phenotypic high throughput screening (hts)...phenotypic high throughput screening (hts) roger clark...
TRANSCRIPT
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Phenotypic High Throughput
Screening (HTS)
Roger Clark
Associate Principal Scientist
Global HTS Centre
Discovery Sciences
Past success & future
challenges
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2
DISCOVERY
SCIENCES
Discovery Sciences | Screening Sciences - Global HTS Centre
1. HTS & the Drug Discovery process
2. Phenotypic HTS – Some definitions
3. The Phenotypic HTS challenge
4. Adding value through High Content annotation
5. When is a RIA target not just a RIA target?
6. Conclusion
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1. Drug Discovery Process
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Global HTS Centre Support for multiple Therapeutic areas & External collaborators
4 Discovery Sciences | Screening Sciences - Global HTS Centre
CVMD
Neuroscience
RIA
Oncology
Infection
HTS
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FBLG
ELT
Sub set
The Drug Discovery process
5
Bleicher KH, Bohm HJ, Muller K, Alanine AI., Nature Reviews, 2003, 2, 369-378
HTS
Discovery Sciences | Screening Sciences - Global HTS Centre
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6 Discovery Sciences | Screening Sciences - Global HTS Centre
Seems simple... What’s the problem?
A screening paradigm that enables coverage of broad chemical diversity
in a single activity, with few target prerequisites. Hundreds of thousands
of compounds can be screened in a given experimental run, in order to
deliver fast, efficient and (most crucially) consistent data.
Determine at what point a compound is active
Select the ‘active’ wells
Follow the remainder workflow (shown opposite)
Find a blockbuster drug that makes a meaningful
difference to patients lives
HTS (Diversity Screening)
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HTS
The problem of false positives
• Single point HTS data can be noisy when compared with XC50 data
• Inactive compounds vastly outnumber active compounds
• We typically underestimate the problem of false positives
• A lot of false positives can make it much harder to find the true positives
• For example:
- Imagine we have a population of 1,000,000 compounds
- Our assay is 99.9% accurate (so 99.9% of active compounds are called correctly and 99.9% of
in-actives are called correctly)
- Let’s assume 1 in 1000 compounds are active (this is actually a pretty high ratio)
- From the 1,000,000 compounds we would expect: • 0.999 x 1000 = 999 true positives
• 0.001 x 999,000 = 999 false positives
- If the true hit rate was 1 in 10,000 then we would have 10 false positives for every true positive • 0.999 x 100 = 99.9 true positives
• 0.001 x 999,900 = 999.9 false positives
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But we do find hits….
1 : 1
1 : 10
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Success varies by target class & technology?
Biochemical & Cellular (target-based & phenotypic)
8 Discovery Sciences | Screening Sciences - Global HTS Centre Clark, R. et al. (2013) European Pharmaceutical Review, 18(6)
** Success taken as campaigns which identified 1 or more chemical series & active chemistry resource deployed to progress these
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2. Phenotypic HTS? … Some definitions
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Phenotypic HTS?
HTS (Diversity Screening) A screening paradigm that enables coverage of broad chemical diversity
in a single activity, with few target prerequisites. Hundreds of thousands
of compounds can be screened in a given experimental run, in order to
deliver fast, efficient and (most crucially) consistent data.
Phenotypic HTS A diversity screening approach which employs a functional cellular assay
as the primary screen. In this instance it will be unclear as to MOA of the
small molecules that appear as ‘hits’
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Why would we run Phenotypic Drug Discovery?
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• Target Based drug discovery alone does not deliver a sustainable big Pharma
model
• Phenotypic Screening offers an opportunity for
• Novel Molecules
• Novel Targets
• Novel indications for existing chemical equity
First-in-class Follower drugs
Swinney and Anthony, Nature Reviews, 2011, 10, 507-519
Discovery Sciences | Screening Sciences - Global HTS Centre
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Historic (Target-based vs. Phenotypic)
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Growth of Cellular HTS campaigns for Oncology
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** Success taken as campaigns which identified 1 or more chemical series & active chemistry resource deployed to progress these
Cellular campaigns appear consistently
more successful
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So why don’t we always screen in phenotypic assays?...
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16 Deconvolution…
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Running phenotypic assays is difficult…
• Complex and time-consuming assays to run at scale
• Automation can be tied-up for long periods of time
• Edge-effects for extended time-point assays can lead to ‘wasted space’ on plates
• Difficult to understand SAR - requires more annotation
• However…. Read-out can be fairly simple & cost-effective e.g. Proliferation • Key is to pick the right cell line (mutant vs. WT)
• It might be logistically complex, but…..
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…. Biology is complex too!…
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3. The phenotypic HTS challenge: HTS can lead to a complex data deluge without proper annotation… How do we progress phenotypic hits?
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Compound set stratification on diversity
20 Discovery Sciences | Screening Sciences - Global HTS Centre
Chemical space (diversity)
Incre
asin
g c
luste
r p
op
ula
tio
n
(as m
ore
‘la
yers
’ scre
en
ed
)
What if we thought in more dimensions?...
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?
? ?
?
?
Stratification on annotation?....
Multi-dimensional Data Cube
21 Discovery Sciences | Screening Sciences - Global HTS Centre
Mining historical compound activity
data vs. cell line expression data can
help to identify pathways
‘Black-holes’ in activity data from
historic layer screening vs. full
collection
Phenotype
Expression
profile
Target
Activity
Mutation
status
Tox
liability
Cell
permeability
Annotation never fully complete
Data cells with higher annotation = screened preferentially
Requires capability to build screening sets on-the-fly?
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Toxicity is a key reason for failure of compounds in the clinic
- Evidence to suggest that compounds with pIC50 >4 are 5 times more likely to
cause whole organ toxicity than compounds with pIC50 <4
Mammalian Tox annotation
Using a phenotypic endpoint to annotate
22 Discovery Sciences | Screening Sciences - Global HTS Centre
Early view of Tox liability should enable early decisions on series
progression or compound set selection for limited phenotypic screens
Keep in mind that certain disease settings (eg. Oncology) may well
want compounds that cause cell death
Key is to annotate compounds to further populate the Data Cube
Simple assay run in THP-1
(monocyte derived line) could allow
pre-emptive full collection screening
% effect at 10uM % effect at 50uM
Compounds active in whole organism phenotypic screen
Profiled for mammalian tox liability
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Proliferation… an easy phenotype to screen?
Particularly for Oncology…
23 Discovery Sciences | Screening Sciences - Global HTS Centre
SYTOX Green (504EX/523EM)
Hoechst nucleic acid stain (350EX/461EM)
CyQUANT Assay (480EX/535EM)
Shouldn’t we just pick the right cell line and screen the whole collection against this line to find hits?
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4. Case study – IDOL (E3 ligase) Adding value through High Content Annotation
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Sawamura T Clin Chem 2009(55:12) 2082-2084 2009
IDOL is expressed in the liver and in peripheral WBCs
IDOL a new player in regulation of
LDL receptor (LDLr) levels
IDOL also targets VLDLr and ApoER2
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HEK293 clone expressing LDLR-GFP, 48 h post
transient transfection with Wild Type or Mutant IDOL
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Hoechst LDLR-GFP
Wild Type IDOL
Untransfected
Mutant IDOL
Hoechst + LDLR-GFP
Science 325, 100(2009), Tontonoz
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Schematic of assay (IDOL LDLR-GFP + wt IDOL) DMSO Max signal control
Assay performance: Quality Control Plate
Discovery Sciences | Screening Sciences - Global HTS Centre
IDOL HTS validation – Whole well FI
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Adding value with imaging
Cell Seeding
Incubation at
37ºC for 20hrs
Compound
dosing
Incubation at
37ºC for 6 hrs
Fixation +
Hoechst
Incubation at
RT for 20mins
Measure FI at
485/520nm
LDLR-GFP HEK293 parental
Image 2x channels
1x fov
Analysis on-the-fly
IDOL
LDLR-GFP
0.14%
HEK293
parental
0.07%
0.09%
GeneData
Screener
Cellomics DB Image Store
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IDOL: Image based phenotypic analysis
Max signal control AZ1
(False positive)
False positive (FP) rate increased
through fluorescent compounds
Images analysed for distinctive
features (granules, texture,
area measurements).
Supervised classification
methods used to cluster false
positives and reject them from
the pipeline
Other forms of FP (toxic
compounds, etc.) can be
integrated in the model.
AZ1
(False positive)
DMSO
Max signal control
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Compound A Compound B Compound C
Active only in LDLR-GFP assay Active in both LDLR-GFP & HEK293
parental assays
False positives characterisation performed using the HTS validation compound set
Different MOAs can potentially be distinguish at this early stage of the pipeline (Compound A vs. B)
View of what ‘active’ means can change with increasing observations over a screen
IDOL: Image based phenotypic analysis
Discovery Sciences | Screening Sciences – Global HTS Centre
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5. Q. When is a RIA target not just a RIA target?
A. When it’s also an Oncology target
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RIA goes looking for inhibitors of T-Cell
proliferation…
… And finds chemical equity with excellent in-vitro efficacy
32 Innovative Medicines | Respiratory Inflammation & Autoimmune
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Target deconvolution
33 Innovative Medicines | Respiratory Inflammation & Autoimmune
Total
protein
Photolabelled
protein
MCT1 target identified by
photo-affinity labelling
• Photo-affinity labelled probes built to pull-down molecular target • Sub cellular fractionation 2D Gel chromatography Mass Spec
• MCT1 identified as probable molecular target
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NH2
COOH
Extracellular
Intracellular
NH2
COOH
Extracellular
Intracellular
MCT % ID
100
27
11 27
12 22 23
9 23
Lactate transporter
MCT
38 4 42 6 7 26
5 28
14
8 22
Lactate transporter
10 22
58 2 1
3
13 31
MCT1 Transporter and family
• 12 TM spanning symporter
• Transports lactate & pyruvate along with protons in / out of cell
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MCT1 activity confirmed in functional assay
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MCT Inhibitor MCT-1
Lactate/H+
Activated
T-cell
MTX Leflunomide
TCR
MHC/Ag
Calcineurin
NFAT IL2
CsA
FK506
IL2R
Rapa
TOR
Gene
transcription
Glycolysis
Glucose Lactate
DNA synthesis
Nucleotide
precursors
Proliferation
Novel mechanism of immunosuppression
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You might think you know where you’re going…
Oncology iMed discovers that certain haematological & solid tumours are
extremely sensitive to MCT1 inhibition
Oncology pick-up chemical equity from RIA project and validate in
relevant cancer lines.
AZD3965 currently in Phase 1 trials in partnership with CRUK
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… but when targets stop being the focus you can end up somewhere different…
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6. Conclusion
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The only way to truly deliver a Phenotypic
portfolio is through teamwork….
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Building the right assays
… in the right cell lines
… screened at the right scale & diversity
…. To enable discovery of:
Novel Molecules
Novel Targets
Novel indications for existing equity
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To conclude….
Phenotypic screening is not a new paradigm, but rather a realisation that the
reductionist approach may not be the only way to identify new molecules of
therapeutic value
Phenotypic screening output will take longer to annotate fully and deconvolute
appropriately.
Rationalising the compound set before screening is an approach to simplify
deconvolution Won’t discover new chemistry, but might find new indications /
targets.
Screening every compound through every target-based screen helps to build
the eternally expanding ‘data cube’
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Of course – Breaking down all the metrics and attempting to rationalise phenotypic screening as a paradigm is a fairly reductionist approach..... You can’t underestimate serendipity!
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Thanks to:
Mark Wigglesworth
Dave Murray
Carolyn Blackett
Sinead Knight
Helen Plant
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Thierry Dorval
Helen Boyd
Johan Brengdahl
Sanna Engberg
Graham Belfield
Clare Murray
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Discovery Sciences | Screening Sciences - Global HTS Centre