Immediately preceding Structure-Based Drug Design, June 15-16

Day 3

Wednesday, June 14

7:45am Morning Coffee 

8:10 Chairperson's Opening Remarks

8:15 Building an Integrated Global Platform for Kinase Selectivity Screening
Dr. Ajith Kamath, Associate Director Discovery Technology Center, Discovery Technology Center, Pfizer Inc. 
This talk will focus on the strategies employed for building an integrated kinase selectivity screening platform to support Pfizer Global Research & Development. These strategies include those employed for reagent sourcing and characterization; assay development; screening platform; data analysis and reporting; and the use of 3D crystallographic data to guide selectivity. In addition, the importance of harmonized workflows across teams, leveraging internal expertise and strategies for outsourcing both reagent provision and expanded kinase profiling will be highlighted. This talk will be of interest to anyone weighing the costs and benefits of building the infrastructure for in-house selectivity profiling thereby creating a balanced internal/external profiling strategy vs an exclusively outsourced strategy.

8:45 Global Analysis of the Phosphoproteome
Dr. Peter Hornbeck, Senior Scientist and PI, PhosphoSite, Cell Signaling Technology 
PhosphoSite® is an expert-curated bioinformatics resource containing over 10,000 public non-redundant phosphorylation sites on over 4000 human and mouse proteins (Proteomics. 2004 4:1551). I will give an overview of known phosphorylation sites in the human proteome, including analyses of kinase signature motifs, the generation of regulatory phosphorylation cascades from curated information, and evolutionary analysis of phosphorylation sites. Analysis of phosphorylation sites associated with various cancers and discovered through PhosphoScan®, our high-throughput MS/MS platform (Nat Biotechnol. 2005 23:94), will also be discussed.

9:45 Networking Coffee Break

10:15 Use of a Kinase Knowledgebase to Accelerate Drug Discovery: Case Studies 
Dr. Francois Petitet, Director, Life Sciences, Aureus-Pharma, France
Use of a unique knowledge management system focused on kinase inhibitors and the associated in vitro and in vivo pharmacological activities in the research of new drug candidates will be illustrated:
• In the hit identification phase, we will focus on a case study where a highly documented source of knowledge can lead to pertinent biological filters and the identification of valuable training sets of active compounds, for focused library design, virtual screening approaches and predictive tools building. 
• In the optimization phase, we will discuss how knowledge bases can help improve the pharmacological activity at the target, selectivity vs other targets, in vivo activities and safety.

10:45 Computational Chemistry Techniques to Analyse and Exploit Kinase Activity Data
Dr. Richard Ward, Computational Chemist, AstraZeneca, UK
Due to the similarity between kinases, identified inhibitors often show activity across a number of kinases, especially in the early stages of inhibitor development. This knowledge can be used to assist the identification and prioritisation of potential chemical series from an HTS or directed screen. This data can also be used when looking to modify the identified series of interest in lead generation.

11:15 The Structure of Dimeric ROCK I Reveals the Mechanism for Ligand Selectivity 
Dr. Marc Jacobs, Scientist, Vertex Pharmaceuticals Incorporated
ROCK or Rho-associated kinase, a serine/threonine kinase, is an effectors of Rho-dependent signaling, and is involved in actin-cytoskeleton assembly and cell motility and contraction. The ROCK protein consists of several domains: an N-terminal region, a kinase catalytic domain, a coiled-coil domain containing a RhoA binding site, and a pleckstrin homology domain. Here we present the structure of the N-terminal region and the kinase domain. In our structure, two N-terminal regions interact to form a dimerization domain linking two kinase domains together. We also determined the structures of ROCK bound to four different ATP-competitive small-molecules inhibitors (Y-27632, fasudil, hydroxyfasudil, and H-1152P). Subtle differences exist between the ROCK and PKA bound conformations of the inhibitors that suggest that interactions with a single amino acid of the active site (Ala215 in ROCK, Thr183 in PKA) determine the relative selectivity of these compounds. 

11:45 Structural Comparison of p38 Inhibitor-Protein Complexes: A Review of Recent p38 Inhibitors Having Unique Binding Interactions 
Dr. Arthur M. Doweyko, Senior Principal Scientist, Computer-Aided Drug Design, Macromolecular Structure, Pharmaceutical Research Institute, Bristol-Myers Squibb
This review will focus on the comparison of the x-ray crystal structures and binding 
models of the most recent p38 inhibitor-enzyme complexes and the identification of the structural elements and interactions that may be important in providing inhibitor potency and selectivity toward the p38 MAP kinase.

12:15pm Lunch on Your Own (Technology Workshop Sponsorship Available)

1:40 Chairperson's Remarks

1:45 Selectivity of Kinase Inhibitors
Dr. Doris Hafenbradl, Director Biochemical Screening, GPC Biotech, Germany
The presentation will address different tools and technologies for the determination of kinase inhibitor selectvity. It will be shown how critical it is to evaluate selctivity with suitale data. The structural aspects of protein kinases determining the selectivity will also be highlighted. It will be discussed how selectivity data can be used within the lead finding and optimization processes.

2:15 Determinants of Selectivity in Targeting the JAK Family of Kinases for Treatment of Cancer and Inflammatory Disease
Dr. Andrew Wilks, CSO, R&D, Cytopia Research Pty Ltd., Australia
The JAK family of PTKs has four members in the human genome (JAK1, JAK2, JAK3 and TYK2) each of which plays an important role in the intracellular signaling downstream of particular cytokines. A single point mutation in the kinase like domain of JAK2 has recently been linked to a significant proportion of cases of Myeloproliferative Disorders, including Polycythemia Vera (PCV) and Essential Thrombocytemia. Parallel computational approaches to molecular modeling, drug design and in silico screening are being explored to generate potent and highly specific small molecule inhibitors of a number of the JAK family of PTKs. Co-crystallography of these potent and specific JAK inhibitors with the JAK2 kinase domain provides important insights into the feasibility of generating drugs against these important targets.

2:45 Networking Refreshment Break

3:15 In silico ADMET Traffic Lights and PhysChem Scores and Their Application to Kinase Inhibitors 
Dr. Mario Lobell, Computational Chemistry, Bayer HealthCare, Germany
The need for in silico characterization of HTS hit structures as part of a data driven hit selection process is demonstrated. A solution is described in form of the in silico ADMET Traffic Light and PhysChem scoring system. The described in silico system has been extensively validated with Bayer in-house data, literature data and a collection of launched small molecule drugs. The system is applied to examples of kinase inhibitor drugs and drug candidates.

3:45 Structural Basis for the Non-Competitive Inhibition of Human MEK1 
Dr. Jeffrey Ohren, Senior Scientist, Structural Biology Group, Department of Chemistry, Pfizer Global Research & Development
MAP kinase kinase 1 (MEK1) plays an integral role in the formation, progression and survival of tumors, in addition to mediating many inflammatory processes. As a result, MEK1 represents an attractive target for pharmacological intervention in both proliferative and inflammatory diseases. The recent X-ray structure of human MEK1 in a complex with ATP and a non-competitive, small molecule inhibitor provides structural insight into a unique mode of kinase inhibition and may provide a platform for the structure-based design of the next generation of protein kinase inhibitors.

4:15 Insights for Design: Differential Binding of Inhibitors to Active and Inactive CDK2
Dr. Campbell McInnes, Head, SBDG, Cyclacel Ltd., Scotland
The cyclin-dependent kinases (CDKs) are important anti-cancer targets and despite having been characterized in complex with a wide variety of inhibitors, the majority of CDK2 structures solved are of the inactive enzyme. Crystallographic data exists for only one ATP-competitive inhibitor in both the active cyclin-bound and inactive CDK2 forms. We have solved the structures of six inhibitors in both the monomeric CDK2 and binary CDK2/cyclin A complexes and demonstrate for the first time that significant differences in binding of CDK2 ligands occur depending on the activation state. The binding mode of two ligands varies substantially as a result of binding site differences induced upon CDK2 activation. Furthermore, an energetic analysis of CDK2/cyclin complexes demonstrates that a good correlation exists between the in vitro potency and calculated energies of interaction, while indicating that no such relationship exists for monomeric CDK2-inhibitor structures. These results confirm that structures solved in complex with the monomeric CDK2 do not fully reflect the active conformation of bound inhibitors. This analysis reveals significant implications for inhibitor design towards active structures since these are distinct from the inactive CDK2 and also suggests that the monomeric CDK2 conformation could be selectively inhibited.

4:45 End of Conference

For more information, please contact:
Margit Eder, Ph.D., Conference Director
Phone: 781-972-5478 • E-mail: meder@healthtech.com

For exhibit and sponsorship information, please contact:
Suzanne Carroll, Manager, Business Development
781-972-5452 • scarroll@healthtech.com