SESSION IV

What’s Druggable – Designing Drugs for CNS

Target Classes

Chair — Mark Frasier, PhD, Michael J. Fox Foundation for Parkinson’s

Research

Session Overview

Mark Frasier, PhD, Michael J. Fox Foundation for Parkinson’s Research

Protein-Protein Interaction: A Growing Trend Towards Feasibility

Gérard Rossé, PhD, Dart Neuroscience

Challenges in Targeting Kinases for Neurodegenerative Diseases

Ravi G. Kurumbail, PhD, Pfizer Inc.

Druggability Considerations for GPCRs and Ion Channels

Shaun R. Stauffer, PhD, Vanderbilt University

Biologics for Challenging Targets: Unique Challenges and Lessons Learned

Guriq S. Basi, PhD, Elan Pharmaceuticals, Inc.

What’s Druggable? Designing Drugs for CNS Target Classes

ADDF MeetingFebruary, 2012

What is in the MJFF pipeline?

Clinical trials

20 ongoing MJFF funded intervention trials

NTN gene therapy (Ceregene), A-synuclein (Affiris)

mGluR5 (Addex), Eltopazine, Dopaminergic improvements (NeuroDerm)

Repurposing: Pioglitazone, Inosine, Isradipine

Promising targets

Disease-modification: Genetics (A-synuclein, LRRK2), inflammation, Nrf2, Nurr1, GDNF, CDNF, antioxidants

Symptomatic: mGluR5, mGluR4, nicotinic, mu opioid

Preclinical development

Over 100 industry led projects moving to the clinic

Dyskinesia therapies

Translational research tools: animal models, antibodies, biomarkers

PD pipeline shows promise

MJFF Resources

Human Tissue and Samples

Arizona Brain Bank collaboration – PD and other tissue

DATATOP (collaboration with PSG) – serum, urine, CSF and DNA

PPMI and supporting studies – serum, plasma, whole blood, CSF, DNA, RNA and urine

Animal Models

Transgenic mice, knockout rats

Standardized characterization

Open access and central repository

Reagents

Novel LRRK2 antibodies

Assay development and optimization

Accessible to the research community

Critical tools to accelerate drug development

Clinical Trial Tools

Dyskinesia rating scale

Cognitive scales

Fox Trial Finder

Target Validation – Target XCATEGORY

Expression & Activity

Untested/

Unknown

Broad Target Organ Broad and

Disease

Modified

Target Organ

and Disease

Modified

Pre-Clinical

Pharmacological

Target Modulation

Untested/

Unknown

In Vitro Pathway

Modulation

Ex Vivo

Pathway

Modulation

In Vivo

Pathway

Modulation

Beneficial

Target

Modulation In

Vivo

Non-Human Genetic

Modulation

Untested/

Unknown

Negative Result

Upon Testing

Model

Organism

Relevant

Phenotype

Rodent/Primat

e Relevant

Phenotype

Human Mutant

Relevant

Phenotype

Human Genetic

Modulation

Untested/

Unknown

Single Study

Association

Multiple Study

Association

Genotype

Phenotype

Relationship

Clinical

Pharmacological

Target Modulation

(non-PD)

Untested/

Unknown

Negative Result

Upon Testing

Symptomatic

without known

target

Effective/Safe

in Proof of

Concept Trials

Effective/Safe in

Pivotal Trials

Clinical

Pharmacological

Target Modulation

(PD)

Untested/

Unknown

Negative Result

Upon Testing

Symptomatic

without known

target

Effective/Safe

in Proof of

Concept Trials

Effective/Safe in

Pivotal Trials

Agenda

Gerard Rosé, PhD: “Protein-Protein Interaction: A Growing Trend Towards Feasibility”

Ravi Kurumbail, PhD: “Challenges in Targeting Kinases for Neurodegenerative Diseases”

Shaun Stauffer, PhD “Druggability Considerations for GPCRs and Ion Channels”

Guriq Basi, PhD “Biologics for Challenging Targets: Unique Challenges and Lessons Learned”

Protein-Protein Interaction: A

Growing Trend Towards

Feasibility

Gérard Rossé, Ph.D., Dart Neuroscience

San Diego, CA

6th DRUG DISCOVERY FOR NEURODEGENERATION

CONFERENCE:

An Intensive Course on Translating Research into Drugs

New York, February 12-14, 2012

Pathways of Drug Discovery

Target & hit

Identification

Marketed Drug

Hit refinement & Lead optimization

Selected Clinical Candidate

Target & hitIdentification

Hit Generation

Hit refinement

Hit Exploration

Lead optimizationstudies

Chemical Optimization

Decision Gates in Pre-Clinical

Drug Discovery

Stage-by-stage quality assessment. Reduce attrition rate, time and cost

Hits LeadsDC(IND)

Validated Hit

Series

Drug(NDA)

Re

Identified Leads

Series

Selected

Clinical

Candidate

Launched

Hit to LeadLO

Advanced

Leads

RegulatoryDevelopment

Clinical studies

Fully

Optimized

Lead

Pre-clinical

Genes Target Families

• 1,357 unique drugs (1204 small

molecules & 166 biologics)

• 324 drug targets for all classes of

approved therapeutics drugs

• 1,048 druggable targets (35% identity)

in human genome

GPCRs 27%

Gene-family Distribution of

Current Drugs

NHRs 13%

Ligand-gated

ion channels 9%

Voltage-gated

ion channels 5%

Overington et al. Nature Reviews Drug Discovery 5, 993–996, 2006

Targets of top 200 selling

prescription drugs (1997)

Protein family

#ofdrugs

#distincttargets

Worldwide sales($US billions)

Birkeland (IM) & Agarwal (BLX): Feb-99

GPCRs

Enzymes*

Ion channels

NHRs

Biotherapeutics

Proteases

Symporters

Pumps

Unknown

38

28

28

20

20

10

6

4

11

25

15

5

8

-

2

3

2

-

21.3

16.8

12.0

7.6

9.02

7.11

6.36

6.02

3.71

*non-proteases

Challenging Targets:

Protein-Protein Interactions

Biochemical Space of Small Molecules

Lipinski C.; A. Hopkins A. Nature, 432, 855, 2004

Druggability/druggable targetFeasibility with which a macromolecular

target can be modulated by a small molecule

that has appropriate properties to be

developed into a drug

Rule of five (Lipinski’s rule)Key properties that should be considered for small

molecules that are intended to be orally

administered. MW < 500, H-donor < 5, H-acceptor

< 10, clogP < 5Chemical space: 1060 (MW<500)

Biologics

Peptides

Small Molecules• Orally bioavailable

• Cell/BBB permeable

• Inadequate selectivity

• Xenobiotic metabolism

• Toxicity

• Limited target binding sites

• Undruggable targets

• High specificity

• Low toxicity

• Block protein interactions

• Poor tissue penetration

• Cell/BBB impermeable

• Immunogenicity

• Limited target binding sites

• Undruggable targets

• High specificity

• Low toxicity

• Block protein interactions

• Pharmacokinetics

• Cell/BBB impermeable

• Undruggable targets

Drug Platforms

Therapeutic Limitations and “The Undruggables”

• 75-80% of all existing targets beyond reach of established drug platforms

Advantages DisadvantagesPlatform

Protein-Protein Interaction (PPI)

PPIs are a crucial element in cellular function

Advances in understanding mechanism of cell signaling are producing

a growing number of potential therapeutic targets

PPIs may provide novel mechanisms to modulate (neural) function

downstream of receptor activation or disrupt localization signals

Human diseases can be caused by aberrant PPIs: (i) loss of essential

interaction (ii) formation/stabilization of protein complex

Rational for Targeting PPI in the CNS

• In the CNS a host of PPIs is required

- neurite outgrowth

- synaptic formation

- signal transduction, neurotransmission

- apoptosis

• PPIs may provide novel mechanisms

to - modulate neural function downstream of

receptor activation

- disrupt localization signals

• Provide a measure of tissue specificity

Amyloid Plaque

NeurofibrillaryTangle

Formation in AD

• Inhibiting protein aggregation

• Targeting downstream members of signaling pathway

Strategies for Neurodegenerative Diseases

Protein Misfolding/Aggregation in

Neurodegeneration

Disease Microscopic lesions Location Aggregated protein

Alzheimer’s

Amyloid plaque

Neurofibrillary tangle

Lewy bodies

Extracellular

Intra-cytoplasmic (neurons)

Intra-cytoplasmic (neurons)

Amyloid- (A )

Tau

-sinuclein

Parkinson’s Lewy bodies Intra-cytoplasmic (neurons) -sinuclein

Huntington’s

Neuronal intra-nuclear

and intra-cytoplasmic

inclusions

Intra-cytoplasmic (neurons)

Huntingtin

(containing poly

glutamine repeat

expansion)

ALSSOD1 and neurofilament

aggregatesIntra-cytoplasmic (neurons) SOD

Disorders may share common targets for therapeutics development

Emerging PPI Targets Downstream of

Signaling Pathway

• Significant hurdles in drug development:

- cell/BBB permeability of compound

- pathway selectivity (druggable networks)

• Selective G inhibitors (M119)

• Potentiating GPCR signaling by inhibiting

RGS proteins:

- selective for specific GPCRs

- tissue specific expression

- RGS4 widely expressed in CNS, inhibitors

increase tissue specificity of an agonist

-effectors

e.g.

Adenyl

cyclase

PLC

MAPK

-effectors

e.g.

PI3K

PLC

GIRK

Ca 2+

PPI

Modulation

Recent Breakthrough:

- Stability of PPI complex is determined by only a small number of

amino acids: proteins “hot spots” (600 Å2)

- Success stories of small molecules PPI inhibitors in oncology

PPI modulation:

An Unsurmontable Problem?

Challenges:

- Large protein-protein contact surfaces (1500-3000 Å2), flat PP

interfaces and lack of suitable binding pockets, IUPs

- Low success rate in HTS campaigns

Evidence of PPI Target Class Tractability

• BCL-2 family protein previously thought to

be undruggable

• ABT-737 is a specific inhibitor of protein-

protein interaction (PPI), (Ki < 1 nM against

Bcl-2, Bcl-xL, Bcl-w)

• Prevent binding of the anti-apoptotic

proteins to apoptotic effectors Bax and

Bak, which may trigger mitochondrial-

induced apoptosis

• Orally bioavailable analog, ABT-263, in

multiple Ph I for lymphoma, CLL, SCLC

Vogler M. et al. Cell Death and Differentiation, 16, 360-367, 2009

N

N

Cl

OHN

S

HN

NO2

N

O OS

ABT-737

N

N

Cl

OHN

S

O

S

N

O OS

ABT-263

F3CO

O

O

Fragment-Based Drug Discovery

• A fragment is just a small weak hit; detection of weak binders

• Find small fragments, then grow/merge fragments to create hit.

• A small number of fragments can sample a large chemical space

- 103 fragments of MW 190 are equivalent to 1018 compounds of MW 450

• Requires protein structure to generate SAR for MedChem efforts

Fragments MW 120 - 250

10 mM 1 mM 100 M 10 M 1 M

Hit compound MW 350 - 500

Scaffolds MW 250 - 350

Affinity

P2

P2

Mechanism of PPI Modulators

= Hot -spots

P1

Targeting hot-spots

= Small molecule

P1

P1

Allosteric sites

P2= Allosteric site

Adapted from Future Medicinal Chemistry, April 2009, Vol. 1, No. 1, Pages 65-93 with permission of Future Science Ltd

Adapted from Future Medicinal Chemistry, with permission of Future Science Ltd

• Two classes of molecules: bifunctional compounds (rapamycin) or

2 moieties linked together

• Thermodynamic aspects of stabilization favorable

• Drawback of PPI stabilizers is large molecular size and weight

Stabilizing PPIs

Mechanism of PPI Modulators

Ligand

Q u ic k T im e ™ a n d a d e c o m p r e s s o r

a r e n e e d e d t o s e e t h is p ic t u r e .

• Historically limited success in HTS of small molecule collections

• PPIs very different from more established targets

• Current small molecule collections decorated in the wrong way

PPI Drug Discovery Problem

• Where is the biologically relevant chemical space of PPIs?

- MW > 500 for PPI inhibitors reaching clinical trial

- Predicted MW of 650-700 Da for small molecule PPI modulators

Wells JC.; McClendon CL Nature, 450, 1001, 2007

HTS(small

molecules &

natural

products)

PPI Modulators

Strategies to Identify Small Molecules

PPI Modulators

Peptides / Peptidomimetics

( -helical,

-strand, -turn)

Fragment-based

(MW < 250,

Ki ~ 100 M)

Chance only favors theprepared mind. — Louis Pasteur

Computational

Chemistry(Hot spots,

binding site)

Project Discovery Flow

HT Screening(PPI binding assay

Phenotypic)

Functional

Assay(s)eADME

PK, brain level

i.p., i.v., p.o.Selectivity

In vivo efficacy in

rodent model

• Selection of compounds libraries

• Choice of primary, secondary

assay(s)

• Understanding selectivity and

brain permeability

• Multidisciplinary team

Key Elements

PoC

Innovative Approaches to Target PPIs

Small Molecule in

Binding Pocket

Antibody Binding

Surface Protrusion

0 500 1,000 200,0002,000

Molecular weight

Staples Peptides

PEM

Synbody

Miniature proteins

Despite significant progress (e.g. oncology),

substantial challenges lie ahead in development of

PPI modulators

Druggability of PPI targets depends heavily on

advances in technologies:

- Improved assays to assess PPI modulators

- High-resolution structure prediction, molecular design

- Design and synthesis of compound libraries for PPIs

screening

- Drug delivery to CNS (neuronal uptake mechanism)

Future Perspective