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Join
over 200 of your colleagues and register today!
Stay on to attend Structure-Based
Design (June 6 - 8)
Wednesday, June 6
7:30 am Morning Coffee
8:10 Chairperson’s Remarks
| CASE STUDY:
8:15 Human MAP3 Kinase COT - The Impact of Early Target
Characterization and Assay Development/Applications in Drug Discovery
Yong Jia, Ph.D., Senior Scientist, Molecular Pharmacology, Abott
Bioresearch Center
Cancer Osaka Thyroid (COT) is essential for lipopolysaccharide activation of
the ERK MAPK cascade in macrophages and is thus emerging as a promising
drug target for immune-mediated diseases. COT alone is difficult to express
and isolate in vitro, yielding only limited quantities of protein with low purity. In
this talk, the purification and kinetic characterization of human recombinant
COT, the development of various in vitro COT assays using both state-of-theart
Homogeneous Time Resolved Fluorescence and conventional radiometric technologies, as well as the applications of each assay format for HTS and hits
confirmation and analysis will be described. This presentation will demonstrate
the critical impact of early target characterization and in vitro assay development
and validation on the drug discovery process. |
8:45 Lead Discovery Strategies for Protein Kinases
Fraser Glickman, Ph.D., Project Team Head, Lead Discovery Center, Novartis Institiutes for BioMedical Research
We will compare and contrast the various miniaturized HTS technologies for measuring
protein kinase activity used at Novartis. We will present the advantages and
disadvantages of each approach, discuss the strategies for kinase assay development and lead
discovery, and present case studies in both successes and pitfalls of various approaches,
including various radiometric, cell-based and fluorimetric assays.
9:15 Kinome Profiling on PepChip Arrays, or How to
Find the Haystack
Jos Joore, Ph.D., VP Array Technologies, Peptide Microarrays, Pepscan
Systems
Pepscan has developed peptide substrate microarrays for the analysis of protein kinases. These PepChip Kinase microarrays allow researchers to perform kinomics , i.e. studying snapshots of total kinase activity in cells and tissues. Using pepchip arrays, we have investigated kinase activity in frozen tumor samples, cell lines, plant tissues and blood cells. This method provides a radically different view of the effects of kinase inhibitors on signal transduction in cells and tissues, allowing novel ways to evaluate such compounds as therapeutics against cancer, inflammatory- and other diseases.
9:45 Coffee Break
10:15 Beyond Kinases: Exploring the Ligand Selectivity of
Diverse ATP-Binding Sites
Robert Lowery, Ph.D., President & Chief Executive Officer, R&D, BellBrook Labs
To explore the ligand selectivity of ATP-binding sites, we are screening a kinasefocused
library across diverse ATP-utilizing enzymes using adenine nucleotide detection as a generic assay method. BellBrook Labs recently developed an HTS
assay platform that enables homogenous, fluorescent detection of nucleotides. The
assays rely on highly selective antibodies that are able to distinguish between
nucleotides on the basis of a single phosphate group. Assays have been developed
for both ADP and AMP, making it possible to detect the majority of ATP-utilizing
enzymes in an HTS format. ADP-producing enzymes used in the study include protein
kinases, lipid kinases, carbohydrate kinases, chaperonin-associated ATPases,
and carboxyltransferases. AMP-producing enzymes (which hydrolyze ATP) include
DNA ligase, Ubiquitin ligase, and acyl-CoA synthetase, as well as phosphodiesterases
(which hydroylze cAMP).
10:45 Poster Snap-Shots
Several carefully selected posters will be presented orally.
| CASE STUDY:
11:15 The Discovery of KXO1: A Highly Selective, Non-ATP
Competitive, Src Inhibitor
David Hangauer, Ph.D., Senior Vice President, Research & Development, Kinex Pharmaceuticals LLC
Utilizing Kinex Pharmaceuticals platform technology, MimeticaTM, KXO1 was
discovered as a novel small molecule Src tyrosine kinase inhibitor. KXO1 targets
the peptide substrate binding site rather than the ATP site wherein most
tyrosine kinase inhibitors bind. This unique binding site provides much higher
selectivity than is obtained with ATP competitive Src inhibitors. KXO1 inhibits
Src kinase activity in whole cells with low nM potency and is >1,000-fold less
active against other tyrosine kinases such as EGFRTK, PDGFRTK, JAK1, JAK2, ZAP70 and Lck. KXO1 is also a low nM potency inhibitor of tumor cell
growth for a broad range of cancer types in vitro and is orally effective in animal
tumor models. KXO1 is currently completing late preclinical development
for oncology applications and is expected to enter Phase I clinical trials in 2007. |
11:45 Lunch on your own
(Lunch and Learn Sponsorship Available)
1:10 pm Chairperson’s Remarks
1:15 Structure-Guided Immune Kinase Drug Discovery
David Borhani, Ph.D., Group Leader, Department of Chemistry, Abbott Bioresearch Center
1:45 Design Strategies for Multiple Kinase Inhibitors
Jagarlapudi Sarma, Ph.D., Senior
Vice President of Informatics, GVK Biosciences PVT Ltd
Sucha Sudarsanam, Chief Scientific Officer, Emilem Inc.
Recent clinical evidence indicates that drugs targeting multiple kinases have proven
to be effective against treatment of cancers. Using crystal structural information of
kinases and pharmacopeia of kinase inhibitors, computational techniques have provided
starting points for designing inhibitors against individual targets. However,
designing compounds that are effective against multiple kinases has remained a
challenge. In this talk, we will outline strategies we have developed for designing
inhibitors active against multiple kinases.
2:15 The Crystal Structure of the p38a-MK2
Heterodimer
Ernst ter Haar, Structural Biology, Vertex Pharmaceuticals
The crystal structure of the unphosphorylated p38a-MK2 heterodimer suggests that both kinases adopt a conformation in the nucleus that prevents their substrates from getting phosphorylated when the cells are devoid of stress signals. In this conformation the C-terminal regulatory domain of MK2 binds in the p38a docking-groove and the ATP-binding sites of both kinases are at the heterodimer interface. Despite this inactive conformation, a small amount of constitutively active MKK6-DD will rapidly phopshorylate and activate p38a, and the activated p38a will subsequently phosphorylate MK2.
2:45 Refreshment Break
| CASE STUDY:
3:15 Allosteric Kinase Inhibitors - Benchtop to Clinic
Christopher Larson, Ph.D., Associate Director of Biology, Kemia, Inc.
Historically, the majority of kinase inhibitor programs have focused on compounds
that target the highly conserved ATP-binding site and compete with ATP for binding
to the activated form of the kinase. In recent years, efforts have begun to focus on
compounds that bind to and stabilize an inactive conformation of the target
kinase. Kemia has been advancing several chemical series that bind to this “allosteric” site.
Targeting this conformation of kinases offers several potential advantages in terms
of selectivity, binding kinetics, kinase activation, etc. This talk will discuss recent
progress in this area as well as characterization of Kemia’s allosteric p38-alpha
inhibitor, KC706, currently in Phase 2 clinical trials. |
3:45 Kinase-Likeness as Viewed by Chemists and by Kinases
Anton Filikov, Ph.D., Principal Investigator, Informatics & Modeling, ArQule Inc.
The in silico rapid evaluation of molecules for promising biological activity is a rich
area of research and a particularly challenging one. The pharmaceutical industry has
long been seeking new kinase inhibitors. At ArQule we asked a simple question: Do
kinase inhibitors carry any particular features that differentiate them from other molecules
and in particular other drugs? Here we describe an approach to address this question which employs a method that uses a 2D Bayesian categorization model
built on a training set obtained by docking a limited number of diverse drug-like compounds.
Once these models are built on a small set of diverse kinase structures, they not only yield the chemical features that are particular to kinase inhibitors, but
also facilitate high thoughput screening of large chemical libraries for
kinase-like compounds. This method will be compared with another technique, which involves
the building of a Bayesian categorization model on an extensive database of known
kinase inhibitors and other drug-like compounds.
4:15 Using Diverse Computational Approaches to Understand
Protein/Ligand Binding Affinities in Structure-Based Drug Design: A Cross-Docking and Quantum
Mechanical Study
Jose S. Duca, Ph.D., Senior Scientist, Computer Assisted Drug Design,
Schering Plough Research Institute
Predicting protein/ligand binding affinity is one of the most challenging computational
chemistry tasks. Numerous methods have been developed to address this challenge,
but they all have limitations. Addressing protein flexibility has been a shortcoming
of many methods. In this study, we used cross-docking of ~150 inhibitors into
the full set of crystal structures for each inhibitor complexed with the kinase CDK2.
In scoring relative binding potency based on multiple combinations of several target
proteins, the dangers of over-fitting became apparent. Examples will be given of
insights gained into ligand properties such as pKa values and relative tautomeric stabilities
computed via ab initio quantum mechanical methods. The estimation of protein/
ligand binding affinities from QM-MM calculations will also be discussed. Finally
various methods of computing binding affinities will be assessed vis-à-vis their
speed and accuracy.
4:45 Discussion with Speakers
5:15 End of Conference
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