Developing Well-Differentiated Antibiotics

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CORPORATE PRESENTATION Developing Well-Differentiated Antibiotics June 2016 PRABHAVATHI FERNANDES, PhD President and CEO

Forward Looking Statement This presentation contains forward-looking statements regarding future events. These statements are just predictions and are subject to risks and uncertainties that could cause the actual events or results to differ materially. These risks and uncertainties include, among others: our and our strategic partners ability to obtain FDA and foreign regulatory approval of our product candidates; risks related to the costs, sources of funding, timing, regulatory review and results of our studies and clinical trials and those of our strategic partners; our need to obtain additional funding and our ability to obtain future funding on acceptable terms; our ability to commercialize and launch whether on our own or with a strategic partner any product that receives regulatory approval; our anticipated capital expenditures and our estimates regarding our capital requirements; our dependence on the success of solithromycin and TAKSTA; the unpredictability of the size of the markets for, and market acceptance of, any of our products, including solithromycin and TAKSTA; our ability to produce and sell any approved products and the price we are able to realize for those products; our ability to retain and hire necessary employees and to staff our operations appropriately; the possible impairment of, or inability to obtain, intellectual property rights and the costs of obtaining such rights from third parties; our ability to compete in our industry; innovation by our competitors; and our ability to stay abreast of and comply with new or modified laws and regulations that currently apply or become applicable to our business. Please refer to the documents that we file from time to time with the Securities and Exchange Commission. [ 2 ]

Highlights Cempra, a Differentiated and Growing Company Cempra has consistently executed on plan the leading antibacterial biotech Cempra has submitted NDAs for solithromycin and expects to launch product Q1 2017 large market potential for CABP New macrolide is urgently needed - resistance to azithromycin and serious adverse event labeling of levofloxacin. Little generic competition, no branded competition Additional indications near term- product within a product Pediatrics, COPD, Gonorrhea Validated by license for Japan, partnerships with BARDA and NIAID Cempra has a second antibiotic in Taksta in Phase 3 - ABSSSI and refractory BJI Only oral antibiotic for long term use with large market potential Cempra owns macrolide platform technology and discovery programs for non-antiinflammatories and motilin agonists Cempra has hired experienced staff in Commercialization, Medical Affairs, Regulatory, Clinical, Chemistry, Finance, IT to support readiness for launch Well financed and ROW (except Japan) licensing potential is still open [ 3 ]

Proven Management Team Prabhavathi Fernandes, PhD President & CEO Mark Hahn, CPA CFO David Moore, MBA CCO Munir Abdullah, PhD EVP Regulatory Gary Horwith, MD EVP Pharmacovigilance & QA David Oldach, MD Chief Medical Officer David Pereira, PhD EVP Chemistry Azactam (Aztreonam) Biaxin (Clarithromycin) Dificid (Fidaxomicin) IPO and M&A Athenix-Bayer CropScience Charles & Colvard (CTHR) E&Y Levaquin (Levofloxacin) Topamax (Topiramate) Ultram (Tramadol) Nucynta (Tapentadol) Flonase (Fluticasone Propionate) Veramyst (Fluticasone Furoate) Avodart (Dutasteride) Tykerb (Lapatinib) S. aureus vaccine Abelcet (Amphotericin B) Viread (Tenofovir) Combinations Against HCV Injectable Penicillins Dobutamine HCI Injection Ranitidine Injection [ 4 ]

Cempra s Late Stage Portfolio PRODUCT CANDIDATE INDICATION FORMULATION PRECLINICAL PHASE 1 PHASE 2 PHASE 3 Community Acquired Bacterial Pneumonia (CABP) Oral Completed IV-to-Oral Completed Pediatric: Capsule/Suspension/IV NDA submitted 4/28/2016 NDA submitted 4/28/2016 SOLITHROMYCIN Biodefense Use Oral/Suspension Urethritis/Gonorrhea Oral Anti-Inflammatory/NASH Oral Anti-Inflammatory/COPD Oral TAKSTA FUSIDIC ACID Chronic Bone and Joint Infections ABSSSI Oral Oral NON-ANTIBIOTIC MACROLIDE Diabetic Gastroparesis and GERD [ 5 ]

NDAs Submitted - with Potential To Be a Successful Antibiotic Solithromycin has completed 2 pivotal Phase 3 trials Positive clinical data from both trials safe and effective Fast Track and Priority review (QIDPs) designations received from the FDA NDA (rolling NDA) submitted 28 April, 2016. EU submission documents preparation on track [ 6 ]

Expected Time-Lines June 30, 2016: Submission of MAA to EMA 3Q 2016: Acceptance of NDAs by FDA EOY 2016: PDUFA date EOY 2016: NDA approval expected Launch Q1 2017 Qualified Infectious Disease Program (QIDP): Two QIDPs for Oral capsules and IV for CABP Provides 8 Month Priority Review Fast Track Designation Rolling NDA [ 7 ]

Community Acquired Bacterial Pneumonia: Prevalent, Deadly and Growing Prevalent and Deadly Growing HOSPITAL DISCHARGES FOR PNEUMONIA 3 5-10M Cases Annually 2,900,000 1.1M Patients Hospitalized #1 Cause of Death from an Infection 1 2,700,000 2,687,991 2,665,904 2,697,392 More Deaths from Pneumococcal Infections in US than Breast or Prostate Cancer 2 Affects Young Children and the Old Disproportionately 2,499,032 2,595,749 2,500,000 2,465,205 2,320,425 2,418,402 2,300,000 2,165,854 2,163,035 2,257,158 2,100,000 2,057,037 2,056,773 1,949,858 1,943,591 2,046,815 1,900,000 1,757,220 1,901,818 1,773,386 1,700,000 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 Appropriate Empiric Therapy Critical for Positive Outcomes Multiple Pathogens (Pneumococcus Most Frequent) 1 Freeman, MK. CABP: A Primer for Pharmacists: US Pharmacist July 1, 2013 2 Xu, et al. Deaths: Final Data for 2007. Natl Vital Stat Rep. 2010;58:1-51. 3 Source: 2011 HCUP, ARHQ.gov [ 8 ]

Resistance Has Created a Large Macrolide Market Opportunity US COMMUNITY ANTIBIOTIC RXs Total = 264 M in 2013 a Cephalosporins (39M) Beta-lactams (79M) Macrolides (62M) Other Fluoroquinolones Antibacterials (36M) (28M) Tetracyclines/ Aminoglycosides (21M) Macrolide Antibiotics - Used Traditionally by Physicians to Treat Respiratory Tract Infections Targeted Spectrum of Activity Good Safety Excellent Tissue / Intracellular Distribution Anti-Inflammatory Activity >60% OF RTI MARKET Azithromycin Leading Macrolide 51M Rx s in US in 2013 b Most Widely Prescribed Treatment for CABP / RTIs (Respiratory Tract Infections) Resistance Driving Need for a New Macrolide Source: a IMS Health (Retail) AMR Hospital Data (Inpatient) b 2013 IMS New Prescription Audit [ 9 ]

Pneumococcal Resistance Drives Need for New Macrolide % Resistance AZITHROMYCIN SOLITHROMYCIN * China** 96.4% 70.5%* 28.0%* 48.0%*** 0% 0% 0% Europe North America Asia Europe North America Asia MIC 90% (µg/ml) >1 >1 >1 0.06 0.25 0.5 * Morrissey, I. ECCMID 2014. Abstr. P1584 ***Jones, RN.DMID 2013; 75:107-109 ** Kim,SH, AAC, 2012, 56: 1418-1426 [ 10 ]

Solithromycin: 4 th Generation Macrolide - The First Fluoroketolide Currently Approved Macrolides ERYTHROMYCIN SOLITHROMYCIN N N H 2 N N CLARITHROMYCIN O N O O O OMe O O HO NMe 2 O O F AZITHROMYCIN CEM - 101 = 3 Changes Made to Make Solithromycin Interacts with Bacterial Ribosome at Three Sites Resistance Rare and Could Only Occur If Mutations Occur at Three Distinct Sites [ 11 ]

What do these three celebrities have in common? Yoko Ono Merle Haggard Michael Moore Hospitalized in the winter of 2015-2016...but why did they have to be hospitalized? [ 12 ]

IDSA / ATS CABP Guidelines Healthy Outpatient Outpatient at Risk of DRSP* Inpatient Non-ICU Inpatient ICU Macrolide Or Doxycycline Respiratory Fluoroquinolone Or Beta-lactam plus Macrolide Beta-lactam plus Macrolide Or Respiratory Fluoroquinolone Or Tigecycline Beta-lactam plus Azithromycin Or Beta-lactam plus Fluoroquinolone * Drug Resistant S. pneumoniae - Recent antimicrobials; comorbidities; Includes healthy patients in regions with high rates of macrolide resistance Treatment of Pseudomonas or MRSA is the main reason to modify standard therapy for ICU Ceftriaxone, cefotaxime, amp/sulbactam, ertapenem, ceftaroline (from CMS list) Mandell L, et al. Clin Infect Dis. 2007;44(Suppl 2):S27-S72; CMS list of antimicrobials. [ 13 ]

Current CABP Therapies Have Use-Limiting Formulations and Safety Issues 2 Primary Options Issues 1 Cephalosporin (e.g. Ceftriaxone) Macrolide (e.g. Azithromycin) NO ORAL OPTION Requires IV Ceftriaxone AND Hospitalization No Oral Switch Therapy Replacement Hospitalization Issues Hospitalized CABP High Mortality Rate 1 Hospital-Acquired Infections Costs and Hazards 2 2 SAFETY CONCERNS Fluoroquinolone (e.g., Levofloxacin, Moxifloxacin) IDSA / ATS Recommends Broad Spectrum, Empiric Coverage 1 Freeman, MK. US Pharmacist. July 1, 2013 2 Magill, SS. And CDC and Emory Authors. NEJM 2014. 1198-1208, 2014 Focus of FDA Advisory Committee, Nov. 5, 2015. Label changes May 2016 Kill Bowel Flora Increased frequency of C. difficile Colitis Tendonitis, Achilles Tendon Rupture, Hepatotoxicity and Peripheral Neuritis, Retinal Detachment Treatment Failures from Resistant Strain Selection Not Approved for Use in Pediatrics No Longer Used for CABP in Several Countries [ 14 ]

Solithromycin Spectrum of Activity That Addresses CABP Pathogens GRAM ORGANISMS SOLITHROMYCIN AZITHROMYCIN CEFTRIAXONE Positive Solithromycin Has Class-Leading Potency Against CABP Pathogens Overcomes macrolide resistance that limits existing macrolides LEVOFLOXACIN or MOXIFLOXACIN Streptococcus pneumoniae Negative Positive Atypical Atypical Atypical Haemophilus influenzae Staphylococcus aureus Legionella pneumophila Mycoplasma pneumoniae / Chlamydophila pneumoniae Azithromycin Monotherapy not used to Treat Moderate to Severe Pneumonia Potency, Spectrum and Resistance Allow Use Only in Simpler Infections or Add-On To Ceftriaxone [ 15 ]

CABP Antibiotic Usage AZ and Levo comprise majority of Retail CABP Rx Ceftriaxone/Azi, Levo and Zosyn ~65-70% of hospital days of therapy 1% 2% 12% 6% 8% 33% 38% Azithromycin Levofloxacin Amoxicillin Amoxicillin/Clavulanic Acid Ciprofloxacin Cefdinir Cephalexin Others Source: 2014 IMS NPA and NDTI Source: AMR Days of Therapy, 2014 2010 2011 2012 2013 2014 Retail Scripts (MM) 8.7 8.5 9.5 9.5 9.7 Retail Levofloxacin Use increasing for CABP and Bronchitis CABP Bronchitis 18.5% 21.7% 25% 25.1% 25% 16.7% 15.5% 17.2% 21.2% 23% Source: 2014 IMS NPA and NDTI [ 16 ]

Oral Phase 2 Trial - Toyama Solithromycin safety and efficacy further validated by Toyama (FUJIFILM) All efficacy outcome measures favored solithromycin SOLITHROMYCIN LEVOFLOXACIN Favors Levofloxacin Favors Solithromycin Population Success Rate % Success Rate % Delta (CI) modified- ITT 77.3 (34/44) 61.7 (29/47) +15.57 (-5.2, 36.4) Per Protocol 85.0 (34/40) 67.4 (29/43) +17.56 (-2.7, 37.8) -24-20 -16-12 -8-4 0 4 8 12 16 20 24 Treatment difference [ 17 ]

Partnership Provides Validation and Adds Value GEOGRAPHY DEVELOPMENT / REGULATORY VALUE Japan Exclusive License (2 nd Largest Antibiotic Market) Global Development Program $30M Upfront / Milestones Rec d Up to $40M Additional Milestones Double Digit Tiered Royalties, Subject to Reaching Sales/Contract Levels ROW ( Europe, China/Asia, South America etc.) is expected to be licensed Growing resistance, exceeding 80% in Asia Large market potential for a macrolide [ 18 ]

Solithromycin May Have Potential In a Broad Range of Indications CABP Primary Indication Special Populations BARDA Funded RESPIRATORY TRACT INFECTIONS (RTI) Hospital-Acquired Pneumonia, Simple RTIs such as Pharyngitis, Acute Exacerbation of Chronic Bronchitis (AECB) ANTIBACTERIAL AND ANTI-INFLAMMATORY COPD, Cystic Fibrosis, NASH PEDIATRICS AND PREGNANCY No Pediatric Drug with Broad Potential in Development Infections in Pregnancy Neonatal Sepsis Infections in Utero Premature, Cerebral Palsy, Autism Biodefense BARDA Funded MULTIPLE UNIDENTIFIED PATHOGENS Anthrax, Tularemia Sexually Transmitted Diseases GENITAL INFECTIONS (GONORRHEA AND CHLAMYDIA) Major Public Health Crisis Multi Drug Resistance, No Oral Therapy GI & Others Ophthalmic OTHER INFECTIONS Helicobacter Gastritis, Tick and Insect Borne Diseases Ophthalmic drops eye infections and blepharitis [ 19 ]

Solithromycin Phase 3 Trial: Gonorrhea BACKGROUND / RATIONALE Gonorrhea: 2 nd Most Common Communicable Disease: 800K US; 500M Globally/Year Drug Resistant Gonorrhea : CDC Emergency Need Current Intramuscular-Only Treatment Precludes Brown Bag Treatment of Partners INDICATION FORMULATION PRECLINICAL PHASE 1 PHASE 2 PHASE 3 Urethritis / Gonorrhea Solithromycin Was 100% Effective in All Culture-Proven Cases of Gonorrhea in a Phase 2 Trial Oral TRIAL DESIGN COMPARATOR PATIENTS (n) PRIMARY ENDPOINT STATUS Single Dose of Solithromycin (1000 mg Oral) Ceftriaxone 500 mg Intramuscular Injection + Azithromycin 1000 mg Oral 300 Patients with Gonorrhea (with or without Chlamydia) Culture Negative at 7 Days (TOC) Study being expanded for women and children with NIAID - NDA expected to be submitted after CABP 1 Unemo, M. Antimicrob. Agents Chemother 2012, 56: 1273-1280 [ 20 ]

Clinical Development for Pediatric Use First antibiotic in over 2 decades being developed for use intravenously/oral capsules or as a suspension formulation dosing flexibility FDA has granted QIDP for suspension formulation Phase 1a completed Enrollment in Phase 1b is proceeding well. Ages 0-17 being enrolled Phase 2/3 pivotal trial is expected initiated 1H 2016 Mostly funded by BARDA ~ 55MM pediatric antibiotic prescriptions annually in the US for all indications* ~ 23% were for azithromycin* Source: http://pediatrics.aappublications.org/content/130/1/23.full.pdf+html [ 21 ]

Solithromycin - Differentiated from Other Recently Approved Antibiotics Community and Hospital Oral and IV product expected to capture the large need in the ER, Urgent care and hospital Generic Competition Alternatives to avoid treatment failures and hospitalization No branded competition 100% share of voice Pricing Pricing expected to be in the hundreds of dollars per prescription Pediatrics Oral suspension for pediatrics in addition to capsules and intravenous formulations Pulmonologists, ER, Urgent Care MDs Respiratory product - 80% of use in pulmonary infections Source: 2013 IMS NPA, NDTI [ 22 ]

Results from recent quantitative Market Research PULM, ID, PCP What is your current level of satisfaction with current CABP treatments? - 66% Somewhat Satisfied, 17% Very Satisfied If you were told that macrolide resistance to pneumococcus has reached 50%, would you seek an alternative treatment? - 96% Yes Are you concerned with safety of fluoroquinolones (levofloxacin/moxifloxacin)? - 65% Yes What is needed is a new antibiotic that has the efficacy of a fluoroquinolone but the safety of the macrolide class Source: Instar Market Research, N = 120 [ 23 ]

Cempra Believes It Can Successfully Launch Solithromycin There is a recognized urgent need for a new macrolide IV/PO formulations allow in-patient and outpatient dosing A select group of providers write a disproportionate share of AZ and LEVO CABP prescriptions Acute CABP prescriptions are not actively managed by 3 rd party payors Cempra has a unique opportunity to own 100% share of voice of the branded antibiotic CABP market We expect the price to be in the hundreds of dollars and not in the thousands - we expect to be a favorable formulary tier with reasonable patient co-pays [ 24 ]

A very small group (4%) writes a disproportionate share of AZ and LEVO CABP prescriptions (40%) CABP Volume (AZ + LEVO TRxs) 40% 60% % TRx Prescribed by Top Deciles 7-10 % TRx Prescribed by Deciles 1-6 4% of Prescribers (34,927) Out of a total of 803,717 PRESCRIBE 40% of AZ/LEVO CABP TRxs SOURCE: IMS Deciler Prescriber Level Data, Time Period: Moving Annual Total (MAT) FEB 2015. Market Definition: Azithromycin and Levofloxacin. Excluded Specialties: Gastroenterology, Urology, Dentistry, Pediatrics, Obstetrics, Gynecology. [ 25 ]

~80,000 Prescribers are Responsible for 60% of TRx volume ~43,000 HCPs ** Targeted thru non-personal XXX 24 Rx s of Rx per per year year ~35,000 HCPs * Targeted thru personal and non-personal 62 Rx s per year DIGITAL & PRINT MEDIA PUBLICATIONS E-DETAIL MARKETING AUTOMATION CONTENT SYNDICATION *SOURCE: IMS Deciler Prescriber Level Data, Time Period: Moving Annual Total (MAT) FEB 2015 Market Definition: Azithromycin and Levofloxacin. Excluded Specialties: Gastroenterology, Urology, Dentistry, Pediatrics, Obstetrics, Gynecology. [ 26 ]

Launch Preparation Underway Planned CABP LAUNCH Pre-launch Activities 1 st Half 2016 Launch API Disease Awareness Commercial Leads MSLs KOL Development Physician Targeting Pre-launch Activities 2 nd Half 2016 Finished Goods Digital Tactics Infrastructure Pricing & Reimbursement Coming Soon Ads Launch Inventory / AR Branded Campaign Sales Force Medical Education Payer Contracting [ 27 ]

Taksta (Fusidic Acid) An ORAL Antibiotic for MRSA Infections Being Developed for ABSSSI and for CHRONIC Use in Bone and Joint Infections in the U.S. INDICATION FORMULATION PRECLINICAL PHASE 1 PHASE 2 PHASE 3 TAKSTA FUSIDIC ACID Chronic Bone and Joint Infections ABSSSI Initiated Dec 2015 Oral Oral [ 28 ]

Taksta Highlights Fusidic Acid 40 Years of Safety and Efficacy in Acute and Chronic Oral Use in Staph Infections (Including MRSA) Ex-U.S. Unique Structure, No Known Cross Resistance No Other Antibiotic Available For Long Term Oral Treatment of Staph Infections CLINICAL TRIALS Well Tolerated in ABSSSI Phase 2 Study; No Resistance Observed Phase 2 PJI Study Data Reported Phase 3 study for ABSSSI and exploratory refractory BJI study enrolling REGULATORY QIDP granted for ABSSSI Exclusivity and priority review Orphan Drug Designation for PJI Granted by FDA (Oct. 2013) Request pending for Orphan Designation for refractory BJI [ 29 ]

Strong IP Protection with Long Patent Runway Loading Dose Patent to 2029 (Plus Patent Term Extensions) 12 Years of Statutory Protections Possible (7 yrs Orphan Drug + 5 yrs GAIN) CEMPRA S LOADING DOSE Concentration (mg/l) 150 125 100 75 TAKSTA 50 25 0 European Dosing EU Dose 500 mg dose Cempra dose 1200 mg Q12h Day followed by 600 mg Q12h 0 24 48 72 96 120 Time (hrs) [ 30 ]

Projected 2016 Milestones 4.28.16: Completed NDA submissions to FDA for Solithromycin Oral capsules and IV formulation 1H 16: Complete MAA submissions to EMA for Solithromycin Oral capsules and IV formulation 7.1.16: Acceptance of NDAs 12.30.16: NDAs Approved 1H 16: EOY 16: EOY 16: EOY 16: Solithromycin: Initiate global Phase 2/3 Pediatrics pivotal trial (BARDA) Solithromycin: Complete Phase 1b - Pediatrics. All formulations Solithromycin: Complete enrollment in Phase 2 NASH Trial Solithromycin: Complete enrollment in Phase 2 COPD Trial [ 31 ]

Finance - Strong Balance Sheet $223.6M $19.7M 48.2M CASH AND EQUIVALENTS 3/31/16 LONG-TERM DEBT 3/31/16 SHARES OUTSTANDING 4/18/16 [ 32 ]