This established and well-recognized kinase conference addresses reoccurring questions about selectivity, safety, resistance and novelty. After many years of research and therapeutic developments of kinase inhibitors, the field still offers new opportunities as novel kinases and their inhibitors are making an appearance. In addition, interest in repurposing of already developed drugs is growing immensely. “Next-Gen Kinase Inhibitors” addresses what lies ahead, what is in store for the pharmaceutical industry and what new avenues are opening up in regards to technologies and methods used, and in regards to novel targets and therapeutic approaches explored.

1. Final Agenda
Next-Gen
Cambridge Healthtech Institute’s Eleventh Annual
Kinase Inhibitors
Moving Towards a Successful Pipeline
June 17-19, 2013 | The Revere Hotel | Boston, MA
TOPIC HIGHLIGHTS:
• Non-Cancer Indications • Overcoming Resistance
• esigning Selective Inhibitors
D • Structure-Based Design
• Property-Based Design • Screening and Validation
Short Course:
The Art and Science of Kinases*
Monday, June 17
Course Instructors:
Kent D. Stewart, Ph.D., Research Fellow, Structural Biology, Abbvie
Maricel Torrent, Ph.D., Senior Scientist III, Molecular
Modeling, AbbVie
*Separate Registration Required.
Co-Located with:
13th Annual Structure-Based Drug
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2. Next-Gen
Cambridge Healthtech Institute’s Eleventh Annual
June 17-19, 2013
The Revere Hotel | Boston, MA
Kinase Inhibitors Moving Towards a
Successful Pipeline
This established and well-recognized kinase conference addresses reoccurring questions about selectivity,
safety, resistance and novelty. After many years of research and therapeutic developments of kinase
inhibitors, the field still offers new opportunities as novel kinases and their inhibitors are making an
appearance. In addition, interest in repurposing of already developed drugs is growing immensely.
“Next-Gen Kinase Inhibitors” addresses what lies ahead, what is in store for the pharmaceutical industry
and what new avenues are opening up in regards to technologies and methods used, and in regards to
novel targets and therapeutic approaches explored.
Monday, June 17 selective PKCθ inhibitors, which show exceptional potency in cells and
in vivo.
8:00 – 9:00 am Pre-Conference Short Course Registration and
Morning Coffee 2:10 JAK Inhibition Suppresses Osteoclast Activation through
Decreased RANKL Production
Timothy P. LaBranche, DVM, Ph.D., Dipl ACVP, Senior Principal Scientist,
9:00 – 12:00 pm Short Course: The Art and Science
Pathologist, Pfizer Drug Safety RD, Cambridge, MA
of Kinases*
Potent inhibition of human T lymphocyte RANKL production by the JAK
Course Instructors: Kent D. Stewart, Ph.D., Research Fellow,
inhibitor tofacitinib (Xeljanz), combined with the lack of an effect on
Structural Biology, Abbvie
human osteoclast differentiation/function suggests that JAK inhibition
Maricel Torrent, Ph.D., Senior Scientist III, Molecular suppresses osteoclast-mediated bone resorption through decreased
Modeling, AbbVie RANKL production. Although T lymphocytes clearly appear to play a role
*Separate Registration Required in osteoclast activation by producing RANKL, it is possible that they do
not represent the totality of RANKL production in the arthritic joint.
11:00 am Main Conference Registration
2:40 Sponsored Presentation (Opportunity Available)
1:30 pm Chairperson’s Opening Remarks
Guido Zaman, Ph.D., Founder, Head, Biology, Netherlands Translational 3:10 Refreshment Break in the Exhibit Hall with Poster Viewing
Research Center B.V.
3:40 Combining Cellular and Biochemical Panel Profiling for the
Non-Cancer Indications Development of Selective Kinase Inhibitors
Guido Zaman, Ph.D., Founder, Head, Biology, Netherlands Translational
1:40 The Design and Optimization of Selective Protein Research Center B.V.
Kinase C theta (PKCθ) Inhibitors for the Treatment of
The Netherlands Translational Research Center B.V. (NTRC) aids in
Autoimmune Diseases
the development of new personalized therapies for the treatment of
Juan-Miguel Jimenez, Ph.D., Director, Chemistry, Vertex cancer, autoimmuneand neurodegenerative diseases. Selective kinase
Pharmaceuticals (Europe) Ltd. inhibitors are optimized for increased target residence time and profiled
Protein kinase C theta (PKCθ) has a central role in T cell activation and on large panels of biochemical and cell-based assays. Genotypic,
survival. Studies in PKCθ-deficient mice have demonstrated that whilst phenotypic and pathway information are combined to determine the
anti-viral responses are PKCθ-independent, T cell responses associated optimal compound for a particular patient responder population. Kinase
with autoimmune diseases are PKCθ- dependent. Thus, potent and inhibitors are tested in combination with existing drugs to identify new
selective inhibition of PKCθ is expected to block autoimmune T cell synergies that improve the efficiency of established therapies
responses without compromising antiviral immunity. The presentation
will describe the design and optimisation of a novel class of potent and 4:10 Structural and Biophysical Insights into Syk Function from
an Allosteric Inhibitor
2 | Next-Gen Kinase Inhibitors healthtech.com/KIN

3. Justin Hall, Ph.D., Senior Scientist, Pfizer The traditional protein kinase inhibitor design process is being
Syk is a soluble kinase responsible for transmission of the B-cell expanded as we learn more about the changing nature of the ATP-
receptor or mast cell FcεRI receptor activation signal from the binding cleft and its switching between active and inactive states. The
membrane to cytosolic targets. Control of Syk function is important presentation will describe the utilization of a new understanding of the
to the human antigenic and inflammation immune response, and an role of hydrophobic residues within the cleft and how the ligand-protein
inhibitor of Syk could provide therapy for autoimmune or inflammation interactions influence conformational changes, providing new inhibitor
diseases. This talk describes the discovery and characterization of a design opportunities.
novel allosteric Syk inhibitor which is noncompetitive against ATP and
substrate peptides, and competitive against activation of Syk by its 9:30 Sponsored Presentations (Opportunities Available)
upstream regulatory kinase LynB.
10:00 Coffee Break in the Exhibit Hall with Poster viewing
4:40 Targeting Aurora A Kinase to Overcome CML
10:45 Structure and Property Based Design of CK2
Acquired Resistance
Kinase Inhibitors
WenYong Chen, Ph.D., Associate Professor, Department of Cancer
James Dowling, Ph.D., Scientist, Astrazeneca
Biology, Beckman Research Institute/City of Hope
CML develops acquired resistance to tyrosine kinase inhibitors by Developing Selective Inhibitors
acquisition of BCR-ABL kinase domain mutations. We found that an
early event for emergence of BCR-ABL mutant cells is mitotic crisis 11:15 Evolutionary and Semantic Web Applications in Protein
of CML cells triggered by tyrosine kinase inhibitor treatment, and it is Kinase Inhibitor Design
controlled by mitotic kinase Aurora A. Specific inhibition of Aurora A is Natarajan Kannan, Ph.D., Assistant Professor, Biochemistry and
able to prevent acquisition of BCR-ABL mutations and block CML cell Molecular Biology Institute of Bioinformatics, University of
relapse from tyrosine kinase inhibitors. Georgia, Athens
Protein kinases display complex sequence-structure-function
5:10 Welcome Reception in the Exhibit Hall with Poster Viewing relationships, a detailed understanding of which is necessary for the
development of selective protein kinase inhibitors. This talk describes
6:45 Close of Day One how evolutionary- and ontology-based analysis of protein kinase data
can provide new insights into sequence-structure-function relationships,
Tuesday, June 18 and aid in the development of selective protein kinase inhibitors.
7:45 am Breakfast Breakout Discussions 11:45 Selective Inhibition of Kinase-Driven Pathways; Exploiting
These are moderated discussions with brainstorming and interactive Demure Features
problem solving, allowing conference participants from diverse Ellen R. Laird, Ph.D. Research Fellow, Array BioPharma
backgrounds to exchange ideas, experiences, and develop future Selective inhibition of nearly any given protein kinase continues to
collaborations around a focused topic. challenge investigators. Literature reviews generally focus upon gross
differences in kinase fold, with emphasis on “inactive” vs. “active”
Table 1: Multi-Parameter Drug Optimization – Is It Working?
conformations, yet many of these compounds remain stubbornly
• Is data quality good enough? promiscuous. We have curated and analyzed a sizeable collection
• How many compounds should be made and in what stage? of X-ray crystal structures of diverse kinases, many of which are
• What is the ideal path for optimization and how do you find proprietary. We have identified additional sources for selectivity by
it efficiently? consideration of nuances at the periphery of active or inactive folds.
• What role does informatics have? – small companies vs Differences in sidechain rotamer preferences and solvation, cleft
large companies dimension, features of the active site floor, the P-loop, and the C-helix
Moderator: Mark Ashwell, Ph.D., Vice President, Chemistry, ArQule often contribute to hypotheses that enable SAR interpretation and
further compound design. This talk will draw upon prominent examples
Table 2: How Can We Leverage Existing Data on Protein Kinases of inhibitors that owe their selectivity to these subtle differences,
for Inhibitor Design? with particular emphasis on our own experiences with AKT, B-Raf,
• Challenges in protein kinase data mining and Erb-B2.
• Resources needed to address data mining challenges 12:15 pm Luncheon Presentation Sponsored by
Moderator: Natarajan Kannan, Ph.D., Assistant Professor, Biochemistry Speaker to be Announced
and Molecular Biology; Institute of Bioinformatics, University of Georgia
1:35 Chairperson’s Remarks
8:55 Chairperson’s Remarks
Natarajan Kannan, Ph.D., Assistant Professor, Biochemistry and
Mark Ashwell, Ph.D., Vice President, Chemistry, ArQule Molecular Biology, Institute of Bioinformatics, University of Georgia
Property-Based Design 1:40 Structure-Based Design of Selective hSmg-1
9:00 Focusing on the Ligand-Protein Relationship in Activation- Kinase Inhibitors
State Dependent Conformational Changes of Protein Kinases Ariamala Gopalsamy Ph.D., Associate Research Fellow, Worldwide
Mark Ashwell, Ph.D., Vice President, Chemistry, ArQule Medicinal Chemistry, Pfizer Global Research and Development
healthtech.com/KIN Next-Gen Kinase Inhibitors | 3

4. hSmg-1 kinase plays a key role in cellular genotoxic stress response
and contributes to tumor growth and resistance to chemotherapy. To »»
Keynote Presentation
understand the functional role of inhibiting this underexplored Ser-Thr 8:30 Kinase Inhibitors: Lessons Learned?
kinase, we identified pyrimidine-based, highly hSmg-1 selective kinase Doriano Fabbro, Ph.D., CSO, Piqur Therapeutics
inhibitors. Use of structure based optimization to achieve selectivity will Our knowledge on the structural determinants of kinase inhibition
be discussed in detail. by small molecules binding to the ATP pocket has advanced
steadily in the past years. We will give an overview on the status
2:10 Sponsored Presentation (Opportunity Available) quo of kinase inhibition and discuss an example on how protein
kinases can be structurally affected by selective kinase inhibitors.
2:40 The SYK–BTK Axis as a Drug Target for In addition we will also discuss on how to target kinases whose
Autoimmune Disorders cellular signaling pathways are only poorly understood.
Thomas Tan, Ph.D., Consultant, Medical Affairs, F- Hoffmann-La
Roche Ltd. Screening and Validation
Spleen Tyrosine Kinase (SYK) and Bruton’s Tyrosine Kinase (BTK) are
non-receptor cytoplasmic tyrosine kinases that are primarily expressed 9:00 Evaluation of the PI4KIIIα Lipid Kinase as a Hepatitis C
in cells of hematopoietic lineage. Both are key mediators in coupling Virus Drug Target: From Inhibitor Screening to Animal Models
activated immunoreceptors to downstream signaling events that affect Frederic Vaillancourt, Ph.D., former Senior Research Scientist,
diverse biological functions, from cellular proliferation, differentiation Department of Biological Sciences, Research and Development,
and adhesion to innate and adaptive immune responses. As such, Boehringer Ingelheim (Canada) Ltd.
pharmacological inhibitors of SYK or BTK are being actively pursued as PI4KIII is an essential host cell factor for HCV replication. Screening,
potential immunomodulatory agents for the treatment of autoimmune using an in vitro biochemical lipid kinase assay, led to the identification
and inflammatory disorders. Here, we review and discuss recent of potent inhibitors. In cell culture studies these inhibitors were used
insights into the emerging role of the SYK–BTK axis in innate immune to demonstrate that the kinase activity was essential for HCV RNA
cell functions, and our experience in developing selective SYK and replication, and a resistance study performed, using two of these
BTK inhibitors. inhibitors, provided additional insight into the potential role of PI4KIIIα
and its product in the HCV viral life cycle. A comprehensive assessment
3:10 Refreshment Break in the Exhibit Hall with Poster Viewing of PI4KIIIα as a drug target in vivo through conditional transgenic murine
lines that mimic target-specific inhibition in adult mice demonstrated an
Case Studies
essential host physiologic role for PI4KIIIα.
4:00 Talk Title to be Announced
Stephen J. Shuttleworth, Ph.D., FRSC CChem, CSO, Karus 9:30 Coffee Break
Therapeutics Ltd. 10:00 Fitting Technology to Screening Strategy: A Probe
4:30 Discovery and Development of Jakafi for Myelofibrosis Displacement Assay to Help Identify Novel Protein
Kinase Inhibitors
Kris Vaddi, DVM, Ph.D., Group Vice President, Pharmacology and
Toxicology, Incyte Pharmaceuticals Ramesh Padmanabha, Ph.D., Principal Scientist, Lead Discovery, Lead
Profiling and Compound Management, Bristol-Myers Squibb RD
Jakafi (ruxolitinib) is a potent, selective and first in-class JAK1 and
JAK2 inhibitor, approved by USFDA for the treatment of patients with The talk will outline assay design process to select the probe
intermediate- and high-risk myelofibrosis. Myelofibrosis is a serious and displacement assay over standard kinase activity assays. The details
life-threatening myeloproliferative neoplasm (MPN), but unlike CML of the HTS will also be discussed and will include validation, quality
is Philadelphia chromosome negative. An important discovery in late control, and data analysis. The outcome from the screen and selectivity
2004 that identified a somatic gain-of-function mutation known as JAK2 data will also be presented.
V617F in MPN patients provided first molecular and genetic evidence
10:30 Talk Title to be Announced
that linked JAK-STAT dysregulation to the pathogenesis of MPNs. Drug
discovery program at Incyte aimed at developing JAK inhibitors began Yaya Liu, Ph.D., Associate Research Fellow, AbbVie Inc.
in early 2003, almost 2 years ahead of the discovery of JAK2V617F with Structure - Based Design
the recognition that JAK-STAT pathway is an important oncogenic and
inflammatory mechanism. This early start allowed Incyte to identify 11:00 Structure-Based Drug Design: Redefining
Jakafi in Protein-Ligand Interactions
Jose Duca, Ph.D., Head, Computer-Aided Drug Discovery, Novartis
5:30 Close of Day Since the introduction of the lock and key hypothesis, structure-based
drug design has been equivalent to understanding and designing
Wednesday, June 19 protein-ligand interactions. A novel theory of binding that encompasses
protein-ligand interactions will be introduced and exemplified.
7:30 am Morning Coffee
11:30 Luncheon Presentation (Opportunity Available) or Lunch on
8:25 Chairperson’s Remarks Your Own
Doriano Fabbro, Ph.D., CSO, Piqur Therapeutics
4 | Next-Gen Kinase Inhibitors healthtech.com/KIN

5. 1:15 pm Chairperson’s Remarks Drug Resistance
Adam C. Palmer, Ph.D., Postdoctoral Fellow, Department of Systems
Biology, Harvard Medical School 4:00 Towards a New Generation of Antimicrobial Antifolates
• the special role that structure-based drug design can play in treating Dennis L. Wright, Ph.D., Professor of Pharmaceutical Sciences and
drug resistant infectious disease Chemistry, University of Connecticut
We are using a structure-based design approach to develop potent
• how considering the evolution of resistance during drug development
and selective inhibitors of the enzyme dihydrofolate reductase (DHFR)
could produce drugs with more long-lasting clinical efficacy
from a variety of pathogenic organisms. Analysis of crystal structures
• how drug resistance can be used as a tool to understand mechanism of trimethoprim-resistant and naturally insensitive enzymes led to the
of drug action design of a series of propargyl-linked antifolates characterized by high
potency, good selectivity over the human form of the enzyme and good
1:20 Structure-Based Design of Potent and Selective Inhibitors of
anti-microbial activity.
PI3-Kinase Delta
Jeremy M. Murray, Ph.D., Scientist, Structural Biology, Genentech 4:30 Understanding Drug Mechanism of Action by Target
Inhibition of PI3Kδ is considered to be an attractive mechanism for the Gene Overexpression
treatment of inflammatory diseases and leukocyte malignancies. Using Adam C. Palmer, Ph.D., Postdoctoral Fellow, Department of Systems
a structure-based design approach, we have identified a series of potent Biology, Harvard Medical School
and selective inhibitors of PI3Kδ. These inhibitors do not occupy the The molecular targets of drugs can sometimes, but not always,
induced selectivity pocket between Trp760 and Met752 that is observed be identified amongst genes that confer drug resistance when
for other families of selective PI3Kδ inhibitors. Instead, the selectivity overexpressed. We quantitatively overexpressed genes encoding
of the compounds for inhibition of PI3Kδ relative to other PI3K isoforms known antibiotic targets and observed that drug resistance does not
appears to be due primarily to the strong interactions these inhibitors only increase; it can remain unchanged, decrease, or even have a
are able to make with Trp760 in the PI3Kδ binding pocket. This talk will non-monotonic dependence on target expression. These diverse effects
discuss the structural understanding of the selectivity of these inhibitors are explained by simple models considering gene toxicity and drug-
against other isoforms, pharmacokinetic properties and the ability of induction of harmful target-catalyzed reactions. The relation between
select compounds to inhibit the function of B-cells in vivo. drug resistance and target expression may reveal unexpectedly complex
mechanisms of drug action.
1:50 MD Simulations of Mutant and WT PI3Kα: Insights into the
Mechanism of Overactivation and Implications for Drug Design 5:00 Close of Conference
Zoe Cournia, Ph.D., Investigator, Biomedical Research Foundation,
Academy of Athens
Understanding how the p110α H1047R mutation causes tumorigenesis
is central to developing new therapeutics for cancer. To this end, MD
simulations in aqueous solution were carried out for 100 ns for both WT
and mutant proteins. Our results indicate that key regions of the protein,
such as the catalytic, activation, membrane binding loops and the
C-terminus, all exhibit significantly different dynamics in the mutant with
respect to the WT protein.
2:20 Sponsored Presentation (Opportunity Available)
2:50 Refreshment Break in the Exhibit Hall with Poster Viewing
3:30 Sponsored Presentation (Opportunity Available)
healthtech.com/KIN Next-Gen Kinase Inhibitors | 5

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