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Wojcik R, Baranowski MR, Markiewicz L, Kubacka D, Bednarczyk M, Baran N, Wojtczak A, Sikorski PJ, Zuberek J, Kowalska J, Jemielity J. Novel N7-Arylmethyl Substituted Dinucleotide mRNA 5' cap Analogs: Synthesis and Evaluation as Modulators of Translation. Pharmaceutics 2021; 13:pharmaceutics13111941. [PMID: 34834356 PMCID: PMC8623273 DOI: 10.3390/pharmaceutics13111941] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
Abstract
Dinucleotide analogs of the messenger RNA cap (m7GpppN) are useful research tools and have potential applications as translational inhibitors or reagents for modification of in vitro transcribed mRNAs. It has been previously reported that replacing the methyl group at the N7-position with benzyl (Bn) produces a dinucleotide cap with superior properties. Here, we followed up on this finding by synthesizing 17 novel Bn7GpppG analogs and determining their structure-activity relationship regarding translation and translational inhibition. The compounds were prepared in two steps, including selective N7-alkylation of guanosine 5'-monophosphate by arylmethyl bromide followed by coupling with imidazole-activated GDP, with total yields varying from 22% to 62%. The compounds were then evaluated by determining their affinity for eukaryotic translation initiation factor 4E (eIF4E), testing their susceptibility to decapping pyrophosphatase, DcpS-which is most likely the major cellular enzyme targeting this type of compound-and determining their translation inhibitory properties in vitro. We also synthesized mRNAs capped with the evaluated compounds and tested their translational properties in A549 cells. Our studies identified N7-(4-halogenbenzyl) substituents as promising modifications in the contexts of either mRNA translation or translational inhibition. Finally, to gain more insight into the consequences at the molecular level of N7-benzylation of the mRNA cap, we determined the crystal structures of three compounds with eIF4E.
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Affiliation(s)
- Radoslaw Wojcik
- Centre of New Technologies, University of Warsaw, 02097 Warsaw, Poland; (R.W.); (L.M.); (M.B.); (N.B.); (P.J.S.)
| | - Marek R. Baranowski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02093 Warsaw, Poland; (M.R.B.); (D.K.); (A.W.); (J.Z.)
| | - Lukasz Markiewicz
- Centre of New Technologies, University of Warsaw, 02097 Warsaw, Poland; (R.W.); (L.M.); (M.B.); (N.B.); (P.J.S.)
| | - Dorota Kubacka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02093 Warsaw, Poland; (M.R.B.); (D.K.); (A.W.); (J.Z.)
| | - Marcelina Bednarczyk
- Centre of New Technologies, University of Warsaw, 02097 Warsaw, Poland; (R.W.); (L.M.); (M.B.); (N.B.); (P.J.S.)
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02093 Warsaw, Poland; (M.R.B.); (D.K.); (A.W.); (J.Z.)
| | - Natalia Baran
- Centre of New Technologies, University of Warsaw, 02097 Warsaw, Poland; (R.W.); (L.M.); (M.B.); (N.B.); (P.J.S.)
| | - Anna Wojtczak
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02093 Warsaw, Poland; (M.R.B.); (D.K.); (A.W.); (J.Z.)
| | - Pawel J. Sikorski
- Centre of New Technologies, University of Warsaw, 02097 Warsaw, Poland; (R.W.); (L.M.); (M.B.); (N.B.); (P.J.S.)
| | - Joanna Zuberek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02093 Warsaw, Poland; (M.R.B.); (D.K.); (A.W.); (J.Z.)
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02093 Warsaw, Poland; (M.R.B.); (D.K.); (A.W.); (J.Z.)
- Correspondence: (J.K.); (J.J.)
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02097 Warsaw, Poland; (R.W.); (L.M.); (M.B.); (N.B.); (P.J.S.)
- Correspondence: (J.K.); (J.J.)
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Mishra RK, Datey A, Hussain T. mRNA Recruiting eIF4 Factors Involved in Protein Synthesis and Its Regulation. Biochemistry 2019; 59:34-46. [DOI: 10.1021/acs.biochem.9b00788] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Rishi Kumar Mishra
- Department of Molecular Reproduction, Development and Genetics, Division of Biological Sciences, Indian Institute of Science, Bangalore 560012, India
| | - Ayushi Datey
- Department of Molecular Reproduction, Development and Genetics, Division of Biological Sciences, Indian Institute of Science, Bangalore 560012, India
| | - Tanweer Hussain
- Department of Molecular Reproduction, Development and Genetics, Division of Biological Sciences, Indian Institute of Science, Bangalore 560012, India
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3
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Pradhan MR, Nguyen MN, Kannan S, Fox SJ, Kwoh CK, Lane DP, Verma CS. Characterization of Hydration Properties in Structural Ensembles of Biomolecules. J Chem Inf Model 2019; 59:3316-3329. [DOI: 10.1021/acs.jcim.8b00453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mohan R. Pradhan
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - Minh N. Nguyen
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Stephen J. Fox
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Chee Keong Kwoh
- School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - David P. Lane
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
| | - Chandra S. Verma
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
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4
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Lama D, Liberatore AM, Frosi Y, Nakhle J, Tsomaia N, Bashir T, Lane DP, Brown CJ, Verma CS, Auvin S. Structural insights reveal a recognition feature for tailoring hydrocarbon stapled-peptides against the eukaryotic translation initiation factor 4E protein. Chem Sci 2019; 10:2489-2500. [PMID: 30881679 PMCID: PMC6385854 DOI: 10.1039/c8sc03759k] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/21/2018] [Indexed: 11/21/2022] Open
Abstract
Stapled-peptides have emerged as an exciting class of molecules which can modulate protein-protein interactions. We have used a structure-guided approach to rationally develop a set of hydrocarbon stapled-peptides with high binding affinities and residence times against the oncogenic eukaryotic translation initiation factor 4E (eIF4E) protein. Crystal structures of these peptides in complex with eIF4E show that they form specific interactions with a region on the protein-binding interface of eIF4E which is distinct from the other well-established canonical interactions. This recognition element is a major molecular determinant underlying the improved binding kinetics of these peptides with eIF4E. The interactions were further exploited by designing features in the peptides to attenuate disorder and increase helicity which collectively resulted in the generation of a distinct class of hydrocarbon stapled-peptides targeting eIF4E. This study details new insights into the molecular basis of stapled-peptide: eIF4E interactions and their exploitation to enhance promising lead molecules for the development of stapled-peptide compounds for oncology.
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Affiliation(s)
- Dilraj Lama
- Bioinformatics Institute , ASTAR (Agency for Science, Technology and Research) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 . ; Tel: +65 6478 8273
| | - Anne-Marie Liberatore
- Ipsen Innovation , 5, Avenue du Canada , Les Ulis , France 91940 . ; Tel: +33 160 922481
| | - Yuri Frosi
- p53 Laboratory , ASTAR (Agency for Science, Technology and Research) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648 . ; Tel: +65 6478 8273
| | - Jessica Nakhle
- Ipsen Innovation , 5, Avenue du Canada , Les Ulis , France 91940 . ; Tel: +33 160 922481
| | - Natia Tsomaia
- Ipsen Bioscience , 650 East Kendall Street , Cambridge , MA 02142 , USA
| | - Tarig Bashir
- Ipsen Innovation , 5, Avenue du Canada , Les Ulis , France 91940 . ; Tel: +33 160 922481
| | - David P Lane
- p53 Laboratory , ASTAR (Agency for Science, Technology and Research) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648 . ; Tel: +65 6478 8273
| | - Christopher J Brown
- p53 Laboratory , ASTAR (Agency for Science, Technology and Research) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648 . ; Tel: +65 6478 8273
| | - Chandra S Verma
- Bioinformatics Institute , ASTAR (Agency for Science, Technology and Research) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 . ; Tel: +65 6478 8273.,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
| | - Serge Auvin
- Ipsen Innovation , 5, Avenue du Canada , Les Ulis , France 91940 . ; Tel: +33 160 922481
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Hashem Y, Frank J. The Jigsaw Puzzle of mRNA Translation Initiation in Eukaryotes: A Decade of Structures Unraveling the Mechanics of the Process. Annu Rev Biophys 2018; 47:125-151. [PMID: 29494255 DOI: 10.1146/annurev-biophys-070816-034034] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Translation initiation in eukaryotes is a highly regulated and rate-limiting process. It results in the assembly and disassembly of numerous transient and intermediate complexes involving over a dozen eukaryotic initiation factors (eIFs). This process culminates in the accommodation of a start codon marking the beginning of an open reading frame at the appropriate ribosomal site. Although this process has been extensively studied by hundreds of groups for nearly half a century, it has been only recently, especially during the last decade, that we have gained deeper insight into the mechanics of the eukaryotic translation initiation process. This advance in knowledge is due in part to the contributions of structural biology, which have shed light on the molecular mechanics underlying the different functions of various eukaryotic initiation factors. In this review, we focus exclusively on the contribution of structural biology to the understanding of the eukaryotic initiation process, a long-standing jigsaw puzzle that is just starting to yield the bigger picture.
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Affiliation(s)
- Yaser Hashem
- INSERM U1212, Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France;
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY 10032, USA;
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6
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Lama D, Pradhan MR, Brown CJ, Eapen RS, Joseph TL, Kwoh CK, Lane DP, Verma CS. Water-Bridge Mediates Recognition of mRNA Cap in eIF4E. Structure 2016; 25:188-194. [PMID: 27916520 DOI: 10.1016/j.str.2016.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/19/2016] [Accepted: 11/07/2016] [Indexed: 11/24/2022]
Abstract
Ligand binding pockets in proteins contain water molecules, which play important roles in modulating protein-ligand interactions. Available crystallographic data for the 5' mRNA cap-binding pocket of the translation initiation factor protein eIF4E shows several structurally conserved waters, which also persist in molecular dynamics simulations. These waters engage an intricate hydrogen-bond network between the cap and protein. Two crystallographic waters in the cleft of the pocket show a high degree of conservation and bridge two residues, which are part of an evolutionarily conserved scaffold. This appears to be a preformed recognition module for the cap with the two structural waters facilitating an efficient interaction. This is also recapitulated in a new crystal structure of the apo protein. These findings open new windows for the design and screening of compounds targeting eIF4E.
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Affiliation(s)
- Dilraj Lama
- Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Mohan R Pradhan
- Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Christopher J Brown
- p53 Laboratory, A(∗)STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648, Singapore
| | - Rohan S Eapen
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Thomas L Joseph
- Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Chee-Keong Kwoh
- School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - David P Lane
- p53 Laboratory, A(∗)STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551, Singapore.
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7
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Lama D, Brown CJ, Lane DP, Verma CS. Gating by Tryptophan 73 Exposes a Cryptic Pocket at the Protein-Binding Interface of the Oncogenic eIF4E Protein. Biochemistry 2015; 54:6535-44. [DOI: 10.1021/acs.biochem.5b00812] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Dilraj Lama
- Bioinformatics
Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis
Street, #07-01 Matrix, Singapore 138671
| | - Christopher J. Brown
- p53
Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
| | - David P. Lane
- p53
Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
| | - Chandra S. Verma
- Bioinformatics
Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis
Street, #07-01 Matrix, Singapore 138671
- 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
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8
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Aumayr M, Fedosyuk S, Ruzicska K, Sousa-Blin C, Kontaxis G, Skern T. NMR analysis of the interaction of picornaviral proteinases Lb and 2A with their substrate eukaryotic initiation factor 4GII. Protein Sci 2015; 24:1979-96. [PMID: 26384734 PMCID: PMC4815241 DOI: 10.1002/pro.2807] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/14/2015] [Accepted: 09/17/2015] [Indexed: 11/09/2022]
Abstract
Messenger RNA is recruited to the eukaryotic ribosome by a complex including the eukaryotic initiation factor (eIF) 4E (the cap-binding protein), the scaffold protein eIF4G and the RNA helicase eIF4A. To shut-off host-cell protein synthesis, eIF4G is cleaved during picornaviral infection by a virally encoded proteinase; the structural basis of this reaction and its stimulation by eIF4E is unclear. We have structurally and biochemically investigated the interaction of purified foot-and-mouth disease virus (FMDV) leader proteinase (Lb(pro)), human rhinovirus 2 (HRV2) 2A proteinase (2A(pro)) and coxsackievirus B4 (CVB4) 2A(pro) with purified eIF4GII, eIF4E and the eIF4GII/eIF4E complex. Using nuclear magnetic resonance (NMR), we completed (13)C/(15) N sequential backbone assignment of human eIF4GII residues 551-745 and examined their binding to murine eIF4E. eIF4GII551-745 is intrinsically unstructured and remains so when bound to eIF4E. NMR and biophysical techniques for determining stoichiometry and binding constants revealed that the papain-like Lb(pro) only forms a stable complex with eIF4GII(551-745) in the presence of eIF4E, with KD values in the low nanomolar range; Lb(pro) contacts both eIF4GII and eIF4E. Furthermore, the unrelated chymotrypsin-like 2A(pro) from HRV2 and CVB4 also build a stable complex with eIF4GII/eIF4E, but with K(D) values in the low micromolar range. The HRV2 enzyme also forms a stable complex with eIF4E; however, none of the proteinases tested complex stably with eIF4GII alone. Thus, these three picornaviral proteinases have independently evolved to establish distinct triangular heterotrimeric protein complexes that may actively target ribosomes involved in mRNA recruitment to ensure efficient host cell shut-off.
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Affiliation(s)
- Martina Aumayr
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, Vienna, A-1030, Austria
| | - Sofiya Fedosyuk
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, Vienna, A-1030, Austria
| | - Katharina Ruzicska
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, Vienna, A-1030, Austria
| | - Carla Sousa-Blin
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, Vienna, A-1030, Austria
| | - Georg Kontaxis
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna, A-1030, Austria
| | - Tim Skern
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, Vienna, A-1030, Austria
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Abstract
The original purification of the heterotrimeric eIF4F was published over 30 years ago (Grifo, J. A., Tahara, S. M., Morgan, M. A., Shatkin, A. J., and Merrick, W. C. (1983) J. Biol. Chem. 258, 5804-5810). Since that time, numerous studies have been performed with the three proteins specifically required for the translation initiation of natural mRNAs, eIF4A, eIF4B, and eIF4F. These have involved enzymatic and structural studies of the proteins and a number of site-directed mutagenesis studies. The regulation of translation exhibited through the mammalian target of rapamycin (mTOR) pathway is predominately seen as the phosphorylation of 4E-BP, an inhibitor of protein synthesis that functions by binding to the cap binding subunit of eIF4F (eIF4E). A hypothesis that requires the disassembly of eIF4F during translation initiation to yield free subunits (eIF4A, eIF4E, and eIF4G) is presented.
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Affiliation(s)
- William C Merrick
- From the Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4935
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10
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Sekiyama N, Arthanari H, Papadopoulos E, Rodriguez-Mias RA, Wagner G, Léger-Abraham M. Molecular mechanism of the dual activity of 4EGI-1: Dissociating eIF4G from eIF4E but stabilizing the binding of unphosphorylated 4E-BP1. Proc Natl Acad Sci U S A 2015; 112:E4036-45. [PMID: 26170285 PMCID: PMC4522750 DOI: 10.1073/pnas.1512118112] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The eIF4E-binding protein (4E-BP) is a phosphorylation-dependent regulator of protein synthesis. The nonphosphorylated or minimally phosphorylated form binds translation initiation factor 4E (eIF4E), preventing binding of eIF4G and the recruitment of the small ribosomal subunit. Signaling events stimulate serial phosphorylation of 4E-BP, primarily by mammalian target of rapamycin complex 1 (mTORC1) at residues T37/T46, followed by T70 and S65. Hyperphosphorylated 4E-BP dissociates from eIF4E, allowing eIF4E to interact with eIF4G and translation initiation to resume. Because overexpression of eIF4E is linked to cellular transformation, 4E-BP is a tumor suppressor, and up-regulation of its activity is a goal of interest for cancer therapy. A recently discovered small molecule, eIF4E/eIF4G interaction inhibitor 1 (4EGI-1), disrupts the eIF4E/eIF4G interaction and promotes binding of 4E-BP1 to eIF4E. Structures of 14- to 16-residue 4E-BP fragments bound to eIF4E contain the eIF4E consensus binding motif, (54)YXXXXLΦ(60) (motif 1) but lack known phosphorylation sites. We report here a 2.1-Å crystal structure of mouse eIF4E in complex with m(7)GTP and with a fragment of human 4E-BP1, extended C-terminally from the consensus-binding motif (4E-BP150-84). The extension, which includes a proline-turn-helix segment (motif 2) followed by a loop of irregular structure, reveals the location of two phosphorylation sites (S65 and T70). Our major finding is that the C-terminal extension (motif 3) is critical to 4E-BP1-mediated cell cycle arrest and that it partially overlaps with the binding site of 4EGI-1. The binding of 4E-BP1 and 4EGI-1 to eIF4E is therefore not mutually exclusive, and both ligands contribute to shift the equilibrium toward the inhibition of translation initiation.
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Affiliation(s)
- Naotaka Sekiyama
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Evangelos Papadopoulos
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Ricard A Rodriguez-Mias
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Mélissa Léger-Abraham
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
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11
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Azzarito V, Miles JA, Fisher J, Edwards TA, Warriner SL, Wilson AJ. Stereocontrolled protein surface recognition using chiral oligoamide proteomimetic foldamers. Chem Sci 2015; 6:2434-2443. [PMID: 29308155 PMCID: PMC5646261 DOI: 10.1039/c4sc03559c] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/29/2015] [Indexed: 12/26/2022] Open
Abstract
An oligoamide helix mimicking foldamer with well-defined conformation is shown to recognize its target protein hDM2 in a manner that depends upon the composition, spatial projection and stereochemistry of functional groups appended to the scaffold.
The development of foldamers capable of selective molecular recognition of solvent exposed protein surfaces represents an outstanding challenge in supramolecular chemical biology. Here we introduce an oligoamide foldamer with well-defined conformation that bears all the hallmarks of an information rich oligomer. Specifically, the foldamer recognizes its target protein hDM2 leading to inhibition of its protein–protein interaction with p53 in a manner that depends upon the composition, spatial projection and stereochemistry of functional groups appended to the scaffold. Most significantly, selective inhibition of p53/hDM2 can be achieved against four other targets and the selectivity for p53/hDM2 inhibition versus Mcl-1/NOXA-B inhibition is critically dependent upon the stereochemistry of the helix mimetic.
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Affiliation(s)
- Valeria Azzarito
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Jennifer A Miles
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Julie Fisher
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK .
| | - Thomas A Edwards
- Astbury Centre for Structural and 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 and 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 and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
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12
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Burslem GM, Kyle HF, Breeze AL, Edwards TA, Nelson A, Warriner SL, Wilson AJ. Small-molecule proteomimetic inhibitors of the HIF-1α-p300 protein-protein interaction. Chembiochem 2014; 15:1083-7. [PMID: 24782431 PMCID: PMC4159589 DOI: 10.1002/cbic.201400009] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Indexed: 11/29/2022]
Abstract
The therapeutically relevant hypoxia inducible factor HIF-1α–p300 protein–protein interaction can be orthosterically inhibited with α-helix mimetics based on an oligoamide scaffold that recapitulates essential features of the C-terminal helix of the HIF-1α C-TAD (C-terminal transactivation domain). Preliminary SAR studies demonstrated the important role of side-chain size and hydrophobicity/hydrophilicity in determining potency. These small molecules represent the first biophysically characterised HIF-1α–p300 PPI inhibitors and the first examples of small-molecule aromatic oligoamide helix mimetics to be shown to have a selective binding profile. Although the compounds were less potent than HIF-1α, the result is still remarkable in that the mimetic reproduces only three residues from the 42-residue HIF-1α C-TAD from which it is derived.
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Affiliation(s)
- George M Burslem
- 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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13
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Lama D, Quah ST, Verma CS, Lakshminarayanan R, Beuerman RW, Lane DP, Brown CJ. Rational optimization of conformational effects induced by hydrocarbon staples in peptides and their binding interfaces. Sci Rep 2013; 3:3451. [PMID: 24336354 PMCID: PMC6506440 DOI: 10.1038/srep03451] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 11/20/2013] [Indexed: 12/26/2022] Open
Abstract
eIF4E is frequently over-expressed in different cancers and causes increased translation of oncogenic proteins via deregulated cap-dependent translation. Inhibitors of the eIF4E:eIF4G interactions represent an approach that would normalize cap-dependent translation. Stapled peptides represent an emerging class of therapeutics that can target protein: protein interactions. We present here molecular dynamics simulations for a set of rationally designed stapled peptides in solution and in complex with eIF4E, supported with biophysical and crystallographic data. Clustering of the simulated structures revealed the favoured conformational states of the stapled peptides in their bound or free forms in solution. Identifying these populations has allowed us to design peptides with improved affinities by introducing mutations into the peptide sequence to alter their conformational distributions. These studies emphasise the effects that engineered mutations have on the conformations of free and bound peptides, and illustrate that both states must be considered in efforts to attain high affinity binding.
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Affiliation(s)
- Dilraj Lama
- 1] Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671 [2]
| | - Soo T Quah
- 1] p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648 [2]
| | - Chandra S Verma
- 1] Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671 [2] Department of Biological sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543 [3] School of Biological sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551
| | | | - Roger W Beuerman
- Singapore Eye Research Institute, 11 Third Hospital Avenue, Singapore 16875
| | - David P Lane
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
| | - Christopher J Brown
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
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14
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O'Brien JP, Mayberry LK, Murphy PA, Browning KS, Brodbelt JS. Evaluating the conformation and binding interface of cap-binding proteins and complexes via ultraviolet photodissociation mass spectrometry. J Proteome Res 2013; 12:5867-77. [PMID: 24200290 DOI: 10.1021/pr400869u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We report the structural analysis of cap-binding proteins using a chemical probe/ultraviolet photodissociation (UVPD) mass spectrometry strategy for evaluating solvent accessibility of proteins. Our methodology utilized a chromogenic probe (NN) to probe the exposed amine residues of wheat eukaryotic translation initiation factor 4E (eIF4E), eIF4E in complex with a fragment of eIF4G ("mini-eIF4F"), eIF4E in complex with full length eIF4G, and the plant specific cap-binding protein, eIFiso4E. Structural changes of eIF4E in the absence and presence of excess dithiothreitol and in complex with a fragment of eIF4G or full-length eIF4G are mapped. The results indicate that there are particular lysine residues whose environment changes in the presence of dithiothreitol or eIF4G, suggesting that changes in the structure of eIF4E are occurring. On the basis of the crystal structure of wheat eIF4E and a constructed homology model of the structure for eIFiso4E, the reactivities of lysines in each protein are rationalized. Our results suggest that chemical probe/UVPD mass spectrometry can successfully predict dynamic structural changes in solution that are consistent with known crystal structures. Our findings reveal that the binding of m(7)GTP to eIF4E and eIFiso4E appears to be dependent on the redox state of a pair of cysteines near the m(7)GTP binding site. In addition, tertiary structural changes of eIF4E initiated by the formation of a complex containing a fragment of eIF4G and eIF4E were observed.
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Affiliation(s)
- John P O'Brien
- Department of Chemistry and Biochemistry and ‡Institute for Cell and Molecular Biology, The University of Texas at Austin , 1 University Station A5300, Austin, Texas 78712, United States
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15
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Carroll M, Borden KLB. The oncogene eIF4E: using biochemical insights to target cancer. J Interferon Cytokine Res 2013; 33:227-38. [PMID: 23472659 DOI: 10.1089/jir.2012.0142] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The eukaryotic translation initiation factor eIF4E is overexpressed in many human malignancies where it is typically a harbinger of poor prognosis. eIF4E is positioned as a nexus in post-transcriptional gene expression. To carry out these functions, eIF4E needs to bind the m(7)G cap moiety on mRNAs. It plays critical roles in mRNA translation, mRNA export, and most likely in mRNA stability as well. Through these activities, eIF4E coordinately modulates the expression of many transcripts involved in proliferation and survival. eIF4E function is controlled by interactions with protein cofactors in concert with many signaling pathways, including Ras, Mnk, Erk, MAPK, PI3K, mTOR, and Akt. This review describes the eIF4E activity and provides several examples of cellular control mechanisms. Further, we describe some therapeutic strategies in preclinical and clinical development.
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Affiliation(s)
- Martin Carroll
- Division of Hematology and Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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16
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Zhou W, Quah ST, Verma CS, Liu Y, Lane DP, Brown CJ. Improved eIF4E binding peptides by phage display guided design: plasticity of interacting surfaces yield collective effects. PLoS One 2012; 7:e47235. [PMID: 23094039 PMCID: PMC3477164 DOI: 10.1371/journal.pone.0047235] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 09/10/2012] [Indexed: 02/07/2023] Open
Abstract
Eukaryotic initiation factor (eIF)4E is over-expressed in many types of cancer such as breast, head and neck, and lung. A consequence of increased levels of eIF4E is the preferential translation of pro-tumorigenic proteins (e.g. c-Myc and vascular endothelial growth factor) and as a result is regarded as a potential therapeutic target. In this work a novel phage display peptide has been isolated against eIF4E. From the phage sequence two amino acids were delineated which improved binding when substituted into the eIF4G1 sequence. Neither of these substitutions were involved in direct interactions with eIF4E and acted either via optimization of the helical capping motif or restricting the conformational flexibility of the peptide. In contrast, substitutions of the remaining phage derived amino acids into the eIF4G1 sequence disrupted binding of the peptide to eIF4E. Interestingly when some of these disruptive substitutions were combined with key mutations from the phage peptide, they lead to improved affinities. Atomistic computer simulations revealed that the phage and the eIF4G1 derivative peptide sequences differ subtly in their interaction sites on eIF4E. This raises the issue, especially in the context of planar interaction sites such as those exhibited by eIF4E, that given the intricate plasticity of protein surfaces, the construction of structure-activity relationships should account for the possibility of significant movement in the spatial positioning of the peptide binding interface, including significant librational motions of the peptide.
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Affiliation(s)
- Weizhuang Zhou
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Soo T. Quah
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Chandra S. Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
- * E-mail: (CJB); (CSV)
| | - Yun Liu
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - David P. Lane
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Christopher J. Brown
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore
- * E-mail: (CJB); (CSV)
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17
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von Stetten D, Batot GO, Noirclerc-Savoye M, Royant A. Alteration of fluorescent protein spectroscopic properties upon cryoprotection. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1578-83. [DOI: 10.1107/s0907444912037900] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 09/04/2012] [Indexed: 05/26/2023]
Abstract
Cryoprotection of a protein crystal by addition of small-molecule compounds may sometimes affect the structure of its active site. The spectroscopic and structural effects of the two cryoprotectants glycerol and ethylene glycol on the cyan fluorescent protein Cerulean were investigated. While glycerol had almost no noticeable effect, ethylene glycol was shown to induce a systematic red shift of the UV–vis absorption and fluorescence emission spectra. Additionally, ethylene glycol molecules were shown to enter the core of the protein, with one of them binding in close vicinity to the chromophore, which provides a sound explanation for the observed spectroscopic changes. These results highlight the need to systematically record spectroscopic data on crystals of light-absorbing proteins and reinforce the notion that fluorescent proteins must not been seen as rigid structures.
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18
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Kinkelin K, Veith K, Grünwald M, Bono F. Crystal structure of a minimal eIF4E-Cup complex reveals a general mechanism of eIF4E regulation in translational repression. RNA (NEW YORK, N.Y.) 2012; 18:1624-34. [PMID: 22832024 PMCID: PMC3425778 DOI: 10.1261/rna.033639.112] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Cup is an eIF4E-binding protein (4E-BP) that plays a central role in translational regulation of localized mRNAs during early Drosophila development. In particular, Cup is required for repressing translation of the maternally contributed oskar, nanos, and gurken mRNAs, all of which are essential for embryonic body axis determination. Here, we present the 2.8 Å resolution crystal structure of a minimal eIF4E-Cup assembly, consisting of the interacting regions of the two proteins. In the structure, two separate segments of Cup contact two orthogonal faces of eIF4E. The eIF4E-binding consensus motif of Cup (YXXXXLΦ) binds the convex side of eIF4E similarly to the consensus of other eIF4E-binding proteins, such as 4E-BPs and eIF4G. The second, noncanonical, eIF4E-binding site of Cup binds laterally and perpendicularly to the eIF4E β-sheet. Mutations of Cup at this binding site were shown to reduce binding to eIF4E and to promote the destabilization of the associated mRNA. Comparison with the binding mode of eIF4G to eIF4E suggests that Cup and eIF4G binding would be mutually exclusive at both binding sites. This shows how a common molecular surface of eIF4E might recognize different proteins acting at different times in the same pathway. The structure provides insight into the mechanism by which Cup disrupts eIF4E-eIF4G interaction and has broader implications for understanding the role of 4E-BPs in translational regulation.
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Affiliation(s)
- Kerstin Kinkelin
- Max-Planck-Institute for Developmental Biology, 71076 Tübingen, Germany
| | - Katharina Veith
- Max-Planck-Institute for Developmental Biology, 71076 Tübingen, Germany
| | - Marlene Grünwald
- Max-Planck-Institute for Developmental Biology, 71076 Tübingen, Germany
| | - Fulvia Bono
- Max-Planck-Institute for Developmental Biology, 71076 Tübingen, Germany
- Corresponding authorE-mail
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19
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Siddiqui N, Tempel W, Nedyalkova L, Volpon L, Wernimont AK, Osborne MJ, Park HW, Borden KLB. Structural insights into the allosteric effects of 4EBP1 on the eukaryotic translation initiation factor eIF4E. J Mol Biol 2011; 415:781-92. [PMID: 22178476 DOI: 10.1016/j.jmb.2011.12.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 11/25/2011] [Accepted: 12/01/2011] [Indexed: 01/11/2023]
Abstract
The eukaryotic translation initiation factor eIF4E plays key roles in cap-dependent translation and mRNA export. These functions rely on binding the 7-methyl-guanosine moiety (5'cap) on the 5'-end of all mRNAs. eIF4E is regulated by proteins such as eIF4G and eIF4E binding proteins (4EBPs) that bind the dorsal surface of eIF4E, distal to the cap binding site, and modulate cap binding activity. Both proteins increase the affinity of eIF4E for 5'cap. Our understanding of the allosteric effects and structural underpinnings of 4EBP1 or eIF4G binding can be advanced by obtaining structural data on cap-free eIF4E bound to one of these proteins. Here, we report the crystal structure of apo-eIF4E and cap-free eIF4E in complex with a 4EBP1 peptide. We also monitored 4EBP1 binding to cap-free eIF4E in solution using NMR. Together, these studies suggest that 4EBP1 transforms eIF4E into a cap-receptive state. NMR methods were also used to compare the allosteric routes activated by 4EBP1, eIF4G, and the arenavirus Z protein, a negative regulator of cap binding. We observed chemical shift perturbation at the dorsal binding site leading to alterations in the core of the protein, which were ultimately communicated to the unoccupied cap binding site of eIF4E. There were notable similarities between the routes taken by 4EBP1 and eIF4G and differences from the negative regulator Z. Thus, binding of 4EBP1 or eIF4G allosterically drives alterations throughout the protein that increase the affinity of eIF4E for the 5'cap.
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Affiliation(s)
- Nadeem Siddiqui
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada H3T 1J4
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20
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Borden KLB, Culjkovic-Kraljacic B. Ribavirin as an anti-cancer therapy: acute myeloid leukemia and beyond? Leuk Lymphoma 2011; 51:1805-15. [PMID: 20629523 DOI: 10.3109/10428194.2010.496506] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ribavirin was discovered nearly 40 years ago as a broad-spectrum antiviral drug. Recent data suggest that ribavirin may also be an effective cancer therapy. In this case, ribavirin targets an oncogene, the eukaryotic translation initiation factor eIF4E, elevated in approximately 30% of cancers including many leukemias and lymphomas. Specifically, ribavirin impedes eIF4E mediated oncogenic transformation by acting as an inhibitor of eIF4E. In a phase II clinical trial, ribavirin treatment led to substantial clinical benefit in patients with poor-prognosis acute myeloid leukemia (AML). Here molecular targeting of eIF4E correlated with clinical response. Ribavirin also targets a key enzyme in the guanosine biosynthetic pathway, inosine monophosphate dehydrogenase (IMPDH), and also modulates immunity. Parallels with known antiviral mechanisms could be informative; however, after 40 years, these are not entirely clear. The antiviral effects of ribavirin appear cell-type specific. This variation likely arises for many reasons, including cell specific variations in ribavirin metabolism as well as virus specific factors. Thus, it seems that the mechanisms for ribavirin action in cancer therapy may also vary in terms of the cancer/tissue under study. Here we review the anticancer activities of ribavirin and discuss the possible utility of incorporating ribavirin into diverse cancer therapeutic regimens.
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Affiliation(s)
- Katherine L B Borden
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal, Montreal, QC, Canada.
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21
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Ashby JA, Stevenson CEM, Jarvis GE, Lawson DM, Maule AJ. Structure-based mutational analysis of eIF4E in relation to sbm1 resistance to pea seed-borne mosaic virus in pea. PLoS One 2011; 6:e15873. [PMID: 21283665 PMCID: PMC3025909 DOI: 10.1371/journal.pone.0015873] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 11/26/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Pea encodes eukaryotic translation initiation factor eIF4E (eIF4E(S)), which supports the multiplication of Pea seed-borne mosaic virus (PSbMV). In common with hosts for other potyviruses, some pea lines contain a recessive allele (sbm1) encoding a mutant eIF4E (eIF4E(R)) that fails to interact functionally with the PSbMV avirulence protein, VPg, giving genetic resistance to infection. METHODOLOGY/PRINCIPAL FINDINGS To study structure-function relationships between pea eIF4E and PSbMV VPg, we obtained an X-ray structure for eIF4E(S) bound to m(7)GTP. The crystallographic asymmetric unit contained eight independent copies of the protein, providing insights into the structurally conserved and flexible regions of eIF4E. To assess indirectly the importance of key residues in binding to VPg and/or m(7)GTP, an extensive range of point mutants in eIF4E was tested for their ability to complement PSbMV multiplication in resistant pea tissues and for complementation of protein translation, and hence growth, in an eIF4E-defective yeast strain conditionally dependent upon ectopic expression of eIF4E. The mutants also dissected individual contributions from polymorphisms present in eIF4E(R) and compared the impact of individual residues altered in orthologous resistance alleles from other crop species. The data showed that essential resistance determinants in eIF4E differed for different viruses although the critical region involved (possibly in VPg-binding) was conserved and partially overlapped with the m(7)GTP-binding region. This overlap resulted in coupled inhibition of virus multiplication and translation in the majority of cases, although the existence of a few mutants that uncoupled the two processes supported the view that the specific role of eIF4E in potyvirus infection may not be restricted to translation. CONCLUSIONS/SIGNIFICANCE The work describes the most extensive structural analysis of eIF4E in relation to potyvirus resistance. In addition to defining functional domains within the eIF4E structure, we identified eIF4E alleles with the potential to convey novel virus resistance phenotypes.
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Affiliation(s)
- Jamie A. Ashby
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Gavin E. Jarvis
- School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom
| | - David M. Lawson
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Andrew J. Maule
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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22
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Brown C, Lim J, Leonard T, Lim H, Chia C, Verma C, Lane D. Stabilizing the eIF4G1 α-Helix Increases Its Binding Affinity with eIF4E: Implications for Peptidomimetic Design Strategies. J Mol Biol 2011; 405:736-53. [DOI: 10.1016/j.jmb.2010.10.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 10/22/2010] [Accepted: 10/25/2010] [Indexed: 12/22/2022]
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23
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Topisirovic I, Svitkin YV, Sonenberg N, Shatkin AJ. Cap and cap-binding proteins in the control of gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:277-98. [PMID: 21957010 DOI: 10.1002/wrna.52] [Citation(s) in RCA: 280] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The 5' mRNA cap structure is essential for efficient gene expression from yeast to human. It plays a critical role in all aspects of the life cycle of an mRNA molecule. Capping occurs co-transcriptionally on the nascent pre-mRNA as it emerges from the RNA exit channel of RNA polymerase II. The cap structure protects mRNAs from degradation by exonucleases and promotes transcription, polyadenylation, splicing, and nuclear export of mRNA and U-rich, capped snRNAs. In addition, the cap structure is required for the optimal translation of the vast majority of cellular mRNAs, and it also plays a prominent role in the expression of eukaryotic, viral, and parasite mRNAs. Cap-binding proteins specifically bind to the cap structure and mediate its functions in the cell. Two major cellular cap-binding proteins have been described to date: eukaryotic translation initiation factor 4E (eIF4E) in the cytoplasm and nuclear cap binding complex (nCBC), a nuclear complex consisting of a cap-binding subunit cap-binding protein 20 (CBP 20) and an auxiliary protein cap-binding protein 80 (CBP 80). nCBC plays an important role in various aspects of nuclear mRNA metabolism such as pre-mRNA splicing and nuclear export, whereas eIF4E acts primarily as a facilitator of mRNA translation. In this review, we highlight recent findings on the role of the cap structure and cap-binding proteins in the regulation of gene expression. We also describe emerging regulatory pathways that control mRNA capping and cap-binding proteins in the cell.
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Affiliation(s)
- Ivan Topisirovic
- Department of Biochemistry and Goodman Cancer Centre, McGill University, Montréal, QC, Canada
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24
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Ruszczyńska-Bartnik K, Maciejczyk M, Stolarski R. Dynamical insight into Caenorhabditis elegans eIF4E recognition specificity for mono-and trimethylated structures of mRNA 5' cap. J Mol Model 2010; 17:727-37. [PMID: 20535623 PMCID: PMC3076583 DOI: 10.1007/s00894-010-0773-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 05/06/2010] [Indexed: 12/01/2022]
Abstract
Specific recognition and binding of the ribonucleic acid 5′ termini (mRNA 5′ cap) by the eukaryotic translation initiation factor 4E (eIF4E) is a key, rate limiting step in translation initiation. Contrary to mammalian and yeast eIF4Es that discriminate in favor of 7-methylguanosine cap, three out of five eIF4E isoforms from the nematode Caenorhabditis elegans as well as eIF4Es from the parasites Schistosome mansoni and Ascaris suum, exhibit dual binding specificity for both 7-methylguanosine-and N2,N2,7-trimethylguanosine cap. To address the problem of the differences in the mechanism of the cap recognition by those highly homologic proteins, we carried out molecular dynamics simulations in water of three factors, IFE-3 and IFE-5 isoforms from C. elegans and murine eIF4E, in the apo form as well as in the complexes with 7-methyl-GDP and N2,N2,7-trimethyl-GDP. The results clearly pointed to a dynamical mechanism of discrimination between each type of the cap, viz. differences in mobility of the loops located at the entrance into the protein binding pockets during the cap association and dissociation. Additionally, our data showed that the hydrogen bond involving the N2-amino group of 7-methylguanosine and the carboxylate of glutamic acid was not stable. The dynamic mechanism proposed here differs from a typical, static one in that the differences in the protein-ligand binding specificity cannot be ascribed to formation and/or disruption of well defined stabilizing contacts.
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Affiliation(s)
- Katarzyna Ruszczyńska-Bartnik
- Nuclear Magnetic Resonance Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
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25
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Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing. Proc Natl Acad Sci U S A 2010; 107:10062-7. [PMID: 20479262 DOI: 10.1073/pnas.1000848107] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human Cleavage Factor Im (CFI(m)) is an essential component of the pre-mRNA 3' processing complex that functions in the regulation of poly(A) site selection through the recognition of UGUA sequences upstream of the poly(A) site. Although the highly conserved 25 kDa subunit (CFI(m)25) of the CFI(m) complex possesses a characteristic alpha/beta/alpha Nudix fold, CFI(m)25 has no detectable hydrolase activity. Here we report the crystal structures of the human CFI(m)25 homodimer in complex with UGUAAA and UUGUAU RNA sequences. CFI(m)25 is the first Nudix protein to be reported to bind RNA in a sequence-specific manner. The UGUA sequence contributes to binding specificity through an intramolecular G:A Watson-Crick/sugar-edge base interaction, an unusual pairing previously found to be involved in the binding specificity of the SAM-III riboswitch. The structures, together with mutational data, suggest a novel mechanism for the simultaneous sequence-specific recognition of two UGUA elements within the pre-mRNA. Furthermore, the mutually exclusive binding of RNA and the signaling molecule Ap(4)A (diadenosine tetraphosphate) by CFI(m)25 suggests a potential role for small molecules in the regulation of mRNA 3' processing.
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26
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Curry S, Kotik-Kogan O, Conte MR, Brick P. Getting to the end of RNA: structural analysis of protein recognition of 5' and 3' termini. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1789:653-66. [PMID: 19619683 DOI: 10.1016/j.bbagrm.2009.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 07/07/2009] [Accepted: 07/09/2009] [Indexed: 10/20/2022]
Abstract
The specific recognition by proteins of the 5' and 3' ends of RNA molecules is an important facet of many cellular processes, including RNA maturation, regulation of translation initiation and control of gene expression by degradation and RNA interference. The aim of this review is to survey recent structural analyses of protein binding domains that specifically bind to the extreme 5' or 3' termini of RNA. For reasons of space and because their interactions are also governed by catalytic considerations, we have excluded enzymes that modify the 5' and 3' extremities of RNA. It is clear that there is enormous structural diversity among the proteins that have evolved to bind to the ends of RNA molecules. Moreover, they commonly exhibit conformational flexibility that appears to be important for binding and regulation of the interaction. This flexibility has sometimes complicated the interpretation of structural results and presents significant challenges for future investigations.
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Affiliation(s)
- Stephen Curry
- Biophysics Section, Blackett Laboratory, Imperial College, Exhibition Road, London, SW7 2AZ, UK.
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