Proteins, Structures, Chemical probes
and Target Discovery – all Open Access.
Chas Bountra
University of Oxford
SGC Toronto
SGC Oxford
SGC Stockholm
Outline
• Public Private Partnership (PPP):
- pool resources
- share risk
• No IP:
- facilitate collaboration
- access best labs quickly and freely
• Disseminate data quickly:
- reduce wastage of resource
- potentially reduce unnecessary patient exposure
• Gene sequence, protein structures, chemical
probes……validation of novel targets in patients –
“proof of clinical mechanism” (POCM)
• Epigenetic proteins are better targets for Drug
Discovery
SGC: Structural Genomics
Consortium
• Established 7 years ago
• Based in Univ. of Toronto, Karolinska Institutet and
Univ. of Oxford
• 200 scientists
• Funded by
- private:
GSK, Merck, Novartis
- govt:
Canada, Sweden
- charities: Wellcome Trust, Wallenberg
Foundation
Objective
Human protein structures
- therapeutically relevant targets
- selected by funders
Achievements
• More than 1000 human protein structures
(nearly 25% of PDB)
• Have purified 2000 human proteins
• >1 publication per week (11 in past two years in
Science, Cell, Nature)
• 500 cDNA clones distributed freely every year
(academia, biotech, pharma)
Our modus operandi
• Do, and enable great science
• Work with the very best (250+ collaborations)
• Disseminate data immediately
• Publish in high impact journals
• Exceed objectives agreed with funders
• No IP
Impact of “no IP”
• Collaborate quickly with any scientist, lab or
institution
• Work closely with multiple private organisations,
on same project
• Generate data quickly
• Place data in public domain quickly
50% of all human protein kinase structures
solved by SGC (in past 5 years)
22 novel structures in one paper
23/ 34 Human Phosphatase
structures solved by SGC
• Compare binding sites
- predict off target activity
• Design allosteric inhibs
• Proteins for
- screening and chemical
probe ID
- antibody production
Epigenetics Chemical Probes Consortium
June 10
June 09
April 09
Jan 09
Pfizer
OICR
(8FTEs) (2FTEs)
Well. Trust (£4.1M)
NCGC (20HTSs)
GSK (8FTEs)
UNC Novartis
(3FTEs) (8FTEs)
Ontario ($5.0M)
15 acad. labs
Sweden ($3.0M)
….more than £30M of resource….now Lilly (8FTEs)
Why epigenetics?
• Potential in many therapeutic areas: oncology,
neuro-psychiatric, inflammation, metabolic….
• Underestimated role of environment, stress, diet,
injury, chronic drug use, early life experiences…
• Early in cascade, not single late stage mediator
PNI induced epigenetic gene silencing
Peripheral nerve injury (PNI)
Increase Neurone Restrictive Silencer Factor (NRSF) in DRG
Bind to Neurone Restrictive Silencer Element (NRSE)
Decreased histone acetylation
Decreased transcription of mu opioid receptor, Nav1.8, Kv4.3
Uchida et al 2010, J of Neuroscience, Uchida et al 2010, Neuroscience
Decreased acetylation of mu opioid
receptor through NRSF binding
Uchida et al 2010, J of Neuroscience
HDACi are anti-hyperalgesic
HDACi
Increased acetylation of p65RelA
Increased mGluR2 expression
Decreased neurotransmitter release from primary afferents
Anti-hyperalgesia
Chiechio et al 09
HDACi increases expression of mGluR2
in lumbar cord (not 1a, 5 and 4)
MS275 (HDAC inhib): 5 days, 3mg/kg sc
Chiechio et al 09
Maternal care, increases GR
expression and dampens stress response
• Maternal care increases TF NGFI-A and histone acetylation,
decreases DNA methylation and increases GR expression
• Methionine promotes methylation and Low LG phenotype
• HDAC inhibs increase acetylation and High LG phenotype
TSA – Trichostatin A (HDAC inhib), SAM – S adenosyl methionine
McGowan et al 08
Childhood abuse decreases
glucocorticoid receptor
Post mortem hippocampus
Decreased GR, leads to increased stress response
Also decreased NGFI-A
McGowan et al 09
Childhood abuse increases methylation
of glucocorticoid receptor
McGowan et al 09
HDAC inhibs have anti-depressant like effects
After 10 days chronic social defeat stress
Infused MS275 or SAHA 100μM
Covington et al 2009
Social defeat stress induced changes in gene expression
are partially reversed by MS275 or fluoxetine
MS275: 100μM infusion into NAc
Fluoxetine: 20mg/kg/day
For 10 days after chronic (10days) social defeat stress
Covington et al 2009
T cell differentiation is associated with
modifications of signature cytokines
•Genome wide
maps - ChIP Seq
•Signature cytokines
as expected
H3K4me3 activating
H3K27me3 repressing
Wei et al 09
JmjD3 is increased in activated macrophages
De Santa et al 07
Transient hyperglycemia produces long
lasting changes in human AECs
Transient hyperglycemia in HAECs
Increased reactive oxygen species
Increase in SET7
Increase in H3K4me1
Increase in NFKβp65
Increase in MCP1 and VCAM1
El-Osta 2008
Transient hyperglycemia produces
sustained elevation of SET7 binding and
H3K4me1
El-Osta 2008
Modulating a late stage mediator
is unlikely to be effective
Birth
Death
Trauma - tissue damage/ nerve injury/ surgery
- infection
- stress/ abuse
- ischemia
- toxins
- drugs
10
100
Nos of genes/ proteins, up/down regulated
1000
Bromodomain proteins
recognise KAc on
histone tails
31 Bromodomain structures
Bromodomain Probes - Target Profile
• <100 nM
• >30-fold selectivity vs
other sub-families
• Cellular potency <1µM
A pre-probe shows sub-family selectivity
BRD4 pre probe shows enantiomeric
specificity
JQ1 reduces proliferation in
two patient derived cell lines
Ki67 Positive ( %)
100
80
60
40
20
0
Vehicle
JQ1
797
KI67 positive = proliferating
Vehicle
403
JQ1
JQ1 induces apoptosis
Annexin V, marker of early apoptosis
PI = propidium iodide, marker of late apoptosis
STA = Staurosporine
JQ1 inhibits tumour growth
Speed, cost and impact of probe
• 2 months: from molecule to submission of
publication
• No cost to us: much of functional data generated
by collaborator at Harvard via network of labs
• Probe has already been sent to 250+ labs
throughout the world for evaluation in multiple
disease areas
Already deposited half of all structures
Family
Number
of
targets
Purified
in SGC
Assays
established in
SGC
Structures
deposited
[SGC/Total]
Lysine demethylase
(KDM)
30
16
16
6/8
Bromodomain (BRD)
42
27
27
14/17
R
O
Y
A
L
Tudor domain
36
15
0
6/19
Chromo domain
34
20
9
10/16
9
8
3
4/7
83
17
14
8
3
5
1/23
5/8
60
31
7
12/18
311
139
70
58/116
MBT domain
PHD
Histone
acetyltransferase (HAT)
Histone
methyltransferase
(HMT)
TOTAL
Creating reagents to accelerate and
improve Target Discovery
Proteins
SGC
Structures
Global
biomedical
community
Chemical
probes
1) Reagents freely available
2) Many collaborations with clinicians and disease experts:
access to assays and new technologies
3) Leveraged resource
Problems with way we do Drug
Discovery
•
Same targets, in parallel, in secret (duplication,
wastage, patients being unnecessarily exposed)
•
Target validation is best done in patients
(preclinical assays have limited utility)
•
No one organisation has all capabilities
•
Early IP is making it even harder (slows
collaboration, restricts competition, makes process more
expensive)
Largest attrition for novel targets
is at clinical POC
Target
ID/
Discovery
HTS
50%
Hit/
Probe/
Lead
ID
LO
10%
Clinical
candidate
ID
Tox./
Pharmacy
30%
Phase
I
Phase
IIa/ b
30%
90+%
this is killing
our industry
…we can generate “safe” molecules, but they
are not developable in chosen patient group
This failure is duplicated, many times
Target
ID/
Discovery
Target
ID/
Discovery
Target
ID/
Target
Discovery
ID/
Discovery
Target
ID/
Discovery
Target
ID/
Discovery
Target
ID/
Discovery
HTS
50%
Hit/
Probe/
Lead
Hit/
ID
Probe/
Lead
Hit/
ID
Probe/
Hit/
Lead
Probe/
ID
Lead
Hit/
ID
Probe/
Lead
Hit/
ID
Probe/
Lead
Hit/
ID
Probe/
Lead
ID
LO
10%
Clinical
candidate
ID
Clinical
candidate
ID
Clinical
candidate
Clinical
ID
candidate
ID
Clinical
candidate
ID
Clinical
candidate
ID
Clinical
candidate
ID
Toxicology/
Pharmacy
Phase
I
Phase
IIa/ b
Toxicology/
Pharmacy
Phase
I
Phase
IIa/ b
Toxicology/
Pharmacy
Toxicology/
30%
Pharmacy
Phase
I
Phase
30%
I
Phase
IIa/ b
Phase
90+%
IIa/ b
Toxicology/
30%
Pharmacy
Phase
30%
I
Phase
90+%
IIa/ b
30%
30%
30%
30%
90+%
90+%
Toxicology/
Pharmacy
Phase
I
Phase
IIa/ b
Toxicology/
Pharmacy
Phase
I
Phase
IIa/ b
30%
30%
90+%
30%
30%
90+%
30%
30%
90+%
…outcomes are not shared
TRPV1 patents by company
TRPV1 patents by disease
– all therapeutic areas
Solution
• A Public Private Partnership to take pioneer targets
through to Phase II (Proof of Clinical Mechanism)
• Create IP only on developable assets, after positive
POCM studies
• Publish all negative studies immediately and positive
studies after a small delay
• Objective is to generate pioneer, clinically validated, derisked targets which pharma can convert into new drugs
Plans post POCM
Invalid
mechanism
Publish
quickly
90%
1 or more
partners
develop
probe
POCM
Developable
probe
10%
10%
Secure IP,
auction IND
to partners
Other
partners
develop
proprietary
molecules
Valid
mechanism
90%
Non
developable
probe
All partners
develop
proprietary
molecules
Proceeds to
independent
research
fund
Benefits of such a model
• Pool resources (charitable, govt,
philanthropic, private) and share risk
• Access global academia quickly and freely
• Rapid publication reduces duplication and
saves patients
Toronto Summit Feb 2011
• Aled Edwards and Stephen Friend
• 5 stakeholder groups: pharma, public funders, patient
groups, regulators, academics
• Outcomes
- Patient groups will facilitate recruitment and minimise
costs of trials
- Regulators will help validate new clinical endpoints and
develop new study designs
- 41/ 43 in favour of model (2 from academic tech
transfer did not vote)
• Recommendation: do now, not pilot
Shifting the pre-competitive
boundary
• 1999
human gene sequence
• 2003
human protein structures
• 2009
chemical probes to enable
target discovery
• 2012
novel, clinically validated
targets
Acknowledgements
• SGC
• Stefan Knapp, Tom Heightman
• Aled Edwards: SGC, Toronto
• Stephen Friend: Sage Bionetworks, Seattle
• Toronto Summit attendees
Sharing costs, sharing risks and
creating benefits
Academia
(probes)
PPP
- novel targets
- through POCM
Clinically
invalidated
targets
(90%)
Clinically
validated
targets
(10%)
Pharma
(probes and
candidates)
National health/ clinical
infrastructures
- patient databases
- stratified patients
- biomarkers
- tissue banks
Where will assets come from?
• Pharma
- “ineffective but safe” clinical candidates
- de-prioritised clinical probes
- short or no patent compounds
• Academia
- new clinical probes
- existing drugs for new indications
probe = good enough to invalidate target
candidate = “potential” to be a drug
Focus of PPP
Target
ID/
Discovery
HTS
50%
Hit/
Probe/
Lead
ID
LO
10%
Clinical
candidate
ID
Clinical
probes
Toxicology/
Pharmacy
30%
Phase
I
30%
De-prioritised assets
Phase
IIa/ b
90+%
How can probe be commercially
viable after a positive POCM?
• Following data will not be published
- route for large scale synthesis
- impurities
- “patient drop-outs”
……
Since Toronto
• Chosen 3 therapeutic areas
- Oncology
- Inflammation
- CNS
• Starting to identify leaders (academic and industrial) and
academic centres (Oxford, Toronto, UCSF)
• Collating input of senior therapeutic heads in pharma
- who are academic leaders?
- which are best academic centres?
- which diseases should we focus on?
• Defining deliverables, timelines and costs with pharma
colleagues
Meeting planned in San
Francisco April 16/17
• Meeting of individuals and organisations that will
operationalise
• Start compiling business plan
• Aim to start Jan 2012
• Calling it ARCH2POCM
- Academics, Regulators, Citizens, Health
industry
- virtual organisation operating as an
ARCHipelago
- Proof Of Clinical Mechanism