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Therapeutic Target Space:
Methods for Druggability Assessment


12:00-1:10 pm Main Conference Registration


(Shared session with Next-Gen Kinase Inhibitors Conference)

1:10 Chairperson’s Remarks

Andrew C. Good, Ph.D., Distinguished Scientific Fellow, Medicinal Chemistry, Genzyme Corp.

1:15 Discovery of Crizotinib (PF-02341066)-A c-Met/ALK Dual Inhibitor for Oncology Applications

Jean CuiJean Cui, Ph.D., Associate Research Fellow, Oncology Medicinal Chemistry, Pfizer, Inc.

Crizotinib (PF-02341066) has shown remarkable efficacy for lung cancer patients with EML4-ALK fusion gene and is currently in Phase III clinical trials. Crizotinib is created as a c-Met/ALk dual inhibitor using structure-based drug design in combination with medicinal chemistry principles.


1:45 A Role for Hydration in Interleukin-2 Inducible T Cell Kinase Selectivity

Ronald Knegtel, Ph.D., Research Fellow I, Molecular Modeling, Vertex Pharmaceuticals (Europe) Ltd.

A series of Itk inhibitors that achieve selectivity through the introduction of a single, solvent exposed aromatic nitrogen atom without direct interactions with the enzyme is reported. By analyzing active site hydration using WaterMap, the selectivity profile can be explained in terms of the replacement of a thermodynamically unfavorable water molecule by the inhibitor and improved hydration of the bound ligand. This hydration site was successfully used to enrich virtual screening results in their content of selective Itk inhibitors.

2:15 Overcoming Drug-Resistant Mutations in Kinase Drug Discovery: Applying Lessons from Ponatinib (AP24534)

David DalgarnoDavid C. Dalgarno, Ph.D.,Vice President, Research Technologies, ARIAD Pharmaceuticals, Inc.

Ponatinib (AP24534) is a novel BCR-ABL inhibitor that inhibits both native and mutant BCR-ABL, including the T315I gatekeeper mutation, and hence acts as a pan-BCR-ABL inhibitor. We recently analyzed the structural basis for this pan-BCR-ABL activity. Here we discuss this analysis and how it can be applied to other kinase targets exhibiting mutation-based resistance, and how the lessons from ponatinib can be applied to the design of other mutant kinase inhibitors.

Sponsored byReaction Biology 2:45 Interrogating the Kinome with HotspotTM Kinase AssaysStephen A. Parent, Ph.D., Director of Business Development, Reaction Biology CorporationRBC provides drug profiling and screening services using HotSpot technology, a high-throughput radioisotopic screening platform with more than 370 kinases.  We will describe its application to kinase inhibitor development and kinase inhibitor selectivity. 


3:00 Networking Refreshment Break in the Exhibit Hall with Poster Viewing

3:30 Structure-Guided Fragment-Based Drug Discovery for Protein Kinase Targets

Stephen BurleyStephen K. Burley, M.D., D.Phil., Distinguished Lilly Research Scholar, Lilly Biotechnology Center, Eli Lilly and Company


4:00 How Molecular Dynamics Simulation May be Applied in Structural Based Design of Kinase Drugs

Yibing Shan, Ph.D., Senior Scientist, Chemistry and Biology, D. E. Shaw Research

The understanding of the extensive conformational heterogeneity of protein kinases is crucial to the understanding of kinase drugs’ binding and specificity. To this end, long molecular dynamics (MD) simulations, which for the first time reached the relevant timescale of micro- to milli-second, may prove a powerful tool. Our MD study of Abl, Src, and EGFR kinases will be discussed as examples of such effort in its early stage.


4:30 Recent Experience Establishing a New Lead ID Capability to Pursue Oncology Kinase Targets 

Hans-Peter Biemann, Ph.D., Associate Scientific Director, In vitro Biology, Genzyme Corporation 

Genzyme’s small molecule discovery unit has incorporated fragment-based and x-ray structure-assisted technologies over the last three years.  Ligands of 150-250 Daltons have undergone structure-assisted elaboration to identify novel potent and selective inhibitors of tyrosine and ser/thr kinases, including Pim-1.  We progressed a tyrosine kinase to late lead optimization in 2.5 years and newer projects have productively commenced outside of the kinase and oncology sectors.   This evolution of our HTS-based drug discovery unit to a multi-platform format enables us to address a number of target classes more expediently than before. 

5:00 Longstanding Kinase Contributor Panel: Structure-Based Kinase Inhibitor Design

Topic: Insights correlating kinase selectivity and toxicity

Andrew C. Good, Ph.D., Distinguished Scientific Fellow, Medicinal Chemistry, Genzyme Corp.

Ravi G. Kurumbail, Ph.D., Research Fellow and Structural Biology Laboratory Head, Pfizer, Inc.

Dirksen Bussiere, Ph.D., M.B.A., Director, Structural Chemistry, Novartis Institutes for BioMedical Research


5:30-6:00 Registration for Dinner Short Course



Wednesday Evening, June 8, 2011

Dinner Short Course* 

6:00-9:00 pm Identification of Druggable Sites for Protein-Protein Interaction Targets

Despite the growing number of examples of small molecule inhibitors that disrupt protein-protein interactions (PPIs), the origin of druggability is poorly understood. This course is designed to demonstrate the use of computational methods to determine the most likely structure of the complex formed by interacting proteins, identify potentially druggable sites in the interface, determine whether the target is druggable, and provide information on potential ligands. Participants will study a number of targets using web-based software (including PIPER and ClusPro, currently the best protein docking tools available) on their laptops.

Course Instructors:

Sandor Vajda, Ph.D., Professor, Departments of Biomedical Engineering and Chemistry, Boston University

Dima Kozakov, Ph.D., Research Assistant Professor, Departments of Biomedical Engineering, Boston University

*Separate Registration Required