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Corporate Presentation January 2017 NASDAQ:WINT Forward Looking Statement To the extent that statements in this presentation are not strictly historical, including statements about the Company’s business strategy, outlook, objectives, plans, intentions, goals, future financial conditions, future collaboration agreements, the success of the Company’s product development, or otherwise as to future events, such statements are forward-looking, and are made pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995. The forward-looking statements contained in this presentation are subject to certain risks and uncertainties that could cause actual results to differ materially from the statements made. These risks are further described in the Company's periodic filings with the Securities and Exchange Commission (SEC), including the most recent reports on Forms 10-K, 8-K and 10-Q, and any amendments thereto (“Company Filings”). Under no circumstances shall this presentation be construed as an offer to sell or as a solicitation of an offer to buy any of the Company’s securities. In addition, the information presented in this deck is qualified in its entirety by the Company Filings. The reader is encouraged to refer to the Company Filings for a fuller discussion of the matters presented here. 2 Windtree Therapeutics Public, small cap biopharmaceutical / medical device company Based in Warrington, PA with approximately 50 employees Technology and development focused in the acute respiratory area with a lead program based in Respiratory Distress Syndrome (RDS) in premature infants Nasdaq: WINT Windtreetx.com 3 Highly Experienced Management Team Craig Fraser CEO Steve Simonson, MD Chief Development Officer John Tattory CFO Mary Templeton General Counsel Kathy Cole Human Resources George Cox Manufacturing & Supply Ron Dundore Regulatory and Quality Larry Weinstein Medical Device 4 Respiratory Distress Syndrome (RDS) Primary characteristic is surfactant deficiency in underdeveloped lungs of premature infants (born with a lack of natural lung surfactant required for open airways and proper gas exchange – O2 in and CO2 out) American Academy of Pediatrics guidelines recommend providing surfactant 1 replacement within the first hours of life Neonatologists believe the highest unmet need in RDS is the ability to deliver surfactant non-invasively to patients2 1. AAP guidelines, 2013 2. WINDTREE primary market research (2014) 5 RDS Treatment Pathways Initial treatment options include invasive and non-invasive methods: ~40% Surfactant Therapy • Animal-derived surfactant • Delivered via intubation, usually in combination with mechanical ventilation ~60% + nCPAP Support until presumptive endogenous surfactant production Invasive mechanical ventilation (IMV) • Requires sustained intubation • Supports breathing until patient can be weaned • Non-invasive nasal delivery of continuous positive airway pressure • Supports breathing until the infant can be weaned TRADE-OFFS Timely therapy delivery vs. Exposure to known significant complications Avoid exposure to known significant complications vs. Cannot deliver surfactant and risk failure >50% intubation and IMV 6 Clinicians seeking a non-invasive way to deliver surfactant What is wanted1: Avoid the risks and complications associated with delivery of surfactant replacement therapy via intubation and mechanical ventilation Possibility of repeat doses Avoid clinical instability associated with administration of liquid surfactant bolus administration Enable administration by nonspecialist staff Reduce cost of treating premature infants “…optimization of less invasive method of surfactant administration will be one of the most important subjects for research in the field of surfactant therapy of RDS in coming years”. Kribs A. How best to administer surfactant to VLBW infants. Arch Dis Child Fetal Neonatal Ed 2011;doi:10.1136. 1. Pillow & Minocchieri: Neonatology, 2012 7 AEROSURF® - Aerosolized Surfactant for RDS Proprietary Synthetic KL4 Surfactant Designed to be structurally similar to human lung surfactant + Proprietary Innovative Aerosol Delivery System (ADS) Designed specifically to aerosolize and deliver KL4 surfactant Liquid KL4 surfactant (intratracheal instillate) for RDS approved by the FDA Lyophilized (freeze-dried) KL4 surfactant – developed initially for AEROSURF® 8 A Closer Look at RDS Treatment Option Trade-Offs RISKS BENEFITS Surfactant Therapy Reversing surfactant deficiency has a profound positive impact on respiration Surfactant therapy delivers nearimmediate clinical improvement BPD Infection, ventilator-induced pneumonia Bradycardia, hypertension, and hypoxemia Peri-dosing events associated with bolus administration Airway trauma Lung injury Pain, discomfort Long-term impacts including vocal cord damage, asthma, lung damage nCPAP Supportive Avoid exposure to the risks of invasive delivery of surfactant therapy Negative impacts of delayed surfactant therapy Extended respiratory distress until either endogenous surfactant production or transfer to invasive SRT Significant nCPAP failure rate leading to delayed surfactant therapy via IMV and the associated risk with that therapy 9 Transformative Potential of AEROSURF® RISKS BENEFITS Surfactant Replacement Therapy (SRT) Reversing surfactant deficiency has a profound positive impact on respiration Surfactant therapy delivers near-immediate clinical improvement BPD Infection, ventilator-induced pneumonia Bradycardia, hypertension, and hypoxemia Peri-dosing events associated with bolus administration Airway trauma Lung injury Pain, discomfort Long-term impacts including vocal cord damage, asthma, lung damage nCPAP Supportive Avoid exposure to the risks of invasive delivery of surfactant therapy The potential for AEROSURF All the benefits of traditional surfactant therapy without the complications associated with intubation and mechanical ventilation Negative impacts of delayed surfactant therapy Eliminates the need to delay surfactant therapy Extended respiratory distress until either endogenous surfactant production or transfer to SRT Physiologic benefits of a synthetic formulation Significant nCPAP failure rate leading to delayed surfactant therapy via IMV and the associated risk with that therapy Reduced morbidity Lower total cost of care Improved peace of mind 10 Potential Drivers of Opportunity in RDS #1 30% Price stated unmet need in RDS reduction in CPAP failure is meaningful (but Total Results in >40% reported, expected patient share 1 Potential for positive Health Economics related to non-invasive approach, cost avoidance, etc.2 “Non-invasive surfactant delivery” = 54% top, unaided response (3x higher 1 than next response) Market Expansion Cost) Potential to bring surfactant therapy to new, lower skilled / certified hospitals and geographies due to non-invasive , less specialized delivery 3 1) N=278 Neonatalogists, US & EU; Quant Research, November 2014 2) Defined Health Payer Research; Quant Research 2014 3) Windtree research and estimates 11 Prevalence of RDS Spans Across Gestational Ages / Severity % of RDS Population RDS Prevalance <26 weeks GA >95% 15% 9% 12% 31% HIGHER LOWER 32% 26-28 weeks GA 85-95% 29-32 weeks GA 65-75% 33-34 weeks GA 40-50% 35-36 weeks GA 5-10% Size of Sub-Population HIGHER GA 26-28 wks GA 29-32 wks GA 33-34 wks 30% nCPAP 1st line 55% nCPAP 1st line 70% nCPAP 1st line HIGHER Severity of RDS & Incidence of CPAP Failure Rate LOWER Source: WINDTREE primary market research (2014); IMS MIDAS data (2012); CDC National Vital Statistics, 2014, Healthcare Costs and Utilization Project (HCUP), 2013; Agency for Healthcare Research and Quality (AHRQ), 2012; Births by birth weight (CDC Website). 12 Initial Clinical Experience AEROSURF® Phase 2a Study in 29 to 34 week gestational age (GA) Phase 2a Gestational Age (wks) Phase 2a Expansion 29 – 34 15 min; 30 min; 45 min ( 25, 50, 75 TPL mg/kg) (8 active, 8 control per group) 60 min; 90 min (100 and 150 TPL mg/kg) (8 active, 8 control per group) Single dose Primarily single dose 48 32 Safety and tolerability Physiological data suggesting delivery of KL4 surfactant to the lungs Safety and tolerability of higher doses and determine therapeutic index (safety window) Performance of Aerosol Delivery System Continue physiological assessment # of sites Initiated with 3; increased to 8 (US) 12 (US) Timeline / Milestones Completed May 2015; key objectives achieved Completed Oct 2015 Dose Groups # of patients Objective(s) 13 AEROSURF® Phase 2a Study (29 to 34 wks GA) Safety and Tolerability - Summary The safety and tolerability profile of AEROSURF was generally comparable to the control group The Aerosol Delivery System delivered KL4 surfactant to the infants in a way that was well tolerated The adverse events and serious adverse events (SAE) seen were expected for this patient population and generally comparable between AEROSURF® and control groups • Most common adverse events were jaundice, constipation, apnea and anemia • Most common SAE’s were air leaks (including pneumothorax, pneumomediastinum and pulmonary interstitial emphysema) There was no pattern of increased adverse events or serious adverse events with increasing doses of AEROSURF 14 AEROSURF® Phase 2a Study (29 to 34 wk GA) nCPAP Failure by Treatment Group through 72 hours 100% % Subjects Failed Through 72 Hrs 90% 70% 60% 50% Focus for dose selection going forward 6/8 80% 5/8 21/40 75% 63% 53% 40% 30% 3/8 3/8 38% 38% 20% 1/7* 14% 10% 0% nCPAP Only 25 mg/kg (15 min) 50 mg/kg 75 mg/kg 100 mg/kg (30 min) (45 min) (60 min) Treatment Group 150 mg/kg (90 min) AEROSURF® treatment, primarily in single doses of 45 minutes and greater, appears to be associated with lower rates of nCPAP failure. * One intubated patient excluded due to being inappropriately enrolled 15 Phase 2a Study (29 to 34 wks GA) 45 and 60 Minute Dose Groups - nCPAP Failure through 72 hours Time to nCPAP Failure Percent Subjects Failed 100% 49% relative reduction 80% 60% 40% 21/40 53% 4/15* 27% 20% 0% nCPAP Only 75 & 100 mg/kg (45 & 60 min) Treatment Group (45 & 60 min) At 72 hours post-dosing, 27% of AEROSURF® patients in the combined 45 and 60 minute dose groups required intubation compared to 53% in the control group; a relative reduction in nCPAP failure of 49% * One intubated patient excluded due to being inappropriately enrolled 16 AEROSURF® Phase 2a Study (29 to 34 wks GA) 45 and 60 Minute Dose Groups - nCPAP Failure through 72 hours 45 and 60 minute Dose Groups Cumulative % Intubated 60% 50% 40% Active nCPAP 53% Potential to repeat dose 27% 30% 27% 30% 27% 25% 18% 20% 15% 10% 0% 0% 3 hrs 0% 6 hrs 12 hrs 24 hrs 72 hrs • Aerosolized KL4 surfactant produces physiological changes that are expected with surfactant replacement therapy • No AEROSURF patients in the 45 and 60 minute dose groups required intubation at 3 or 6 hours post-dosing compared to 18% (7/40) of control patients • AEROSURF 45 and 60 minute doses may be reducing the rates of intubation and also prolonging the time to intubation – repeat dosing may be important to extend this effect until the patient’s endogenous surfactant production is adequate * One intubated patient excluded due to being inappropriately enrolled 17 Comprehensive AEROSURF® Phase 2 Program Ongoing Trials Phase 2a Gestational Age (wks) Dose Groups Phase 2a Expansion 29 – 34 15 min; 30 min; 45 min ( 25, 50, 75 TPL mg/kg) (8 active, 8 control per group) Single dose # of patients 60 min; 90 min (100 and 150 TPL mg/kg) (8 active, 8 control per group) Primarily single dose Phase 2a Phase 2b 26 - 28 28– 32 30 min; 45 min; 60 min; 90 min (if needed) (50, 75, 100 and 150 TPL mg/kg) (8 active, 8 control per group) Up to two doses 25 min; 50 min; Control (40 and 80 TPL mg/kg) Up to 3 doses 48-64 Up to 240 Safety and tolerability Provide evidence of efficacy on an acceptable endpoint Physiological assessment Identify dose regimens for phase 3 study 48 32 Safety and tolerability Physiological data suggesting delivery of KL4 surfactant to the lungs Safety and tolerability of higher doses and determine therapeutic index (safety window) Performance of Aerosol Delivery System Continue physiological assessment # of sites Initiated with 3; increased to 8 (US) 12 (US) Up to 20 (US) 50+ (US, EU, Canada, LATAM) Timeline / Milestones Completed May 2015; key objectives achieved Completed Oct 2015 Target top line data for first three dose groups – Q1’17 Target top line data – Mid-Year’17 Objective(s) Provide est. of effect size 18 Prospective Observational Study Study Overview Findings Prospective observational study of approximately 2,000 premature infants (U.S., Canada, E.U.) to collect data on the treatment and outcomes in the gestational ages we are studying Approximately 75% of the 26-28 week GA infants required intubation. Gain further understanding of nCPAP use, intubations, oxygen requirements and other treatments that impact nCPAP success/failure and the need for intubation to better inform our development and forecasts A lower proportion of the 29-34 week GA infants require intubation, however, the number of babies in this GA group is much larger than the number of babies in the younger GA group and actually account for more intubations Infants whose oxygen requirement is lower than used in our trial (including “room air” / no oxygen requirement) had a higher rate of nCPAP failure and need for intubation than expected 19 Implications for the AEROSURF® Program What we have learned There is a greater clinical need and potential market opportunity in the larger population of 29-34 week gestational age infants than many previously considered The total addressable market opportunity for AEROSURF may extend to neonates with a lower severity level of RDS at presentation and may begin earlier in the treatment pathway (i.e. Delivery Room) for RDS treatment optimization These and other observations help inform our current and future trial design related to oxygen requirements, mix of gestational age groups, etc. 20 Encouraging clinical results suggest ADS is delivering KL4 surfactant to the lungs but can we obtain direct evidence? Can we demonstrate and quantify that aerosolized KL4 surfactant is actually getting into the lung? Factors to consider: • Pulmonary drug delivery through inhalation is challenging • Characteristics of surfactants • Device needed that can deliver a constant and acceptable output rate and particle size 21 Pulmonary Drug Delivery Through Inhalation Pulmonary drug delivery through inhalation can be very advantageous but comes with significant challenges: • Creating the appropriate particle size and aerosol concentration • Producing consistent drug output from the aerosol device • Delivering the drug through the patient’s anatomy and other breathing apparatus • Delivering the drug in different breathing characteristics 22 Aerosolizing surfactant has been a daunting task Currently available liquid surfactants are generally effective for treating RDS but are administered via invasive intubation, which increases the risk of serious complications – thus the pursuit for a noninvasive approach Surfactant characteristics make it a particularly challenging substance to aerosolize due to: • High viscosity; tendency to foam and bubble • The need to avoid clogging or obstruction in the delivery system • The need to deliver an adequate dose in the right particle size in a reasonable amount of time Many have tried but there has been little success in aerosolizing surfactants and there are no commercially available devices Given the characteristics of RDS and of premature infants, as well as the heightened need for efficacy and safety in this fragile patient population, the performance standard is high 23 Aerosol Delivery System Summary Aerosol Delivery System allows for a very well controlled and consistent KL4 surfactant delivery system: • High output • Pre- and post-aerosolization characteristics of KL4 surfactant are comparable • Consistent output rate and particle size from device to device • Consistent output rate and particle size throughout the dosing period Controlled and reproducible experience A solid platform for potential life-cycle advancements 24 Lung Deposition Study in Non-Human Primates • Use of non-human primates (cynomolgus macaques) – Nose, throat, & lung anatomy comparable to infants – Respiratory function similar to preterm infants – Lightly anesthetized, spontaneously breathing via nasal cannula • In vitro studies performed to validate that admixed technetium-99m (99mTc) travels with the aerosolized KL4 surfactant in a measurable and consistent manner • Radiolabeled KL4 surfactant aerosolized using Aerosol Delivery System (ADS), delivered via nasal cannula in 3-10 min exposures inhaled from a nCPAP circuit (3 L/min aerosol flow & 3 L/min CPAP flow) by 3 cynomolgus macaques • Measured total & regional pulmonary deposition by a series of gamma images with SPECT data used to determine regional lung deposition using a quantitative model 25 Lung Deposition Study - Distribution Information nCPAP: NHP-3 Gamma Images Planar 1 Planar Planar 1 SPECT SPECT Planar Planar22 1 Scintigraphy provided qualitative images indicating wide spread distribution throughout entire lung 26 Lung Deposition Study – Quantitative Analysis of Distribution Model divides the lung into 10 equal volume shells Total Deposition Across 10 Equal Shells 52% 48% Drug deposition observed across all areas of the lung after 3 to 10 min of inhalation demonstrating generally uniform distribution of drug between the inner half and the outer half of the lungs 27 Lung Deposition Study Summary • Aerosolized KL4 surfactant, delivered using the Aerosol Delivery System (ADS) via nCPAP, is deposited within a few minutes throughout the lungs of NHPs • The aerosol is observed to be homogeneously deposited in all regions of the lungs • These results are complemented by the clinical evidence seen in our phase 2a clinical trial in premature infants 29 to 34 weeks gestational age • This study, along with other testing and studies, should serve as a validation of our ADS ability to effectively aerosolize and deliver KL4 surfactant 28 Windtree as a Platform Company KL4 surfactant + innovative Aerosol Delivery System (ADS) technology create a platform strategy that could enable potential prevention / protection, treatment, and delivery of therapeutics in an array of diseases RDS Phase 2b Program Focus ALI - Radiation Preclinical development Prevention of acute & chronic changes (fibrotic) Mitigate lung injury, prevent vent. / ECMO Potential Application Metastatic Breast & Lung Rad.Onc; Biodefense SARS, H1N1, MERS, Viral pneumo (peds), etc. ALI - Viral Preclinical ALI - Chemical Preclinical Mitigate lung injury, prevent vent. / ECMO Defense, industrial Drug Delivery Preclinical Better delivery of drugs to lungs / higher concentration Antivirals, Antibiotics, chemo agents, anti-fibrotic… Planned Assessment & Prioritization in Q4’16 Cystic Fibrosis ECMO Liberation Acute Asthma Severe Pneumonia Post Surgical Adhesion COPD + Others? Chronic Sinusitis Lung Transplant 29 Fast Track Designation and Regulatory Interactions The company held a Type C meeting with the FDA in April 2016 to obtain FDA input on several aspects of our clinical development program • In our assessment, the discussion reaffirmed our current and planned direction for the AEROSURF® clinical development program In September 2016, the FDA granted Windtree a Fast Track designation for our AEROSURF RDS program • The Fast Track program was created by the FDA to facilitate the development and expedite the review of new drugs that are intended to treat serious or lifethreatening conditions that demonstrate the potential to address an unmet medical need • This designation underscores the significant need to reduce the use of invasive intubation and mechanical ventilation, which are currently required to administer life-saving surfactant therapy to premature infants with RDS 30 Platform Exclusivities Broad Multi-Faceted Exclusivity Portfolio Regulatory Exclusivities • Orphan Drug Designation in RDS for the U.S. and EU Patents Lyophilized KL4 Surfactant Portfolio - to 2033 Aerosol Delivery System Portfolio - through 2031+ Trade Secrets/Know-How Methods of Manufacture Non-USP Analytical Processes Potential Challenges to Generic Entry Bioequivalence Complexities – Surfactants are Non-Receptor Based 31 Significant RDS Global Revenue Opportunity 8 to 10 Million LBW Children Born Every Year Globally Developed World – 250k to 350k RDS Patients • Only 50% to 60% of RDS patients currently treated with surfactant therapy • Current market: invasive, undifferentiated, animal-derived products • Opportunity to expand treatment population and increase the pharmacoeconomic value of surfactant therapy Developing World – 1.0 million+ RDS Patients • Current surfactant market as large as the developed world – fewer than 50% treated with surfactant therapy • Opportunity for growth as access to neonatal care continues to increase world-wide Regions Estimated 2014 Annual Revenue Invasive surfactant therapy only† US $70 - $75 million EU $60 - $70 million LATAM $50 - $100 million China $50 - $100 million GLOBAL $250 - $345 million Revenue Potential of AEROSURF‡ $600 million to $1.0B+ † Current global revenue based on ~$900 to $1000 per treatment ‡ Windtree primary market research (2014) In addition to expanding the number of patients treated, value of AEROSURF® therapy potentially significantly higher than current treatments – potentially reduces the largest cost-drivers for treating premature infants with RDS: in the U.S. the average cost to treat low birth weight (LBW) infants with RDS on MV is over $50,000; cost to treat patient with chronic lung disease is over $100,000 CDC National Vital Statistics; UNICEF data; Windtree market research; IMS MIDAS data; private companies with access to government purchasing records for Latin America, China and Middle East 32 Financial Update as of September 30, 2016 • Cash and cash equivalents of $12.4 million as of September 30, 2016 – The Company anticipates that existing cash (before any additional financings) is sufficient to fund operations through February 2017; the Company is pursuing potential strategic and other transactions to secure needed additional capital to ensure adequate financial resources through phase 2b data with a modest cushion • $25 million long-term debt with Deerfield: $12.5 million due in each February 2018 (subject to potential deferral if specified milestone is achieved) and in February 2019 33 Windtree’s Organizational Core Focus - 2017 Deliver Positive Phase 2b Results Value Creation Position for Phase 3 Readiness Successful Transaction / Major Partnership 34 Focus on Execution for Value Creation Initiate priority life cycle studies Initiate RDS phase 3 Milestone End of phase 2 FDA & EMA meetings Phase 2b results in 28-32 wk GA Phase 2a Lung Deposition Study (completed) Phase 2a results in 29-34wk GA (Completed) 2016 in 26-28wk GA 2018 Transaction / Strategic Partnership Deliver positive phase 2 results 2017 Position Company as attractive, “phase 3 ready” • Device: phase 3 / “go to market” validated and efficient • Regulatory strategy and clarity • Manufacturing efficiency and scale • Commercial / access needs reflected in development • Vetted and valued life cycle and platform opportunities • Any potential risk or concerns mitigated Strategic Path 35 High Value-Creating Potential Well characterized asset and target application in RDS Potentially transformative therapy for the important, acute neonatology market that has a clear unmet medical need and is growing Building data base of potential in safety, clinical effect and benefit Opportunity to build a positive health economic position as well as expand use globally Broad IP with the potential to build a pipeline of aerosolized surfactant therapies to address a variety of respiratory diseases Experienced management team focused on rigorous clinical execution and effective cash management Significant near-term milestones 36 Windtree Therapeutics “Striving to deliver Hope for a Lifetime!” 37