1. PTI-428-01 CF Subjects North American Cystic Fibrosis Conference October 27-29, 2016 Orlando, Florida CFTR amplifier is genotype agnostic with a distinct mechanism of action Figure 1: Pharmacokinetic Data – PTI-428-02 and PTI-428-01, SAD Phase 1 Initial Results Evaluating Safety, Tolerability, PK, and Biomarker Data Using PTI-428, A Novel CFTR Modulator M Mouded 1, D Layish 2, GS Sawicki 3, C Milla 4, PA Flume 5, NF Mehdi 6, J Tolle 7, L Vansaghi 8, C Watson 1, B Munoz 1, A Bhalla 1, P-S Lee 1 1 Proteostasis Therapeutics, Inc., Cambridge, MA, USA; 2 Central Florida Pulmonary Group, Orlando, FL, USA; 3 Boston Children’s Hospital, Boston, MA, USA; 4 The Stanford Cystic Fibrosis Center, Palo Alto, CA, USA; 5 Medical University of South Carolina, Charleston, SC, USA; 6 Oklahoma University Medicine, Oklahoma City, OK, USA 7 Vanderbilt University Medical Center, Nashville, TN, USA; 8 Quintiles, Overland Park, KS, USA Amplifiers are a new class of CFTR modulators Exposure to PTI-428 increases in a dose proportional manner Steady state achieved by day 4 with repeat dosing PK profile similar in healthy volunteers and CF subjects No safety concerns identified based on SRC review of laboratory and AE data to date Two-fold increase in CFTR mRNA and protein 8 hours following a single dose of PTI-428 An HTS strategy that enriches for small molecules acting on the translated sequence of CFTR protein was used to identify a new class of modulator. This modulator has been termed a CFTR amplifier. It is mutation agnostic and ultimately leads to increased levels of immature CFTR protein, along with stabilization and increase in CFTR mRNA. Production of additional CFTR protein allows for more substrate for other CFTR modulators, such as correctors and potentiators, to act upon. In vitro data using amplifier demonstrated improvement in chloride currents across multiple CFTR mutations. PTI-428 is an amplifier entering a first-in- human trial to demonstrate safety and tolerability in CF subjects and HV. Introduction CF subjects (PTI-428-01): A randomized, double-blind, placebo-controlled phase 1 clinical study –CF subjects between ages 18-55 years –Not on either KALYDECO ® or ORKAMBI ® HV subjects (PTI-428-02): A randomized, double-blind, placebo-controlled phase 1 and drug-drug interaction study –Females between ages 18-55 years Primary objective: Assessment of safety and tolerability Secondary objective: Assessment of the PK of PTI-428 Exploratory objectives: Include CFTR expressions from nasal brushings 187 Conclusions Abbreviations AE, adverse event; ALT, alanine aminotransferase; AST, aspartate aminotransferase; AUC, area under the curve; BMI, body mass index; CF, cystic fibrosis; CFTR, cystic fibrosis transmembrane conductance regulator; C max, maximum serum concentration; EC 50, half maximal effective concentration; FEV 1, forced expiratory volume in 1 second; HBE, human bronchial epithelial; HCT, hematocrit; HTS, high-throughput screen; HV, healthy volunteer; ITT, intent-to-treat; MAD, multiple ascending dose; NHV, normal healthy volunteer; PK, pharmacokinetics; PLAT, platelet; PTI-428, novel amplifier; SAD, single ascending dose; SRC, scientific review committee; TEAE, treatment-emergent adverse event; WBC, white blood count. Figure 5: Measurement of CFTR mRNA and protein have been developed as a clinical biomarker HV PK Shows Dose Proportionality Clinical Biomarker Development BA Potentiators, such as ivacaftor, act by increasing the opening time of the CFTR channel, resulting in higher ion flow. Correctors, such as lumacaftor, are thought to facilitate the processing of mutated CFTR protein, leading to improved delivery of CFTR protein to the cell membrane. Amplifiers selectively increase the amount of immature CFTR protein in the cell, providing additional substrate for correctors and potentiators to act upon. Each cohort followed by SRC review of PK and safety data Biomarker data collected pre- and post-dosing Studies ongoing in both CF and HV subjects Interim analysis performed on SAD, PTI-428-02 Methods Mechanism of Action Study Designs –FEV 1 >50% of predicted –All CFTR mutations are eligible Cohort 1 Cohort 2 Cohort 3 Cohort 1 Cohort 2 Cohort 3 SAD One single daily dose 7-day follow-up MAD Single daily dose for 7 days 14-day follow-up Interim Analysis PTI-428-02 Healthy Volunteer Subjects Cohort 1 Cohort 2 Cohort 3 Cohort 1 Cohort 2 Cohort 3 SAD One single daily dose 7-day follow-up MAD Single daily dose for 7 days 14-day follow-up Study population demographics reflect the population expected under the inclusion/exclusion criteria Baseline Demographics (PTI-428-02, SAD) ITT Population Parameter/SummaryPlacebo (N=6)PTI 10 mg (N=6)PTI 30 mg (N=6)PTI 100 mg (N=6) Age Mean27.034.039.224.5 Std Dev6.0311.4711.004.32 Minimum20.023.022.020.0 Maximum36.053.0 31.0 Race American Indian or Alaska Native1 Black or African American415 White6241 BMI Mean26.025.324.624.8 Std Dev2.753.013.613.07 Minimum22.420.519.320.5 Maximum28.8 28.429.7 Height Mean164.0166.2165.1166.1 Std Dev4.337.396.167.80 Minimum158.8158.2157.8156.8 Maximum169.0176.6172.4177.3 Weight Mean70.070.567.768.2 Std Dev8.9413.2511.748.82 Minimum55.851.751.657.9 Maximum81.884.182.878.2 Results Data from SAD cohorts in HV suggest PTI-428 is biologically active in subjects where specific threshold concentration was achieved In 5 of 6 subjects, the maximum concentration of PTI-428 observed at 8 hours after a single dose was comparable to the EC 50 achieved in vitro On average, an approximate 2-fold increase in CFTR protein as compared to baseline was observed at 8 hour post-dosing in the 100 mg cohort Amplifiers are the only known CFTR modulators that lead to an increase in immature CFTR protein that results in an increase in mRNA. Thus, a clinical biomarker was designed to detect an increase in CFTR mRNA and protein Nasal swab biomarker is a noninvasive technique to sample the respiratory epithelium No clinically significant changes in hematologic parameters No clinically significant changes in liver enzymes No safety concerns were identified at SRC review Table 1: Safety summary – adverse events (PTI-428-02, SAD) Number (%) of Subjects Category Placebo (N = 6) PTI-428 10 mg (N = 6) PTI-428 30 mg (N = 6) PTI-428 100 mg (N = 6) PTI-428 All Active Doses (N = 18) At Least One TEAE 0 (0.0%) 1 (16.7%) 2 (33.3%) 1 (16.7%) 4 (22.2%) At Least One Related TEAE 0 (0.0%) At Least One Severe TEAE 0 (0.0%) 1 (16.7%) 0 (0.0%) 1 (5.6%) At Least One Severe Related TEAE 0 (0.0%) At Least One Serious AE 0 (0.0%) TEAEs Leading to Discontinuation 0 (0.0%) TEAEs Leading to Death 0 (0.0%) No treatment-related adverse events noted Preliminary data suggests PK is increased when PTI-428 is administered with food Exposure to PTI-428 increased in an approximately dose proportional manner PK profile is similar in HV and CF subjects T ½ ~ 14-15 hours Steady state achieved by day 4 Minimal accumulation after repeat dosing with accumulation ratio for C max and AUC (0-24) approximately 1.4 Figure 6: PTI-428 is biologically active in humans after a single 100 mg dose B A Nasal brushing samples from subjects in SAD cohorts collected on multiple time points RNA extracted and analyzed for mRNA expression of CFTR and actin Biomarker Results Over Time Modeling of PK Log 10 AUC and Relative mRNA at Day 1 8-Hour by SAD Cohort Time Point 08 hr24 hr48 hr72 hr Relative CFTR mRNA 0 4 3 2 1 2.43.83.72.52.62.73.63.92.83.43.32.93.03.13.23.5 Relative mRNA (QR) 0 11 8 6 3 1 10 5 4 2 9 7 Log 10 AUC (hr*ng/mL) Cohort100 mg 30 mg 10 mg Placebo PTI-428 10 mg PTI-428 30 mg PTI-428 100 mg Biomarker Discovery ~1.5-2 fold CFTR mRNA and protein increase with PTI-428 in both normal and CF patient HBE cells Biomarker Discovery ~1.5-2 fold CFTR mRNA and protein increase with PTI-428 in both normal and CF patient HBE cells Biomarker Development CFTR mRNA and protein expression measurable in nasal epithelial cells of rats, monkeys, NHV, and CF patients Biomarker Development CFTR mRNA and protein expression measurable in nasal epithelial cells of rats, monkeys, NHV, and CF patients Biomarker Implementation CFTR mRNA and protein expression measured in nasal epithelial cells with PTI-428 in phase 1 NHV and CF subjects Biomarker Implementation CFTR mRNA and protein expression measured in nasal epithelial cells with PTI-428 in phase 1 NHV and CF subjects SAD PK in Subjects With CF vs HV Concentration (ng/mL) 081624 0 100 80 40 Time (h) Concentration (ng/mL) 020406080 Time (h) 60 20 100 mg 30 mg 10 mg CF Cohort 1 HV Cohort 1 0.1 100 10 0 10,000 1000 Design: Once per day dosing for 7 days Repeat dosing of 20 mg of PTI-428 PK sample collection through day 1 and day 7 Figure 2: Pharmacokinetic Data – PTI-428-02, MAD MAD Day 1 vs MAD Day 7 Concentration (ng/mL) 020406080 0 300 200 100 Time (h) Day 1 Day 7 Figure 3: Positive food effect in healthy volunteers Concentration (ng/mL) Design: 2 x 2 crossover, 12 healthy female subjects Single dose of 100 mg of PTI-428 administered with and without food (overnight fasted vs high fat meal) PK sample collection up to 72 h post dose 01020304050607080 0 1500 1000 500 Time (h) Fasted Fed Figure 4: Safety summary – laboratory results (PTI-428-02, SAD) AB ALTASTHCT C Description of Planned Arm PTI-428 10 mg PTI-428 100 mg PTI-428 30 mg Placebo 0 50 40 30 20 0 50 30 20 10 0 50 40 30 20 Average Values 24682468 Visit WBC E PLAT D 24682468 Visit 24682468 24682468 24682468 100 300 250 150 0 10 4 Nasal Brushing Protocol Retain the tip of curettes in the same Eppendorf tube Store at -80°C immediately and ship to analysis lab on dry ice Repeat with the other nostril Repeat brushing motion at least 3 times Place in pre-prepared lysis buffer ASI Rhino-Pro Curettes X3 Average Values 10 40 10 6 8 2 200