Structure-Based Design of a Novel Series of Nonpeptide Ligands That Bind to the pp60<sup>src</sup> SH2 Domain

Lunney, Elizabeth A.; Para, Kimberly S.; Rubin, John R.; Humblet, Christine; Fergus, James H.; Marks, and James S.; Sawyer, Tomi K.

doi:10.1021/ja971794t

Cited by 61 publications

(45 citation statements)

References 30 publications

(37 reference statements)

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“…In this regard, a reported nonpeptide template developed for the Src SH2 domain (13,14) provided a prototype for the structurebased design of our bicyclic template (see below). Relative to the nonpeptide 3 (Fig.…”

Section: Resultsmentioning

confidence: 99%

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Structure-based design of an osteoclast-selective, nonpeptide Src homology 2 inhibitor with in vivo antiresorptive activity

Shakespeare¹,

Yang²,

Bohacek³

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

137

102

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Targeted disruption of the pp60 src (Src) gene has implicated this tyrosine kinase in osteoclast-mediated bone resorption and as a therapeutic target for the treatment of osteoporosis and other bone-related diseases. Herein we describe the discovery of a nonpeptide inhibitor (AP22408) of Src that demonstrates in vivo antiresorptive activity. Based on a cocrystal structure of the noncatalytic Src homology 2 (SH2) domain of Src complexed with citrate [in the phosphotyrosine (pTyr) binding pocket], we designed 3,4-diphosphonophenylalanine (Dpp) as a pTyr mimic. In addition to its design to bind Src SH2, the Dpp moiety exhibits bone-targeting properties that confer osteoclast selectivity, hence minimizing possible undesired effects on other cells that have Src-dependent activities. The chemical structure AP22408 also illustrates a bicyclic template to replace the post-pTyr sequence of cognate Src SH2 phosphopeptides such as Ac-pTyr-Glu-Glu-Ile (1). An x-ray structure of AP22408 complexed with Lck (S164C) SH2 confirmed molecular interactions of both the Dpp and bicyclic template of AP22408 as predicted from molecular modeling. Relative to the cognate phosphopeptide, AP22408 exhibits significantly increased Src SH2 binding affinity (IC50 ‫؍‬ 0.30 M for AP22408 and 5.5 M for 1). Furthermore, AP22408 inhibits rabbit osteoclast-mediated resorption of dentine in a cellular assay, exhibits bone-targeting properties based on a hydroxyapatite adsorption assay, and demonstrates in vivo antiresorptive activity in a parathyroid hormone-induced rat model.

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Section: Resultsmentioning

confidence: 99%

“…To date, most Src SH2 inhibitors have been phosphopeptides (12) or peptidomimetics (13,14), which incorporate pTyr or pTyr-like mimics. pTyr-containing inhibitors suffer from poor transport properties and are rapidly degraded by phosphatases.…”

mentioning

confidence: 99%

Structure-based design of an osteoclast-selective, nonpeptide Src homology 2 inhibitor with in vivo antiresorptive activity

Shakespeare¹,

Yang²,

Bohacek³

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

137

102

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“…Researchers at ARIAD have conducted structure-based design studies examining various types of scaffolds for Src SH2 inhibitors, including ureido-type peptide mimetics [223], di-substituted thiazoles [224], oxazoles [220] and benzamide [225]. Notably, X-ray crystallography revealed the benzamide template forms hydrogen bonds with LysßDö, displacing water molecules found in the previous X-ray structure.…”

Section: Importance Of the Scaffoldmentioning

confidence: 99%

“…For example, inhibitors containing various scaffolds were docked onto the Src SH2 domain, using the pTyr residue as an anchor based on the known binding mode of poYEEl high-affinity peptides, leading to the choice of benzamide scaffolds [225]. However, subsequent X-ray crystal structures demonstrated significant differences in the details of the actual mode of binding compared to modeling predictions.…”

Section: Structure-based Design and Binding Modementioning

confidence: 99%

Probing the Tyrosine Phosphorylation State in Breast Cancer by Src Homology 2 Domain Binding

Mayer¹

2004

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Pubhc reporting burden for Ms collection of information is estimated to average 1 hour per response, Including the lime for reviewing instructions, searching existing data sources gathering and maintaininn the data neededI andcompletingland renewing this collection of information. Send comments regarding this burden estimate or any other asped of this collection of InfoirnaBorf iffsSÄto" educing this burden to Washington Headquarters AUTHOR(S)Bruce J. Mayer PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES)University Abstract (Maximum 200 Words) (abstract should contain no proprietary or confidential information)Improved molecular diagnostic methods that can classify tumors and predict their response to therapy have enormous potential to improve the effectiveness breast cancer treatments. The overall goal of this project is to develop a novel molecular diagnostic method, i: termed SH2 profiling, that can classify cell samples based on their global protein tyrosine phosphorylation state. The first aim is to use an existing SH2 profiling method, based on far-Western blotting, to analyze fresh surgical breast cancer samples. The second aim is to o develop a more high-throughput quantitative reversed-phase SH2 profiling format, and test its usefulness in classifying breast cancer samples. The third aim is to develop histochemical SH2 profiling methods that can be used to analyze archived, formalin-fixed tissue sections, and perform pilot retrospective studies to determine whether SH2 binding patterns have potential prognostic value. In the past year we have made great progress in developing the reversed-phase array and histochemical SH2 profiling formats, and results suggest that these quantitative methods will be useful in classifying breast cancer samples. In the coming year, once HSRRB approval for use of human samples is secured, we will begin to apply these new methods to the analysis of actual breast cancer specimens. SUBJECT TERMS Conclusions 9References 10 Appendices 10-93Mayer, B.J. INTRODUCTIONThe focus is this study is to test whether a novel molecular diagnostic approach, SH2 profiling, can serve as a useful prognostic tool to classify breast cancer. SH2 domains are small protein modules that bind specifically to tyrosine phosphorylated peptides. These domains play an important role in normal signal transduction, mediating the formation of multiprotein complexes in response to changes in tyrosine phosphorylation [1,2]. There are ~116 SH2 domains in the human genome, and different SH2 domains recognize different tyrosine phosphorylated proteins. SH2 profiling is a method in which a battery SH2 domain probes is used to provide a snapshot of the global state of tyrosine phosphorylation in a cell sample [3,4]. Different breast cancers are likely to have different patterns of tyrosine phosphorylation, reflecting differences in the signal transduction pathways active in the tumor, and thus SH2 profiling has the potential to provide a biologically relevant means to classify these tumors. In this project we prop...

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“…tures of the target protein complexed with a modified pTyr containing peptidomimetic 11 as well as a de novo designed nonpeptide 12 (vide infra, section on SH2 domain drug discovery).…”

Section: Figurementioning

confidence: 99%

Src homology-2 domains: Structure, mechanisms, and drug discovery

Sawyer¹

1998

Biopolymers

Self Cite

126

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Src homology‐2 (SH2) domains and their associated catalytic or noncatalytic proteins constitute critical signal transduction targets for drug discovery. Such SH2 proteins are found in the regulation of a number of cellular processes, including growth, mitogenesis, motility, metabolism, immune response, and gene transcription. From the relationship of tyrosine phosphorylation and intracellular regulation by protein–tyrosine kinases (PTKs) and protein–tyrosine phosphatases (PTPs), the dynamic and reversible binding interactions of SH2 domain containing proteins with their cognate phosphotyrosine (pTyr) containing proteins provide a third dimensionality to the orchestration of signal transduction pathways that exist as a result of pTyr formation, degradation, and molecular recognition events. This review highlights several key research achievements impacting our current understanding of SH2 structure, mechanisms, and drug discovery that underlie the role(s) of SH2 domains in signal transduction processes, cellular functions, and disease states. © 1998 John Wiley & Sons, Inc. Biopoly 47: 243–261, 1998

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Structure-Based Design of a Novel Series of Nonpeptide Ligands That Bind to the pp60^src SH2 Domain

Cited by 61 publications

References 30 publications

Structure-based design of an osteoclast-selective, nonpeptide Src homology 2 inhibitor with in vivo antiresorptive activity

Structure-based design of an osteoclast-selective, nonpeptide Src homology 2 inhibitor with in vivo antiresorptive activity

Probing the Tyrosine Phosphorylation State in Breast Cancer by Src Homology 2 Domain Binding

Src homology-2 domains: Structure, mechanisms, and drug discovery

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Structure-Based Design of a Novel Series of Nonpeptide Ligands That Bind to the pp60src SH2 Domain

Cited by 61 publications

References 30 publications

Structure-based design of an osteoclast-selective, nonpeptide Src homology 2 inhibitor with in vivo antiresorptive activity

Structure-based design of an osteoclast-selective, nonpeptide Src homology 2 inhibitor with in vivo antiresorptive activity

Probing the Tyrosine Phosphorylation State in Breast Cancer by Src Homology 2 Domain Binding

Src homology-2 domains: Structure, mechanisms, and drug discovery

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Structure-Based Design of a Novel Series of Nonpeptide Ligands That Bind to the pp60^src SH2 Domain