We strive to develop innovative solutions that improve and extend the lives of people with cystic fibrosis

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1 Nivalis Therapeutics, Inc., October 2015 Analyst Breakfast at NACFC We strive to develop innovative solutions that improve and extend the lives of people with cystic fibrosis

2 Disclaimer Regarding Forward Looking Statements This presentation contains forward-looking statements that are based on our management's belief and assumptions and on information currently available to our management. Although we believe that the expectations reflected in these forward-looking statements are reasonable, these statements relate to future events or our future financial performance, and involve known and unknown risks, uncertainties and other factors that may cause our actual results, levels of activity, performance or achievements to be materially different from any future results, levels of activity, performance or achievements expressed or implied by these forward-looking statements. In some cases, you can identify forward-looking statements by terminology such as "may," "might," "could," "would," "will," "should," "expect," "intend," "plan," "anticipate," "believe," "estimate," "predict," "project," "target," "potential," "continue" or the negative of these terms or other comparable terminology. These statements are only predictions. You should not place undue reliance on forward-looking statements because they involve known and unknown risks, uncertainties and other factors, which are, in some cases, beyond our control and which could materially affect results. These risks, uncertainties and other factors include, among others, the risk that there is a delay in the initiation or completion of our planned clinical trials, that unanticipated costs or expenditures arise in connection with our clinical trials that affect our need for capital and/or that results from clinical trials fail to meet primary or secondary endpoints. Any forward-looking statements made in this presentation are also subject to the risks and uncertainties that are described more fully in our filings with the SEC, including our most recent quarterly report on Form 10-Q and our registration statement on Form S-1, including the prospectus contained therein. If one or more of these risks, uncertainties or other factors occurs, or if our underlying assumptions prove to be incorrect, actual events or results may vary significantly from those implied or projected by the forward-looking statements. The forward-looking statements in this presentation represent our views as of the date of this presentation. We anticipate that subsequent events and developments will cause our views to change but we undertake no obligation to update these forward-looking statements in the future, except to the extent required by applicable law. All trademarks and registered trademarks are the property of their respective owners. Such use should not be construed as an endorsement of our business. Certain data in this presentation was obtained from various external sources, and neither we nor our affiliates, advisers or representatives has verified such data with independent sources. Accordingly, neither we nor any of our affiliates, advisers or representatives makes any representations as to the accuracy or completeness of that data or to update such data after the date of this presentation. Such data is subject to change based on various factors. This presentation shall not constitute an offer to sell or the solicitation of an offer to buy any securities in any jurisdiction in which such offer or solicitation is not permitted under applicable law. 2

3 Expertise in Drug Development, Cystic Fibrosis & Inflammation Management Team Jon Congleton President and Chief Executive Officer Janice Troha Chief Operating Officer Mike Carruthers Chief Financial Officer Sherif Gabriel, PhD Vice President Research & Discovery Steven Shoemaker, MD Vice President Clinical R&D / Medical Director Prior Experience Teva Pharmaceuticals; Sanofi (Aventis) Endo Pharmaceuticals; RxKinetix; Cortech; Boehringer Ingelheim Array BioPharma; Ionics; Sievers Instruments; Dover (Waukesha Bearings); Coopers & Lybrand University of North Carolina Cystic Fibrosis Center Nicosof; Cephalon; Anesta 3

4 Michael Knowles, MD University of North Carolina Professor of Pulmonary and Critical Care medicine at UNC Over 3 decades of research and clinical development Currently head of two large multicenter studies: Genetic Modifiers of disease phenotype (severity) in cystic fibrosis lung and liver disease Consortium with 8 sites to study rare genetic disorders of mucociliary clearance 4

5 Summary Highlights First-in-class CFTR stabilizer to treat cystic fibrosis (CF) N91115 significantly increases and prolongs CFTR activity through GSNOR inhibition N91115 initially targets the most common mutation in CF F508del mutation present in ~86% of CF patients (1) Positioned to become a new standard of care in CF Phase 2 to explore N91115 in triple therapy along with lumacaftor/ivacaftor N91115 complementary and agnostic to other CFTR modulators Effective across multiple mutations and in all age groups Strong proprietary portfolio of GSNOR inhibitors N91115 composition of matter patent protection until at least 2031 (1) Decision Resources Report, 2014; European Registry Report,

6 Preclinical Data Update Sherif Gabriel, Vice President Research & Discovery

7 N91115 Improves CFTR Stability in F508del Addition of N91115 to potentiator + corrector approach could improve patient outcomes 7

8 AUC (fold change) N91115 Significantly Increases and Prolongs CFTR Activity N91115 stabilizes F508del CFTR in human lung cells (1) 50% increase in net chloride secretion (1) Ussing chamber studies. 50% increase in net chloride secretion with N

9 DMSO VX-770 VX-809 VX VX-770 VX-661 VX VX-770 PM density (% of DMSO) N91115 Increases Surface Expression of F508del CFTR N91115 Increases Surface Expression of F508del CFTR in CFBe41o- Cells Effects Demonstrated with corrector + potentiator combinations DMSO N91115 * P = 0.05 ** p = 0.01 * * ** ** * Human Bronchial Cell Line CFBE41o- Performed by Dr. Guido Veit and Dr. Gergely Lukacs McGill University 9

10 N91115 Caused a Significant Increase in Chloride Secretion N91115 increases F508del CFTR activity in CF mice (1) (1) Intestinal current measurement studies 10

11 Phase 1b N91115 Trial F508del Homozygous Monotherapy Trial with N91115 to Evaluate Safety and Determine Phase 2 dosing

12 Phase 1b Trial of N91115 in F508del Homozygous Patients Double-blind, randomized, placebo-controlled, parallel group 51 total patients recruited at 19 TDN clinical sites patients each arm placebo, 50, 100, and 200 mg twice daily 28 days followed by 2 week withdrawal and follow-up period Primary endpoints safety, PK and determine Phase 2 study doses Exploratory endpoints included pulmonary function, sweat chloride, inflammatory biomarkers Study was not powered or optimized to show an efficacy signal. For example, there was no upper limit placed on FEV at entry 12

13 Baseline and Demographic Characteristics 13

14 Adverse Event Summary N91115 mg BID Placebo N= Patients with any adverse event, n (%) 11 (92%) 11(92%) 12 (92%) 12 (86%) Patients with any serious adverse event, n Discontinuation due to adverse event Adverse Event by Preferred Term Cough 5 (42%) 2 (17%) 3 (23%) 6 (43%) Chest discomfort 0 2 (17%) 0 2 (14%) Fatigue 1 (8%) 1 (8%) 0 3 (21%) Pulmonary exacerbation of CF During 28-day treatment period 1 (8%) 1 (8%) 1 (8%) 0 During 14-day withdrawal period 1 (8%) 0 1 (8%) 3 (21%) hscrp 0 1 (8%) 2 (15%) 1 (7%) Dyspnea 0 1 (8%) 0 2 (14%) Nasal congestion 1 (8%) (14%) Oropharyngeal pain 1 (8%) 0 1 (8%) 2 (14%) Weight (21%) Wheezing (14%) 14

15 N91115 Safe and Well Tolerated No dose-limiting toxicities identified by independent DMC No adverse effects on pulmonary function No cardiac toxicity No liver toxicity No adverse effect on body weight No immunosuppressive effects No effects on white blood cell and absolute neutrophil counts No effects on CRP No effects on sputum bacterial count 15

16 Δ ppfev1 (mean ± SD) Mean Absolute Change in ppfev 1 No adverse effect on ppfev 1 during the study 8 Placebo 50 mg 100 mg 200 mg Days Per protocol population 16

17 Effects on ppfev 1 Compared with Placebo 17 Dose of N91115 BID Placebo N = ppfev 1 : Relative Change from Baseline at Day 28 Mean (SD) -2.2 (4.4) 0.1 (6.1) -3.5 (4.7) 0.6 (5.9) Median ppfev 1 : Absolute Change from Baseline at Day 28 Mean (SD) -2.1 (3.5) 0.3 (4.3) -2.5 (3.6) 0.2 (4.1) Median ppfev 1 : Relative treatment response (versus placebo) at Day 28 Mean Median ppfev 1 : Absolute treatment response (versus placebo) at Day 28 Mean Median

18 Mean Change in Sweat Chloride (mmol/l ± 95% CI) Mean Change in Sweat Chloride (95% CI) at 28 days Placebo 50 mg 100 mg 200 mg Modest trend toward improvement at 28 days on 200 mg BID Data suggests that 200 mg is a threshold dose for sweat chloride signal -4-6 Placebo difference at 28 days of -5.2 mmol/l Day D28 - Baseline -D1 18

19 Sweat Chloride More Patients in 200 mg Arm Show Improvement Placebo 50 mg 100 mg 200 mg Day 7 - Baseline Day 14 - Baseline Day 21 - Baseline Day 28 - Baseline 19

20 Change in Sweat Chloride (mmol/l) Difference From Placebo Comparison of Sweat Chloride Treatment Differences to Vertex Compounds mg N mg VX IVA IVA The magnitude of the sweat chloride response on N91115 is similar to VX-661 plus ivacaftor currently being studied in Phase 3 Day 28 Wk 16 (onset at D15) 1. VX-661+IVA: Data extrapolated from Donaldson 2013 NACFC presentation 2. IVA: Flume et al 2012 Chest 142(3): ; Ivacaftor monotherapy D1 to Week 16; 150 mg BID; p=0.04; onset of effect at D15 20

21 Conclusions There were no dose limiting toxicities N91115 was well-tolerated at all doses for 28 days Sweat chloride response may suggest a threshold dose effect at 200mg Testing a higher dose warranted Phase 2 active arms planned at both 200 and 400 mg 21

22 N91115 Phase 2 Study Design Janice Troha, COO

23 Safety Margins Support Higher Dosing in Phase 2 Species & Design Estimated Safety Margins at 200 mg Twice Daily Based on C max Based on AUC last Estimated Safety Margins at 400 mg Twice Daily Based on C max Based on AUC last Dose Limiting Toxicity Rat 90-day NOAEL 150 mg/kg Dog 90-day NOAEL 50 mg/kg Dog CV Safety 13-fold 4-fold 7-fold 2-fold 29-fold 22-fold 15-fold 12-fold 48-fold 34-fold 24-fold 18-fold At 1000 mg/kg: Mild reversible anemia Liver weight increases Kidney weight increases At 500 mg/kg: Mild biliary hyperplasia Mild tubular changes in kidney Anemia 1 dog euthanized At 1000 mg/kg: Increased heart rate and decreased blood pressure Compared with efficacious doses in preclinical in vivo models, these doses provide 4 to 8-fold the exposure (2 to 4-fold based 23 on protein binding differences)

24 N91115 Phase 2 Study Design N91115 added to Orkambi in adults with CF who are homozygous for F508del Double-blind, randomized, placebo controlled, parallel group study Three arms, 45 patients per arm, total 135 Placebo N91115 at 200 and 400mg BID Primary Endpoint Absolute change from baseline in ppfev 1 at 12 weeks Sample Size Provides > 90% power to detect 5% absolute change in ppfev 1 Study Duration 12 weeks followed by 4-week follow-up period Study Start First Patient First Visit targeted for late

25 N91115 Milestones in Homozygous F508del Patients Complete Phase 3 program File NDA for treatment of adult CF patients Initiate Phase 3 program (two trials) - show clinically meaningful benefit of triple therapy Complete Phase 2 clinical trial Request Breakthrough 2016 Initiate Phase 2 randomized, controlled clinical trial - demonstrate safety and efficacy of triple therapy Request Orphan/Fast Track Complete Phase 1b clinical trial (dose-finding safety study) 2015 Demonstrate efficacy and safety of N91115 in triple therapy along with lumacaftor/ivacaftor 25

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