 Developing Well-Differentiated Antibiotics to Meet Medical Needs Cempra Corporate Presentation September 2012 Developing Well-Differentiated Antibiotics to Meet Medical Needs Exhibit 99.1 |
 Forward Looking Statement 2 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: risks related to the costs, timing, regulatory review and results of our studies and clinical trials; our ability to obtain FDA approval of our product candidates; our dependence on the success of Solithromycin and Taksta; our need to obtain additional funding and our ability to obtain future funding on acceptable terms; our anticipated capital expenditures and our estimates regarding our capital requirements; the possible impairment of, or inability to obtain, intellectual property rights and the costs of obtaining such rights from third parties; 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; 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. |
 Lead program, Solithromycin, has the potential to be the first Oral and IV macrolide approved since Zithromax/Z-PAK - Oral Phase 3 trial in CABP is expected to begin 2H 2012 Solithromycin Phase 2 trial for bacterial urethritis is running - Results expected 2H 2012 Antibiotic-resistant gonorrhea is a major global threat and new treatment options for gonorrhea are urgently needed Second program, Taksta, is an oral drug that is effective against MRSA, which we are developing for long-term treatment of Prosthetic Joint Infections (PJI)- Phase 2 trial expected to begin 2H 2012 - a potential orphan indication New FDA guidance provides regulatory pathway – The GAIN Act provides incentives for antibacterial development Large market opportunity with global antibiotic sales in the multibillions Significant need for new antibiotics driven by resistance and tolerability issues Strong management team with extensive, successful experience in antibiotic drug development and approval - Azactam, Biaxin, Fidaxomicin, Synercid, Viread Highlights 3 |
 Significant need for new treatment driven by: Resistance Adverse events/lack of tolerability Inappropriate spectrum Lack of IV-oral Lack of pediatric dosing formulation Acceptability for long term use Developing Differentiated Antibiotics to Meet Significant Needs 4 Global antibiotic sales in 2009 Total $42B From B. Hamad, IMS Health Nature Drug Discovery, 2010, 9: 675-676. Cephalosporins beta-lactams Fluoroquinolones Macrolides Other antibacterials Tetracyclines / aminoglycosides $11.9B $11.5B $7.1B $4.8B $4B $2.6B At least 30% of pneumococci in the U.S. are resistant to azithromycin (Z-Pak) – the leading macrolide Anti-gonorrhea antibiotics are slowly losing their effectiveness. CDC has announced new guidelines, removing Cefixime, the last oral drug available for treating gonorrhoea Growing need for oral therapies to address chronic staphyloccocal infections (MRSA) infections – chronic therapy of prosthetic joint infections The growing need: |
 Cempra’s Portfolio Addresses The Critical Needs in The Antibiotic Market Non-Antibiotic Macrolide Program: GERD/Diabetic gastroparesis and COPD are in preclinical stage Product Formulation Preclinical Phase 1 Phase 2 Phase 3 CEM-101 (Solithromycin) Community Acquired Bacterial Pneumonia (CABP) Oral Intravenous (IV) Oral Suspension/Pediatric Future CEM-101 indications: Urethritis, Other respiratory tract infections (RTI’s), chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF), malaria, eye infections, etc. Oral – Urethritis Taksta Fusidic Acid Acute and Chronic Treatment of Staph (MRSA) Oral – Chronic Prosthetic Joint Infections Oral – ABSSSI Oral Suspension/Pediatric 5 TM |
 6 Solithromycin – (CEM-101) A next generation macrolide for respiratory tract infections, including CABP, entering Phase 3 |
 7 Community-Acquired Bacterial Pneumonia (CABP) Pneumococci (80% of cases) Haemophilus Staphylococcus Moraxella Legionella Mycoplasma Chlamydophila Hospital-Acquired Pneumonia (HAP) Pseudomonas Enteric gram-negatives (E.coli, Klebsiella, Serratia, etc.) Staphyloccci, MRSA Pneumococcus Haemophilus Ventilator-Associated Pneumonia (VAP) Pseudomonas Enteric gram-negatives (Klebsiella, Serratia, etc.) Acinetobacter Staphyloccci, MRSA Burkholderia Viral Pneumonia Influenza Other viruses All Pneumonias Are Not Created Equal |
 Community-Acquired Bacterial Pneumonia (CABP) No. 1 cause of death due to infection Pneumococcus is the most common cause of fatal CABP Most common cause of chronic bronchitis, sinusitis, meningitis and otitis media 5-6 million cases/year ~1 million hospital admissions/year ~1.6 million fatal cases of pneumococcal disease worldwide annually Pneumococcal diseases cause more deaths per year in U.S. than breast or prostate cancer Centers for Disease Control and Prevention. 2010. Active Bacterial Core Surveillance Report, Emerging Infections Program Network, Streptococcus pneumoniae, 2009. http://www.cdc.gov/abcs/reports- findings/survreports/spneu09.pdf. Accessed February 3, 2011. Xu. et al. Deaths: Final Data for 2007. Natl Vital Stat Rep. 2010; 58: 1-51 8 Drug Discovery News May 2012. Report forecasts increases in respiratory disease incidence, market. |
 9 Monotherapy, IV-Oral in CABP - Currently Possible Only With Fluoroquinolones Although FQs are approved and used widely for treatment of CABP – Adverse events are associated with their use – It is not approved for use in pediatrics Fluoroquinolones affect bowel flora and select for CDAD Far more could be done to stop the deadly bacteria C. diff By Peter Eisler, USA TODAY August 17, 2012 Tendonitis - That can lead to spontaneous rupture of multiple tendons, commonly Achilles, which may occur during therapy or typically within 12 weeks, but can occur years after therapy has been discontinued. Adverse events from FQ treatment increase cost to hospitals, insurance companies and patients Look, I know its ruptured doc.. But surely I’ll still be able to run in the marathon next week… |
 Azithromycin’s long, low blood/tissue levels favors selection of resistant bacteria A new macrolide is needed Impact of Macrolide Therapy on Mortality in Severe CABP Restrepo, MI. et al. Eur Resp J. 2009; 33: 153-159. Survival of CABP patients treated in accordance with IDSA/ATS guideline using combinations with a macrolide or a quinolone - macrolide Martin-Loeches, I. et al. Intensive Care Med. 2010; 36: 612-620. CONFIDENTIAL 10 IDSA and KOLs recommend a ß-lactam plus Several reports show that addition of a macrolide results in better patient outcome Addition of macrolide decreases mortality by >50% in patients with highest PORT scores + macrolide a macrolide for CABP |
 Solithromycin Opportunity 11 Azithromycin (Zithromax/Z-Pak), the leading macrolide, went generic in 2005 52 million prescriptions and $1.1 billion in sales in 2010 Widespread azithromycin use has led to resistance issues Lack of new macrolides with improved resistance profiles has led physicians to turn to fluoroquinolones (Levaquin) despite side effect concerns Total 2009 Pneumonia Oral Prescriptions – By Class (Branded and Generic) Source: IMS Macrolides are the most widely prescribed treatment for CABP and other RTIs Broad spectrum of activity Good safety Excellent tissue/intracellular distribution and anti-inflammatory activity Pneumococcal resistance rate in China – 96.4% Asian Network Surveillance. AAC. 2012; 56: 1418-1426. Canadian Bacterial Surveillance Network. http://microbiology.mtsinai.on.ca/research/cbsn/. Accessed March 2011 62.6% 25.5% 11.9% Extended Spectrum Macrolides Quinolones Other Erythromycin-Resistant S. pneumoniae Isolates in NA |
 History of Macrolide Development 12 In vitro activity is similar. Better PK, acid stable, fewer GI effects Resistance is now widespread More potent than 2 generation macrolides Active against macrolide-resistant strains, 2 binding sites, acid stable, good PK, better tissue distribution Telithromycin – major adverse events Others have failed – no other new macrolides More potent than 3 generation macrolides Active against 1 , 2 and 3 generation macrolide-resistant strains, 3 ribosomal binding sites, extended spectrum, good PK and tissue distribution, intravenous and oral dosing Effective in Phase 2 oral and well-tolerated (Solithromycin) First Generation Macrolide Second Generation Macrolide Third Generation Macrolides, “Ketolides” Fourth Generation Macrolide, Fluoroketolide nd rd st nd rd |
 # of Organisms Solithromycin Azithromycin MIC 90 (µg/ml) Streptococcus pneumoniae (150) 0.25 >16 Haemophilus influenzae (100) 2 2 Streptococcus pyogenes (100) 0.03 >16 Legionella pneumophila (30) 0.015 2 Mycoplasma pneumoniae (36) 0.000125 0.0005 Chlamydophila pneumoniae (10) 0.25 0.125 Solithromycin: Spectrum of Activity That Addresses CABP Pathogens Solithromycin (CEM-101) is several fold more potent than azithromycin against S. pneumoniae, a critical pathogen in CABP and respiratory tract infections 13 Solithromycin has demonstrated class-leading potency in vitro against macrolide-resistant pneumococcus CEM-101’s unique chemical structure necessitates mutations at three distinct sites for resistance to develop – no other macrolide has more than two |
 Population Solithromycin Levofloxacin Success rate, % Success rate, % ITT* 72.3 71.6 MITT 77.8 71.4 Solithromycin: Comparable Efficacy to Standard of Care (Levaquin) - Oral Phase 2 Trial 14 Solithromycin performed favorably in mITT at TOC when CABP pathogens were isolated - key criteria used by the FDA Randomized 132 patients received either Solithromycin or Levofloxacin: * Early Clinical Response defined as: Improvement at 72 hours in severity from baseline in at least two of the following signs/symptoms: cough, dyspnea, chest pain, sputum production Without worsening in any of the above 4 signs/symptoms - patient is clinically stable Proposed by FDA, November 3 rd 2011 for future CABP trial design and defined by the Foundation for the NIH (FNIH) |
 Solithromycin demonstrated a favorable safety and tolerability profile, with a lower incidence of AEs than levofloxacin Fewer treatment emergent AEs (30% vs 46%) Fewer study subjects with SAEs (2 vs 7 subjects) Fewer drug discontinuations due to AEs (0 vs 6 subjects) Fewer GI related AEs (14% vs 24%) No significant liver safety issues No QT signals of concern No bitter after-taste 15 Solithromycin: Favorable Safety and Tolerability – Oral Phase 2 Trial |
 Community-Acquired Bacterial Pneumonia (CABP) – Standard-of-Care 16 Macrolides have kept a large segment of the global antibiotic market in spite of fluoroquinolones Macrolide segment not crowded Mostly occupied by azithromycin and clarithromycin – rising incidence of resistance No new macrolides except solithromycin Solithromycin is being developed for monotherapy for CABP – replacing current standard of care - a cephalosporin plus azithromycin cost of two drugs No oral cephalosporin for step down Side effects of two drugs Solithromycin has the spectrum of activity that provides coverage for CABP pathogens, including azithromycin-resistant bacteria Step down IV to oral therapy could give a pharmacoeconomic advantage over current treatment options |
 Solithromycin: Intravenous Development First Injectable Macrolide in 20 Years 17 High plasma levels after IV administration to address the most resistant bacteria. Well tolerated No QT effects. Intravenous macrolides have not been developed because of safety and tolerability issues FDA interest in IV dose - Allows enrollment of PORT III – IV patients IV toxicology, 28-day in dog and monkey – well-tolerated Intravenous and oral formulation allow: Flexibility for treating severe or moderate pneumonia Severely ill patients begin treatment in the hospital and then go home earlier on oral therapy Pharmacoeconomic advantage Phase 1 IV clinical trial underway |
 Plan for Phase 3 CABP Studies 18 Phase 3 CABP trial design and end points are consistent with the proposed FDA CABP guidance Nov 2011 Two phase 3 trials are planned. One oral trial and one IV-to-oral step-down trial Phase 3 oral planned to begin second half 2012 and complete in 2014 Global study – <50% PORT II, 50% PORT III and PORT IV Enroll ~800 patients Comparator moxifloxacin – a fluoroquinolone that is used worldwide at same dose Enrollment criteria controlled strictly as per FDA guidance Success criteria: as specified by newly proposed FDA guidance Primary endpoint: Non-inferiority of early response (at 72 hours) compared to a fluoroquinolone Secondary endpoints: Safety and pooled mITT at early response |
 19 Solithromycin for CABP and Multiple Indications – Potential Broad Use Campylobacter diarrhea Helicobacter gastritis Gonococcal and non-gonococcal urethritis Simple Skin Infections Group B Strep infections in pregnancy Lyme disease and other tick borne diseases Other Diseases: Ophthalmic Infections Pediatric Infections Malaria prophylaxis Biodefense GI Tract Diseases: Antibacterial and Anti- inflammatory: Primary Indication: CABP Simple RTI’s, Pharyngitis, Sinusitis, Bronchitis, Acute Exacerbation of Chronic Bronchitis (AECB) GU Tract Diseases: Respiratory Tract Infections (RTI): COPD Cystic fibrosis Panbronchiolitis Solithromycin- The Next Generation Macrolide- First Fluoroketolide |
 20 Urethral Neisseria gonorrhoeae isolates (n= 32,794) with elevated MICs (>0.25 g/mL) and Ceftriaxone MICs (>0.125 g/mL). Gonococcal Surveillance project, US. 2006-2011) Gonococcal Isolate Surveillance Project (Bolan et al. NEJM 2012. 366:485-487) D. Gopalrian, et al. WHO Collaborating Center for Gonorrhoea and other STIs. AAC, 56: 2739-2742, 2012, MIC 90 ( g/mL) Range ( g/mL) 0.25 0.001 - 32 In Vitro Activity of Solithromycin against 256 gonococci The proportion of N. gonorrhoeae in the US with elevated cefixime MICs has increased 17- fold between 2006 and the first half of 2011 Last Oral Antibiotic Removed from Recommended Therapy for Gonococcus - 2 nd most common Communicable Disease |
 21 30 patients with uncomplicated gonorrhea Patient Population Gram stain/culture NAAT Clinical Symptoms Day 1 Screen and Diagnosis Treat with single dose of Solithromycin 1200 mg Day 2 Proven gonorrhoeae Test of cure Symptom Free Negative culture Day 7 (+ 3) TOC Uncomplicated Gonococcal Urethritis - Phase 2 Trial Plan Current Treatment: Ceftriaxone 250 mg IM in a single dose OR, IF NOT AN OPTION, Cefixime 400 mg orally in a single dose OR Single dose injectable cephalosporin regimens PLUS Azithromycin 1g orally in a single dose OR Doxycycline 100 mg orally twice a day for 7 days Study Design: Open label, single site, oral treatment of uncomplicated gonorrhea Success Criteria: The primary outcome – bacterial eradication at TOC (7 day after treatment) Other outcome measures: Safety and tolerability th |
 22 TAKSTA™ (Fusidic acid) An oral antibiotic for MRSA infections being developed for chronic use in the U.S. |
 23 What is Taksta ? Taksta is Cempra’s proprietary fusidic acid dosing regimen Fusidic acid approved in Western Europe, Australia, and other countries 40 years of established safety and efficacy profile in acute and chronic use in staph infections ex-U.S. NCE in the US, Hatch Waxman exclusivity, 5 years obtained by Cempra, dosing regimen patent, supply agreement of drug substance - a fermentation product GAIN Act adds an additional 5 years of data exclusivity - A minimum of 10 years of data exclusivity Unique structure, no cross resistance with any other antibiotic Orally bioavailable Targeted against gram-positive pathogens, including MRSA - a pathogen of great concern that causes bone and joint infections requiring long-term treatment TM |
 Tetracyclines and Bactrim (TMP/SMX) have significant limitations for oral, outpatient use Linezolid is the only oral antibiotic approved for MRSA but is not recommended for long term use TAKSTA has Excellent Activity Against S. aureus in the U.S. (1,710 U.S. strains) 24 Taksta is highly effective against S. aureus strains found in the U.S. Antimicrobial agents MIC (µg/ml) 90% % susceptible Fusidic acid 0.12 99.6 Clindamycin >2 69.7 Erythromycin >4 11.2 Levofloxacin >4 30.2 Linezolid 1 99.9 Tetracycline 1 95.8 TMP/SMX 97.9 Compared with other Oral Agents Almost all staph and MRSA in the U.S. are susceptible 0.5 |
 25 Osteomyelitis/Prosthetic Joint Infection is a Significant Opportunity Growing need for oral therapies to address MRSA infections Physicians cite staph (MRSA) as top pathogen of concern in prosthetic joint infections and osteomyelitis Prosthetic joint replacement is increasing Risk of life-long bacterial infection of implant Minimum duration of treatment is 4-6 weeks, with many patients requiring life-long treatment Leading drugs for prosthetic joint infections and osteomyelitis are the same as those for ABSSSI: vancomycin, daptomycin and linezolid Total prosthetic-joint infections 1990-2004 (Kurtz et. al) N Engl J Med. 2009; 361: 787-794 Total arthroplasties performed from 1990-2006 (CDC) |
 European dosing Cempra’s loading dose 1500 mg BID loading dose followed by 600 mg BID maintenance dose – minimizes resistance development Loading dose regimen validated – resistance not noted in Phase 2 study Patent pending Cempra’s Proprietary TAKSTA Loading Dose Validated - Phase 2 Study With MRSA Infections Cempra developed a proprietary loading dose regimen to prevent resistance to fusidic acid that has occurred outside the U.S. 26 Data from 155-patient Phase 2 trial demonstrates efficacy and safety in ABSSSI Comparable efficacy to Zyvox (linezolid) Proprietary loading dose regimen was well tolerated and overcame resistance Comparable safety to linezolid, despite trial design excluding patients for whom linezolid is contra- indicated (e.g., those on SSRIs) End of Phase 2 meeting for ABSSSI with FDA completed |
 Use In Prosthetic Joint Infections 27 Used outside the U.S. in Osteomyelitis/PJI Significant physician interest for chronic use in the U.S. Eur J Clin Microbiol Infect Dis. 2010; 29: 171-180 Several reports from ex-USA that PJI can be successfully treated by adding FA to the standard of care Taksta could address the need for a safe, oral product for acute and chronic treatment in prosthetic joint infections |
 28 Two compassionate use cases of bone/prosthesis infections in North America Efficacy is comparable to linezolid but has better safety – useful for oral chronic use in all patient populations PJI Facts: 200,000 Hip Replacements; 550,000 Knee Replacements in 2007 Surgeries increase by 3% per year 1% of hips and 2% of knees develop PJI's Chronic daily therapy Total Joint and Hardware Procedures - 3,286,000/year a,b Potential use in osteomyelitis, septic arthritis, diabetic foot Potential of Taksta for Chronic Use in Prosthetic Joint Device Infections Tedizolid Linezolid Taksta a Life Science Intelligence market research report. U.S. Markets for Large Replacement Technologies in 2012. March, 2012. b Life Science Intelligence market research report. U.S. Markets for Small Joint Implants and Hardware for the Extremities. January, 2012. |
 Current Treatment: Debride and treat intravenously and orally for months – replace prosthesis if possible, Study Design: Success Criteria: The primary outcome – retention of a functional prosthesis at the end of 3 months Other outcome measures: longer term safety and tolerability, joint & mobility function Cempra will confirm trial design with the FDA – Orphan indication potential 29 50 patients with Knee or Hip PJI Patient Population IV vancomycin + Taksta + rifampin Discontinue vancomycin at 7-28 days Add Taksta to Current Standard of Care Continue with Taksta + rifampin for 3 months Continue for 3 Months Taksta as oral monotherapy beyond 3 months Long-Term Therapy Prosthetic Joint Infection Phase 2 Trial Plan – Chronic Oral Treatment of MRSA may not be possible in older patients |
 2012 Milestones 2H 12: CEM-101 Initiation of dosing of Phase 3 Oral Global Trial for CABP 2H 12: CEM-101 Completion of Phase 1 IV 4Q 12: Taksta Initiation of dosing of Phase 2 Prosthetic Joint Infection Trial 4Q 12 Solithromycin top line data of Phase 2 Gonococcal Urethritis Study 2013 Milestones 1H 13: CEM-101 Initiation of Phase 3 IV-to-Oral CABP Trial (Financing TBD) 4Q 13: Taksta top line Prosthetic Joint Infection results 2014 Milestones 1H 14: Taksta Phase 2 Prosthetic Joint Study Results 1H 14: CEM-101 Phase 3 Oral CABP Top line data 30 Clinical Development Plan and Estimated Milestones |
 31 Capitalization Cash & Equivalents (at 6/30/12) $ 57.8M Long-Term Debt (at 6/30/12) $ 9.6M Shares Outstanding 21.0M Market Capitalization (at 8/30/12) $167.0M Cash Runway * 1H 2014 * Includes initiation of CEM-101 P3 oral trial and Taksta P2 PJI trial; Does not include any potential partnerships. |
 Kenneth Touw, PhD EVP Regulatory Carl Foster EVP Business Development Mark Hahn, CPA CFO David Oldach, MD SVP Clinical GILEAD Prabhavathi Fernandes, PhD President & CEO Proven Management Team David Pereira, PhD SVP Chemistry • Azactam (aztreonam) • Biaxin (clarithromycin) • Dificid (fidaxomicin) • Plenaxis (abarelix) • Zavesca (miglustat) • OncoVax • Prilosec (omeprazole) • IPO and M&A • Athenix-Bayer CropScience • Charles & Colvard (CTHR) • E&Y • Viread • GS-9190 • Combinations against HCV • Synercid (quinupristin/ dalfopristin) • Altace (ramipril) • Embeda (morphine and naltrexone) • Acurox • Injectable Penicillins • Dobutamine HCl Injection • Ranitidine Injection 32 (oxycodone) |
 Highlights 33 Lead program, Solithromycin, has the potential to be the first Oral and IV macrolide approved since Zithromax/Z-PAK - Oral Phase 3 trial in CABP is expected to begin 2H 2012 Solithromycin Phase 2 trial for bacterial urethritis is running - Results expected 2H 2012 Antibiotic-resistant gonorrhea is a major global threat and new treatment options for gonorrhea are urgently needed Second program, Taksta, is an oral drug that is effective against MRSA, which we are developing for long-term treatment of Prosthetic Joint Infections (PJI)- Phase 2 trial expected to begin 2H 2012 - a potential orphan indication New FDA guidance provides regulatory pathway – The GAIN Act provides incentives for antibacterial development Large market opportunity with global antibiotic sales in the multibillions Significant need for new antibiotics driven by resistance and tolerability issues Strong management team with extensive, successful experience in antibiotic drug development and approval - Azactam, Biaxin, Fidaxomicin, Synercid, Viread |