Aquinox R&D Day

Aquinox R&D Day February 9, 2018 David Main President & CEO

Forward Looking Statements/ Safe Harbor This presentation and the accompanying oral commentary contain

forward-looking statements that involve substantial risks and uncertainties. All statements other than statements of historical facts contained in this presentation and the accompanying oral commentary, including statements regarding our

future financial condition, business strategy and plans and objectives of management for future operations, are forward looking statements. In some cases, you can identify forward-looking statements by terminology such as believe,

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could, potentially or the negative of these terms or other similar expressions. Forward looking statements appear in a number of places throughout this presentation and the accompanying oral commentary and include statements

regarding our intentions, beliefs, projections, outlook, analyses or current expectations concerning, among other things, our ongoing and planned preclinical development and clinical trials, the timing of and our ability to make regulatory filings

and obtain and maintain regulatory approvals for rosiptor (AQX-1125) and our future product candidates, our intellectual property position, the degree of clinical utility of rosiptor and our future product candidates, particularly in specific

patient populations, our ability to develop commercial functions, expectations regarding clinical trial data, our results of operations, cash needs, financial condition, liquidity, prospects, growth and strategies, the industry in which we operate

and the trends that may affect the industry or us. Forward-looking statements involve known and unknown risks, uncertainties, assumptions and other factors that may cause our actual results, performance or achievements to be materially different

from any future results, performance or achievements expressed or implied by the forward looking statements. In evaluating these statements, you should specifically consider various factors, including the risks outlined under the caption Risk

Factors set forth in our Quarterly Report on Form 10-Q for the quarter-end ended Sept 30, 2017, which we filed with the Securities and Exchange Commission ( SEC ) on November 8, 2017 and other reports and filings we will make with

the SEC from time to time. Forward-looking statements represent our management s beliefs and assumptions only as of the date of this presentation. Except as required by law, we assume no obligation to update these forward-looking statements

publicly, or to update the reasons why actual results could differ materially from those anticipated in the forward-looking statements, even if new information becomes available in the future. Aquinox 2

Agenda Overview of IC/BPS Diagnosis & Treatment Landscape Dr. Phillip Hanno, Stanford University Dept. of

Urology Dr. Hanno Q & A IC/BPS Clinical Program Update: Barbara Troupin, MD, MBA - Aquinox CMO, VP Clinical Development & Regulatory Affairs IC/BPS Commercial Landscape & Opportunity: Abigail Jenkins -Chief Commercial Officer & US

Business Head Open Lunch Aquinox 3

Aquinox Pharmaceuticals, Inc. Founded 2006; Founder/CEO David Main NASDAQ 2014: AQXP Aquinox is discovering and

developing novel drug candidates to treat inflammation, inflammatory pain, & blood cancers: Primary focus is anti-inflammatory product candidates targeting SHIP1 As of 2017: 50+ employees and growing Vancouver, BC 2 locations: Vancouver, BC and

San Bruno, CA San Bruno, CA Aquinox Aquinox 4

Aquinox Summary Well capitalized into 2019 First-in-Class drug targeting novel enzyme (SHIP1) with broad

anti-inflammatory potential Lead disease indication: Rosiptor (AQX-1125) for Interstitial Cystitis / Bladder Pain Syndrome (IC/BPS) Encouraging Phase 2 results in IC/BPS; published in Journal of Urology in 2016 Competitive advantage in IC/BPS;

large, underserved market, suitable for independent commercialization in the US with RoW partner Achieved Enrollment Target of 300 Females in Phase 3 Clinical Trial Top-Line Data Expected Q3 2018 Aquinox 5

Prospective Near-Term Milestones Near-term Data, Expanded Market Opportunities and Pipeline Advancement

Publication of LEADERSHIP 201 Data S Initiation of Ethnobridging Trial (Q1 2018) Initiation of IC/BPS - LEADERSHIP 301 S Initiation of Drug/Drug Interaction Trial (Q1 2018) Complete ADME Trial S LEADERSHIP 301 Last Patient Randomized (Q1 2018)

Initiate Carcinogenicity Studies S CP/CPPS Phase 2 Trial 1st Patient Randomized (Early 2018) FDA Advisory Committee Meeting on IC/BPS S LEADERSHIP 301 Top-Line Data (Q3 2018) Aquinox 6

Dr. Philip Hanno Clinical Professor of Urology at Stanford University Specializes in the treatment of urologic

chronic pain syndromes including IC/BPS and CP/CPPS Extensively published (over 100 publications) Editor of multiple books on IC/BPS: most recently the 2018 Bladder Pain Syndrome -An Evolution published by Springer International Relevant experience

Former Chairman of Urology at Temple University School of Medicine Former medical officer for the FDA Co-chair of the Medical Advisory Board of the Interstitial Cystitis Association (ICA) Executive board of the International Society for the Study of

Bladder Pain Syndrome (ESSIC) Chair of the IC/BPS Guideline Committee of the AUA Aquinox 7

Aquinox IC/BPS Rosiptor Clinical Program Update February 9, 2018 Barbara Troupin, MD, MBA CMO, VP Clinical

Development & Regulatory Affairs

Rosiptor (AQX-1125) & Leadership 201

Rosiptor Overview: A Novel, First-in-Class Anti-Inflammatory Therapy First-in-Class SHIP1 activator with broad

anti-inflammatory potential Favorable ADME profile in humans Once-daily oral administration High oral bioavailability; minimal metabolism - Predominantly eliminated through renal clearance as rosiptor T1/2= 21 hours, Tmax= 1.25 hours Dose

proportional PK, no food effect Well tolerated in 8 completed clinical trials More than 395 subjects dosed to date Aquinox 10

Phase 2 LEADERSHIP Trial: A Comprehensive IC/BPS Trial Population and entry demographics: 69 female patients

across US and Canadian sites with moderate to severe IC/BPS symptoms: Mean bladder pain >5/10 Mean BPIC-SS and O Leary Sant ICSI/PI symptom scores >19 and >8, respectively On background medication (excluding opioids) Primary endpoint:

Reduction of average daily bladder pain at 6 weeks with once daily rosiptor (AQX-1125) vs. placebo Pre-specified secondary endpoints: Maximum daily bladder pain based on an 11-point NRS recorded by eDiary Average and maximum daily bladder pain score

measured by 11-point NRS recorded at clinic Multiple urological and QoL symptom assessments (O Leary-Sant ICSI/PI, BPIC-SS) Voiding frequency over a 24-hour period Safety, pharmacokinetics IC/BPS=interstitial cystitis/bladder pain syndrome;

BPIC-SS=Bladder Pain/Interstitial Cystitis Symptom Score; ICSI=interstitial cystitis symptom index; ICPI=interstitial cystitis problem index; NRS=numerical rating scale; QoL=quality of life Nickel JC, et al. J Urol. 2016;196(3):747-754 Aquinox 11

Rosiptor Reduced Maximum Daily Bladder Pain Over 6 Weeks 10 Week Follow-up -1.0 -1.3 -2.3 -2.6 -1.4 Follow-up 0

-0.5 -1.0 -1 -1.3 -1.4 -1.4 -1.5 -1.7 -1.8 -2 P=0.115 -2.3 -2.6 P=0.434 -2.5 P=0.060 -3 P=0.030 -3.5 Baseline 2 Weeks 4 Weeks 6 Weeks 10 Week Follow-up Based on 11-point NRS recorded with an e-diary Adapted from Nickel JC, et al. J Urol.

2016;196(3):747-754 Aquinox 12

Rosiptor: Significant Improvement in Secondary Endpoints at Week 6 1 Endpoint Placebo (N=32) Rosiptor 200 mg

(N=37) Difference in LS Mean Rosiptor-placebo P value 1 BLADDER PAIN (11-POINT NRS, CLINIC) Average daily pain -1.1 -2.6 -1.6 0.008 Maximum daily pain -1.1 -2.8 -1.6 0.028 SYMPTOM QUESTIONNAIRES O Leary-Sant IC Symptom Index (ICSI) -1.4 -3.8

-2.7 0.005 O Leary-Sant IC Problem Index (ICPI) -1.6 -3.6 -2.5 0.014 Combined O Leary-Sant ICSI/ICPI -3.0 -7.3 -5.1 0.007 BPIC-SS -4.0 -8.8 -5.4 0.011 VOIDING FREQUENCY Number of Voids/24h (e-diary) -0.8 -3.6 -2.8 0.040 Nickel JC, et al. J

Urol. 2016;196(3):747-754 Aquinox 13

\Rosiptor Demonstrated Similar AE Profile to Placebo in Phase 2 Trials LEADERSHIP 201 COMBINED SAFETY DATA

IC/BPS (6-week dosing) Three Phase 2 Trials (LEADERSHIP 201, KINSHIP, FLAGSHIP) Placebo N=32 n (%) Rosiptor N=37 n (%) Placebo N=260 n (%) Rosiptor N=263 n (%) TEAE 25 (78) 19 (51) 143 (55) 148 (56) GI Disorders 11 (34) 11 (30) 42 (16) 54 (21) Eye

Disorders 3 (9) 2 (5) 25 (10) 18 (7) SAEs 0 (0) 0 (0) 18 (7) 12 (5) Deaths 0 (0) 0 (0) 1 (0.4) 1 (0.4) TEAEs Leading to Discontinuation 1 (3) 2 (5) 12 (5) 15 (6) Nonclinical studies showed lens changes in animals, which led us to conduct ocular

monitoring in clinical trials Monitoring includes slit lamp biomicroscopy, visual acuity, intraocular pressure There was no substantial difference in observations at the ophthalmic examination between rosiptor and placebo or between start and end of

the 6-week treatment period of the LEADERSHIP 201 trial AE=adverse events; GI=gastrointestinal; SAE=serious adverse events; TEAE=treatment emergent adverse events Nickel JC, et al. J Urol. 2016;196(3):747-754 Aquinox 14

LEADERSHIP 301 Update

LEADERSHIP 301: Assessing Bladder Pain and Urinary Symptoms 12-week treatment period followed by 52-week

extension period Primary endpoint: Change from baseline at Week 12 in the maximum daily bladder pain score based on an 11-point NRS recorded by e-diary Key secondary endpoints: Change from baseline at Week 12 for the following: Voiding frequency

over a 24-hour period BPIC-SS Subjects Global Response Assessment (GRA) at Week 12 AEs over 12-week treatment period followed by 52-week extension period Aquinox 16

LEADERSHIP 301: Initiated in September 2016 Screening (up to 2 or 6 Weeks) Treatment Period (12 Weeks) Topline

Results Extension Period (52 Weeks) Follow-up Period Safety Follow-Up Visit (4 weeks post-dose) Follow-Up Telephone Call (3 months post-dose) Ophthalmic Safety Follow-Up Visit (6 months post-dose) Rosiptor 200 mg Rosiptor 100 mg Rosiptor 200 mg

Rosiptor 100 mg Rosiptor 200 mg Rosiptor 100 mg Placebo Randomization (1:1:1) Day - Day -28/- Day -14 Day 1 Day 42 Day 84 Day 126 Day 182 Day 238 Day 294 Day 364 Day 448 Day 476 Day 539 Day 630 42 14 ( 3) Baseline ( 3) ( 3)

( 7) ( 7) ( 7) ( 7) ( 7) ( 7) ( 7) ( 7) Visit 12 ( 3) Visit 1 Visit 2 Visit 3 Visit 4 Visit 5 Visit 6 Visit 7 Visit 8 Visit 9 Visit 10 Visit 11 Phone Ophthalmic Visit 1 Visit 1a

(Follow-up) Visit - 11a Assessment subjects not subjects requiring a requiring a cystoscopy cystoscopy Extension period will Visit 1 Visit 1a subjects requiring a cystoscopy subjects not requiring a cystoscopy afford all patients treatment with

LEADERSHIP 301: Enrollment Update (As of February 6, 2018) 410 Patients Enrolled 322 (79%) Females (Target

Enrollment was 300) 88 (21%) Males 297 (72%) Through Treatment Period 63% Have Transitioned into Extension Period 129 Trial Sites 12 Countries 57% of Sites in North America ~50% Screen Failures (consistent with LEADERSHIP 201) < 9% Dropouts in

Treatment Period (consistent with LEADERSHIP 201) Topline Data Expected Q3 2018 Data on File, AQX 2017 Aquinox 18

Blinded LEADERSHIP 301 Baseline Data (As of December 31, 2017) North America Europe Female (N = 148)

Allsubjects (N =188) Female (N = 126) Allsubjects (N =163) Age (years; mean SD) 48.9 13.5 50.1 13.7 51.3 16.5 50.9 16.3 Race, White (n, %) 129 (87.2) 168 (89.4) 124 (98.4) 161 (98.8) Duration of Diagnosis

(months; mean SD) 66.7 60.2 63.5 59.5 35.3 42.2 35.1 42.4 Hunner Lesions (%) 8.1 11.7 30.2 28.2 NRS Average Pain (mean SD) 6.3 1.0 6.3 1.0 6.4 1.0 6.4 0.9 BPIC-SS

(mean SD) 28.8 4.5 28.8 4.4 27.1 4.2 26.5 4.3 ICPI (mean SD) 12.5 2.6 12.6 2.6 12.7 2.3 12.5 2.3 ICSI (mean SD) 14.4 3.3 14.5 3.2 13.9

3.0 13.7 3.0 Voids per 24hrs (mean SD) 18.5 9.7 18.9 10.0 18.3 10.7 17.6 9.8 Total N includes all randomized subjects as of 31-Dec-2017; n for individual parameters may vary Aquinox Data on

File 2018 Aquinox 19

LEADERSHIP 301 Topline Data Preview

Powering Assumptions for LEADERSHIP 301 Trial has 90% power to detect a 1-point difference in the change from

baseline in maximum daily bladder pain between rosiptor and placebo in female subjects with a two-sided 0.05 alpha Aquinox 21

The change from Baseline (Visit 2) at Week 12 (Visit 4) for rosiptor 100 mg or 200 mg, compared to placebo in

the maximum daily bladder pain score based on a standardized 11-point NRS recorded by e-diary as measured by the mean of the maximum bladder pain scores recorded once daily for a minimum of 5 of the 7 days prior to each visit Aquinox 22

11-Point NRS for Bladder Pain Daily assessment of bladder pain using an electronic diary 11-point scale,

responses of 0 to 10 Assessment of average and maximum (worst) bladder pain evening diary Please assess your average and worst bladder pain for each day on a scale from 0-10 0= No pain 10 = Pain As bad as you can imagine Welcome to the evening diary

Please complete your assessment in the evening at approximately the same time 1.What number would you give your average pain over the last 24 hours Back Next Back Next 0 1 2 3 4 5 6 7 8 9 10 0 1 2 3 4 5 6 7 8 9 10 2.What number would you give your

worst pain over the last 24 hours Aquinox 23

Primary Analysis (ITT) Repeated measures analysis of change from baseline at Week 12 (female subjects only) Two

step process Step 1: Global test Placebo vs rosiptor 100 mg vs rosiptor 200 mg treatment arms Step 2: If global test is significant, two pairwise comparisons Placebo vs rosiptor 100 mg and placebo vs rosiptor 200 mg At least one of these two

comparisons must also be significant to have a successful trial By first doing the global test, we preclude the need for any alpha adjustment, and all p-values are compared to an alpha of 0.050 ITT=intent to treat Aquinox 24

Primary Analysis Primary analysis in females will be stratified by Hunner lesion status Randomization is

stratified by sex (male, female) and Hunner lesion status (present, absent) Aquinox 25

Secondary Endpoints - Female Subjects (ITT) The change from Baseline (Visit 2) at Week 12 (Visit 4) for

rosiptor 100 mg or 200 mg compared to placebo in the following: Voiding frequency (24-hour period) BPIC-SS Overall response to treatment for rosiptor 100 mg or 200 mg compared to placebo as measured by the subject s GRA at Week 12 Aquinox 26

Assessment of Urinary Frequency For a 24-hour period prior to a scheduled trial visit, subjects are asked to

complete a diary For each urination, they are asked whether the need to void woke them from sleep Urination Diary welcome to the urination diary your urination diary is now available for input. Please complete the diary each time you urinate from

the time you got up this morning and for the next 24 hours. Urination Diary info for this urination, did the need to urinate wake you from sleep? If you forget to report a urination, please record it as soon as possible. Back next There are no

urinations reported yet.report urination date time nothing further to report Aquinox 27

Bladder Pain/Interstitial Cystitis Symptom Score (BPIC-SS) Developed and validated as a clinical screening tool

8 questions about urinary symptoms and bladder pain over past 7 days Questions 1-5 pain and symptoms Questions 6-7 bother Question 8 worst bladder pain (based on 11-point NRS) Total Score up to 38 points Bladder PainZ Interstitial Cystitis Symptom

Score (BPIC-SS) When answering the following questions, please think about the PAST 7 DAYS Never Rarely Sometimes Most of the time Always In the past 7 days when you urinated, how often was it because of pain in your bladder? li -I, L_, lj3 u*

2. In the past 7 days, how often did you still feel the need to urinate just after you urinated? LI, -Ir Lls lj3 Ul, 3. In the past 7 days, how often did you urinate to avoid pain in your bladder from getting worse? lj -I, u. lj3 I* 4. In the

past 7 days, how often did you have a feeling of pressure in your bladder? li -I, L_, lj3 U* 5. In the past 7 days, how often did you have pain in your bladder? u. -If u, lj3 L. Not at all A little Somewhat Moderately A great deal 6. In the past 7

days, how bothered were you by frequent urination during the daytime? LI, -If L: u3 Ul< 7. In the past 7 days how bothered were you by having to get up during the night to urinate? u. -If u. lj3 I* No bladder Pain Worst possible bladder pain I-

l_ 1- 1- u LI u L L U L 0 1 2 3 4 5 6 7 8 9 10 8. Select the number that best descnbes your worst bladder pain in the past 7 days : To be : completed : by study t staff Add the scores for each question together to give a total BPIC-SS score TOTAL

SCORE = Total score ranges from 0 - 38. A total score can only be calculated if ALL questions are completed by the patient Aquinox 28

Bladder Pain/Interstitial Cystitis Symptom Score (BPIC-SS) Developed and validated as a clinical screening tool