©Copyright 2015 Galapagos NV

YFP-halide assays for CFTR drug discovery using the FDSS/μcell Joseline Ratnam, PhD Team Leader Biochemical Pharmacology Hamamatsu 11th FDSS User Meeting 11 June 2015

2

Outline • Introduction to Cystic Fibrosis Disease and cause

Approved therapies and remaining challenges

Targeting underlying mutations

• Cell-based assays used for CFTR drug discovery YFP-Halide Assay

Principle and advantages

Assay development on FDSS/µCell

HTS to find CFTR modulators

• Conclusion

3

Cystic Fibrosis: Facts & Biology

• Cystic Fibrosis (CF) is the most frequent life-threatening autosomal recessive disease in the Caucasian population

1 in 2500 newborns diagnosed with CF

1 in 25 Caucasians carry at least 1 CF allele

• Characterized by thick mucus in lumen of several organs

Airways, pancreas, gastro-intestinal tract, reproductive tract

Frequent lung infections, sinus infections, poor growth, and infertility

Life expectancy: mid-30s

• Caused by mutations in the CFTR gene (~1900)

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Cystic Fibrosis Transmembrane Conductance Regulator (CFTR)

ATP

ADP + Pi

ATP

ADP + Pi

PKA + ATP

Domaine R

NBD-1NBD-2

Extracellulaire

Intracellulaire

N

C

MSD-1 MSD-2

ATP

ADP + Pi

ATP

ADP + Pi

PKA + ATP

Domaine R

NBD-1NBD-2

Extracellulaire

Intracellulaire

N

C

MSD-1 MSD-2

• Chloride channel from ABC transporter family, expressed on the apical membrane of epithelial cells

• In normal cells, water follows chloride ions onto surface of lung, hydrates lung surface and cilia beat normally

• Defective CFTR channels don’t transport chloride ions out of cells

• Reduced hydration of lung surfaces impairs normal functioning of cilia

CFTR : ATP-gated Cl- channel

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Approved CF Therapies Stem Cell and Gene Therapy

Treatments

Small-Molecule CFTR Modulators Kalydeco®, Kalydeco®

/Lumacaftor combination (ORKAMBI™

FDA decision July 5, 2015 )

Targeting the cause

Infection Treatments Tobramycin, Azithromycin,

Cayston®

Anti-inflammatory Treatments Ibuprofen

Mucus Alteration and Airway Surface Liquid Modulation Therapy

Hypertonic saline, Pulmozyme®

Targeting the symptoms

CFTR gene mutation

CFTR protein dysfunction

Defective mucociliary clearance

Airways obstruction

Inflammation Infection

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Challenges in CF drug discovery

• Gene therapy : Lack of efficient gene transfer to cellular targets required to correct in vivo CFTR function -> 25 failed clinical trials to date

• Lack of good animal models

• Paucity of structural information on full-length wild-type and mutant CFTR

• Complexity of defects caused by various CFTR mutations

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• Class 1 – Synthesis Premature stop codon, ~10% freq

• Class 2 – Maturation Includes F508del, ~70% freq

• Class 3 – Regulation Includes G551D, ~3-5% freq

• Class 4 – Conductance Includes R117H, ~2% freq

• Class 5 – Quantity • Class 6 - Turnover

Classes of CFTR mutations

ICFTR = n x Po x g n = number of channels Po = open probability g = channel conductance

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Combination approaches to fix the most severe CFTR mutations

Maturation Defect (Class II , eg. F508del)

Corrector

Functional Defects (Class III / IV, eg. G551D, R117H)

Cl- Cl- Cl-

Cl- Cl-

Cl- Cl-

Cl-

Cl- Cl-

Adapted from Dr. Scott Donaldson’s Plenary Session (NACFC, 2013)

Potentiator

PKA PKA

Potentiators restore the flow of ions through activated CFTR

Correctors restore the processing of CFTR from the ER to the surface

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CFTR phenotypic assays

• CFTR channel function:

Membrane potential or halide-sensitive fluorescent dyes to measure CFTR-dependent chloride influx

YFP-Halide assays to measure CFTR-dependent halide influx

• CFTR cell surface expression:

Epitope-tagged CFTR detection on cell surface via ELISA

Beta galactosidase enzyme fragment complementation for detection of membrane localized enzyme fragment fusion CFTR construct (DiscoveRx™)

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YFP-Halide Assay • Fluorescence of Yellow Fluorescent Protein mutant ( YFP-H148Q/I521L)

quenched by halides (selectivity: iodide > chloride)

• Cell lines expressing mutant CFTR and YFP are generated, CFTR activated via cAMP ↑ (Forskolin) in the presence of iodide

• Compound mediated restoration of anion channel function estimated by fluorescence quenching of iodide

Cell-based assay for high-throughput quantitative screening of CFTR chloride transport agonists Luis V. J. Galietta, Sujatha Jayaraman, A. S. Verkman American Journal of Physiology - Cell Physiology Nov 2001, 281 (5)

YFP YFP

Cl-/ I-

I-

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Detection of CFTR potentiators Cells over-expressing F508d-CFTR and YFP-H148/I152L

YFP

27oC

(24h)

YFP

Cl- → I-

I-

YFP

Fsk + CFTR potentiator

YFP (10min)

Fsk + inactive cpd NaI

CFTR potentiator

Vehicle/inactive

-12 -10 -8 -6 -40.0

0.2

0.4

0.6

0.8

log conc (M)

1-F

/F0

Dose response CFTR potentiator

YFP

Cl-

Cl-

YFP Cl- → I-

I-

I-

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Detection of CFTR correctors

YFP

YFP

YFP YFP

Cl- → I-

I-

YFP

+ CFTR corrector

(24h)

+ inactive compound

Cells over-expressing F508del-CFTR and YFP-H148/I152L

YFP

Cl-

Cl-

YFP Cl- → I-

I-

I-

Fsk + Potentiator

(20 min)

NaI

CFTR corrector

Vehicle/inactive

-10 -9 -8 -7 -6 -50

25

50

75

100

125

log conc (M)

% a

ctiv

ity v

s Po

s C

trl Dose response CFTR corrector

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Advantages • Sensitive quantitative assay to measure restoration of

deficient cellular chloride transport – HTS compatible

• Excellent optical properties and retention in cells

• Fluorescence indicator loading and washing not necessary

• Applicable to physiologically relevant bronchial epithelial cells - show minimal basal halide permeability before stimulation

• Anion co-transporters like NKCC and exchangers like AE1 transport I- poorly, whereas CFTR transports I- efficiently -> better selectivity

• Can be run in different flavours : to detect potentiators, correctors and compound synergies

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HTS to identify CFTR potentiators Assay optimization

• Evaluation of HEK-293 cells vs CF bronchial epithelial (CFBE41o-) cells

• Transfection/transduction conditions

• Using the µcell/FDSS for increased throughput - comparison with EnVision®

• Analysis method

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Z’ is generally poor for HEK-293 transfected cells

HEK-293 Cell number and YFP transfection conditions

Baseline fluorescence and Z’ in HEK-293 cells transfected with YFP-H148/I152L

1 2 3 4 5 1 2 3 4 5 1 2 3 4 5 1 2 3 4 50

5000

10000

15000

20000 15.000c/w20.000c/w25.000c/w30.000c/w

F0 (b

asel

ine)

1 2 3 4 5 1 2 3 4 5 1 2 3 4 5 1 2 3 4 5-20-10

-0.8-0.6-0.4-0.20.00.20.40.60.81.0

15.000c/w20.000c/w25.000c/w30.000c/w

z'

16

10 20 30 40 50 10 20 30 40 50 10 20 30 40 50 10 20 30 40 50

-0.4

-0.2

0.0

0.2

0.4

0.6

0.8

1.0

z'

CFBE41o- cells Cell number and YFP transduction conditions

• Adenoviral transduction in CFBE cells gives more uniform YFP signals • More physiologically relevant cell line for CF

Baseline fluorescence and Z’ in CFBE cells transduced with YFP-H148/I152L

10 20 30 40 50 10 20 30 40 50 10 20 30 40 50 10 20 30 40 50

0

5000

10000

15000

20000

25000

30000

35000 1000c/w

1500c/W

2000c/w

2500c/w

base

line

F 0

YFP MOI YFP MOI

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Comparison of instruments EnVision® (Perkin Elmer)

Dual-detector multilabel Plate reader

Label specific optical mirror modules and filter optics

Temperature control Well per well reading

High precision dispenser unit:

Well per well dispensing -96w plates

Dispense volume: 2 - 475 µL

Dispense speed: 100 - 500 µL/sec

FDSS/µCELL (Hamamatsu) Kinetic plate reader for fluorescence and

luminescence Filter optics

No temperature control High speed, high - sensitivity CCD camera

for detection of entire plate 384 well dispenser head:

Simultaneous 384w dispensing

Dispense volume: 1 - 30 µL

Dispense speed: 2 - 50 µL/sec

Multiple compound/ligand dispensing

Active wash station allowing reuse of tips, with wipe function

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Comparison of methods EnVision® Assay conditions FDSS/µCELL

Day 1: Cell seeding

96 well Plate format 384 well

6,000 cells/well in 100 µL Cell density 2,000 cells/well in 50µL

Day 2: Transduction of cells

MOI 20 YFP virus MOI 30

MOI 30 CFTRdelF508 virus MOI 30

Day 3: Low temperature correction

20 hours incubation at 27 °C, 5% CO2

Day 4: Washing of cells, compound addition & activation of CFTR

Manual washing (2 x 40 µL) Washing of cells with DPBS Plate washer (5x 90 µL, 20 µL remaining after last wash)

Addition of compounds and forskolin using multichannel (40 µL added on dry cells)

Compound addition + activation of CFTR with 10 µM forskolin

Compound and forskolin addition using FDSS/µCELL (10 µL added on cell plates

containing 20 µL PBS)

150 µL/sec Injection of I- 30 µL/sec

16 minutes (34 readings per well every 0.2 sec) with excitation at 485 nm and emission

at 530 nm Reading

3 minutes including washing of tips (384 wells read simultaneously) with excitation

at 480 nm and emission at 540 nm

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Analysis method

Analysis based on slope

Analysis based on fluorescence at 36 sec

Analysis based on fluorescence at 105 sec

S/B 1.7 2.2 1.4

Z’ 0.67 0.76 0.76

F0 = fluorescence before injection F = fluorescence at a fixed time point after injection.

-12 -10 -8 -6 -40.0

0.2

0.4

0.6

0.8

log conc (M)

1-F

/F0

Dose response CFTR potentiator

Positive control Vehicle

0 5 10

15

20

25

30

35

40

45

50

55

60

65

70

75

80

85

90

95

100

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Comparison of compound activities

Good correlation between pEC50 values obtained on both platforms

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Comparison of QC parameters

0.00

0.40

0.80

1.20

Expt. No.

Z' (EnVision) Z' (FDSS/µCELL)

0.00

4.00

8.00

12.00

Expt. No.

S/B (EnVision) S/B (FDSS/µCELL)

• Z’ values comparable between platforms • S/B considerably reduced on the FDSS/µCELL but more

stable over runs

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HTS to identify potentiators of F508del-CFTR • Library

A diverse selection of 76,000 compounds was screened (40 plates/day, 6 runs)

• HTS QC criteria

Plates accepted if Z’>=0.35

Pharmacology QC by reference compound IC50 +/- 3 fold the historical average

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YHA potentiator HTS Normalized data

• High hit rate observed • Consistent data after normalization over the different runs • Reproducible pharmacology for reference compounds

% A

ctiv

ity

Compound #

HTS data normalized to positive control

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0

0.2

0.4

0.6

0.8

1

1.2

1.4

1.6

1.8

2

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

0 50 100 150 200 250

YHA potentiator HTS QC results

• Good assay S:B and plate Z’ for most plates screened • Only 1 plate rejected for the whole screen

HTS plates Quality Control

Plat

e Z’

Plat

e S:

B

Plate #

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YHA potentiator HTS Hit identification

• Asymmetric distribution due to high hit rate, hit calling using IQR method • Percentage activation ≥ Q3+3.5*IQR (62%) • 909 hits identified with > 62% activity, being further profiled

% activity distribution for controls and samples

Binned Ra data PIN

Hits selection at 62%

Row

cou

nt

Binned normalized data

Row

cou

nt

Binned normalized data

Row

cou

nt

Binned normalized data

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Conclusions • Quantitative functional assay to identify compounds that

improve chloride channel function in CFBE cells

• Robust protocol with an average S/B of 1.8 and a Z’>0.5.

• Optimized protocol using the plate washer and the FDSS/µCELL led to a 20-fold increase in the assay throughput – suitable for HTS

• Good correlation between EC50 data obtained on the EnVision® and the FDSS/µCELL

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Acknowledgments CF team at Galapagos Mechelen

Thierry Christophe

Luc Nelles

Katja Conrath

Jan Van Der Schueren

Mia Jans

Anne-Sophie Wesse

Kim Carrein

Katleen Verdonck

Ann Vandevelde

YFP-halide assays for CFTR drug discovery using the FDSS/μcell Outline�Cystic Fibrosis: Facts & BiologyCystic Fibrosis Transmembrane Conductance Regulator (CFTR)Approved CF TherapiesChallenges in CF drug discoveryClasses of CFTR mutations�Combination approaches to fix the most severe CFTR mutationsCFTR phenotypic assaysYFP-Halide Assay Detection of CFTR potentiators �Detection of CFTR correctors�Advantages HTS to identify CFTR potentiators�Assay optimizationHEK-293�Cell number and YFP transfection conditionsCFBE41o- cells�Cell number and YFP transduction conditionsComparison of instrumentsComparison of methodsAnalysis methodComparison of compound activitiesComparison of QC parametersHTS to identify potentiators of F508del-CFTRYHA potentiator HTS�Normalized dataYHA potentiator HTS�QC resultsYHA potentiator HTS�Hit identificationConclusionsAcknowledgments