The development of protein kinase substrate biomarkers to assess the specificities ofkinase inhibitors in vivo

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We will accumulate huge datasets that record the signatures of those target proteins
that are phosphorylated on specific serine and threonine residues, and captured by
binding to 14-3-3s, in response to many extracellular stimuli and drugs. Creating a
searchable system to mine these datasets will identify new mechanisms underlying
diseases and drug actions, and new biomarkers reflecting which signalling pathways
are operational in cell cultures, and healthy and diseased tissues, and how they change
in response to drugs. Based on our initial data, the major pharmaceutical companies
with whom we collaborate in the Division of Signal Transduction Therapy (DSTT) are
excited by the potential for these methods to help in prioritizing candidate drugs for
human clinical trials. In essence, we will be able to determine whether a pre-clinical
drug specifically blocks the phosphorylation of the protein kinase that the drug was
designed to inhibit, and/or also affects other signalling pathways in ways that may
interfere with drug efficacy or cause unacceptable side effects. Two companysponsored
postdoctoral positions have therefore been earmarked to develop the
protein/phosphopeptide purification and analysis aspects of this work. However, our
recent experimental success means that data analysis is fast becoming rate-limiting:
both in the peptide-searching/programming steps of mass spectrometry, and in
tracking, cross-referencing and mining the large datasets generated by each
experiment. This application is therefore a request for one programmer/analyst and
one bioinformatician to underpin this programme, providing matching support for the
two postdoctoral scientists funded by the pharmaceutical industry. This support will
enable us to provide the information required by the companies with the required high
throughput, and create robust systems that will help us develop new insights into
signalling pathways, diseases and drugs. The portends are high for this project making
a major impact, due to the timely convergence of advances in the MRC Protein
Phosphorylation Unit's research, technological improvements in mass spectrometry,
and the major collaboration with pharma. Success will be measured by the ability of
our methods to accelerate new drug discovery programmes, generation of user-friendly
data systems that can be interrogated to track how specific targets are (de)regulated in
health and disease, the filing of patents protecting new drug targets identified during
the work, the training of researchers at the interface of biochemistry and
bioinformatics, and the publication of high quality papers.