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Martinez JC, Castillo F, Ruiz-Sanz J, Murciano-Calles J, Camara-Artigas A, Luque I. Understanding binding affinity and specificity of modular protein domains: A focus in ligand design for the polyproline-binding families. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:161-188. [PMID: 35534107 DOI: 10.1016/bs.apcsb.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Within the modular protein domains there are five families that recognize proline-rich sequences: SH3, WW, EVH1, GYF and UEV domains. This chapter reviews the main strategies developed for the design of ligands for these families, including peptides, peptidomimetics and drugs. We also describe some studies aimed to understand the molecular reasons responsible for the intrinsic affinity and specificity of these domains.
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Affiliation(s)
- Jose C Martinez
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain.
| | - Francisco Castillo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Granada, Spain
| | - Javier Ruiz-Sanz
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Javier Murciano-Calles
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Ana Camara-Artigas
- Departamento de Química Física, Universidad de Almería, Campus de Excelencia Internacional Agroalimentario ceiA3 y CIAMBITAL, Almeria, Spain
| | - Irene Luque
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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2
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Mardani Z, Golsanamlou V, Jabbarzadeh Z, Moeini K, Khodavandegar S, Carpenter-Warren C, Slawin AMZ, Woollins JD. Structural conversion of an oxazolidine ligand upon treatment with copper(I) and (II) halides; structural, spectral, theoretical and docking studies. J COORD CHEM 2018. [DOI: 10.1080/00958972.2018.1536268] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Zahra Mardani
- Inorganic Chemistry Department, Faculty of Chemistry, Urmia University, Urmia, I. R. Iran
| | - Vali Golsanamlou
- Inorganic Chemistry Department, Faculty of Chemistry, Urmia University, Urmia, I. R. Iran
| | - Zahra Jabbarzadeh
- Inorganic Chemistry Department, Faculty of Chemistry, Urmia University, Urmia, I. R. Iran
| | - Keyvan Moeini
- Chemistry Department, Payame Noor University, Tehran, I. R. Iran
| | - Saba Khodavandegar
- Inorganic Chemistry Department, Faculty of Chemistry, Urmia University, Urmia, I. R. Iran
| | | | | | - J. Derek Woollins
- EaStCHEM School of Chemistry, University of St Andrews, St Andrews Fife, UK
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3
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Chaume G, Simon J, Caupène C, Lensen N, Miclet E, Brigaud T. Incorporation of CF3–Pseudoprolines into Peptides: A Methodological Study. J Org Chem 2013; 78:10144-53. [DOI: 10.1021/jo401494q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Grégory Chaume
- Laboratoire SOSCO, Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Julien Simon
- Laboratoire SOSCO, Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Caroline Caupène
- Laboratoire SOSCO, Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Nathalie Lensen
- Laboratoire SOSCO, Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Emeric Miclet
- Laboratoire des
BioMolécules, UMR 7203, Ecole Normale Supérieure, UPMC Paris 06, 4 Place Jussieu, 75005 Paris, France
| | - Thierry Brigaud
- Laboratoire SOSCO, Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
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4
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The impact of either 4-R-hydroxyproline or 4-R-fluoroproline on the conformation and SH3m-cort binding of HPK1 proline-rich peptide. Amino Acids 2012; 44:607-14. [DOI: 10.1007/s00726-012-1383-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 07/30/2012] [Indexed: 10/27/2022]
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5
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Liu F, Giubellino A, Simister PC, Qian W, Giano MC, Feller SM, Bottaro DP, Burke TR. Application of ring-closing metathesis to Grb2 SH3 domain-binding peptides. Biopolymers 2011; 96:780-8. [PMID: 21830199 PMCID: PMC3402909 DOI: 10.1002/bip.21692] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Molecular processes depending on protein–protein interactions can use consensus recognition sequences that possess defined secondary structures. Left-handed polyproline II (PPII) helices are a class of secondary structure commonly involved with cellular signal transduction. However, unlike -helices, for which a substantial body of work exists regarding applications of ring-closing metathesis (RCM), there are few reports on the stabilization of PPII helices by RCM methodologies. The current study examined the effects of RCM macrocyclization on left-handed PPII helices involved with the SH3 domain-mediated binding of Sos1–Grb2. Starting with the Sos1-derived peptide “Ac-V1-P2-P3-P4-V5-P6-P7-R8-R9-R10-amide,” RCM macrocyclizations were conducted using alkenyl chains of varying lengths originating from the pyrrolidine rings of the Pro4 and Pro7 residues. The resulting macrocyclic peptides showed increased helicity as indicated by circular dichroism and enhanced abilities to block Grb2–Sos1 interactions in cell lysate pull-down assays. The synthetic approach may be useful in RCM macrocyclizations, where maintenance of proline integrity at both ring junctures is desired.
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Affiliation(s)
- Fa Liu
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702
| | - Alessio Giubellino
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20989
| | - Philip C. Simister
- Cell Signalling Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Wenjian Qian
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702
| | - Michael C. Giano
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702
| | - Stephan M. Feller
- Cell Signalling Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Donald P. Bottaro
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20989
| | - Terrence R. Burke
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702
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6
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Yu L, Zhou W, Wang Z. Synthesis and in vitro antibacterial activity of oxazolidine LBM-415 analogs as peptide deformylase inhibitors. Bioorg Med Chem Lett 2010; 21:1541-4. [PMID: 21288715 DOI: 10.1016/j.bmcl.2010.12.097] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 12/20/2010] [Indexed: 10/18/2022]
Abstract
The drug resistant bacteria pose a severe threat to human health. The increasing resistance of those pathogens to traditional antibacterial therapy renders the identification of new antibacterial agents with novel antibacterial mechanisms an urgent need. In this study, a series of (2S)-N-substituted-1-[(formyhydroxyamino)methyl]-1-oxohexyl]-2-oxazolidinecarboxamides were designed, synthesized and evaluated for in vitro antibacterial activity. Most of these compounds displayed good activities against Gram-positive organisms comparable to reference agent LBM-415.
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Affiliation(s)
- Linliang Yu
- State Key Lab of New Drug & Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, Shanghai, PR China.
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7
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Chaume G, Barbeau O, Lesot P, Brigaud T. Synthesis of 2-trifluoromethyl-1,3-oxazolidines as hydrolytically stable pseudoprolines. J Org Chem 2010; 75:4135-45. [PMID: 20481551 DOI: 10.1021/jo100518t] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Trifluoromethyl group containing oxazolidines (Fox) are conveniently synthesized by condensation of serine esters with trifluoroacetaldehyde hemiacetal or trifluoroacetone. These oxazolidines can undergo N-acylation and amidification reactions and are completely configurationally and hydrolytically stable. Therefore, they can be considered as highly valuable proline surrogates (Tfm-pseudoprolines).
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Affiliation(s)
- Grégory Chaume
- Laboratoire SOSCO, Université de Cergy-Pontoise, 5 Mail Gay-Lussac, Neuville sur Oise, 95000 Cergy-Pontoise cedex, France
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8
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Bentabed-Ababsa G, Derdour A, Roisnel T, Sáez JA, Pérez P, Chamorro E, Domingo LR, Mongin F. A combined experimental and theoretical study of the polar [3 + 2] cycloaddition of electrophilically activated carbonyl ylides with aldehydes and imines. J Org Chem 2010; 74:2120-33. [PMID: 19199802 DOI: 10.1021/jo8027104] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Numerous 2,5-diaryl-1,3-dioxolane-4,4-dicarbonitriles and 2,4-diphenyl-1,3-oxazolidine-5,5-dicarbonitriles have been synthesized by [3 + 2] cycloaddition reactions between carbonyl ylides generated from epoxides and aldehydes or imines. In contrast to the use of aldehydes (3,4,5-trimethoxybenzaldehyde, piperonal, 1-naphthaldehyde, indole-3-carboxaldehyde, furan-2-carboxaldehyde, and thiophene-2-carboxaldehyde), the reactions performed with imines (N-(phenylmethylene)methanamine, N-(1,3-benzodioxol-5-ylmethylene)propylamine, N-(1,3-benzodioxol-5-ylmethylene)butylamine, and N-(1,3-benzodioxol-5-ylmethylene)benzylamine) proceed diastereoselectively. The effect of microwave irradiation on the outcome of the reaction was studied. The mechanism of these [3 + 2] cycloaddition reactions has been theoretically investigated using DFT methods. These cycloadditions, which have one-step mechanisms, consist of the nucleophilic attack of the aldehyde oxygen or imine nitrogen on the carbonyl ylide. For the reaction with aldehydes, a back-donation effect is responsible for the unexpected reverse charge transfer found at the transition structure. The analysis of the reactivity indexes indicates that the large electrophilic character of the carbonyl ylides induces them to act as strong electrophiles in these polar [3 + 2] cycloaddition reactions.
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Affiliation(s)
- Ghenia Bentabed-Ababsa
- Chimie et Photonique Moléculaires, UMR 6510 CNRS, Université de Rennes 1, Campus Scientifique de Beaulieu, 35042 Rennes, France
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9
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Maurer J, Linseis M, Sarkar B, Schwederski B, Niemeyer M, Kaim W, Záliš S, Anson C, Zabel M, Winter RF. Ruthenium Complexes with Vinyl, Styryl, and Vinylpyrenyl Ligands: A Case of Non-innocence in Organometallic Chemistry. J Am Chem Soc 2007; 130:259-68. [DOI: 10.1021/ja075547t] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Jörg Maurer
- Contribution from the Institut für Anorganische Chemie der Universität Regensburg, D-93040 Regensburg, Germany, Institut für Anorganische Chemie der Universität Stuttgart, D-70563 Stuttgart, Germany, J. Heyrovský Institute of Physical Chemistry v.v.i., Academy of Sciences of the Czech Republic, Czech Republic, Institut für Anorganische Chemie der Universität Karlsruhe, D-76131 Karlsruhe, Germany
| | - Michael Linseis
- Contribution from the Institut für Anorganische Chemie der Universität Regensburg, D-93040 Regensburg, Germany, Institut für Anorganische Chemie der Universität Stuttgart, D-70563 Stuttgart, Germany, J. Heyrovský Institute of Physical Chemistry v.v.i., Academy of Sciences of the Czech Republic, Czech Republic, Institut für Anorganische Chemie der Universität Karlsruhe, D-76131 Karlsruhe, Germany
| | - Biprajit Sarkar
- Contribution from the Institut für Anorganische Chemie der Universität Regensburg, D-93040 Regensburg, Germany, Institut für Anorganische Chemie der Universität Stuttgart, D-70563 Stuttgart, Germany, J. Heyrovský Institute of Physical Chemistry v.v.i., Academy of Sciences of the Czech Republic, Czech Republic, Institut für Anorganische Chemie der Universität Karlsruhe, D-76131 Karlsruhe, Germany
| | - Brigitte Schwederski
- Contribution from the Institut für Anorganische Chemie der Universität Regensburg, D-93040 Regensburg, Germany, Institut für Anorganische Chemie der Universität Stuttgart, D-70563 Stuttgart, Germany, J. Heyrovský Institute of Physical Chemistry v.v.i., Academy of Sciences of the Czech Republic, Czech Republic, Institut für Anorganische Chemie der Universität Karlsruhe, D-76131 Karlsruhe, Germany
| | - Mark Niemeyer
- Contribution from the Institut für Anorganische Chemie der Universität Regensburg, D-93040 Regensburg, Germany, Institut für Anorganische Chemie der Universität Stuttgart, D-70563 Stuttgart, Germany, J. Heyrovský Institute of Physical Chemistry v.v.i., Academy of Sciences of the Czech Republic, Czech Republic, Institut für Anorganische Chemie der Universität Karlsruhe, D-76131 Karlsruhe, Germany
| | - Wolfgang Kaim
- Contribution from the Institut für Anorganische Chemie der Universität Regensburg, D-93040 Regensburg, Germany, Institut für Anorganische Chemie der Universität Stuttgart, D-70563 Stuttgart, Germany, J. Heyrovský Institute of Physical Chemistry v.v.i., Academy of Sciences of the Czech Republic, Czech Republic, Institut für Anorganische Chemie der Universität Karlsruhe, D-76131 Karlsruhe, Germany
| | - Stanislav Záliš
- Contribution from the Institut für Anorganische Chemie der Universität Regensburg, D-93040 Regensburg, Germany, Institut für Anorganische Chemie der Universität Stuttgart, D-70563 Stuttgart, Germany, J. Heyrovský Institute of Physical Chemistry v.v.i., Academy of Sciences of the Czech Republic, Czech Republic, Institut für Anorganische Chemie der Universität Karlsruhe, D-76131 Karlsruhe, Germany
| | - Chris Anson
- Contribution from the Institut für Anorganische Chemie der Universität Regensburg, D-93040 Regensburg, Germany, Institut für Anorganische Chemie der Universität Stuttgart, D-70563 Stuttgart, Germany, J. Heyrovský Institute of Physical Chemistry v.v.i., Academy of Sciences of the Czech Republic, Czech Republic, Institut für Anorganische Chemie der Universität Karlsruhe, D-76131 Karlsruhe, Germany
| | - Manfred Zabel
- Contribution from the Institut für Anorganische Chemie der Universität Regensburg, D-93040 Regensburg, Germany, Institut für Anorganische Chemie der Universität Stuttgart, D-70563 Stuttgart, Germany, J. Heyrovský Institute of Physical Chemistry v.v.i., Academy of Sciences of the Czech Republic, Czech Republic, Institut für Anorganische Chemie der Universität Karlsruhe, D-76131 Karlsruhe, Germany
| | - Rainer F. Winter
- Contribution from the Institut für Anorganische Chemie der Universität Regensburg, D-93040 Regensburg, Germany, Institut für Anorganische Chemie der Universität Stuttgart, D-70563 Stuttgart, Germany, J. Heyrovský Institute of Physical Chemistry v.v.i., Academy of Sciences of the Czech Republic, Czech Republic, Institut für Anorganische Chemie der Universität Karlsruhe, D-76131 Karlsruhe, Germany
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10
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Kang YK, Park HS. Conformational Preferences of Pseudoproline Residues. J Phys Chem B 2007; 111:12551-62. [DOI: 10.1021/jp074128f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea, and Department of Radiotechnology, Cheju-halla College, Cheju 690-708, Republic of Korea
| | - Hae Sook Park
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea, and Department of Radiotechnology, Cheju-halla College, Cheju 690-708, Republic of Korea
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11
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Solid Phase Synthesis of Phosphopeptides Incorporating 2,2-Dimethyloxazolidine Pseudoproline Analogs: Evidence for trans Leu-Pro Peptide Bonds in Stat3 Inhibitors. Int J Pept Res Ther 2007. [DOI: 10.1007/s10989-007-9099-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Feller SM, Tuchscherer G, Voss J. High affinity molecules disrupting GRB2 protein complexes as a therapeutic strategy for chronic myelogenous leukaemia. Leuk Lymphoma 2003; 44:411-27. [PMID: 12688310 DOI: 10.1080/1042819021000037930] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Chronic myelogenous leukaemia (CML) is one of the most intensively studied human malignancies. It has been the focus of major efforts to develop potent drugs for several decades, but until recently cure rates remained low. A breakthrough in CML therapy was very likely accomplished with the clinical introduction of STI-571 [imatinib mesylate; Gleevec (USA); Glivec (other countries)] in 2000/2001. Despite the hope that STI-571 has generated for many CML patients, development of resistance to this drug is already apparent in some cases, especially if the CML is diagnosed in its later stages. Therefore, novel drugs which can be used alone or in combination with STI-571 are highly desirable. This review briefly summarises the current understanding and therapy of CML and then discusses in more detail basic laboratory research that attempts to target Grb2, an adaptor protein known to directly interact with the Bcr portion of the Bcr-Abl fusion protein. Blocking the binding of Grb2 to the GDP-releasing protein SoS is well known to abrogate the activation of the GTPase Ras, a major driving force of the central mitogenic (MAP kinase) pathway. Additional Grb2 effector proteins may also contribute to the proliferation-inhibiting effects observed upon uncoupling Grb2 from its downstream signalling system. Since Grb2 is a known signal transducer for several major human oncogenes, this approach may have applications for a wider range of human cancers.
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MESH Headings
- Adaptor Proteins, Signal Transducing
- Animals
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Benzamides
- Drug Design
- Enzyme Inhibitors/administration & dosage
- Enzyme Inhibitors/therapeutic use
- Fatty Acids, Unsaturated/pharmacology
- Forecasting
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/metabolism
- GRB2 Adaptor Protein
- Humans
- Imatinib Mesylate
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Macromolecular Substances
- Mice
- Neoplasm Proteins/antagonists & inhibitors
- Neoplasm Proteins/metabolism
- Peptide Fragments/metabolism
- Phosphatidylinositol 3-Kinases/physiology
- Piperazines/administration & dosage
- Piperazines/therapeutic use
- Protein Binding/drug effects
- Proteins/antagonists & inhibitors
- Proteins/chemistry
- Proteins/metabolism
- Pyrimidines/administration & dosage
- Pyrimidines/therapeutic use
- Signal Transduction/drug effects
- Son of Sevenless Proteins/physiology
- Structure-Activity Relationship
- Transcription Factors/physiology
- ras Proteins/antagonists & inhibitors
- src Homology Domains
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Affiliation(s)
- Stephan M Feller
- Cell Signalling Group, Molecular Oncology Laboratory, Cancer Research UK, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK. stephan.feller@.cancer.org.uk
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13
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Guichou JF, Patiny L, Mutter M. Pseudo-prolines (ΨPro): direct insertion of ΨPro systems into cysteine containing peptides. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)00755-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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