, plays a pivotal role in regulating the activity of the tumor suppressor protein p53 by restricting p53 transcriptional activity and stimulating the E3 ubiquitin ligase activity of another key regulatory protein, MDM2, to promote p53 degradation. MDMX is ubiquitously expressed in most tissue types and overexpression of MDMX has been implicated in many forms of cancer. MDMX has been shown to require an intact N-terminal p53-binding domain and C-terminal RING domain to exert inhibitory effects on p53. The presence of a tryptophan-rich sequence in the central acidic domain of MDMX has also been implicated in regulating the interaction between MDMX and p53, directly interacting with the p53 DNA-binding domain. To date, little structural information has been obtained for this acidic region of MDMX that encompasses the Trp-rich sequence. In order to gain insight into the structure and function of this region, we have carried out solution-state NMR spectroscopy studies utilizing the segment of MDMX spanning residues 181-300-with bounds specifically chosen through multiple sequence alignment-which encompasses nearly 25% of MDMX. Here, we report the 1H, 15N and 13C backbone chemical shift assignments of the acidic domain of MDMX and show that it exhibits hallmarks of intrinsic disorder and localized variation in inferred secondary structure propensity.
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Affiliation(s)
- Qinyan Song
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Xiang-Qin Liu
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
| | - Jan K Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
- Department of Chemistry, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
- School of Biomedical Engineering, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
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7
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Kukushkin M, Novotortsev V, Filatov V, Ivanenkov Y, Skvortsov D, Veselov M, Shafikov R, Moiseeva A, Zyk N, Majouga A, Beloglazkina E. Synthesis and Biological Evaluation of S-, O- and Se-Containing Dispirooxindoles. Molecules 2021; 26:molecules26247645. [PMID: 34946727 PMCID: PMC8703884 DOI: 10.3390/molecules26247645] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
A series of novel S-, O- and Se-containing dispirooxindole derivatives has been synthesized using 1,3-dipolar cycloaddition reaction of azomethine ylide generated from isatines and sarcosine at the double C=C bond of 5-indolidene-2-chalcogen-imidazolones (chalcogen was oxygen, sulfur or selenium). The cytotoxicity of these dispiro derivatives was evaluated in vitro using different tumor cell lines. Several molecules have demonstrated a considerable cytotoxicity against the panel and showed good selectivity towards colorectal carcinoma HCT116 p53+/+ over HCT116 p53−/− cells. In particular, good results have been obtained for LNCaP prostate cell line. The performed in silico study has revealed MDM2/p53 interaction as one of the possible targets for the synthesized molecules. However, in contrast to selectivity revealed during the cell-based evaluation and the results obtained in computational study, no significant p53 activation using a reporter construction in p53wt A549 cell line was observed in a relevant concentration range.
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Affiliation(s)
- Maksim Kukushkin
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory, 1/3, GSP-1, 119991 Moscow, Russia; (M.K.); (V.N.); (V.F.); (D.S.); (R.S.); (A.M.); (N.Z.); (A.M.)
- Research Laboratory of Biophysics, National University of Science and Technology MISiS, 119049 Moscow, Russia
| | - Vladimir Novotortsev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory, 1/3, GSP-1, 119991 Moscow, Russia; (M.K.); (V.N.); (V.F.); (D.S.); (R.S.); (A.M.); (N.Z.); (A.M.)
| | - Vadim Filatov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory, 1/3, GSP-1, 119991 Moscow, Russia; (M.K.); (V.N.); (V.F.); (D.S.); (R.S.); (A.M.); (N.Z.); (A.M.)
| | - Yan Ivanenkov
- Laboratory of Medicinal Chemistry and Bioinformatic, Moscow Institute of Physics and Technology (MIPT), Institutski Pereulok 9, 141701 Dolgoprudny, Russia; (Y.I.); (M.V.)
| | - Dmitry Skvortsov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory, 1/3, GSP-1, 119991 Moscow, Russia; (M.K.); (V.N.); (V.F.); (D.S.); (R.S.); (A.M.); (N.Z.); (A.M.)
| | - Mark Veselov
- Laboratory of Medicinal Chemistry and Bioinformatic, Moscow Institute of Physics and Technology (MIPT), Institutski Pereulok 9, 141701 Dolgoprudny, Russia; (Y.I.); (M.V.)
| | - Radik Shafikov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory, 1/3, GSP-1, 119991 Moscow, Russia; (M.K.); (V.N.); (V.F.); (D.S.); (R.S.); (A.M.); (N.Z.); (A.M.)
| | - Anna Moiseeva
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory, 1/3, GSP-1, 119991 Moscow, Russia; (M.K.); (V.N.); (V.F.); (D.S.); (R.S.); (A.M.); (N.Z.); (A.M.)
| | - Nikolay Zyk
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory, 1/3, GSP-1, 119991 Moscow, Russia; (M.K.); (V.N.); (V.F.); (D.S.); (R.S.); (A.M.); (N.Z.); (A.M.)
| | - Alexander Majouga
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory, 1/3, GSP-1, 119991 Moscow, Russia; (M.K.); (V.N.); (V.F.); (D.S.); (R.S.); (A.M.); (N.Z.); (A.M.)
- Dmitry Mendeleev University of Chemical Technology of Russia, Miusskaya Sq. 9, 125047 Moscow, Russia
| | - Elena Beloglazkina
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory, 1/3, GSP-1, 119991 Moscow, Russia; (M.K.); (V.N.); (V.F.); (D.S.); (R.S.); (A.M.); (N.Z.); (A.M.)
- Correspondence:
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8
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Attri P, Kurita H, Koga K, Shiratani M. Impact of Reactive Oxygen and Nitrogen Species Produced by Plasma on Mdm2-p53 Complex. Int J Mol Sci 2021; 22:ijms22179585. [PMID: 34502494 PMCID: PMC8431430 DOI: 10.3390/ijms22179585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 12/11/2022] Open
Abstract
The study of protein–protein interactions is of great interest. Several early studies focused on the murine double minute 2 (Mdm2)–tumor suppressor protein p53 interactions. However, the effect of plasma treatment on Mdm2 and p53 is still absent from the literature. This study investigated the structural changes in Mdm2, p53, and the Mdm2–p53 complex before and after possible plasma oxidation through molecular dynamic (MD) simulations. MD calculation revealed that the oxidized Mdm2 bounded or unbounded showed high flexibility that might increase the availability of tumor suppressor protein p53 in plasma-treated cells. This study provides insight into Mdm2 and p53 for a better understanding of plasma oncology.
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Affiliation(s)
- Pankaj Attri
- Center of Plasma Nano-Interface Engineering, Kyushu University, Fukuoka 819-0395, Japan;
- Graduate School of Information Science and Electrical Engineering, Kyushu University, Fukuoka 819-0395, Japan
- Correspondence:
| | - Hirofumi Kurita
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi 441-8580, Aichi, Japan;
| | - Kazunori Koga
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka 819-0395, Japan;
- Center for Novel Science Initiatives, National Institute of Natural Science, Tokyo 105-0001, Japan
| | - Masaharu Shiratani
- Center of Plasma Nano-Interface Engineering, Kyushu University, Fukuoka 819-0395, Japan;
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka 819-0395, Japan;
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9
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Huang L, Agrawal T, Zhu G, Yu S, Tao L, Lin J, Marmorstein R, Shorter J, Yang X. DAXX represents a new type of protein-folding enabler. Nature 2021; 597:132-137. [PMID: 34408321 PMCID: PMC8485697 DOI: 10.1038/s41586-021-03824-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 07/15/2021] [Indexed: 12/31/2022]
Abstract
Protein quality control systems are crucial for cellular function and organismal health. At present, most known protein quality control systems are multicomponent machineries that operate via ATP-regulated interactions with non-native proteins to prevent aggregation and promote folding1, and few systems that can broadly enable protein folding by a different mechanism have been identified. Moreover, proteins that contain the extensively charged poly-Asp/Glu (polyD/E) region are common in eukaryotic proteomes2, but their biochemical activities remain undefined. Here we show that DAXX, a polyD/E protein that has been implicated in diverse cellular processes3-10, possesses several protein-folding activities. DAXX prevents aggregation, solubilizes pre-existing aggregates and unfolds misfolded species of model substrates and neurodegeneration-associated proteins. Notably, DAXX effectively prevents and reverses aggregation of its in vivo-validated client proteins, the tumour suppressor p53 and its principal antagonist MDM2. DAXX can also restore native conformation and function to tumour-associated, aggregation-prone p53 mutants, reducing their oncogenic properties. These DAXX activities are ATP-independent and instead rely on the polyD/E region. Other polyD/E proteins, including ANP32A and SET, can also function as stand-alone, ATP-independent molecular chaperones, disaggregases and unfoldases. Thus, polyD/E proteins probably constitute a multifunctional protein quality control system that operates via a distinctive mechanism.
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Affiliation(s)
- Liangqian Huang
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Trisha Agrawal
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Wilson Sonsini Goodrich & Rosati LP, New York, NY, USA
| | - Guixin Zhu
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sixiang Yu
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Liming Tao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - JiaBei Lin
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ronen Marmorstein
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiaolu Yang
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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10
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Sakai H, Kawakami H, Teramura T, Onodera Y, Somers E, Furuuchi K, Uenaka T, Kato R, Nakagawa K. Folate receptor α increases chemotherapy resistance through stabilizing MDM2 in cooperation with PHB2 that is overcome by MORAb-202 in gastric cancer. Clin Transl Med 2021; 11:e454. [PMID: 34185411 PMCID: PMC8167866 DOI: 10.1002/ctm2.454] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The main function of folate receptor α (FOLRα) has been considered to mediate intracellular folate uptake and induce tumor cell proliferation. Given the broad spectrum of expression among malignant tumors, including gastric cancer (GC) but not in normal tissue, FOLRα represents an attractive target for tumor-selective drug delivery. However, the efficacy of anti-FOLRα monoclonal antibodies (mAbs) has not been proved so far, with the reason for this failure remaining unclear, raising the need for a better understanding of FOLRα function. METHODS The distribution of FOLRα in GC cells was evaluated by immunohistochemistry. The impacts of FOLRα expression on the survival of GC patients and GC cell lines were examined with the Gene Expression Omnibus database and by siRNA of FOLRα. RNA-sequencing and Microarray analysis was conducted to identify the function of FOLRα. Proteins that interact with FOLRα were identified with shotgun LC-MS/MS. The antitumor efficacy of the anti-FOLRα mAb farletuzumab as well as the antibody-drug conjugate (ADC) consists of the farletuzumab and the tublin-depolymerizing agent eribulin (MORAb-202) was evaluated both in vitro and in vivo. RESULTS FOLRα was detected both at the cell membrane and in the cytoplasm. Shorter overall survival was associated with FOLRα expression in GC patients, whereas reduction of FOLRα attenuated cell proliferation without inducing cell death in GC cell lines. Transcriptomic and proteomic examinations revealed that the FOLRα-expressing cancer cells possess a mechanism of chemotherapy resistance supported by MDM2, and FOLRα indirectly regulates it through a chaperone protein prohibitin2 (PHB2). Although reduction of FOLRα brought about vulnerability for oxaliplatin by diminishing MDM2 expression, farletuzumab did not suppress the MDM2-mediated chemoresistance and cell proliferation in GC cells. On the other hand, MORAb-202 showed significant antitumor efficacy. CONCLUSIONS The ADC could be a more reasonable choice than mAb as a targeting agent for the FOLRα-expressing tumor.
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Affiliation(s)
- Hitomi Sakai
- Department of Medical OncologyKindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Hisato Kawakami
- Department of Medical OncologyKindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Takeshi Teramura
- Division of Cell Biology for Regenerative MedicineInstitute of Advanced Clinical MedicineKindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Yuta Onodera
- Division of Cell Biology for Regenerative MedicineInstitute of Advanced Clinical MedicineKindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Elizabeth Somers
- AD Franchise Special Mission, Eisai Inc.Woodcliff LakeNew JerseyUSA
| | - Keiji Furuuchi
- Epochal Precision Anti‐Cancer Therapeutics (EPAT), Eisai Inc.ExtonPennsylvaniaUSA
| | - Toshimitsu Uenaka
- Epochal Precision Anti‐Cancer Therapeutics (EPAT), Eisai Inc.ExtonPennsylvaniaUSA
| | - Ryoji Kato
- Department of Medical OncologyKindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Kazuhiko Nakagawa
- Department of Medical OncologyKindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
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11
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Eltamany EE, Abdelmohsen UR, Hal DM, Ibrahim AK, Hassanean HA, Abdelhameed RFA, Temraz TA, Hajjar D, Makki AA, Hendawy OM, AboulMagd AM, Youssif KA, Bringmann G, Ahmed SA. Holospiniferoside: A New Antitumor Cerebroside from The Red Sea Cucumber Holothuria spinifera: In Vitro and In Silico Studies. Molecules 2021; 26:1555. [PMID: 33809026 PMCID: PMC8001240 DOI: 10.3390/molecules26061555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 11/16/2022] Open
Abstract
Chemical investigation of the methanolic extract of the Red Sea cucumber Holothuria spinifera led to the isolation of a new cerebroside, holospiniferoside (1), together with thymidine (2), methyl-α-d-glucopyranoside (3), a new triacylglycerol (4), and cholesterol (5). Their chemical structures were established by NMR and mass spectrometric analysis, including gas chromatography-mass spectrometry (GC-MS) and high-resolution mass spectrometry (HRMS). All the isolated compounds are reported in this species for the first time. Moreover, compound 1 exhibited promising in vitro antiproliferative effect on the human breast cancer cell line (MCF-7) with IC50 of 20.6 µM compared to the IC50 of 15.3 µM for the drug cisplatin. To predict the possible mechanism underlying the cytotoxicity of compound 1, a docking study was performed to elucidate its binding interactions with the active site of the protein Mdm2-p53. Compound 1 displayed an apoptotic activity via strong interaction with the active site of the target protein. This study highlights the importance of marine natural products in the design of new anticancer agents.
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Affiliation(s)
- Enas E. Eltamany
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (E.E.E.); (D.M.H.); (A.K.I.); (H.A.H.); (R.F.A.A.)
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, New Minia 61111, Egypt;
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
| | - Dina M. Hal
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (E.E.E.); (D.M.H.); (A.K.I.); (H.A.H.); (R.F.A.A.)
| | - Amany K. Ibrahim
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (E.E.E.); (D.M.H.); (A.K.I.); (H.A.H.); (R.F.A.A.)
| | - Hashim A. Hassanean
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (E.E.E.); (D.M.H.); (A.K.I.); (H.A.H.); (R.F.A.A.)
| | - Reda F. A. Abdelhameed
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (E.E.E.); (D.M.H.); (A.K.I.); (H.A.H.); (R.F.A.A.)
| | - Tarek A. Temraz
- Department of Marine Science, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt;
| | - Dina Hajjar
- Department of Biochemistry, Collage of Science, University of Jeddah, Jeddah 80203, Saudi Arabia; (D.H.); (A.A.M.)
| | - Arwa A. Makki
- Department of Biochemistry, Collage of Science, University of Jeddah, Jeddah 80203, Saudi Arabia; (D.H.); (A.A.M.)
| | - Omnia Magdy Hendawy
- Department of Chemistry of Pharmacology, Faculty of Pharmacy, Jouf University, Skaka 2014, Saudi Arabia;
- Department of Clinical Pharmacology, Faculty of Medicine, Beni Suef University, Beni-Suef 62513, Egypt
| | - Asmaa M. AboulMagd
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Nahda University, Beni Suef 62513, Egypt;
| | - Khayrya A. Youssif
- Department of Pharmacognosy, Faculty of Pharmacy, Modern University for Technology and Information, Cairo 12585, Egypt;
| | - Gerhard Bringmann
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Safwat A. Ahmed
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (E.E.E.); (D.M.H.); (A.K.I.); (H.A.H.); (R.F.A.A.)
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12
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Magnussen HM, Huang DT. Identification of a Catalytic Active but Non-Aggregating MDM2 RING Domain Variant. J Mol Biol 2021; 433:166807. [PMID: 33450248 PMCID: PMC7895813 DOI: 10.1016/j.jmb.2021.166807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/28/2020] [Accepted: 01/02/2021] [Indexed: 11/26/2022]
Abstract
As a key regulator of the tumour suppressor protein p53, MDM2 is involved in various types of cancer and has thus been an attractive drug target. So far, small molecule design has primarily focussed on the N-terminal p53-binding domain although on-target toxicity effects have been reported. Targeting the catalytic RING domain of MDM2 resembles an alternative approach to drug MDM2 with the idea to prevent MDM2-mediated ubiquitination of p53 while retaining MDM2's ability to bind p53. The design of RING inhibitors has been limited by the extensive aggregation tendency of the RING domain, making it challenging to undertake co-crystallization attempts with potential inhibitors. Here we compare the purification profiles of the MDM2 RING domain from several species and show that the MDM2 RING domain of other species than human is much less prone to aggregate although the overall structure of the RING domain is conserved. Through sequence comparison and mutagenesis analyses, we identify a single point mutation, G443T, which greatly enhances the dimeric fraction of human MDM2 RING domain during purification. Neither does the mutation alter the structure of the RING domain, nor does it affect E2(UbcH5B)-Ub binding and activity. Hence, MDM2-G443T facilitates studies involving binding partners that would be hampered by the low solubility of the wild-type RING domain. Furthermore, it will be valuable for the development of MDM2 RING inhibitors.
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Affiliation(s)
- Helge M Magnussen
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Danny T Huang
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, United Kingdom.
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13
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Zhao J, Blayney A, Liu X, Gandy L, Jin W, Yan L, Ha JH, Canning AJ, Connelly M, Yang C, Liu X, Xiao Y, Cosgrove MS, Solmaz SR, Zhang Y, Ban D, Chen J, Loh SN, Wang C. EGCG binds intrinsically disordered N-terminal domain of p53 and disrupts p53-MDM2 interaction. Nat Commun 2021; 12:986. [PMID: 33579943 PMCID: PMC7881117 DOI: 10.1038/s41467-021-21258-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 01/11/2021] [Indexed: 12/19/2022] Open
Abstract
Epigallocatechin gallate (EGCG) from green tea can induce apoptosis in cancerous cells, but the underlying molecular mechanisms remain poorly understood. Using SPR and NMR, here we report a direct, μM interaction between EGCG and the tumor suppressor p53 (KD = 1.6 ± 1.4 μM), with the disordered N-terminal domain (NTD) identified as the major binding site (KD = 4 ± 2 μM). Large scale atomistic simulations (>100 μs), SAXS and AUC demonstrate that EGCG-NTD interaction is dynamic and EGCG causes the emergence of a subpopulation of compact bound conformations. The EGCG-p53 interaction disrupts p53 interaction with its regulatory E3 ligase MDM2 and inhibits ubiquitination of p53 by MDM2 in an in vitro ubiquitination assay, likely stabilizing p53 for anti-tumor activity. Our work provides insights into the mechanisms for EGCG's anticancer activity and identifies p53 NTD as a target for cancer drug discovery through dynamic interactions with small molecules.
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Affiliation(s)
- Jing Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemistry and Chemical Biology, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Alan Blayney
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Xiaorong Liu
- Department of Chemistry, University of Massachusetts, Amherst, MA, USA
| | - Lauren Gandy
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemistry and Chemical Biology, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Weihua Jin
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemistry and Chemical Biology, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Lufeng Yan
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemistry and Chemical Biology, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Ashley J Canning
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Michael Connelly
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Chao Yang
- Department of Chemistry, New York University, New York, NY, USA
| | - Xinyue Liu
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemistry and Chemical Biology, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Yuanyuan Xiao
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemistry and Chemical Biology, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Michael S Cosgrove
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Sozanne R Solmaz
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY, USA
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY, USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
| | - David Ban
- Merck Research Laboratories, Mass Spectrometry and Biophysics, Kenilworth, NJ, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA, USA
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemistry and Chemical Biology, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA.
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14
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Abstract
Molecular dynamics simulations can now routinely access the microsecond timescale, making feasible direct sampling of ligand association events. While Markov State Model (MSM) approaches offer a useful framework for analyzing such trajectory data to gain insight into binding mechanisms, accurate modeling of ligand association pathways and kinetics must be done carefully. We describe methods and good practices for constructing MSMs of ligand binding from unbiased trajectory data and discuss how to use time-lagged independent component analysis (tICA) to build informative models, using as an example recent simulation work to model the binding of phenylalanine to the regulatory ACT domain dimer of phenylalanine hydroxylase. We describe a variety of methods for estimating association rates from MSMs and discuss how to distinguish between conformational selection and induced-fit mechanisms using MSMs. In addition, we review some examples of MSMs constructed to elucidate the mechanisms by which p53 transactivation domain (TAD) and related peptides bind the oncoprotein MDM2.
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Affiliation(s)
- Yunhui Ge
- Department of Chemistry, Temple University, Philadelphia, PA, USA
| | - Vincent A Voelz
- Department of Chemistry, Temple University, Philadelphia, PA, USA.
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15
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El-Kalyoubi S, Agili F. Synthesis, In Silico Prediction and In Vitro Evaluation of Antitumor Activities of Novel Pyrido[2,3- d]pyrimidine, Xanthine and Lumazine Derivatives. Molecules 2020; 25:molecules25215205. [PMID: 33182318 PMCID: PMC7672615 DOI: 10.3390/molecules25215205] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/21/2020] [Accepted: 10/30/2020] [Indexed: 12/24/2022] Open
Abstract
Ethyl 5-arylpyridopyrimidine-6-carboxylates 3a–d were prepared as a one pot three component reaction via the condensation of different aromatic aldehydes and ethyl acetoacetate with 6-amino-1-benzyluracil 1a under reflux condition in ethanol. Additionally, condensation of ethyl 2-(2-hydroxybenzylidene) acetoacetate with 6-amino-1-benzyluracil in DMF afforded 6-acetylpyridopyrimidine-7-one 3e; a facile, operationally, simple and efficient one-pot synthesis of 8-arylxanthines 6a–f is reported by refluxing 5,6-diaminouracil 4 with aromatic aldehydes in DMF. Moreover, 6-aryllumazines 7a–d was obtained via the reaction of 5,6-diaminouracil with the appropriate aromatic aldehydes in triethyl orthoformate under reflux condition. The synthesized compounds were characterized by spectral (1H-NMR, 13C-NMR, IR and mass spectra) and elemental analyses. The newly synthesized compounds were screened for their anticancer activity against lung cancer A549 cell line. Furthermore, a molecular-docking study was employed to determine the possible mode of action of the synthesized compounds against a group of proteins highly implicated in cancer progression, especially lung cancer. Docking results showed that compounds 3b, 6c, 6d, 6e, 7c and 7d were the best potential docked compounds against most of the tested proteins, especially CDK2, Jak2, and DHFR proteins. These results are in agreement with cytotoxicity results, which shed a light on the promising activity of these novel six heterocyclic derivatives for further investigation as potential chemotherapeutics.
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Affiliation(s)
- Samar El-Kalyoubi
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Nasr City, Cairo 11651, Egypt
- Correspondence: ; Tel.: +20-111-995-2620
| | - Fatimah Agili
- Chemistry Department, Faculty of Science (Female Section), Jazan University, Jazan 82621, Saudi Arabia;
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16
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Orts J, Riek R. Protein-ligand structure determination with the NMR molecular replacement tool, NMR 2. J Biomol NMR 2020; 74:633-642. [PMID: 32621003 DOI: 10.1007/s10858-020-00324-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
We recently reported on a new method called NMR Molecular Replacement that efficiently derives the structure of a protein-ligand complex at the interaction site. The method was successfully applied to high and low affinity complexes covering ligands from peptides to small molecules. The algorithm used in the NMR Molecular Replacement program has until now not been described in detail. Here, we present a complete description of the NMR Molecular Replacement implementation as well as several new features that further reduce the time required for structure elucidation.
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Affiliation(s)
- Julien Orts
- Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, Wolgang-Pauli-Strasse 10, 8093, Zürich, Switzerland.
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, Wolgang-Pauli-Strasse 10, 8093, Zürich, Switzerland
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17
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Popov SA, Semenova MD, Baev DS, Frolova TS, Shestopalov MA, Wang C, Qi Z, Shults EE, Turks M. Synthesis and cytotoxicity of hybrids of 1,3,4- or 1,2,5-oxadiazoles tethered from ursane and lupane core with 1,2,3-triazole. Steroids 2020; 162:108698. [PMID: 32687846 DOI: 10.1016/j.steroids.2020.108698] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/05/2020] [Accepted: 07/11/2020] [Indexed: 12/21/2022]
Abstract
Ursane and lupane type (1-((5-aryl-1,3,4-oxadiazol-2-yl)methyl)-1H-1,2,3-triazol-4-yl)methyl and (1-((4-methyl-2-oxido-1,2,5-oxadiazol-3-yl)methyl)-1H-1,2,3-triazol-4-yl)methyl hybrids were prepared by 1,3-cycloaddition reactions of azole-derived azides with alkyne esters connected to positions C-3 and C-28 of triterpene core and tested for cytotoxicity. Hybrid compounds of 1,3,4-oxadiazoles attached at positions 3- and 28- of triterpenoid frame via triazole spacer and combinations of 1,2,5-oxadiazole or 1,3,4-oxadiazole, tethered with succinate linker and 1,2,3-triazole at the position 3- of the ursane backbone, were inactive in relation to all the cancer cells tested. Eventually, combinations of furoxan fragment and 1,2,3-triazole linked to C-28 position of triterpene backbone demonstrated marked cytotoxic activity towards MCF-7 and HepG2 cells. The most active ester of ursolic acid with (1-((4-methyl-2-oxido-1,2,5-oxadiazol-3-yl)methyl)-1H-1,2,3-triazol-4-yl)methyl substituent and 3-O-acetyl group was superior in activity and selectivity over doxorubicin and ursolic acid on MCF-7 cells. The length of the carbon spacer group may be of crucial importance for cytotoxicity. The introduction of the additional ester linker between the C-28 of triterpenoid and triazole or changing triazole spacer between furoxan moiety and triterpenoid core resulted in activity decrease against all the tested cells. In accordance with molecular modeling results, the activity of new derivatives may be explained in terms of the interaction of the new hybrid molecules and Mdm2 binding sites.
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Affiliation(s)
- Sergey A Popov
- Novosibirsk Institute of Organic Chemistry, Acad. Lavrentyev ave. 9, Novosibirsk 630090, Russia.
| | - Marya D Semenova
- Novosibirsk Institute of Organic Chemistry, Acad. Lavrentyev ave. 9, Novosibirsk 630090, Russia
| | - Dmitry S Baev
- Novosibirsk Institute of Organic Chemistry, Acad. Lavrentyev ave. 9, Novosibirsk 630090, Russia
| | - Tatiana S Frolova
- The Federal Research Center Institute of Cytology and Genetics, Acad. Lavrentyev Ave., 10, 630090 Novosibirsk, Russia; Novosibirsk State University, Pirogova Street, 2, 630090 Novosibirsk, Russia
| | - Michael A Shestopalov
- Nikolaev Institute of Inorganic Chemistry SB RAS, Acad. Lavrentiev ave., 3, 630090 Novosibirsk, Russia
| | - Chengzhang Wang
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing 210042, China
| | - Zhiwen Qi
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing 210042, China
| | - Elvira E Shults
- Novosibirsk Institute of Organic Chemistry, Acad. Lavrentyev ave. 9, Novosibirsk 630090, Russia
| | - Māris Turks
- Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry, Riga Technical University, P. Valdena Str. 3, Riga LV-1048, Latvia
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18
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Conlon IL, Drennen B, Lanning ME, Hughes S, Rothhaas R, Wilder PT, MacKerell AD, Fletcher S. Rationally Designed Polypharmacology: α-Helix Mimetics as Dual Inhibitors of the Oncoproteins Mcl-1 and HDM2. ChemMedChem 2020; 15:1691-1698. [PMID: 32583936 PMCID: PMC8477420 DOI: 10.1002/cmdc.202000278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/19/2020] [Indexed: 02/06/2023]
Abstract
Protein-protein interactions (PPIs), many of which are dominated by α-helical recognition domains, play key roles in many essential cellular processes, and the dysregulation of these interactions can cause detrimental effects. For instance, aberrant PPIs involving the Bcl-2 protein family can lead to several diseases including cancer, neurodegenerative diseases, and diabetes. Interactions between Bcl-2 pro-life proteins, such as Mcl-1, and pro-death proteins, such as Bim, regulate the intrinsic pathway of apoptosis. p53, a tumor-suppressor protein, also has a pivotal role in apoptosis and is negatively regulated by its E3 ubiquitin ligase HDM2. Both Mcl-1 and HDM2 are upregulated in numerous cancers, and, interestingly, there is crosstalk between both protein pathways. Recently, synergy has been observed between Mcl-1 and HDM2 inhibitors. Towards the development of new anticancer drugs, we herein describe a polypharmacology approach for the dual inhibition of Mcl-1 and HDM2 by employing three densely functionalized isoxazoles, pyrazoles, and thiazoles as mimetics of key α-helical domains of their partner proteins.
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Affiliation(s)
- Ivie L Conlon
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Brandon Drennen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Maryanna E Lanning
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Samuel Hughes
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Rebecca Rothhaas
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Paul T Wilder
- Department of Biochemistry and Molecular Biology Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
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19
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Quartararo AJ, Gates ZP, Somsen BA, Hartrampf N, Ye X, Shimada A, Kajihara Y, Ottmann C, Pentelute BL. Ultra-large chemical libraries for the discovery of high-affinity peptide binders. Nat Commun 2020; 11:3183. [PMID: 32576815 PMCID: PMC7311396 DOI: 10.1038/s41467-020-16920-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/27/2020] [Indexed: 11/22/2022] Open
Abstract
High-diversity genetically-encoded combinatorial libraries (108-1013 members) are a rich source of peptide-based binding molecules, identified by affinity selection. Synthetic libraries can access broader chemical space, but typically examine only ~ 106 compounds by screening. Here we show that in-solution affinity selection can be interfaced with nano-liquid chromatography-tandem mass spectrometry peptide sequencing to identify binders from fully randomized synthetic libraries of 108 members-a 100-fold gain in diversity over standard practice. To validate this approach, we show that binders to a monoclonal antibody are identified in proportion to library diversity, as diversity is increased from 106-108. These results are then applied to the discovery of p53-like binders to MDM2, and to a family of 3-19 nM-affinity, α/β-peptide-based binders to 14-3-3. An X-ray structure of one of these binders in complex with 14-3-3σ is determined, illustrating the role of β-amino acids in facilitating a key binding contact.
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Affiliation(s)
- Anthony J Quartararo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Zachary P Gates
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Bente A Somsen
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600, MB, Eindhoven, Netherlands
| | - Nina Hartrampf
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Xiyun Ye
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Arisa Shimada
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yasuhiro Kajihara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600, MB, Eindhoven, Netherlands
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02142, USA.
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.
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20
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Abstract
About 50% of human cancers across the globe arise due to a mutation in the p53 gene which gives rise to its functional inactive form, and in the rest of the cancer the efficacy of active p53 (wild-type) is hindered by MDM2-mediated degradation. Breakdown of the p53-MDM2 association may constitute an effective strategy to stimulate or reinstate the activity of wild type p53, thereby reviving the p53 tumor suppressor capability. S100A1 has been revealed to associate with the N-terminal domain of MDM2 and p53 protein. We utilized NMR spectroscopy to study the interface amongst the S100A1 and N-terminal domain of MDM2. Additionally, the S100A1-MDM2 complex generated through the HADDOCK program was then superimposed with the p53 (peptide) -MDM2 complex reported earlier. The overlay indicated that a segment of S100A1 could block the interaction of p53 (peptide) -MDM2 complex significantly. To further justify our assumption, we performed HSQC-NMR titration for the S100A1 and p53 N-terminal domain (p53-TAD). The data obtained indicated that the S100A1 segment comprising nearly 17 residues have some common residues that interact with both MDM2 and p53-TAD. Further, we synthesized the 17-residue peptide derived from the S100A1 protein and attached it to the cell-penetrating HIV-TAT peptide. The HSQC-NMR competitive binding experiment revealed that Peptide 1 could successfully interfere with the p53-MDM2 interaction. Furthermore, functional effects of the peptide was validated in cancer cells. The results showed that Peptide 1 effectively inhibited cell proliferation, and increased the protein levels of p53 and its downstream p21 in MCF-7 cells. Treatment of Peptide 1 resulted in cell cycle arrest at G2/M phase, and also induced apoptotic cell death at higher concentration. Taken together, the results suggest that disruption of the interaction of p53 and MDM2 by Peptide 1 could activate normal p53 functions, leading to cell cycle arrest and apoptotic cell death in cancer cells. We proposed here that S100A1 could influence the p53-MDM2 interaction credibly and possibly reactivates the wild type p53 pathway.
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Affiliation(s)
- Deepu Dowarha
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Ruey-Hwang Chou
- Graduate Institute of Biomedical Sciences and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
- Department of Biotechnology, Asia University, Wufeng, Taichung, Taiwan
- * E-mail: (CY); (RHC)
| | - Chin Yu
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
- * E-mail: (CY); (RHC)
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21
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Taliani S, Da Settimo F, Martini C, Laneri S, Novellino E, Greco G. Exploiting the Indole Scaffold to Design Compounds Binding to Different Pharmacological Targets. Molecules 2020; 25:molecules25102331. [PMID: 32429433 PMCID: PMC7287756 DOI: 10.3390/molecules25102331] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 12/14/2022] Open
Abstract
Several indole derivatives have been disclosed by our research groups that have been collaborating for nearly 25 years. The results of our investigations led to a variety of molecules binding selectively to different pharmacological targets, specifically the type A γ-aminobutyric acid (GABAA) chloride channel, the translocator protein (TSPO), the murine double minute 2 (MDM2) protein, the A2B adenosine receptor (A2B AR) and the Kelch-like ECH-associated protein 1 (Keap1). Herein, we describe how these works were conceived and carried out thanks to the versatility of indole nucleus to be exploited in the design and synthesis of drug-like molecules.
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Affiliation(s)
- Sabrina Taliani
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano, 6, 56126 Pisa, Italy; (F.D.S.); (C.M.)
- Correspondence: (S.T.); (G.G.); Tel.: +39-050-2219547 (S.T.); +39-081-678645 (G.G.)
| | - Federico Da Settimo
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano, 6, 56126 Pisa, Italy; (F.D.S.); (C.M.)
| | - Claudia Martini
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano, 6, 56126 Pisa, Italy; (F.D.S.); (C.M.)
| | - Sonia Laneri
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano, 49, 80131 Naples, Italy; (S.L.); (E.N.)
| | - Ettore Novellino
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano, 49, 80131 Naples, Italy; (S.L.); (E.N.)
| | - Giovanni Greco
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano, 49, 80131 Naples, Italy; (S.L.); (E.N.)
- Correspondence: (S.T.); (G.G.); Tel.: +39-050-2219547 (S.T.); +39-081-678645 (G.G.)
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22
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Magnussen HM, Ahmed SF, Sibbet GJ, Hristova VA, Nomura K, Hock AK, Archibald LJ, Jamieson AG, Fushman D, Vousden KH, Weissman AM, Huang DT. Structural basis for DNA damage-induced phosphoregulation of MDM2 RING domain. Nat Commun 2020; 11:2094. [PMID: 32350255 PMCID: PMC7190642 DOI: 10.1038/s41467-020-15783-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/27/2020] [Indexed: 01/30/2023] Open
Abstract
Phosphorylation of MDM2 by ATM upon DNA damage is an important mechanism for deregulating MDM2, thereby leading to p53 activation. ATM phosphorylates multiple residues near the RING domain of MDM2, but the underlying molecular basis for deregulation remains elusive. Here we show that Ser429 phosphorylation selectively enhances the ubiquitin ligase activity of MDM2 homodimer but not MDM2-MDMX heterodimer. A crystal structure of phospho-Ser429 (pS429)-MDM2 bound to E2-ubiquitin reveals a unique 310-helical feature present in MDM2 homodimer that allows pS429 to stabilize the closed E2-ubiquitin conformation and thereby enhancing ubiquitin transfer. In cells Ser429 phosphorylation increases MDM2 autoubiquitination and degradation upon DNA damage, whereas S429A substitution protects MDM2 from auto-degradation. Our results demonstrate that Ser429 phosphorylation serves as a switch to boost the activity of MDM2 homodimer and promote its self-destruction to enable rapid p53 stabilization and resolve a long-standing controversy surrounding MDM2 auto-degradation in response to DNA damage.
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Affiliation(s)
- Helge M Magnussen
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Syed F Ahmed
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Gary J Sibbet
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Ventzislava A Hristova
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Koji Nomura
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Andreas K Hock
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- AstraZeneca, AstraZeneca R&D, Innovative Medicines, Discovery Sciences, Darwin (Building 310), Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, UK
| | - Lewis J Archibald
- School of Chemistry, University of Glasgow, Joseph Black Building, G12 8QQ, Glasgow, UK
| | - Andrew G Jamieson
- School of Chemistry, University of Glasgow, Joseph Black Building, G12 8QQ, Glasgow, UK
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | | | - Allan M Weissman
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Danny T Huang
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK.
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23
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Tomorowicz Ł, Sławiński J, Żołnowska B, Szafrański K, Kawiak A. Synthesis, Antitumor Evaluation, Molecular Modeling and Quantitative Structure-Activity Relationship (QSAR) of Novel 2-[(4-Amino-6- N-substituted-1,3,5-triazin-2-yl)methylthio]-4-chloro-5-methyl- N-(1 H-benzo[ d]imidazol-2(3 H)-ylidene)Benzenesulfonamides. Int J Mol Sci 2020; 21:E2924. [PMID: 32331219 PMCID: PMC7215599 DOI: 10.3390/ijms21082924] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 02/08/2023] Open
Abstract
A series of novel 2-[(4-amino-6-R2-1,3,5-triazin-2-yl)methylthio]-4-chloro-5-methyl-N-(5-R1-1H-benzo[d]imidazol-2(3H)-ylidene)benzenesulfonamides 6-49 was synthesized by the reaction of 5-substituted ethyl 2-{5-R1-2-[N-(5-chloro-1H-benzo[d]imidazol-2(3H)-ylidene)sulfamoyl]-4-methylphenylthio}acetate with appropriate biguanide hydrochlorides. The most active compounds, 22 and 46, showed significant cytotoxic activity and selectivity against colon (HCT-116), breast (MCF-7) and cervical cancer (HeLa) cell lines (IC50: 7-11 µM; 15-24 µM and 11-18 µM), respectively. Further QSAR (Quantitative Structure-Activity Relationships) studies on the cytotoxic activity of investigated compounds toward HCT-116, MCF-7 and HeLa were performed by using different topological (2D) and conformational (3D) molecular descriptors based on the stepwise multiple linear regression technique (MLR). The QSAR studies allowed us to make three statistically significant and predictive models for them. Moreover, the molecular docking studies were carried out to evaluate the possible binding mode of the most active compounds, 22 and 46, within the active site of the MDM2 protein.
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Affiliation(s)
- Łukasz Tomorowicz
- Department of Organic Chemistry, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland; (Ł.T.); (K.S.)
| | - Jarosław Sławiński
- Department of Organic Chemistry, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland; (Ł.T.); (K.S.)
| | - Beata Żołnowska
- Department of Organic Chemistry, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland; (Ł.T.); (K.S.)
| | - Krzysztof Szafrański
- Department of Organic Chemistry, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland; (Ł.T.); (K.S.)
| | - Anna Kawiak
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, ul. Abrahama 58, 80-307 Gdansk, Poland;
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24
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Kannan S, Partridge AW, Lane DP, Verma CS. The Dual Interactions of p53 with MDM2 and p300: Implications for the Design of MDM2 Inhibitors. Int J Mol Sci 2019; 20:ijms20235996. [PMID: 31795143 PMCID: PMC6928821 DOI: 10.3390/ijms20235996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/26/2022] Open
Abstract
Proteins that limit the activity of the tumour suppressor protein p53 are increasingly being targeted for inhibition in a variety of cancers. In addition to the development of small molecules, there has been interest in developing constrained (stapled) peptide inhibitors. A stapled peptide ALRN_6924 that activates p53 by preventing its interaction with its negative regulator Mdm2 has entered clinical trials. This stapled peptide mimics the interaction of p53 with Mdm2. The chances that this peptide could bind to other proteins that may also interact with the Mdm2-binding region of p53 are high; one such protein is the CREB binding protein (CBP)/p300. It has been established that phosphorylated p53 is released from Mdm2 and binds to p300, orchestrating the transcriptional program. We investigate whether molecules such as ALRN_6924 would bind to p300 and, to do so, we used molecular simulations to explore the binding of ATSP_7041, which is an analogue of ALRN_6924. Our study shows that ATSP_7041 preferentially binds to Mdm2 over p300; however, upon phosphorylation, it appears to have a higher affinity for p300. This could result in attenuation of the amount of free p300 available for interacting with p53, and hence reduce its transcriptional efficacy. Our study highlights the importance of assessing off-target effects of peptide inhibitors, particularly guided by the understanding of the networks of protein-protein interactions (PPIs) that are being targeted.
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Affiliation(s)
- Srinivasaraghavan Kannan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
- Correspondence: (S.K.); (C.S.V.); Tel.: +65-6478-8353 (S.K.); +65-6478-8273 (C.S.V.); Fax: +65-6478-9048 (S.K.); +65-6478-9048(C.S.V.)
| | - Anthony W. Partridge
- MSD International, Translation Medicine Research Centre, Singapore 138665, Singapore;
| | - David P. Lane
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648, Singapore;
| | - Chandra S. Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
- Correspondence: (S.K.); (C.S.V.); Tel.: +65-6478-8353 (S.K.); +65-6478-8273 (C.S.V.); Fax: +65-6478-9048 (S.K.); +65-6478-9048(C.S.V.)
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25
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Abstract
It has been demonstrated that MMP13 enzyme is related to most cancer cell tumors. The world's largest traditional Chinese medicine database was applied to screen for structure-based drug design and ligand-based drug design. To predict drug activity, machine learning models (Random Forest (RF), AdaBoost Regressor (ABR), Gradient Boosting Regressor (GBR)), and Deep Learning models were utilized to validate the Docking results, and we obtained an R2 of 0.922 on the training set and 0.804 on the test set in the RF algorithm. For the Deep Learning algorithm, R2 of the training set is 0.90, and R2 of the test set is 0.810. However, these TCM compounds fly away during the molecular dynamics (MD) simulation. We seek another method: peptide design. All peptide database were screened by the Docking process. Modification peptides were optimized the interaction modes, and the affinities were assessed with ZDOCK protocol and Refine Docked protein protocol. The 300 ns MD simulation evaluated the stability of receptor-peptide complexes. The double-site effect appeared on S2, a designed peptide based on a known inhibitor, when complexed with BCL2. S3, a designed peptide referred from endogenous inhibitor P16, competed against cyclin when binding with CDK6. The MDM2 inhibitors S5 and S6 were derived from the P53 structure and stable binding with MDM2. A flexible region of peptides S5 and S6 may enhance the binding ability by changing its own conformation, which was unforeseen. These peptides (S2, S3, S5, and S6) are potentially interesting to treat cancer; however, these findings need to be affirmed by biological testing, which will be conducted in the near future.
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Affiliation(s)
- Jian-Qiang Chen
- School of Intelligent Systems Engineering, Artificial Intelligence Medical Center , Sun Yat-sen University , Shenzhen 510275 , China
| | - Hsin-Yi Chen
- School of Intelligent Systems Engineering, Artificial Intelligence Medical Center , Sun Yat-sen University , Shenzhen 510275 , China
| | - Wen-Jie Dai
- School of Pharmacy , Sun Yat-sen University , Shenzhen 510275 , China
| | - Qiu-Jie Lv
- School of Intelligent Systems Engineering, Artificial Intelligence Medical Center , Sun Yat-sen University , Shenzhen 510275 , China
| | - Calvin Yu-Chian Chen
- School of Intelligent Systems Engineering, Artificial Intelligence Medical Center , Sun Yat-sen University , Shenzhen 510275 , China
- Department of Medical Research , China Medical University Hospital , Taichung 40447 , Taiwan
- Department of Bioinformatics and Medical Engineering , Asia University , Taichung 41354 , Taiwan
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26
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Charoenpattarapreeda J, Tan YS, Iegre J, Walsh SJ, Fowler E, Eapen RS, Wu Y, Sore HF, Verma CS, Itzhaki L, Spring DR. Targeted covalent inhibitors of MDM2 using electrophile-bearing stapled peptides. Chem Commun (Camb) 2019; 55:7914-7917. [PMID: 31225847 DOI: 10.1039/c9cc04022f] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Herein, we describe the development of a novel staple with an electrophilic warhead to enable the generation of stapled peptide covalent inhibitors of the p53-MDM2 protein-protein interaction (PPI). The peptide developed showed complete and selective covalent binding resulting in potent inhibition of p53-MDM2 PPI.
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Affiliation(s)
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Jessica Iegre
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.
| | - Stephen J Walsh
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.
| | - Elaine Fowler
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.
| | - Rohan S Eapen
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Yuteng Wu
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.
| | - Hannah F Sore
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore and Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore and School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 673551, Singapore
| | - Laura Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.
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27
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Partridge AW, Kaan HYK, Juang YC, Sadruddin A, Lim S, Brown CJ, Ng S, Thean D, Ferrer F, Johannes C, Yuen TY, Kannan S, Aronica P, Tan YS, Pradhan MR, Verma CS, Hochman J, Chen S, Wan H, Ha S, Sherborne B, Lane DP, Sawyer TK. Incorporation of Putative Helix-Breaking Amino Acids in the Design of Novel Stapled Peptides: Exploring Biophysical and Cellular Permeability Properties. Molecules 2019; 24:E2292. [PMID: 31226791 PMCID: PMC6632053 DOI: 10.3390/molecules24122292] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/14/2019] [Accepted: 06/16/2019] [Indexed: 12/21/2022] Open
Abstract
Stapled α-helical peptides represent an emerging superclass of macrocyclic molecules with drug-like properties, including high-affinity target binding, protease resistance, and membrane permeability. As a model system for probing the chemical space available for optimizing these properties, we focused on dual Mdm2/MdmX antagonist stapled peptides related to the p53 N-terminus. Specifically, we first generated a library of ATSP-7041 (Chang et al., 2013) analogs iteratively modified by L-Ala and D-amino acids. Single L-Ala substitutions beyond the Mdm2/(X) binding interfacial residues (i.e., Phe3, Trp7, and Cba10) had minimal effects on target binding, α-helical content, and cellular activity. Similar binding affinities and cellular activities were noted at non-interfacial positions when the template residues were substituted with their d-amino acid counterparts, despite the fact that d-amino acid residues typically 'break' right-handed α-helices. d-amino acid substitutions at the interfacial residues Phe3 and Cba10 resulted in the expected decreases in binding affinity and cellular activity. Surprisingly, substitution at the remaining interfacial position with its d-amino acid equivalent (i.e., Trp7 to d-Trp7) was fully tolerated, both in terms of its binding affinity and cellular activity. An X-ray structure of the d-Trp7-modified peptide was determined and revealed that the indole side chain was able to interact optimally with its Mdm2 binding site by a slight global re-orientation of the stapled peptide. To further investigate the comparative effects of d-amino acid substitutions we used linear analogs of ATSP-7041, where we replaced the stapling amino acids by Aib (i.e., R84 to Aib4 and S511 to Aib11) to retain the helix-inducing properties of α-methylation. The resultant analog sequence Ac-Leu-Thr-Phe-Aib-Glu-Tyr-Trp-Gln-Leu-Cba-Aib-Ser-Ala-Ala-NH2 exhibited high-affinity target binding (Mdm2 Kd = 43 nM) and significant α-helicity in circular dichroism studies. Relative to this linear ATSP-7041 analog, several d-amino acid substitutions at Mdm2(X) non-binding residues (e.g., d-Glu5, d-Gln8, and d-Leu9) demonstrated decreased binding and α-helicity. Importantly, circular dichroism (CD) spectroscopy showed that although helicity was indeed disrupted by d-amino acids in linear versions of our template sequence, stapled molecules tolerated these residues well. Further studies on stapled peptides incorporating N-methylated amino acids, l-Pro, or Gly substitutions showed that despite some positional dependence, these helix-breaking residues were also generally tolerated in terms of secondary structure, binding affinity, and cellular activity. Overall, macrocyclization by hydrocarbon stapling appears to overcome the destabilization of α-helicity by helix breaking residues and, in the specific case of d-Trp7-modification, a highly potent ATSP-7041 analog (Mdm2 Kd = 30 nM; cellular EC50 = 600 nM) was identified. Our findings provide incentive for future studies to expand the chemical diversity of macrocyclic α-helical peptides (e.g., d-amino acid modifications) to explore their biophysical properties and cellular permeability. Indeed, using the library of 50 peptides generated in this study, a good correlation between cellular permeability and lipophilicity was observed.
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Affiliation(s)
- Anthony W Partridge
- MSD International, 8 Biomedical Grove, #04-01/05 Neuros Building, Singapore 138665, Singapore.
| | - Hung Yi Kristal Kaan
- MSD International, 8 Biomedical Grove, #04-01/05 Neuros Building, Singapore 138665, Singapore.
| | - Yu-Chi Juang
- MSD International, 8 Biomedical Grove, #04-01/05 Neuros Building, Singapore 138665, Singapore.
| | - Ahmad Sadruddin
- MSD International, 8 Biomedical Grove, #04-01/05 Neuros Building, Singapore 138665, Singapore.
| | - Shuhui Lim
- MSD International, 8 Biomedical Grove, #04-01/05 Neuros Building, Singapore 138665, Singapore.
| | - Christopher J Brown
- p53Lab, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648, Singapore.
| | - Simon Ng
- p53Lab, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648, Singapore.
| | - Dawn Thean
- p53Lab, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648, Singapore.
| | - Fernando Ferrer
- p53Lab, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648, Singapore.
| | - Charles Johannes
- Institute of Chemical and Engineering Sciences (ICES), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07, Neuros Building, Singapore 138665, Singapore.
| | - Tsz Ying Yuen
- Institute of Chemical and Engineering Sciences (ICES), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07, Neuros Building, Singapore 138665, Singapore.
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Pietro Aronica
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Yaw Sing Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Mohan R Pradhan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Chandra S Verma
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | | | | | - Hui Wan
- Merck & Co., Inc., Kenilworth, NJ 07033, USA.
| | - Sookhee Ha
- Merck & Co., Inc., Kenilworth, NJ 07033, USA.
| | | | - David P Lane
- p53Lab, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648, Singapore.
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28
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Verhoork SJM, Jennings CE, Rozatian N, Reeks J, Meng J, Corlett EK, Bunglawala F, Noble MEM, Leach AG, Coxon CR. Tuning the Binding Affinity and Selectivity of Perfluoroaryl-Stapled Peptides by Cysteine-Editing. Chemistry 2019; 25:177-182. [PMID: 30255959 DOI: 10.1002/chem.201804163] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Indexed: 11/08/2022]
Abstract
A growing number of approaches to "staple" α-helical peptides into a bioactive conformation using cysteine cross-linking are emerging. Here, the replacement of l-cysteine with "cysteine analogues" in combinations of different stereochemistry, side chain length and beta-carbon substitution, is explored to examine the influence that the thiol-containing residue(s) has on target protein binding affinity in a well-explored model system, p53-MDM2/MDMX, which is constituted by the interaction of the tumour suppressor protein p53 and proteins MDM2 and MDMX, which regulate p53 activity. In some cases, replacement of one or more l-cysteine residues afforded significant changes in the measured binding affinity and target selectivity of the peptide. Computationally constructed homology models indicate that some modifications, such as incorporating two d-cysteine residues, favourably alter the positions of key functional amino acid side chains, which is likely to cause changes in binding affinity, in agreement with measured surface plasmon resonance data.
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Affiliation(s)
- Sanne J M Verhoork
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom St, Liverpool, L3 3AF, UK
| | - Claire E Jennings
- Northern Institute for Cancer Research, Newcastle University, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Neshat Rozatian
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK
| | - Judith Reeks
- Northern Institute for Cancer Research, Newcastle University, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Jieman Meng
- Northern Institute for Cancer Research, Newcastle University, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Emily K Corlett
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK
| | - Fazila Bunglawala
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom St, Liverpool, L3 3AF, UK
| | - Martin E M Noble
- Northern Institute for Cancer Research, Newcastle University, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Andrew G Leach
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom St, Liverpool, L3 3AF, UK
| | - Christopher R Coxon
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom St, Liverpool, L3 3AF, UK
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Chae H, Kwak DK, Lee MK, Chi SW, Kim KB. Solid-state nanopore analysis on conformation change of p53TAD-MDM2 fusion protein induced by protein-protein interaction. Nanoscale 2018; 10:17227-17235. [PMID: 30191243 DOI: 10.1039/c8nr06423g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Although protein-protein interactions (PPIs) are emerging therapeutic targets for human diseases, development of high-throughput screening (HTS) technologies against PPI targets remains challenging. In this study, we propose a protein complex structure to effectively detect conformational changes of protein resulting from PPI using solid-state nanopore for a novel, widely-applicable drug screening method against various PPI targets. To effectively detect conformational changes resulting from PPI, we designed a fusion protein MLP (MDM2-linker-p53TAD), where p53TAD and MDM2 are connected by a 16 amino acid linker. The globular conformation of MLP exhibited a single-peak translocation event, whereas the dumbbell-like conformation of nutlin-3-bound MLP revealed as a double-peak signal. The proportion of double-peak to single-peak signals increased from 9.3% to 23.0% as nutlin-3 concentration increased. The translocation kinetics of the two different MLP conformations with varied applied voltage were analyzed. Further, the fractional current of the intra-peak of the double-peak signal was analyzed, probing the structure of our designed protein complex. This approach of nanopore sensing may be extendedly employed in screening of PPI inhibitors and protein conformation studies.
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Affiliation(s)
- Hongsik Chae
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Korea.
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30
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Morimoto J, Hosono Y, Sando S. Isolation of a peptide containing d-amino acid residues that inhibits the α-helix-mediated p53-MDM2 interaction from a one-bead one-compound library. Bioorg Med Chem Lett 2018; 28:231-234. [PMID: 29326019 DOI: 10.1016/j.bmcl.2018.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/29/2017] [Accepted: 01/01/2018] [Indexed: 11/19/2022]
Abstract
α-Helix-mediated protein-protein interactions (PPIs) are important targets in biological research and drug development. Peptides containing d-amino acid residues are attractive molecules for inhibiting α-helix-mediated PPIs because of their wide surface area and high protease resistance. In this study, a peptide library was constructed using a one-bead one-compound format designed to isolate left-handed α-helical peptides, which are promising molecules as inhibitors of α-helix-mediated PPIs. Screening of the library against an α-helix-mediated PPI between MDM2 and p53 yielded an inhibitor of the PPI. Design and screening of the library, and biochemical and spectroscopic studies of the discovered peptide are presented.
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Affiliation(s)
- Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Yuki Hosono
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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31
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Chee SMQ, Wongsantichon J, Siau J, Thean D, Ferrer F, Robinson RC, Lane DP, Brown CJ, Ghadessy FJ. Structure-activity studies of Mdm2/Mdm4-binding stapled peptides comprising non-natural amino acids. PLoS One 2017; 12:e0189379. [PMID: 29228061 PMCID: PMC5724825 DOI: 10.1371/journal.pone.0189379] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/24/2017] [Indexed: 11/24/2022] Open
Abstract
As primary p53 antagonists, Mdm2 and the closely related Mdm4 are relevant cancer therapeutic targets. We have previously described a series of cell-permeable stapled peptides that bind to Mdm2 with high affinity, resulting in activation of the p53 tumour suppressor. Within this series, highest affinity was obtained by modification of an obligate tryptophan residue to the non-natural L-6-chlorotryptophan. To understand the structural basis for improved affinity we have solved the crystal structure of this stapled peptide (M011) bound to Mdm2 (residues 6–125) at 1.66 Å resolution. Surprisingly, near identity to the structure of a related peptide (M06) without the 6-chloro modification is observed. Further analysis of linear and stapled peptides comprising 6-Me-tryptophan provides mechanistic insight into dual Mdm2/Mdm4 antagonism and confirms L98 of Mdm4 as a mutable steric gate. The results also highlight a possible role of the flexible hinge region in determining Mdm2/Mdm4 plasticity.
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Affiliation(s)
- Sharon Min Qi Chee
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | | | - Jiawei Siau
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Dawn Thean
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Fernando Ferrer
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Robert C. Robinson
- Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore
| | - David P. Lane
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Christopher J. Brown
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
- * E-mail: (CJB); (FJG)
| | - Farid J. Ghadessy
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
- * E-mail: (CJB); (FJG)
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Frolova TS, Lipeeva AV, Baev DS, Tsepilov YA, Sinitsyna OI. [Apoptosis as the basic mechanism of cytotoxic action of ursolic and pomolic acids in glioma cells]. Mol Biol (Mosk) 2017; 51:809-816. [PMID: 29116067 DOI: 10.7868/s002689841705007x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/03/2016] [Indexed: 11/23/2022]
Abstract
Pentacyclic triterpene acids are of great interest as compounds that exhibit selective cytotoxicity against malignant tumor cells. If earlier studies were carried out mainly in cancer cells of epithelial origin, in the present work the cytotoxic effect of ursolic and pomolic acids on the primary and permanent glioma cell lines was analyzed. Both compounds are toxic to oncotransformed cells and induce apoptosis in U-87 MG line. Using molecular docking, it has been shown that Akt1 and MDM2 may be potential targets of the studied triterpene acids. It has been suggested that ursolic and pomolic acids induce apoptosis in glioma cells through inhibition of the PI3K/Akt signaling pathway, and they can be considered as potentially promising agents for the treatment of glioblastoma.
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Affiliation(s)
- T S Frolova
- Vorozhtsov Novosibirsk Institute of Organic ChemistrySiberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
- Institute of Cytology and GeneticsSiberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
- Novosibirsk State University, Novosibirsk, 630090 Russia
| | - A V Lipeeva
- Vorozhtsov Novosibirsk Institute of Organic ChemistrySiberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - D S Baev
- Vorozhtsov Novosibirsk Institute of Organic ChemistrySiberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
- Novosibirsk State University, Novosibirsk, 630090 Russia
| | - Y A Tsepilov
- Institute of Cytology and GeneticsSiberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
- Novosibirsk State University, Novosibirsk, 630090 Russia
| | - O I Sinitsyna
- Institute of Cytology and GeneticsSiberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
- Novosibirsk State University, Novosibirsk, 630090 Russia
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Abstract
BACKGROUND The p53 signalling pathway, which controls cell fate, has been extensively studied due to its prominent role in tumor development. The pathway includes the tumor supressor protein p53, its vertebrate paralogs p63 and p73, and their negative regulators MDM2 and MDM4. The p53/p63/p73-MDM system is ancient and can be traced in all extant animal phyla. Despite this, correct phylogenetic trees including both vertebrate and invertebrate species of the p53/p63/p73 and MDM families have not been published. RESULTS Here, we have examined the evolution of the p53/p63/p73 protein family with particular focus on the p53/p63/p73 transactivation domain (TAD) and its co-evolution with the p53/p63/p73-binding domain (p53/p63/p73BD) of MDM2. We found that the TAD and p53/p63/p73BD share a strong evolutionary connection. If one of the domains of the protein is lost in a phylum, then it seems very likely to be followed by loss of function by the other domain as well, and due to the loss of function it is likely to eventually disappear. By focusing our phylogenetic analysis to p53/p63/p73 and MDM proteins from phyla that retain the interaction domains TAD and p53/p63/p73BD, we built phylogenetic trees of p53/p63/p73 and MDM based on both vertebrate and invertebrate species. The trees follow species evolution and contain a total number of 183 and 98 species for p53/p63/p73 and MDM, respectively. We also demonstrate that the p53/p63/p73 and MDM families result from whole genome duplications. CONCLUSIONS The signaling pathway of the TAD and p53/p63/p73BD in p53/p63/p73 and MDM, respectively, dates back to early metazoan time and has since then tightly co-evolved, or disappeared in distinct lineages.
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Affiliation(s)
- Emma Åberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Fulvio Saccoccia
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Manfred Grabherr
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Wai Ying Josefin Ore
- 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
| | - Greta Hultqvist
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, BMC, Box 591, SE-75124, Uppsala, Sweden
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Nomura K, Klejnot M, Kowalczyk D, Hock AK, Sibbet GJ, Vousden KH, Huang DT. Structural analysis of MDM2 RING separates degradation from regulation of p53 transcription activity. Nat Struct Mol Biol 2017; 24:578-587. [PMID: 28553961 PMCID: PMC6205632 DOI: 10.1038/nsmb.3414] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/01/2017] [Indexed: 02/08/2023]
Abstract
MDM2-MDMX complexes bind the p53 tumor-suppressor protein, inhibiting p53's transcriptional activity and targeting p53 for proteasomal degradation. Inhibitors that disrupt binding between p53 and MDM2 efficiently activate a p53 response, but their use in the treatment of cancers that retain wild-type p53 may be limited by on-target toxicities due to p53 activation in normal tissue. Guided by a novel crystal structure of the MDM2-MDMX-E2(UbcH5B)-ubiquitin complex, we designed MDM2 mutants that prevent E2-ubiquitin binding without altering the RING-domain structure. These mutants lack MDM2's E3 activity but retain the ability to limit p53's transcriptional activity and allow cell proliferation. Cells expressing these mutants respond more quickly to cellular stress than cells expressing wild-type MDM2, but basal p53 control is maintained. Targeting the MDM2 E3-ligase activity could therefore widen the therapeutic window of p53 activation in tumors.
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Affiliation(s)
- Koji Nomura
- Cancer Research-UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, United Kingdom
| | - Marta Klejnot
- Cancer Research-UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, United Kingdom
| | - Dominika Kowalczyk
- Cancer Research-UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, United Kingdom
| | - Andreas K. Hock
- Cancer Research-UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, United Kingdom
| | - Gary J. Sibbet
- Cancer Research-UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, United Kingdom
| | | | - Danny T. Huang
- Cancer Research-UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, United Kingdom
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35
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Bai F, Morcos F, Cheng RR, Jiang H, Onuchic JN. Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis. Proc Natl Acad Sci U S A 2016; 113:E8051-E8058. [PMID: 27911825 PMCID: PMC5167203 DOI: 10.1073/pnas.1615932113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Protein-protein interactions play a central role in cellular function. Improving the understanding of complex formation has many practical applications, including the rational design of new therapeutic agents and the mechanisms governing signal transduction networks. The generally large, flat, and relatively featureless binding sites of protein complexes pose many challenges for drug design. Fragment docking and direct coupling analysis are used in an integrated computational method to estimate druggable protein-protein interfaces. (i) This method explores the binding of fragment-sized molecular probes on the protein surface using a molecular docking-based screen. (ii) The energetically favorable binding sites of the probes, called hot spots, are spatially clustered to map out candidate binding sites on the protein surface. (iii) A coevolution-based interface interaction score is used to discriminate between different candidate binding sites, yielding potential interfacial targets for therapeutic drug design. This approach is validated for important, well-studied disease-related proteins with known pharmaceutical targets, and also identifies targets that have yet to be studied. Moreover, therapeutic agents are proposed by chemically connecting the fragments that are strongly bound to the hot spots.
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Affiliation(s)
- Fang Bai
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
| | - Faruck Morcos
- Department of Biological Sciences, University of Texas at Dallas, Dallas, TX 75080
- Department of Bioengineering, University of Texas at Dallas, Dallas, TX 75080
- Center for Systems Biology, University of Texas at Dallas, Dallas, TX 75080
| | - Ryan R Cheng
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China;
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005;
- Department of Physics and Astronomy, Rice University, Houston, TX 77005
- Department of Chemistry, Rice University, Houston, TX 77005
- Department of Biosciences, Rice University, Houston, TX 77005
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36
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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37
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Menéndez CA, Accordino SR, Gerbino DC, Appignanesi GA. Hydrogen Bond Dynamic Propensity Studies for Protein Binding and Drug Design. PLoS One 2016; 11:e0165767. [PMID: 27792778 PMCID: PMC5085089 DOI: 10.1371/journal.pone.0165767] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/17/2016] [Indexed: 12/04/2022] Open
Abstract
We study the dynamic propensity of the backbone hydrogen bonds of the protein MDM2 (the natural regulator of the tumor suppressor p53) in order to determine its binding properties. This approach is fostered by the observation that certain backbone hydrogen bonds at the p53-binding site exhibit a dynamical propensity in simulations that differs markedly form their state-value (that is, formed/not formed) in the PDB structure of the apo protein. To this end, we conduct a series of hydrogen bond propensity calculations in different contexts: 1) computational alanine-scanning studies of the MDM2-p53 interface; 2) the formation of the complex of MDM2 with the disruptive small molecule Nutlin-3a (dissecting the contribution of the different molecular fragments) and 3) the binding of a series of small molecules (drugs) with different affinities for MDM2. Thus, the relevance of the hydrogen bond propensity analysis for protein binding studies and as a useful tool to complement existing methods for drug design and optimization will be made evident.
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Affiliation(s)
- Cintia A. Menéndez
- INQUISUR-UNS-CONICET and Departamento de Química, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Sebastián R. Accordino
- INQUISUR-UNS-CONICET and Departamento de Química, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Darío C. Gerbino
- INQUISUR-UNS-CONICET and Departamento de Química, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Gustavo A. Appignanesi
- INQUISUR-UNS-CONICET and Departamento de Química, Universidad Nacional del Sur, Bahía Blanca, Argentina
- * E-mail:
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38
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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39
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Sarkar D, Patra P, Ghosh A, Saha S. Computational Framework for Prediction of Peptide Sequences That May Mediate Multiple Protein Interactions in Cancer-Associated Hub Proteins. PLoS One 2016; 11:e0155911. [PMID: 27218803 PMCID: PMC4878775 DOI: 10.1371/journal.pone.0155911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 05/08/2016] [Indexed: 01/26/2023] Open
Abstract
A considerable proportion of protein-protein interactions (PPIs) in the cell are estimated to be mediated by very short peptide segments that approximately conform to specific sequence patterns known as linear motifs (LMs), often present in the disordered regions in the eukaryotic proteins. These peptides have been found to interact with low affinity and are able bind to multiple interactors, thus playing an important role in the PPI networks involving date hubs. In this work, PPI data and de novo motif identification based method (MEME) were used to identify such peptides in three cancer-associated hub proteins—MYC, APC and MDM2. The peptides corresponding to the significant LMs identified for each hub protein were aligned, the overlapping regions across these peptides being termed as overlapping linear peptides (OLPs). These OLPs were thus predicted to be responsible for multiple PPIs of the corresponding hub proteins and a scoring system was developed to rank them. We predicted six OLPs in MYC and five OLPs in MDM2 that scored higher than OLP predictions from randomly generated protein sets. Two OLP sequences from the C-terminal of MYC were predicted to bind with FBXW7, component of an E3 ubiquitin-protein ligase complex involved in proteasomal degradation of MYC. Similarly, we identified peptides in the C-terminal of MDM2 interacting with FKBP3, which has a specific role in auto-ubiquitinylation of MDM2. The peptide sequences predicted in MYC and MDM2 look promising for designing orthosteric inhibitors against possible disease-associated PPIs. Since these OLPs can interact with other proteins as well, these inhibitors should be specific to the targeted interactor to prevent undesired side-effects. This computational framework has been designed to predict and rank the peptide regions that may mediate multiple PPIs and can be applied to other disease-associated date hub proteins for prediction of novel therapeutic targets of small molecule PPI modulators.
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Affiliation(s)
| | - Piya Patra
- Maulana Abdul Kalam Azad University of Technology, Kolkata, India
| | - Abhirupa Ghosh
- Maulana Abdul Kalam Azad University of Technology, Kolkata, India
| | - Sudipto Saha
- Bioinformatics Centre, Bose Institute, Kolkata, India
- * E-mail: ;
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40
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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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41
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Estrada-Ortiz N, Neochoritis CG, Dömling A. How To Design a Successful p53-MDM2/X Interaction Inhibitor: A Thorough Overview Based on Crystal Structures. ChemMedChem 2016; 11:757-72. [PMID: 26676832 PMCID: PMC4838565 DOI: 10.1002/cmdc.201500487] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/23/2015] [Indexed: 01/10/2023]
Abstract
A recent therapeutic strategy in oncology is based on blocking the protein-protein interaction between the murine double minute (MDM) homologues MDM2/X and the tumor-suppressor protein p53. Inhibiting the binding between wild-type (WT) p53 and its negative regulators MDM2 and/or MDMX has become an important target in oncology to restore the antitumor activity of p53, the so-called guardian of our genome. Interestingly, based on the multiple disclosed compound classes and structural analysis of small-molecule-MDM2 adducts, the p53-MDM2 complex is perhaps the best studied and most targeted protein-protein interaction. Several classes of small molecules have been identified as potent, selective, and efficient inhibitors of the p53-MDM2/X interaction, and many co-crystal structures with the protein are available. Herein we review the properties as well as preclinical and clinical studies of these small molecules and peptides, categorized by scaffold type. A particular emphasis is made on crystallographic structures and the observed binding modes of these compounds, including conserved water molecules present.
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Affiliation(s)
- Natalia Estrada-Ortiz
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD, Groningen, The Netherlands
| | - Constantinos G Neochoritis
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD, Groningen, The Netherlands
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD, Groningen, The Netherlands.
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42
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Azzarito V, Rowell P, Barnard A, Edwards TA, Macdonald A, Warriner SL, Wilson AJ. Probing Protein Surfaces: QSAR Analysis with Helix Mimetics. Chembiochem 2016; 17:768-73. [PMID: 26690307 PMCID: PMC6591138 DOI: 10.1002/cbic.201500504] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Indexed: 12/17/2022]
Abstract
α-Helix-mediated protein-protein interactions (PPIs) are important targets for small-molecule inhibition; however, generic approaches to inhibitor design are in their infancy and would benefit from QSAR analyses to rationalise the noncovalent basis of molecular recognition by designed ligands. Using a helix mimetic based on an oligoamide scaffold, we have exploited the power of a modular synthesis to access compounds that can readily be used to understand the noncovalent determinants of hDM2 recognition by this series of cell-active p53/hDM2 inhibitors.
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Affiliation(s)
- Valeria Azzarito
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Philip Rowell
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Anna Barnard
- Department of Chemistry, Imperial College London, London, London, SW7 2AZ, UK
- Institue of Chemical Biology, Imperial College London, London, SW7 2AZ, UK
| | - Thomas A Edwards
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Andrew Macdonald
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Stuart L Warriner
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
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43
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Wu Y, Olsen LB, Lau YH, Jensen CH, Rossmann M, Baker YR, Sore HF, Collins S, Spring DR. Development of a Multifunctional Benzophenone Linker for Peptide Stapling and Photoaffinity Labelling. Chembiochem 2016; 17:689-92. [PMID: 26919579 PMCID: PMC4862033 DOI: 10.1002/cbic.201500648] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Indexed: 01/18/2023]
Abstract
Photoaffinity labelling is a useful method for studying how proteins interact with ligands and biomolecules, and can help identify and characterise new targets for the development of new therapeutics. We present the design and synthesis of a novel multifunctional benzophenone linker that serves as both a photo-crosslinking motif and a peptide stapling reagent. Using double-click stapling, we attached the benzophenone to the peptide via the staple linker, rather than by modifying the peptide sequence with a photo-crosslinking amino acid. When applied to a p53-derived peptide, the resulting photoreactive stapled peptide was able to preferentially crosslink with MDM2 in the presence of competing protein. This multifunctional linker also features an extra alkyne handle for downstream applications such as pull-down assays, and can be used to investigate the target selectivity of stapled peptides.
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Affiliation(s)
- Yuteng Wu
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Lasse B Olsen
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Yu Heng Lau
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Claus Hatt Jensen
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Maxim Rossmann
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Ysobel R Baker
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Hannah F Sore
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Súil Collins
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - David R Spring
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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44
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Thayer KM, Beyer GA. Energetic Landscape of MDM2-p53 Interactions by Computational Mutagenesis of the MDM2-p53 Interaction. PLoS One 2016; 11:e0147806. [PMID: 26992014 PMCID: PMC4798270 DOI: 10.1371/journal.pone.0147806] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/01/2015] [Indexed: 11/18/2022] Open
Abstract
The ubiquitin ligase MDM2, a principle regulator of the tumor suppressor p53, plays an integral role in regulating cellular levels of p53 and thus a prominent role in current cancer research. Computational analysis used MUMBO to rotamerize the MDM2-p53 crystal structure 1YCR to obtain an exhaustive search of point mutations, resulting in the calculation of the ΔΔG comprehensive energy landscape for the p53-bound regulator. The results herein have revealed a set of residues R65-E69 on MDM2 proximal to the p53 hydrophobic binding pocket that exhibited an energetic profile deviating significantly from similar residues elsewhere in the protein. In light of the continued search for novel competitive inhibitors for MDM2, we discuss possible implications of our findings on the drug discovery field.
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Affiliation(s)
- Kelly M. Thayer
- Department of Chemistry, 124 Raymond Avenue, Poughkeepsie, New York 12604, United States of America
- Wesleyan University, Hall Atwater Laboratories, Middletown, Connecticut 06459, United States of America
- * E-mail:
| | - George A. Beyer
- Biochemistry Program, Vassar College, 124 Raymond Avenue, Poughkeepsie, New York 12604, United States of America
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45
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Lau YH, Wu Y, Rossmann M, Tan BX, de Andrade P, Tan YS, Verma C, McKenzie GJ, Venkitaraman AR, Hyvönen M, Spring DR. Double Strain-Promoted Macrocyclization for the Rapid Selection of Cell-Active Stapled Peptides. Angew Chem Int Ed Engl 2015; 54:15410-3. [PMID: 26768531 PMCID: PMC5868729 DOI: 10.1002/anie.201508416] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 12/11/2022]
Abstract
Peptide stapling is a method for designing macrocyclic alpha-helical inhibitors of protein-protein interactions. However, obtaining a cell-active inhibitor can require significant optimization. We report a novel stapling technique based on a double strain-promoted azide-alkyne reaction, and exploit its biocompatibility to accelerate the discovery of cell-active stapled peptides. As a proof of concept, MDM2-binding peptides were stapled in parallel, directly in cell culture medium in 96-well plates, and simultaneously evaluated in a p53 reporter assay. This in situ stapling/screening process gave an optimal candidate that showed improved proteolytic stability and nanomolar binding to MDM2 in subsequent biophysical assays. α-Helicity was confirmed by a crystal structure of the MDM2-peptide complex. This work introduces in situ stapling as a versatile biocompatible technique with many other potential high-throughput biological applications.
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Affiliation(s)
- Yu Heng Lau
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW (UK)
| | - Yuteng Wu
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW (UK)
| | - Maxim Rossmann
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA (UK)
| | - Ban Xiong Tan
- p53Lab, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648 (Singapore)
| | - Peterson de Andrade
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW (UK)
| | - Yaw Sing Tan
- Bioinformatics Institute, A*STAR, 30 Biopolis St, #07-01 Matrix, Singapore 138671 (Singapore)
| | - Chandra Verma
- Bioinformatics Institute, A*STAR, 30 Biopolis St, #07-01 Matrix, Singapore 138671 (Singapore)
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
- School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551
| | | | | | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA (UK)
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW (UK).
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46
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Shi S, Zhang S, Zhang Q. Probing Difference in Binding Modes of Inhibitors to MDMX by Molecular Dynamics Simulations and Different Free Energy Methods. PLoS One 2015; 10:e0141409. [PMID: 26513747 PMCID: PMC4625964 DOI: 10.1371/journal.pone.0141409] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 10/08/2015] [Indexed: 01/20/2023] Open
Abstract
The p53-MDMX interaction has attracted extensive attention of anti-cancer drug development in recent years. This current work adopted molecular dynamics (MD) simulations and cross-correlation analysis to investigate conformation changes of MDMX caused by inhibitor bindings. The obtained information indicates that the binding cleft of MDMX undergoes a large conformational change and the dynamic behavior of residues obviously change by the presence of different structural inhibitors. Two different methods of binding free energy predictions were employed to carry out a comparable insight into binding mechanisms of four inhibitors PMI, pDI, WK23 and WW8 to MDMX. The data show that the main factor controlling the inhibitor bindings to MDMX arises from van der Waals interactions. The binding free energies were further divided into contribution of each residue and the derived information gives a conclusion that the hydrophobic interactions, such as CH-CH, CH-π and π-π interactions, are responsible for the inhibitor associations with MDMX.
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Affiliation(s)
- Shuhua Shi
- School of Science, Shandong Jianzhu University, Jinan, China
- * E-mail: ;
| | - Shaolong Zhang
- College of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Qinggang Zhang
- College of Physics and Electronics, Shandong Normal University, Jinan, China
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47
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Yu B, Sun XN, Shi XJ, Qi PP, Zheng YC, Yu DQ, Liu HM. Efficient synthesis of novel antiproliferative steroidal spirooxindoles via the [3+2] cycloaddition reactions of azomethine ylides. Steroids 2015; 102:92-100. [PMID: 26256638 DOI: 10.1016/j.steroids.2015.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 08/04/2015] [Indexed: 12/31/2022]
Abstract
A series of novel steroidal spirooxindoles 3a-h were synthesized from pregnenolone in a high regioselective manner using the 1,3-dipolar cycloaddition as the key step. This protocol resulted in the formation of two C-C bonds, one C-N bond and the creation of one pyrrolidine ring and three contiguous stereocenters in a single operation. Biological evaluation showed that these synthesized steroidal spirooxindoles exhibited moderate to good antiproliferative activity against the tested cell lines and some of them were more potent than 5-FU. Among them, compounds 3e and 3f displayed the best antiproliferative activity against MCF-7 cells with the IC50 values of 4.0 and 3.9μM, respectively. Flow cytometry analysis demonstrated that compound 3d caused the cellular apoptosis and cell cycle arrest at G2/M phase in a concentration-dependent manner. Docking results indicated that compound 3d fitted well into the MDM2 active site 1RV1 by interacting with Lys94 and Thr101 residues.
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Affiliation(s)
- Bin Yu
- School of Pharmaceutical Sciences and New Drug Research & Development Center, Zhengzhou University, Zhengzhou 450001, PR China.
| | - Xiao-Nan Sun
- The Affiliated Hospital of Huanghe Sanmenxia of Henan University of Science and Technology, Sanmenxia 472000, PR China
| | - Xiao-Jing Shi
- School of Pharmaceutical Sciences and New Drug Research & Development Center, Zhengzhou University, Zhengzhou 450001, PR China
| | - Ping-Ping Qi
- School of Pharmaceutical Sciences and New Drug Research & Development Center, Zhengzhou University, Zhengzhou 450001, PR China
| | - Yi-Chao Zheng
- School of Pharmaceutical Sciences and New Drug Research & Development Center, Zhengzhou University, Zhengzhou 450001, PR China
| | - De-Quan Yu
- School of Pharmaceutical Sciences and New Drug Research & Development Center, Zhengzhou University, Zhengzhou 450001, PR China.
| | - Hong-Min Liu
- School of Pharmaceutical Sciences and New Drug Research & Development Center, Zhengzhou University, Zhengzhou 450001, PR China.
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48
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Pettersson M, Quant M, Min J, Iconaru L, Kriwacki RW, Waddell MB, Guy RK, Luthman K, Grøtli M. Design, Synthesis and Evaluation of 2,5-Diketopiperazines as Inhibitors of the MDM2-p53 Interaction. PLoS One 2015; 10:e0137867. [PMID: 26427060 PMCID: PMC4591261 DOI: 10.1371/journal.pone.0137867] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/23/2015] [Indexed: 11/19/2022] Open
Abstract
The transcription factor p53 is the main tumour suppressor in cells and many cancer types have p53 mutations resulting in a loss of its function. In tumours that retain wild-type p53 function, p53 activity is down-regulated by MDM2 (human murine double minute 2) via a direct protein-protein interaction. We have designed and synthesised two series of 2,5-diketopiperazines as inhibitors of the MDM2-p53 interaction. The first set was designed to directly mimic the α-helical region of the p53 peptide, containing key residues in the i, i+4 and i+7 positions of a natural α-helix. Conformational analysis indicated that 1,3,6-trisubstituted 2,5-diketopiperazines were able to place substituents in the same spatial orientation as an α-helix template. The key step of the synthesis involved the cyclisation of substituted dipeptides. The other set of tetrasubstituted 2,5-diketopiperazines were designed based on structure-based docking studies and the Ugi multicomponent reaction was used for the synthesis. This latter set comprised the most potent inhibitors which displayed micromolar IC50-values in a biochemical fluorescence polarisation assay.
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Affiliation(s)
- Mariell Pettersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Maria Quant
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, United States of America
| | - Luigi Iconaru
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, United States of America
| | - Richard W. Kriwacki
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, United States of America
| | - M. Brett Waddell
- Molecular Interaction Analysis Shared Resource, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, United States of America
| | - R. Kiplin Guy
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, United States of America
| | - Kristina Luthman
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
- * E-mail:
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49
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Menéndez CA, Accordino SR, Gerbino DC, Appignanesi GA. "Chameleonic" backbone hydrogen bonds in protein binding and as drug targets. Eur Phys J E Soft Matter 2015; 38:107. [PMID: 26486885 DOI: 10.1140/epje/i2015-15107-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 07/27/2015] [Accepted: 09/14/2015] [Indexed: 06/05/2023]
Abstract
We carry out a time-averaged contact matrix study to reveal the existence of protein backbone hydrogen bonds (BHBs) whose net persistence in time differs markedly form their corresponding PDB-reported state. We term such interactions as "chameleonic" BHBs, CBHBs, precisely to account for their tendency to change the structural prescription of the PDB for the opposite bonding propensity in solution. We also find a significant enrichment of protein binding sites in CBHBs, relate them to local water exposure and analyze their behavior as ligand/drug targets. Thus, the dynamic analysis of hydrogen bond propensity might lay the foundations for new tools of interest in protein binding-site prediction and in lead optimization for drug design.
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Affiliation(s)
- C A Menéndez
- INQUISUR-UNS-CONICET and Departamento de Química, Universidad Nacional del Sur, Avenida Alem 1253, 8000, Bahıa Blanca, Argentina
| | - S R Accordino
- INQUISUR-UNS-CONICET and Departamento de Química, Universidad Nacional del Sur, Avenida Alem 1253, 8000, Bahıa Blanca, Argentina
| | - D C Gerbino
- INQUISUR-UNS-CONICET and Departamento de Química, Universidad Nacional del Sur, Avenida Alem 1253, 8000, Bahıa Blanca, Argentina
| | - G A Appignanesi
- INQUISUR-UNS-CONICET and Departamento de Química, Universidad Nacional del Sur, Avenida Alem 1253, 8000, Bahıa Blanca, Argentina.
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50
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Zaytsev A, Dodd B, Magnani M, Ghiron C, Golding BT, Griffin RJ, Liu J, Lu X, Micco I, Newell DR, Padova A, Robertson G, Lunec J, Hardcastle IR. Searching for Dual Inhibitors of the MDM2-p53 and MDMX-p53 Protein-Protein Interaction by a Scaffold-Hopping Approach. Chem Biol Drug Des 2015; 86:180-9. [PMID: 25388787 DOI: 10.1111/cbdd.12474] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 09/18/2014] [Accepted: 10/15/2014] [Indexed: 12/19/2022]
Abstract
Two libraries of substituted benzimidazoles were designed using a 'scaffold-hopping' approach based on reported MDM2-p53 inhibitors. Substituents were chosen following library enumeration and docking into an MDM2 X-ray structure. Benzimidazole libraries were prepared using an efficient solution-phase approach and screened for inhibition of the MDM2-p53 and MDMX-p53 protein-protein interactions. Key examples showed inhibitory activity against both targets.
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Affiliation(s)
- Andrey Zaytsev
- Newcastle Cancer Centre, Northern Institute for Cancer Research and School of Chemistry, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Barry Dodd
- Newcastle Cancer Centre, Northern Institute for Cancer Research and School of Chemistry, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Matteo Magnani
- Siena Biotech S.p.A., Strada del Petriccio e Belriguardo 35, Siena, 53100, Italy
| | - Chiara Ghiron
- Siena Biotech S.p.A., Strada del Petriccio e Belriguardo 35, Siena, 53100, Italy
| | - Bernard T Golding
- Newcastle Cancer Centre, Northern Institute for Cancer Research and School of Chemistry, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Roger J Griffin
- Newcastle Cancer Centre, Northern Institute for Cancer Research and School of Chemistry, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Junfeng Liu
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Xiaohong Lu
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Iolanda Micco
- Siena Biotech S.p.A., Strada del Petriccio e Belriguardo 35, Siena, 53100, Italy
| | - David R Newell
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Alessandro Padova
- Siena Biotech S.p.A., Strada del Petriccio e Belriguardo 35, Siena, 53100, Italy
| | - Graeme Robertson
- Siena Biotech S.p.A., Strada del Petriccio e Belriguardo 35, Siena, 53100, Italy
| | - John Lunec
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Ian R Hardcastle
- Newcastle Cancer Centre, Northern Institute for Cancer Research and School of Chemistry, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, UK
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