Protein Kinases: Structure-Guided Drug Discovery

X-ray crystallography and solution NMR spectroscopy are playing ever increasing roles in the drug discovery process. Both technologies have matured to the point where they are being used for screening of fragment (or scaffold) libraries to identify privileged scaffolds that bind to the drug target for the desired inhibitory effect. Once scaffold starting points are identified, these same structural methods, combined with biophysical studies and biochemical and cellular assays, guide chemical elaboration of the scaffolds to optimize potency, achieve the desired selectivity, and build in favorable drug-like properties.

This strategy has proved particularly useful for oncology drug discovery programs targeting protein kinases, for which selectivity represents a particularly significant challenge. Many of the protein kinase inhibitors now in the clinic have turned out to be promiscuous in inhibiting a variety of "off-target" kinases that may be responsible for producing undesirable side effects. Application of structural biology techniques to lead identification and lead optimization should enable more robust discovery of highly selective inhibitors.

Moreover, recent advances in high-throughput X-ray crystallography of membrane proteins hold significant promise that structure-guided approaches will soon find utility in developing small molecule inhibitors of proteins not typically amenable to crystallization. Although these techniques have been typically applied to kinase targets in cancer, they may also be used for protein targets associated with central nervous system, cardiovascular, and other disorders. At this symposium leading scientists from academe and the pharmaceutical/biotech industry will discuss recent advances and future challenges of this burgeoning field.

The BPDG at the New York Academy of Sciences represents a diverse group of scientists and others with an interest in biochemistry, molecular biology, biomedical research, and related areas. Members are from pharmaceutical and biotechnology companies, and university and medical center research facilities across the Eastern United States. The group also serves as the Biochemical Topical Group for the American Chemical Society's New York Section. The purpose of the BPDG is to bring together diverse institutions and communities, industrial and academic, to share new and relevant information at the frontiers of research and development.

Organizers: Stephen K. Burley, Eli Lilly and Company and George B. Zavoico, Westport Capital Markets, LLC

Speakers: Susan Taylor, University of California, San Diego; Vincent Stoll, Abbott Laboratories, Inc.; Harren Jhoti, Astex Therapeutics, Inc.; Stephen Burley, Eli Lilly and Co.

Abstracts

Protein Kinases: Dynamic Targets For Drug Design
Susan Taylor, University of California, San Diego

cAMP-dependent Protein Kinase (PKA) continues to serve as a prototype for the protein kinase superfamily. Our understanding of the catalytic subunit has allowed us not only to elucidate the roles of many key active site and allosteric residues but also led us to discover non-linear hydrophobic motifs that define the architectural framework for this enzyme family. The catalytic and regulatory spines anchored to the buried hydrophobic F-Helix provides a framework for understanding both catalysis and regulation. It also provides a strategy for therapeutic design. The catalytic subunits of PKA are inhibited by regulatory (R) subunit dimers in the absence of cAMP, while in the presence of cAMP the R-subunits dissociate thereby unleashing the catalytic activity. Solving structures of holoenzyme complexes containing both R and C-subunits revealed a dramatic cAMP-induced rearrangement of the R-subunit structure that was not anticipated previously. This allowed us to elucidate the allosteric mechanism of PKA regulation by cAMP, providing an entirely new strategy for therapeutic intervention. Another level of regulation of PKA activity is provided by a family of A Kinase Anchoring Proteins (AKAPs) that localize PKA in an isoform-specific manner to different cell compartments. AKAPs serve as polyvalent scaffolds for multiple proteins and orchestrate cAMP signaling at specific sites. The AKAP docking site provides another mechanism for disrupting signaling of PKA isoforms.
Support for this work was provided by NIH DK54441, GM19301, and GM34921

Structure-based Drug Design on Kinase Targets: Key Lessons Learned
Vincent Stoll, Abbott Laboratories, Inc.

This presentation will provide an overview of the challenges faced in drug discovery on kinase targets, common problems, the impact of structure-based drug design and the lessons learned from finding solutions. The challenges of selectivity, toxicity, pharmacokinetic properties and novelty will be reviewed and how structural information can be used to address these issues. In addition, the difficulties in executing structure based drug design on kinase targets such as, understanding kinase structure and function, obtaining kinase structures and the use and value of surrogates to support chemistry programs will be discussed

Fragment-Based Drug Discovery
Harren Jhoti, Astex Therapeutics, Inc.

Fragment-based discovery has recently emerged as a new approach for the generation of novel small molecule therapeutic agents and involves the use of biophysical techniques to screen fragment libraries. The resulting "fragment hits" are then rapidly optimized using iterative cycles of medicinal chemistry and structure-based drug design. This approach was used to discovery a CDK inhibitor (AT7519) and an Aurora kinase inhibitor (AT9283) which are both now being tested in clinical trials as potential anti-cancer therapies.

SGX523 is an Exquisitely Selective ATP-Completive Inhibitor of the MET Receptor Tyrosine Kinase
Stephen Burley, Eli Lilly and Co.

We describe the potency and selectivity of SGX523 in enzyme assays, its activity in various cell based assays and in tumor models, and the crystal structure of SGX523 bound to MET. We also describe a structural bioinformatics analysis to explain the selectivity.