Meeting report: targeting the kinome--20 years of tyrosine kinase inhibitor research in Basel

Phosphoproteomics by mass spectrometry: insights, implications, applications and limitations

Phosphorylation of proteins is a predominant, reversible post-translational modification. It is central to a wide variety of physiological responses and signaling mechanisms. Recent advances have allowed the global scope of phosphorylation to be addressed by mass spectrometry using phosphoproteomic approaches. In this perspective, we discuss four aspects of phosphoproteomics: the insights and implications from recently published phosphoproteomic studies and the applications and limitations of current phosphoproteomic strategies. Since approximately 50,000 known phosphorylation sites do not yet have any ascribed function, we present our perspectives on a major function of protein phosphorylation that may be of predictive value in hypothesis-based investigations. Finally, we discuss strategies to measure the stoichiometry of phosphorylation in a proteome-wide manner that is not provided by current phosphoproteomic approaches.

BlockMaster: partitioning protein kinase structures using normal-mode analysis

Protein kinases are key signaling enzymes which are dysregulated in many health disorders and therefore represent major targets of extensive drug discovery efforts. Their regulation in the cell is exerted via various mechanisms, including control of the 3D conformation of their catalytic domains. We developed a procedure, BlockMaster, for partitioning protein structures into semirigid blocks and flexible regions based on residue-residue correlations calculated from normal modes. BlockMaster provided correct partitioning into domains and subdomains of several test set proteins for which documented expert annotation of subdomains exists. When applied to representative structures of protein kinases, BlockMaster identified semirigid blocks within the traditional N-terminal and C-terminal lobes of the kinase domain. In general, the block regions had elevated helical content and reduced, but significant, coil content compared to the nonblock (flexible) regions. The specificity-determining regions, previously used to derive inhibitory peptides, were found to be more flexible in the tyrosine kinases than in serine/threonine kinases. Two blocks were identified which spanned both lobes. The first, which we termed the "pivot" block, included the alphaC-beta4 loop in the N-terminal lobe and part of the activation loop in the C-terminal lobe and appeared in both the active and inactive conformations of the kinases. The second, which we termed the "loop" block, differed between the active and inactive conformations. In the structures of active kinases, this block included part of the activation loop in the C-terminal lobe and the alphaC helix in the N-terminal lobe, representing a known interaction that stabilizes the active conformation. In the inactive structures, this block included G loop residues instead of the alphaC residues. This novel inactive "loop" block may stabilize the inactive conformation and thus downregulate kinase activity.

Targeted therapies: the rare cancer paradigm

This review analyzes the state of the art of targeted therapies for several tumors, starting from the paradigmatic example of Imatinib treatment in chronic myelogenous leukemia (CML). We discuss how rare tumors can be models for various mechanisms of receptor tyrosine kinase (RTK) activation, and provide the opportunity to develop new therapies also for more common cancer types. We discuss the activation of the downstream RTK effectors as further targets for therapies in colorectal cancer. Finally, we highlight how a novel multidimensional approach which adds an in silico dimension to the in vitro and in vivo approach, can predict clinical results.

Peptidic modulators of protein-protein interactions: progress and challenges in computational design

With the decline in productivity of drug-development efforts, novel approaches to rational drug design are being introduced and developed. Naturally occurring and synthetic peptides are emerging as novel promising compounds that can specifically and efficiently modulate signaling pathways in vitro and in vivo. We describe sequence-based approaches that use peptides to mimic proteins in order to inhibit the interaction of the mimicked protein with its partners. We then discuss a structure-based approach, in which protein-peptide complex structures are used to rationally design and optimize peptidic inhibitors. We survey flexible peptide docking techniques and discuss current challenges and future directions in the rational design of peptidic inhibitors.

Treatment for chronic myelogenous leukemia: the long road to imatinib

The scientists of today have become accustomed to the extremely rapid pace of progress in the biomedical sciences spurred on by the discovery of recombinant DNA and the advent of automated DNA sequencing and PCR, with progress usually being measured in months or years at most. What is often forgotten, however, are the many prior advances that were needed to reach our present state of knowledge. Here I illustrate this by discussing the scientific discoveries made over the course of the past century and a half that ultimately led to the recent successful development of drugs, particularly imatinib mesylate, to treat chronic myelogenous leukemia.