Design, Synthesis, and Cocrystal Structure of a Nonpeptide Src SH2 Domain Ligand

Plummer, Mark S.; Holland, Debra R.; Shahripour, Aurash; Lunney, Elizabeth A.; Fergus, James H.; Marks, James S.; McConnell, Patrick I.; Mueller, W. Tom; Sawyer, Tomi K.

doi:10.1021/jm970402q

Cited by 52 publications

(56 citation statements)

References 31 publications

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“…A cyclic peptide containing a simple Tyr in place of Tyr(P) has been shown to inhibit Grb2 SH2 domain at 20 M potency (22), suggesting that establishment of stronger interactions to other regions of the binding pocket is possible. This crystal structure provides a starting point for the design of such carboxylatecontaining inhibitors of the p56 lck and other SH2 domains, preferably with nonpeptide moieties at the other positions (9). The carboxymethyl group as a phosphate replacement could also prove useful in the development of inhibitors against other protein targets that normally recognize phosphate groups.…”

Section: Discussionmentioning

confidence: 99%

Carboxymethyl-phenylalanine as a Replacement for Phosphotyrosine in SH2 Domain Binding

Tong

Warren

Lukas

et al. 1998

Journal of Biological Chemistry

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The crystal structure of human p56 lck SH2 domain in complex with an inhibitor containing the singly charged p-(carboxymethyl)phenylalanine residue (cmF) as a phosphotyrosine (Tyr(P) or pY) replacement has been determined at 1.8 Å resolution. The binding mode of the acetyl-cmF-Glu-Glu-Ile (cmFEEI) inhibitor is very similar to that of the pYEEI inhibitor, confirming that the cmFEEI inhibitor has a similar mechanism of SH2 domain inhibition despite its significantly reduced potency. Observed conformational differences in the side chain of the cmF residue can be interpreted in terms of maintaining similar interactions with the SH2 domain as the Tyr(P) residue. The crystal structure of the free p56 lck SH2 domain has been determined at 1.9 Å resolution and shows an open conformation for the BC loop and an open phosphotyrosine binding pocket, in contrast to earlier studies on the src SH2 domain that showed mostly closed conformation. The structural information presented here suggests that the carboxymethyl-phenylalanine residue may be a viable Tyr(P) replacement and represents an attractive starting point for the design and development of SH2 domain inhibitors with better pharmaceutical profiles.Protein tyrosine phosphorylation is among the first intracellular events in the transduction of many external signals into the cell. The phosphotyrosyl (Tyr(P) or pY) 1 proteins can affect many biological processes by interacting with receptors that recognize the Tyr(P) and its neighboring residues. The src homology 2 (SH2) domain is a specific recognition module for phosphotyrosyl peptides and proteins (1) and has been identified from a variety of enzymes and proteins in general. Individual SH2 domains appear to have a good degree of selectivity toward the sequences of phosphotyrosyl peptides (2). Recognition of a phosphotyrosyl protein by the proper SH2 domain is an important step in many signal transduction processes. Therefore, SH2 domains are attractive targets for the development of therapeutic agents against various human diseases (3).Phosphotyrosyl peptides containing 4 -6 residues can bind SH2 domains with high affinity (2). However, it is unlikely that inhibitors containing the phosphotyrosyl residue can become successful therapeutic agents. This is due both to the lability of the phosphate group toward hydrolysis and to its doubly negative charge at physiological pH, which significantly reduces cell permeability. Therefore, a phosphate replacement that is metabolically stable and possesses lesser (or preferably no) charge at physiological pH may be a crucial component for the development of SH2 domain inhibitors. Most efforts to date have used phosphonates, difluorophosphonates, dicarboxylic acids, and prodrugs as phosphate replacements (4 -10), but these still contain at least two negative charges. The carboxymethyl functionality is an attractive phosphate replacement because it is metabolically stable and contains only a single negative charge. The carboxymethyl-phenylalanyl (cmF) residue was used as a mimetic fo...

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Section: Discussionmentioning

confidence: 99%

Carboxymethyl-phenylalanine as a Replacement for Phosphotyrosine in SH2 Domain Binding

Tong

Warren

Lukas

et al. 1998

Journal of Biological Chemistry

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“…The crystal structure of protein tyrosine kinase pp60 c-src (PDB code: 1skj), 23 which is a c-src tyrosine kinase of Rous sarcoma virus, was used in this docking study. The 3D structure of 1skj was reported by Plummer et al 23 …”

Section: Docking Studymentioning

confidence: 99%

Antitumor studies. Part 1: Design, synthesis, antitumor activity, and AutoDock study of 2-deoxo-2-phenyl-5-deazaflavins and 2-deoxo-2-phenylflavin-5-oxides as a new class of antitumor agents

Ali

Tomita

Akaho

et al. 2007

Bioorganic & Medicinal Chemistry

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Abstract--Novel 2-deoxo-2-phenyl-5-deazaflavins and 2-deoxo-2-phenylflavin-5-oxides were prepared as a new class of antitumor agents and showed significant antitumor activities against NCI-H 460, HCT 116, A 431, CCRF-HSB-2, and KB cell lines. In vivo investigation, 2-deoxo-10-methyl-2-phenyl-5-deazaflavin exhibited the effective antitumor activity against A 431 human adenocarcinoma cells transplanted subcutaneously into nude mouse. Furthermore, AutoDock study has been done by binding of the flavin analogs into PTK pp60 c-src , where a good correlation between their IC 50 and AutoDock binding free energy was exhibited. In particular, 2-deoxo-2-phenylflavin-5-oxides exhibited the highest potential binding affinity within the binding pocket of PTK.

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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%

“…However, subsequent X-ray crystal structures demonstrated significant differences in the details of the actual mode of binding compared to modeling predictions. These differences suggest difficulties in de novo prediction of binding mode by computational modeling, and emphasize the importance of confirmation by structural analysis for each SH2 inhibitor [223,227]. Such structural studies sometimes reveal new and unexpected binding modes, which in turn provide valuable information for further inhibitor design.…”

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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Design, Synthesis, and Cocrystal Structure of a Nonpeptide Src SH2 Domain Ligand

Cited by 52 publications

References 31 publications

Carboxymethyl-phenylalanine as a Replacement for Phosphotyrosine in SH2 Domain Binding

Carboxymethyl-phenylalanine as a Replacement for Phosphotyrosine in SH2 Domain Binding

Antitumor studies. Part 1: Design, synthesis, antitumor activity, and AutoDock study of 2-deoxo-2-phenyl-5-deazaflavins and 2-deoxo-2-phenylflavin-5-oxides as a new class of antitumor agents

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

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