Bonnie Ramsey, M.D.

1. Roadmap to a Cure (II)AClinical Research Path Ensuring Benefit for All Patients with CF Bonnie Ramsey, M.D. CF Endowed Professor of Pediatrics, University of Washington School of Medicine Director, CFF Therapeutics Development Network Coordinating Center October 18, 2013

2. Faculty Disclosure Bonnie W. Ramsey, M.D. In my capacity as Director of the Cystic Fibrosis Foundation Therapeutics Development Network Coordinating Center, I have received grants or contracts from the following companies in the past 3 years: 12th Man Technologies Achaogen Aires Apartia Bayer Healthcare AG Celtaxsys Bristol – Myers Squibb Cornerstone Therapeutics Eli Lilly Genentech Gilead Sciences GlaxoSmithKline Grifols Therapeutics, Inc Hall Bioscience InsmedCorporation* KaloBios* RempexPharmaceuticals, Inc. N30 Pharmaceuticals, LLC Nikan Pharmaceuticals Nordmark Novartis Pharmaceuticals Corp. Pharmagenesis PTC Therapeutics, Inc.* Pulmatrix SavaraPharmaceuticals* Talecris Vectura Ltd. Vertex Pharmaceuticals Incorporated* *Companies mentioned in this presentation

3. Our Dream All patients with Cystic Fibrosis will live full, healthy lives.

4. Mucociliary clearance and obstruction Periciliary Liquid (PCL) Surface Epithelial Cells CFTR normal CF Tenacious Mucus

5. How much CFTR is enough? Pancreatic Insufficient CF Pancreatic Sufficient Carriers Normal ≈ 30% CFTR activity associated with symptom reduction Adapted from Accurso et al JCF 2013 in press

6. CF is Not One Genetic DisorderCFTR mutation classes Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- X X X X X Normal Class I synthesis Class II maturation Class III regulation Class IV conductance Class V quantity ‘severe’ mutations ‘mild’ mutations pancreatic insufficiency decreased survival pancreatic sufficiency Adapted from http://www.umd.be/CFTR/W_CFTR/gene.html

7. So, there must be mutation specific treatment approaches Reduced Quantity Reduced Function Normal CFTR quantity and function Little to no CFTR Some CFTR Gating Conductance Class I Class II Class III Class IV Class V Treatment approaches Correctors Potentiators MacDonald et al. Pediatr Drugs 2007;9:1-10; Zielenski. Respiration 2000;67:117-33; Welsh et al. Cystic fibrosis In: Valle et al, eds. OMMBID. McGraw-Hill Companies Inc;2004:part 21,chap 201; O’Sullivan et al. Lancet 2009;373:1891-1904

8. Our challenge is finding therapies to correct CFTR for all CF mutations First Allele Second Allele CFFPR* Patients Among 25,976 patients with at least one allele recorded in the 2012 CFFPR *Cystic Fibrosis Foundation Patient Registry, 2012

9. Patients with two copies of F508del predominate in the US First Allele Second Allele CFFPR* Patients *Cystic Fibrosis Foundation Patient Registry, 2012

10. Our challenge is finding therapies to correct CFTR for all CF mutations First Allele Second Allele CFFPR* Patients Log scale *Cystic Fibrosis Foundation Patient Registry, 2012

11. Proof-of-concept for mutation-specific therapy Class III gating mutations- G551D Cl- Cl- Cl- Cl- Cl- Cl- X X Most common CF gating mutation Mutant protein is present on the epithelial cell surface - ion transport is reduced High throughput screening of small molecules identified ‘potentiators’: molecules that increased G551D function at the cell surface

12. How Much CFTR is Enough?The Ivacaftor – G551D Benchmark Study Baseline 150 mg Adapted from Accurso et al New Engl J Med 2010

13. Ivacaftor has a profound impact on lung function J Davis, AJRCCM, 2012 Ramsey, New Engl J Med, 2011 http://www.accessdata.fda.gov/drugsatfda_docs/nda/2012/203188Orig1s000SumR.pdf.

14. The ivacaftor effect persists for many months Open Label Follow-On See: McKone et al. NACFC 2013 Poster #227

15. Effect of 150 mg BID ivacaftor on hospitalization rate in G551D patients From the GOAL presentation and kindly provided by S. Rowe

16. Important lessons learned from approval of the CFTR potentiator ivacaftor High throughput screening In vitro models In vitro models: HBE Cells High throughput screening to find candidates

17. Important lessons learned from approval of the CFTR potentiator ivacaftor High throughput screening In vitro models In vivo biomarkers in vivo Biomarkers (Sweat Chloride)

18. Important lessons learned from approval of the CFTR potentiator ivacaftor High throughput screening In vitro models In vivo Biomarkers Clinical Outcome Clinical Outcome (Lung Function)

19. Important lessons learned from approval of the CFTR potentiator ivacaftor High throughput screening In vitro models In vivo biomarkers Approval Clinical outcome A successful drug approval pathway Approval

20. Yet, questions remain • For example, sweat chloride and lung function changes correlate poorly for individual patients DurmowiczChest 2013

21. Ivacaftor coverage of G551D mutations in the US First Allele Second Allele 1,138 patients CFFPR* Patients 19 homozygotes *Cystic Fibrosis Foundation Patient Registry, 2012

22. Progress towards our goal Ivacaftor G551D 4.4%* 95.6% Remaining *- at some point in their lives (no data in infants and young children) Cystic Fibrosis Foundation Patient Registry, 2012

23. Are there other patients with CF who may benefit from ivacaftor monotherapy? • Other gating mutations • Infants and toddlers with G551D • Mutations, like R117H, that result in residual CFTR function

24. Ivacaftor coverage of other gating mutations • In vitro studies have shown that ivacaftor improves chloride transport in CF cells with other CFTR gating mutations1 • G178R, S549N, S549R, G551S, G970R, G1244E, S1251N, G1349D, S1255P • KONNECTION Study: Blinded, placebo-controlled 8 week crossover study of ivacaftor in other CFTR gating mutations with open label extension2 • At 8 weeks, FEV1 change from baseline favored ivacaftor treatment by 10.7% predicted (P < .0001) • Comparable to ivacaftor treatment effect seen at 24 weeks in G551D patients (10.6% predicted, P < .0001) Study Status: Crossover portion complete, supplemental New Drug Application filed 1- Yu et al. J Cyst Fibros. 2012;11(3):237-45. 2- DeBoeck et al. NACFC 2013 Symposium 3.15 and Poster #241 Kindly provided by Vertex Pharmaceuticals

25. Ivacaftor Phase 3 Study: VX770-108 KIWI (2-5 years) • A two-part, open-label study to evaluate the safety, pharmacokinetics, and pharmacodynamics of ivacaftor • Patients with CF aged 2 through 5 years with a CFTR gating mutation: • G551D, G178R, S549N, S549R, G551S, G970R, G1244E, S1251N, G1349D, S1255P Part A Multiple dose safety and PK trial Part B Ivacaftor Week -4 Week 0 Wk 12 Wk 24 Study Status: Fully enrolled with data anticipated second quarter 2014 Kindly provided by Vertex Pharmaceuticals

26. Phase 3 Study: R117Hmutations - Konduct • Multi-center, randomized, double-blind, placebo-controlled study (1:1) Follow Up Ivacaftor 150mg q12h Screen Run In Placebo W-5 W-2 0 W2 W4 W8 W16 W24 W28 Key Inclusion Criteria • ≥ 6 years of age • Sweat chloride ≥60 mmol/L • At least 1 R117H allele FEV1 at screening • 6 – 11 years old, 40 to 105 % predicted • ≥ 12 years old, 40 to 90% predicted Study Status: Fully enrolled with first results expected by end of 2013 Kindly provided by Vertex Pharmaceuticals

27. Potential coverage of ivacaftor: infants and children, other gating mutations, R117H G551D/R117H 6.8% 93.2% Remaining Cystic Fibrosis Foundation Patient Registry, 2012

28. CFTR proteins with Class II mutations do not reach the cell surface Cl- Cl- Cl- Cl- Cl- Cl- Cultured F508del/F508del-human bronchial epithelial cells X cilia cytoplasmic F508del CFTR F508del Class II mutation nuclei Normal CFTR Van Goor et al., PNAS 2011

29. F508del dominates the Class II common mutations G551D/R117H 6.8% 9.9% Remaining 5.1% F508del Heterozygotes 40.1% (10,409 in US) F508del Homozygotes 48.0% (12,469 in US) Cystic Fibrosis Foundation Patient Registry, 2012

30. Lumacaftor increases the amount of F508del-CFTR at the cell surface Cultured F508del/F508del-human bronchial epithelial cells cilia CFTR nuclei untreated + lumacaftor Van Goor et al., PNAS 2011

31. The function of lumacaftor corrected F508del-CFTR can be further enhanced by a CFTR potentiator F508del/F508del-HBE (N = 7 donor bronchi) Chloride transport (% Normal CFTR) Van Goor et al., PNAS 2011

32. Phase 2: lumacaftor with and without ivacaftor in F508del homozygotes Boyle et al NACFC 2012

33. Lumacaftor + ivacaftor Phase 3 studies: VX809-103 & 104, TRAFFIC & TRANSPORT Randomized, placebo-controlled double-blind Phase 3 studies in F508del homozygotes TRAFFIC (103) TRANSPORT (104) Rollover/Extension Up to 96 Weeks lumacaftor 600mg QD + ivacaftor 250mg q12h OR lumacaftor 400mg q12h+ ivacaftor 250mg q12h lumacaftor 600mg QD + ivacaftor 250mg q12h Homozygous F508del lumacaftor 400mg q12h + ivacaftor 250mg q12h placebo Week 1 24 • Primary Endpoints: • Relative change in FEV1 % predicted through Week 24 compared to placebo • Examples of Key Secondary Endpoints: • Absolute change in body mass index (BMI) from baseline at Week 24 • Number of pulmonary exacerbations through Week 24 • Safety and tolerability assessments Study Status: Fully enrolled and data anticipated mid 2014 Kindly provided by Vertex Pharmaceuticals, Inc.

34. CFTR correctors • Good news: significant progress in patients who have two F508del mutations • Ongoing challenges: • Correction is a multi-step process which may require more than one drug • If a patient has only one F508del mutation (i.e., F508del heterozygote), the overall clinical response is often reduced.

35. Strategic planning for back-up correctors began 4 years go • Reviewed lessons learned from first generation correctors • Created road map for more robust second generation compounds • Strong partners in place • Amazing progress • Novel screens developed • Up to 6 million compounds will be reviewed

36. Wild-type CFTR channel formation Folding and assembly of membrane and cytoplasmic domains Reaches cell surface M1 M1 M2 M2 M1 M1 N1 N2 N1 N1 M1 M2 CL1 CL4 Phenylalanine 508 M= membrane spanning domain N= nuclear binding domain F508 N2 N1 Thomas et al. FEBS Lett. 1992;312(1):7-9. Du et al. Nat StructMol Biol. 2005;12(1):17-25 Rabehet al. Cell. 2012;148(1-2):150-63. Mendoza et al. Cell. 2012;148(1-2):164-74.

37. Multiple correctors may be required for optimal F508del folding cotranslational folding posttranslational folding Target 2 Target 1 M1 M1 M1 M1 M2 M2 M2 M2 M1 M1 M1 M1 M2 M2 M2 N2 N2 N1 N1 N1 N1 N2 N1 N1 N1 N1 R N2 N2 R R R R R R Folded CFTR Target 3 Okiyoneda, Nature ChemBiol 2013

38. A second corrector further enhances in vitro F508del CFTR function F508del/F508del F508del/G542X Kindly provided by Vertex Pharmaceuticals, Inc.

39. Remaining CFTR genotypes 9.9% Remaining Nonsense Mutations 8.8% G551D, R117H, F508del 90.1% 2.8% 7.1% Remaining

40. Class I nonsense mutations Nonsense mutation Readthrough compound Full-length protein Shortened protein Adapted from Schmitz A, Famulok M. Nature 2007

41. Ataluren(PTC 124) induces functional CFTR protein in nonsense (Class I) -mutation-mediated mouse model of CF ataluren control • Novel molecule discovered by high throughput screening • Induces selective dose-dependent ribosomal readthrough of premature stop codons but not normal stop codons • Activity in nonsense-mutation-mediated mouse models of CF and DMD Transepithelial Short-Circuit Current No Chloride Channel Activity Chloride Channel Activity Du X et al., PNAS2008

42. Ataluren Phase 3: Mean relative change in FEV1 % predicted at week 48 Konstan, M. – European CF Conference, Dublin 2012 Kindly provided by TemitayoAjayi, PTC Pharmaceuticals

43. Inhaled aminoglycosides may affect ataluren response Week 48 ∆ = 5.7% p = 0.008* Week 48 ∆ = -1.4% p = 0.43* In 2014, PTC is initiating an ataluren Phase 3 efficacy and safety trial in patients not receiving inhaled aminoglycosides Kindly provided by TemiAjayi Konstan, M. – European CF Conference, Dublin 2012

44. Class I (nonsense mutation) next generation possibilities • Cystic Fibrosis Foundation has initiated new discovery programs with both academic and industry partners • With support from CFF, University of Alabama and Southern Research Institute, are currently screening approved drugs for read-through activity • in vitro proof of concept studies using primary nasal epithelial cell cultures from Y 122 X homozygotes to test topical gentamicin effect in progress* * personal communication – Isabelle Sermet-Gaudelus

45. How close are we to our goal using allele-specific approaches? Both alleles One allele Unidentified alleles First Allele Second Allele CFFPR* Patients > 90% are covered *Cystic Fibrosis Foundation Patient Registry, 2012

46. How close are we to our goal using allele-specific approaches? Both alleles One allele Unidentified AND MISSING alleles First Allele Second Allele 1,768 patients CFFPR* Patients *Cystic Fibrosis Foundation Patient Registry, 2012

47. 100% of patients with CF should have two identified mutations – the Mutation Analysis Program • Genetic testing is available free of charge to all U.S. patients with CF who do not have 2 identified mutations • For more information, go to cff.org http://www.cff.org/LivingWithCF/AssistanceResources/MAP

48. CFTR2: An Emerging Tool for Diagnosis, Prognosis, and Therapeutics (supported by CFF) http://www.cftr2.org/

49. What about other rare mutations? Personalized medicine 2013 and beyond Clinical trial model for screening drug effects on rare alleles

50. Model for studying rare mutations: Individual (n=1) trials for clinical response to CFTR modulators • Single-center, randomized, double-blind, multiple within-subject (N-of-One) crossover study in patients with rare mutations Cycle 1 Cycle 2 Open-Label Active Drug Daily Home Monitoring Wk -2 Day 1 Wk4 Wk 8 Wk12 Wk16 Wk 24 Key outcome measures: • Primary: Change from baseline in % predicted FEV1 after 2 weeks of treatment • Multiple secondary outcomes may be measured Vertex is currently using this approach to study ivacaftor response in patients with residual CFTR function and splice variants Kindly provided by Vertex Pharmaceuticals, Inc.