Reaching for High Hanging Fruit in Drug Discovery

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Reaching for High Hanging Fruit in Drug Discovery

• Jim Wells
• Michelle Arkin
• UCSF

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Our Mission

• Provide UCSF with small molecule discovery
  capabilities to
• advance understanding of cell/protein function
• identify promising new targets and leads
• advance technologies for challenging targets

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High-Hanging Fruit in Drug Discovery
Protein-protein
Allosteric effectors
Transcrip.factors
Phospha-tases
proteases
kinases
GPCRs
Targets which have not yielded to HTS need a new
approach
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Why Fragment-based Lead Discovery

• Definition discovering a drug lead in pieces
  (in a way
• that facilitates rapid optimization)

• Potential benefits of Fragment Discovery
• Solving the diversity problem pieces are
  preselected for binding
• Solving the complexity problem simple compounds
  with high ligand efficiency

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Integrated Approach to Fragment-based Discovery
HT-SPR Disulfide trapping Structural biology
HT-chemistry Hit-to-lead
Library development Binding-site
prediction DOCKing
The Fragment Discovery Center is a research
collaborative
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Fragment Discovery by HT-SPR

• Surface Plasmon Resonance allows real-time
  detection of binding interactions
  stoichiometry, affinity, kinetics
• HT-SPR with the AP3000 (Fujifilm) 3840 data
  points in 24 hrs

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Targeting the Inactive Conformation of NEK2

• Screened 800 compounds for binding to kinase
  domain
• 2 major scaffolds show low stoichiometry, SAR,
  Kd 40-500 mM

1C02
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Targeting Regulatory PPI on Enzymes
Signaling complexes are often allosteric
regulators of activity
Arkin, Whitty COCB (2009)
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Example Targeting Kinase Complexes
N-lobe
Allosteric Activator
active site
C-lobe

• Binding assay
• Screen for binding in presence of active-site
  ligand
• Determine functional activity, binding site in
  2nd assays

• Functional assay
• Screen for activators in absence of allosteric
  protein
• Determine MOA, binding site in 2nd assay

Kate Engel, Preeti Chugha, John Kuriyan
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Two Approaches Converge on a Scaffold
Kinase activity
HT-SPR
KD20 µM LE0.34 stoichiometry1.2
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We hope to provide benefit to the CBC by

• Proposing high hanging cancer targets from our
  lab and UC collaborators
• Providing approaches to harvesting these targets
• Contributing expertise in fragment screening,
  computational chemistry, structural biology, and
  medicinal chemistry

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Turning caspases ON with small molecules
Jim Wells, Dennis Wolan, Julie Zorn, Dan Gray,
UCSF NCI August 10, 2009
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Chemo?Apoptosis a long and bumpy road
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Caspases are Dynamic
activation
Active-site Inhibitor
Allosteric Inhibitor
Allosteric
On Off
Active
Romanowski et al., Structure 12, 1361 (2004)
Hardy et al., PNAS 101, 12461 (2004) Scheer et
al., PNAS 103, 7579 (2006) Datta et al., J. Mol.
Biol. 381, 1157 (2008)
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Can we stabilize the on form the pro-caspase-3 ?
activation
Active-site Inhibitor
Allosteric Inhibitor
Apo
Allosteric
Active
Romanowski et al., Structure 12, 1361 (2004)
Hardy et al., PNAS 101, 12461 (2004) Scheer et
al., PNAS 103, 7579 (2006) Datta et al., J. Mol.
Biol. 381, 1157 (2008)
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HTS for Executioner Procaspase 3 Activators
Dennis Wolan
Slide 17
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Small Molecule Activation Model

• Shows lag then burst activation
• Instantly enhances pro-caspase catalytic
  efficiency 50X
• Single site binding activates, two-site binding
  inhibits
• Resistance mutants near active site
• Increases susceptibility to proteolysis
• Shows feedback activation

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Instantly enhances procaspase catalytic
efficiency by 50-fold
1/KM
kcat
E S
E.S
E P
Relative kcat/KM
KM
kcat
kcat/KM
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Enhances susceptibility to proteolysis
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1541 rapidly induced cellular apoptosis

• Induces apoptosis in pC3 containing cells
• Can circumvent upsteam blocks in intrinsic
• or extrinsic pathways
• Apoptotic mechanism blocked by caspase inhibitors
  

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Activators vs Inhibitors

• Sufficiency vs Necessity
• IC10 vs IC90
• Expands to Different Target Class
• Challenge of Allosteric vs Active Site compds