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Abstract
Tyrosine phosphorylation is a critical component of signal transduction for multicellular organisms, particularly for pathways that regulate cell proliferation and differentiation. While tyrosine kinase inhibitors have become FDA-approved drugs, inhibitors of the other important components of these signaling pathways have been harder to develop. Specifically, direct phosphotyrosine (pTyr) isosteres have been aggressively pursued as inhibitors of Src homology 2 (SH2) domains and protein tyrosine phosphatases (PTPs). Medicinal chemists have produced many classes of peptide and small molecule inhibitors that mimic pTyr. However, balancing affinity with selectivity and cell penetration has made this an extremely difficult space for developing successful clinical candidates. This review will provide a comprehensive picture of the field of pTyr isosteres, from early beginnings to the current state and trajectory. We will also highlight the major protein targets of these medicinal chemistry efforts, the major classes of peptide and small molecule inhibitors that have been developed, and the handful of compounds which have been tested in clinical trials.
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Affiliation(s)
- Robert A Cerulli
- Cellular, Molecular and Developmental Biology Program, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA.
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2
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Debnath S, Kosek D, Tagad HD, Durell SR, Appella DH, Acevedo R, Grishaev A, Dyda F, Appella E, Mazur SJ. A trapped human PPM1A-phosphopeptide complex reveals structural features critical for regulation of PPM protein phosphatase activity. J Biol Chem 2018; 293:7993-8008. [PMID: 29602904 DOI: 10.1074/jbc.ra117.001213] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/29/2018] [Indexed: 01/09/2023] Open
Abstract
Metal-dependent protein phosphatases (PPM) are evolutionarily unrelated to other serine/threonine protein phosphatases and are characterized by their requirement for supplementation with millimolar concentrations of Mg2+ or Mn2+ ions for activity in vitro The crystal structure of human PPM1A (also known as PP2Cα), the first PPM structure determined, displays two tightly bound Mn2+ ions in the active site and a small subdomain, termed the Flap, located adjacent to the active site. Some recent crystal structures of bacterial or plant PPM phosphatases have disclosed two tightly bound metal ions and an additional third metal ion in the active site. Here, the crystal structure of the catalytic domain of human PPM1A, PPM1Acat, complexed with a cyclic phosphopeptide, c(MpSIpYVA), a cyclized variant of the activation loop of p38 MAPK (a physiological substrate of PPM1A), revealed three metal ions in the active site. The PPM1Acat D146E-c(MpSIpYVA) complex confirmed the presence of the anticipated third metal ion in the active site of metazoan PPM phosphatases. Biophysical and computational methods suggested that complex formation results in a slightly more compact solution conformation through reduced conformational flexibility of the Flap subdomain. We also observed that the position of the substrate in the active site allows solvent access to the labile third metal-binding site. Enzyme kinetics of PPM1Acat toward a phosphopeptide substrate supported a random-order, bi-substrate mechanism, with substantial interaction between the bound substrate and the labile metal ion. This work illuminates the structural and thermodynamic basis of an innate mechanism regulating the activity of PPM phosphatases.
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Affiliation(s)
- Subrata Debnath
- Laboratory of Cell Biology, Center for Cancer Research, NCI, Bethesda, Maryland 20892
| | - Dalibor Kosek
- Laboratories of Molecular Biology, Bethesda, Maryland 20892
| | - Harichandra D Tagad
- Laboratory of Cell Biology, Center for Cancer Research, NCI, Bethesda, Maryland 20892
| | - Stewart R Durell
- Laboratory of Cell Biology, Center for Cancer Research, NCI, Bethesda, Maryland 20892
| | - Daniel H Appella
- Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Roderico Acevedo
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850
| | - Alexander Grishaev
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850; National Institute of Standards and Technology, Gaithersburg, Maryland 20899
| | - Fred Dyda
- Laboratories of Molecular Biology, Bethesda, Maryland 20892
| | - Ettore Appella
- Laboratory of Cell Biology, Center for Cancer Research, NCI, Bethesda, Maryland 20892
| | - Sharlyn J Mazur
- Laboratory of Cell Biology, Center for Cancer Research, NCI, Bethesda, Maryland 20892.
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3
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Hoang HN, Wu C, Beyer RL, Hill TA, Fairlie DP. Alpha Helix Nucleation by a Simple Cyclic Tetrapeptide. Aust J Chem 2017. [DOI: 10.1071/ch16591] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The simple cyclic tetrapeptide cyclo-(1,4)-[Ala-Arg-Ala-homoGlu]-NH2 (3) is shown to adopt an unusual α-turn structure, which is not α-helical but can nucleate α-helicity when attached to the N-terminus of either model peptides or two biologically relevant peptides. This new N-terminal helix-capping macrocycle provides very simple and rapid synthetic access to α-helical peptide structures.
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4
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Iwata T, Tanaka K, Tahara T, Nozaki S, Onoe H, Watanabe Y, Fukase K. A conformationally fixed analog of the peptide mimic Grb2–SH2 domain: synthesis and evaluation against the A431 cancer cell. MOLECULAR BIOSYSTEMS 2013; 9:1019-25. [DOI: 10.1039/c3mb25462c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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5
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Tanaka K, Shirotsuki S, Iwata T, Kageyama C, Tahara T, Nozaki S, Siwu ERO, Tamura S, Douke S, Murakami N, Onoe H, Watanabe Y, Fukase K. Template-assisted and self-activating clicked peptide as a synthetic mimic of the SH2 domain. ACS Chem Biol 2012; 7:637-45. [PMID: 22239652 DOI: 10.1021/cb2003175] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A new synthetic strategy for obtaining artificial receptors that selectively regulate and/or control specific protein/protein interactions was developed based on the template-assisted and the self-activating click reaction applied to a combinatorial library. Synthetic mimics of the Grb2-SH2 domain, examined as a model case, selectively bound to a target signaling protein to induce cytotoxicity and inhibit tumor growth in vivo.
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Affiliation(s)
- Katsunori Tanaka
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
| | - Sanae Shirotsuki
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
| | - Takayuki Iwata
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
| | - Chika Kageyama
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
| | - Tsuyoshi Tahara
- RIKEN Center for Molecular Imaging Science, 6-7-3 Minatojima-minamimachi,
Chuo-ku, Kobe-shi, Hyogo 650-0047, Japan
| | - Satoshi Nozaki
- RIKEN Center for Molecular Imaging Science, 6-7-3 Minatojima-minamimachi,
Chuo-ku, Kobe-shi, Hyogo 650-0047, Japan
| | - Eric R. O. Siwu
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
| | - Satoru Tamura
- Graduate School of Pharmaceutical
Sciences, Osaka University, 1-6 Yamada-oka,
Suita-shi, Osaka 565-0871, Japan
| | - Shunsuke Douke
- Graduate School of Pharmaceutical
Sciences, Osaka University, 1-6 Yamada-oka,
Suita-shi, Osaka 565-0871, Japan
| | - Nobutoshi Murakami
- Graduate School of Pharmaceutical
Sciences, Osaka University, 1-6 Yamada-oka,
Suita-shi, Osaka 565-0871, Japan
| | - Hirotaka Onoe
- RIKEN Center for Molecular Imaging Science, 6-7-3 Minatojima-minamimachi,
Chuo-ku, Kobe-shi, Hyogo 650-0047, Japan
| | - Yasuyoshi Watanabe
- RIKEN Center for Molecular Imaging Science, 6-7-3 Minatojima-minamimachi,
Chuo-ku, Kobe-shi, Hyogo 650-0047, Japan
| | - Koichi Fukase
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
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6
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Smith DJ, Yap GPA, Kelley JA, Schneider JP. Enhanced stereoselectivity of a Cu(II) complex chiral auxiliary in the synthesis of Fmoc-L-γ-carboxyglutamic acid. J Org Chem 2011; 76:1513-20. [PMID: 21291260 PMCID: PMC3488861 DOI: 10.1021/jo101940k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
L-γ-Carboxyglutamic acid (Gla) is an uncommon amino acid that binds avidly to mineral surfaces and metal ions. Herein, we report the synthesis of N-α-Fmoc-L-γ-carboxyglutamic acid γ,γ'-tert-butyl ester (Fmoc-Gla(O(t)Bu)(2)-OH), a suitably protected analogue for Fmoc-based solid-phase peptide synthesis. The residue was synthesized using a novel chiral Cu(II) complex, whose structure-based design was inspired by the blue copper protein rusticyanin. The five-coordinate complex is formed by Shiff base formation between glycine and the novel ligand (S)-2-(N-(2-methylthio)benzylprolyl)aminobenzophenone in the presence of copper. Michael addition of di-tert-butyl methylenemalonate to the α-carbon of the glycine portion of the complex occurs in a diastereoselective fashion. The resulting (S,S)-complex diastereomer can be easily purified by chromatography. Metal complex decomposition followed by Fmoc protection affords the enantiomerically pure amino acid. With the use of this novel chiral complex, the asymmetric synthesis of Fmoc-Gla(O(t)Bu)(2)-OH was completed in nine steps from thiosalicylic acid in 14.5% overall yield.
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Affiliation(s)
- Daniel J. Smith
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702 USA
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716 USA
| | - Glenn P. A. Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716 USA
| | - James A. Kelley
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702 USA
| | - Joel P. Schneider
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702 USA
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Song YL, Tan J, Luo XM, Long YQ. Utilization of 3′-carboxy-containing tyrosine derivatives as a new class of phosphotyrosyl mimetics in the preparation of novel non-phosphorylated cyclic peptide inhibitors of the Grb2–SH2 domain. Org Biomol Chem 2006; 4:659-66. [PMID: 16467940 DOI: 10.1039/b515432d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new class of phosphotyrosyl (pTyr) mimetics, distinct from the conventional pTyr mimetic design of adding non-hydrolyzable acidic functionalities to the 4'-position of phenylalanine, was created by introducing carboxy-containing groups to the 3'-position of tyrosine. The effect of the chain length of the carboxy substituent was examined. Reported herein is the chiral pool synthesis of the new pTyr mimetics, and their first use in a novel non-phosphorylated Grb2-SH2 domain binding motif with the 5-amino-acid sequence Xx1-Leu-(3'-substituted-Tyr)-Ac6c-Asn. The highest affinity was exhibited by the 3-L-(2-carboxyethyl)tyrosine-containing sulfoxide-cyclized peptide , with an IC50 = 1.1 microM, providing a promising new template for further development of potent Grb2-SH2 domain inhibitors with reduced charge and peptidic nature, but improved selectivity and bioavailability.
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Affiliation(s)
- Yan-Li Song
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, CAS, 555 Zuchongzhi Road, Shanghai, 201203, China
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9
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Roberts KD, Lambert JN, Ede NJ, Bray AM. Efficient methodology for the cyclization of linear peptide libraries via intramolecularS-alkylation using Multipin™ solid phase peptide synthesis. J Pept Sci 2006; 12:525-32. [PMID: 16710870 DOI: 10.1002/psc.761] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Methodology is described here for the efficient parallel synthesis and cyclization of linear peptide libraries using intramolecular S-alkylation chemistry in combination with Multipin solid phase peptide synthesis (Multipin SPPS). The effective use of this methodology was demonstrated with the synthesis of a 72-member combinatorial library of cyclic thioether peptide derivatives of the conserved four-residue structural motif DD/EXK found in the active sites of the five crystallographically defined orthodox type II restriction endonucleases, EcoRV, EcoRI, PvuII, BamHI and BglI.
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Affiliation(s)
- Kade D Roberts
- School of Chemistry, The University of Melbourne, Grattan Street, Parkville, Victoria 3010, Australia.
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10
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Abstract
New ligands for a variety of biological targets can be selected from biological or synthetic combinatorial peptide libraries. The use of different libraries to select novel peptides with potential therapeutic applications is reviewed. The possible combination of molecular diversity provided by combinatorial libraries and a rational approach derived from computational modeling is also considered. Advantages and disadvantages of different approaches are compared. Possible strategies to bypass loss of peptide bioactivity in the transition from ligand selection to in vivo use are discussed.
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Affiliation(s)
- Chiara Falciani
- Department of Molecular Biology, University of Siena, I-53100 Siena, Italy
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11
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Shi YH, Song YL, Lin DH, Tan J, Roller PP, Li Q, Long YQ, Song GQ. Binding affinity difference induced by the stereochemistry of the sulfoxide bridge of the cyclic peptide inhibitors of Grb2-SH2 domain: NMR studies for the structural origin. Biochem Biophys Res Commun 2005; 330:1254-61. [PMID: 15823578 DOI: 10.1016/j.bbrc.2005.03.110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2005] [Indexed: 11/19/2022]
Abstract
The SAR study on a phage library-derived non-phosphorylated cyclic peptide ligand of Grb2-SH2 domain indicates that the configuration of the cyclization linkage is crucial for assuming the active binding conformation. When the thioether linkage was oxidized to the two chiral sulfoxides, the R-configured sulfoxide-cyclized peptide displayed 10-30 times more potency than the corresponding S-configured one in binding affinity to the Grb2-SH2 domain. In this paper, the solution structures of such a pair of sulfoxide-bridged cyclic peptide diastereoisomers, i.e., cyclo[CH(2)CO-Gla(1)-L-Y-E-N-V-G-NPG-Y-(R/S)C(O)(10)]-amide, were determined by NMR and molecular dynamics simulation. Results indicate that the consensus sequence of Y(3)-E(4)-N(5)-V(6) in both diastereoisomers adopt a beta-turn conformation; however, the R-configured peptide forms an extended structure with a circular backbone conformation, while the S-configured isomer forms a compact structure with key residues buried inside the molecule. The average root-mean-square deviations were found to be 0.756 and 0.804 A, respectively. It is apparent that the chiral S-->O group played a key role in the solution structures of the sulfoxide-bridged cyclic peptides. The R-sulfoxide group forms an intramolecular hydrogen bond with the C-terminal amide, conferring a more rigid conformation with all residues protruding outside except for Leu2, in which the Gla1 and Tyr3 share an overlapping function as previous SAR studies proposed. Additionally, the extended structure endows a more hydrophilic binding surface of the R-configured peptide to facilitate its capture by its targeted protein. In comparison, the S-configured sulfoxide was embedded inside the ligand peptide leading to a compact structure, in which the essential residues of Gla1, Tyr3, and Asn5 form multiple intramolecular hydrogen bonds resulting in an unfavorable conformational change and a substantial loss of the interaction with the protein. The solution structures disclosed by our NMR and molecular dynamics simulation studies provide a molecular basis for understanding how the chirality of the cyclization linkage remarkably discriminates in terms of the binding affinity, thus advancing the rational design of potent non-phosphorylated inhibitors of Grb2-SH2 domain as antitumor agents.
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Affiliation(s)
- Yan-hong Shi
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, CAS, 555 Zuchongzhi Road, Shanghai 201203, China
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12
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Abstract
In the year 2003 there was a 17% increase in the number of publications citing work performed using optical biosensor technology compared with the previous year. We collated the 962 total papers for 2003, identified the geographical regions where the work was performed, highlighted the instrument types on which it was carried out, and segregated the papers by biological system. In this overview, we spotlight 13 papers that should be on everyone's 'must read' list for 2003 and provide examples of how to identify and interpret high-quality biosensor data. Although we still find that the literature is replete with poorly performed experiments, over-interpreted results and a general lack of understanding of data analysis, we are optimistic that these shortcomings will be addressed as biosensor technology continues to mature.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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13
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Song YL, Roller PP, Long YQ. Development of l-3-aminotyrosine suitably protected for the synthesis of a novel nonphosphorylated hexapeptide with low-nanomolar Grb2-SH2 domain-binding affinity. Bioorg Med Chem Lett 2004; 14:3205-8. [PMID: 15149676 DOI: 10.1016/j.bmcl.2004.03.103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2004] [Revised: 03/29/2004] [Accepted: 03/31/2004] [Indexed: 11/30/2022]
Abstract
Synthesis of orthogonally protected (2S)-2-amino-3-(3-amino-4-hydroxy-phenyl)-propionic acid (10) suitable for solid phase peptide synthesis and its first use for the preparation of nonphosphorylated Grb2-SH2 domain antagonists (4a-c) are reported. The 3-aminotyrosine containing sulfoxide-cyclized hexapeptide (4b) exhibited potent Grb2-SH2 domain binding affinity with IC50 = 50 nM, which represents the highest affinity yet reported for a peptide inhibitor against Grb2-SH2 domain with only 6 residues free of phosphotyrosine or phosphotyrosine mimics. This potent small peptidomimetic 4b may be representative of a new class of therapeutically relevant Grb2-SH2 domain-directed agents, and acts as a chemotherapeutic lead for the treatment of erbB2-related cancers.
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Affiliation(s)
- Yan-Li Song
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, CAS, 555 Zuchongzhi Road, Shanghai 201203, China
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14
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Long YQ, Guo R, Luo JH, Yang D, Roller PP. Potentiating effect of distant sites in non-phosphorylated cyclic peptide antagonists of the Grb2-SH2 domain. Biochem Biophys Res Commun 2003; 310:334-40. [PMID: 14521914 DOI: 10.1016/j.bbrc.2003.09.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Without the presence of a phosphotyrosyl group, a phage library derived non-phosphorylated cyclic peptide ligand of Grb2-SH2 domain attributed its high affinity and specificity to well-defined and highly favored interactions of its structural elements with the binding pocket of the protein. We have disclosed a significant compensatory role of the Glu(2-) sidechain for the absence of the phosphate functionality on Tyr(0) in the peptide ligand, cyclo(CH(2)CO-Glu(2-)-Leu-Tyr(0)-Glu-Asn-Val-Gly-Met(5+)-Tyr-Cys)-amide (termed G1TE). In this study, we report the importance of hydrophobic residue at the Tyr+5 site in G1TE. Both acidic and basic amino acid substitutes are disfavored at this position, and replacement of Met with beta-tert-butyl-Ala was found to improve the antagonist properties. Besides, the polarity of the cyclization linkage was implicated as important in stabilizing the favored binding conformation. Oxidation of the thioether linkage into sulfoxide facilitated the binding to Grb2-SH2 markedly. Simultaneous modification of the three distant sites within G1TE provided the best agent with an IC(50) of 220 nM, which is among the most potent non-phosphorous- and non-phosphotyrosine-mimic containing Grb2-SH2 domain inhibitors yet reported. This potent peptidomimetic provides a novel template for the development of chemotherapeutic agents for the treatment of erbB2-related cancer. Biological assays on G1TE(Gla(2-)) in which the original residue of Glu(2-) was substituted by gamma-carboxyglutamic acid (Gla) indicated that it could inhibit the interaction between activated GF receptor and Grb2 protein in cell homogenates of MDA-MB-453 breast cancer cells at the 2 microM level. More significantly, both G1TE(Gla(2-)) alone and the conjugate of G1TE(Gla(2-)) with a peptide carrier can effectively inhibit intracellular association of erbB2 and Grb2 in the same cell lines with IC(50) of 50 and 2 microM, respectively.
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Affiliation(s)
- Ya-Qiu Long
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
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