INNOVATIVE SCIENCE DRIVES ANTIBIOTIC LEADERSHIP Corporate Presentation June 2018 Nasdaq: AKAO
Forward Looking Statements This presentation contains forward-looking statements. All statements other than statements of historical facts contained in this presentation, including statements regarding future operational and financial results and positions, business strategy, commercial availability and potential of ZEMDRI, growth in and potential demand for ZEMDRI, potential indications and uses for ZEMDRI, prospective products, commercial opportunity and market share, availability and potential sources of funding, clinical trial results, product approvals and regulatory pathways, research and development costs, timing (including but limited to timing of clinical timelines), strategies for completion and likelihood of success for our business activities, and plans for future operations, are forward-looking statements reflecting the current beliefs and expectations of management made pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995. These statements involve known and unknown risks, uncertainties and other important 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. Because forward-looking statements are inherently subject to risks and uncertainties, some of which cannot be predicted and some of which are beyond our control, you should not rely on these forward-looking statements as predictions. The events and circumstances reflected in our forward-looking statements may not be achieved or occur and actual results could differ materially from those projected in the forward-looking statements. Such risks and uncertainties include, among others, those inherent in the preclinical and clinical development process; the risks and uncertainties of the regulatory approval process; commercialization and gaining market acceptance; manufacturing and supply development and conditions; conditions when bacteria will evolve resistance to ZEMDRI, C- Scape or other antibiotics; third party claims alleging infringement of patents and proprietary rights or seeking to invalidate Achaogen's patents or proprietary rights; efficacy, safety and tolerability of ZEMDRI and our product candidates; and the risk that Achaogen's proprietary rights may be insufficient to protect its product candidates. For a further description of the risks and uncertainties that could cause actual results to differ from those expressed in these forward-looking statements, as well as risks relating to our business in general, see our Annual Report on Form 10-K for the fiscal year ended December 31, 2017 filed with the Securities and Exchange Commission on February 27, 2018 and our Form 10-Q for the quarter ended March 31, 2018, filed with the Securities and Exchange Commission on May 7, 2018 and our future periodic Form 10-Ks or Form 10-Qs. Except as required by applicable law, we assume no obligation to publicly update or revise any forward-looking statements contained herein, whether as a result of any new information, future events, changed circumstances or otherwise. This presentation concerns products which, other than ZEMDRI, have not been approved for commercialization. They are currently limited to research or investigational use. 2
Achaogen: Innovative Products for Serious Infections Unique Antibacterial Company Committed to addressing threat of multi-drug resistant (MDR) bacterial infections Pipeline of innovative product candidates Proven R&D and Commercial teams Significant Commercial Opportunity Large and growing patient populations Strong physician interest; value-based pricing ZEMDRI Approved for use in cuti June 25, 2018 Novel once-daily therapy and differentiated class for infections in the inpatient setting and for use in the outpatient setting Activity against CRE and ESBL- producing Enterobacteriaceae Innovative Pipeline C-Scape: oral candidate for ESBL- producing cuti infections Preclinical assets: MDR gram-negative infections, other diseases 3
Multi-Drug Resistance Poses an Urgent and Growing Threat Priority Pathogens Resistance rising rapidly 2 High morbidity and mortality (up to 50% in BSI due to CRE) 1,3 Limited treatment options 4 Significant economic burden to healthcare system & society 5 CDC Urgent 1 CDC Serious 1 1 CDC Antibiotic Resistance Threats in the United States, 2013 http://www.cdc.gov/drugresistance/threat-report-2013/ 2 The Surveillance Network database: CDDEP.org Resistance Map; Braykov et. al., 2013 3 Ben-David et al. Clin Microbiol Infect 2012;18(1):54 60. 4 Daikos et al., Clin Microbiol Rev. 2012 Oct;25(4):682-707. 5 Bartsch et al., Clin Microbiol Infect. 2016 Sep 15. pii: S1198-743X(16)30389-5. WHO published Feb. 27, 2017 4
% ESBL+ Patients Nonsusceptible Isolates There is a Demand for New Therapies to Fight MDR Infections Increase in ESBL Prevalence Increasing Reliance on Carbapenem Therapy Rise in Carbapenem Resistance U.S. Prevalence of ESBL Production in E.coli from Urinary Sources 1 UTI Inpatients Receiving a Carbapenem In- Hospital or Upon Discharge, U.S. 2 Carbapenem Resistance in Klebsiella spp. 30 400,000 9% Europe 3 25 350,000 300,000 8% 7% US 4 20 15 10 5 250,000 200,000 150,000 100,000 50,000 6% 5% 4% 3% 2% 1% 0 Community-Acquired Hospital-Associated 0 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 0% 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2011 2012 2013 2014 1 Diagn Microbiol Infect Dis 2016, http://dx.doi.org/10.1016/j.diagmicrobio.2016.04.022 E.coli is the causative pathogen in 79% of complicated UTI (incl. pyelonephritis): Lancet 2015;385:1949. 2. Source: Decision Resources AMR Hospital Antibiotic Market Guide; Data annualized from half-year datasets: 2004-H2, 2006-H2, 2009-H2, 2011-H1, 2014-H1. UTI diagnosis codes include UTI/cystitis/urosepsis and pyelonephritis/perinephric abscess. 3 Europe: Population-weighted average of 30 European countries, calculated from: Non-susceptibility: ECDC EARS-Net, http://ecdc.europa.eu/, 2016 (Klebsiella pneumoniae); Population: Eurostat, http://ec.europa.eu/eurostat/data/database/, 2016. 4 US: Curve extrapolated from multiple data sources: 2005-2010: The Surveillance Network database USA as published in Braykov et. al., 2013 (Klebsiella pneumoniae); 2011: Antimicrob Agents Chemother. 2013 Apr;57(4):1982-8. (Klebsiella spp., non-susceptibility to meropenem; 2011 data point represents combined data from isolates collected in 2010 and 2011); 2012: ICAAC 2013, poster C2-1630 (Klebsiella pneumoniae, non-susceptibility to meropenem); 2014-2015: JMI Laboratories, surveillance conducted for Achaogen (Klebsiella pneumoniae, non-susceptibility to 1 or more carbapenems: meropenem, imipenem, doripenem). 5
Achaogen Pipeline Stage Funding Partners ZEMDRI (plazomicin) For patients with cuti, including pyelonephritis, due to certain Enterobacteriaceae FDA Approved C-Scape ESBL- producing Enterobacteriaceae Phase 1 Novel Aminoglycoside Enterobacteriaceae, P. aeruginosa, A. baumannii Preclinical Small Molecule Discovery Program Infections due to MDR gram-negative pathogens Preclinical Therapeutic Antibody Discovery Program Infections due to MDR gram-negative pathogens Other therapeutic antibodies against multiple novel targets (e.g., Nav 1.7 for non-opioid pain) Preclinical cuti: complicated Urinary Tract Infection; MDR: multi-drug resistant; ESBL: expanded spectrum beta-lactamases Only ZEMDRI has been approved for commercial use. See full prescribing information. All other product candidates are investigational only, potential treatments, and have not been approved for commercial use. 6
Plazomicin: A Next Generation Aminoglycoside for the Treatment of MDR Enterobacteriaceae Discovered at Achaogen; U.S. patent protection currently estimated 2031-2032 Uniquely engineered to overcome aminoglycoside-modifying enzymes (AME) that inactivate existing aminoglycosides AMEs co-travel with other resistance mechanisms, including β-lactamases and carbapenemases AMEs ) AMEs AMEs AMEs Rapidly bactericidal AMEs Adapted from Aggen JB, et al. Antimicrob Agents Chemother. Figure 1. Plazomicin has Potent In-vitro Activity Against MDR Enterobacteriaceae, Including ESBL-Producers, CRE Strains and AG-Resistant Isolates 7
Plazomicin Clinical Trial Results 8
Composite Cure (%) EPIC Results Plazomicin met FDA co-primary endpoints at Day 5 and test of cure (TOC) 100 Composite Cure Over Time (mmitt) 80 Plazomicin 60 Meropenem 40 20 0 0 2 3 4 5 6 7 8 TOC (~17) Study Day Lower clinical relapse at LFU (clinical relapse of 1.8% for plazomicin, 7.9% for meropenem for all clinical cures at TOC) LFU: Late follow-up For patients with EOIV visit before Study Day 8, the EOIV observation was carried forward. 609 patients randomized in EPIC, 388 patients in mmitt (plazomicin: N=191; meropenem: N=197) LFU (~28) 9
EPIC Overall Summary of TEAEs and SAEs Incidence across treatment groups were not different Patients with Any of the Following: (Safety Population) Plazomicin (N=303) n (%) Meropenem (N=301) n (%) TEAE 59 (19.5) 65 (21.6) IV Study Drug Related 18 (5.9) 16 (5.3) Led to Discontinuation of IV Study Drug 6 (2.0) 6 (2.0) Related to Renal Function 11 (3.6) 4 (1.3) SAE 5 (1.7) 5 (1.7) IV Study Drug Related 1 (0.3) 1 (0.3) Death 1 (0.3) 0 (0.0) TEAE: Treatment Emergent Adverse Event; SAE: Serious Adverse Event Most common adverse reactions ( 1%) occurring in plazomicin-treated patients were decreased renal function (3.6%), diarrhea (2.3%), hypertension (2.3%), headache (1.3%), nausea (1.3%), vomiting (1.3%), and hypotension (1.0%). One case of potential ototoxicity in each treatment group; both cases mild and recovered 10
EPIC Laboratory Parameters Associated With Renal Function Low incidence of serum creatinine increase Serum Creatinine (Safety Population) Plazomicin n/n (%) Meropenem n/n (%) 0.5 mg/dl increase any time on study (including on and/or post IV therapy) 21/300 (7.0) 12/297 (4.0) 0.5 mg/dl increase while on IV therapy 11/300 (3.7) 9/297 (3.0) Full recovery at EOIV 6/11 4/9 Full recovery at last follow-up visit 9/11 9/9 Full recovery defined as serum creatinine value <0.5 mg/dl above the baseline value at the EOIV visit or last post-baseline measurement, respectively 11
Patients (%) CARE Primary Results Difference [Plazomicin minus Colistin] (90% CI) Results: Lower values are better 60 50-26.5% (-51.2 to 0.7%) 50.0% -28.2% (-52.5 to -0.7%) 40 30 40.0% Cohort 1 mmitt Population 20 23.5% Plazomicin (N=17) Colistin (N=20) 10 11.8% 0 Day 28 all-cause mortality or significant disease related complications Day 28 all-cause mortality Two-sided 90% confidence interval (CI) calculation based on the unconditional extact method 12
CARE Kaplan-Meier Survival Curve 1.0 Censored 0.8 Plazomicin (N=17) 0.6 Survival Probability 0.4 Plazomicin:Colistin Through Day 28: HR (90% CI): 0.25 (0.07, 0.93): p=0.03 Through Day 60: HR (90% CI): 0.47 (0.22, 1.02): p=0.05 Colistin (N=20) 0.2 0.0 0 10 20 30 40 50 60 Time to Event (Days) Estimate of hazard ratio (HR) calculated as plazomicin:colistin based on Cox proportional hazards regression model. Data from Cohort 1 (mmitt) 13
CARE Overall Summary of TEAEs and SAEs Safety Population Plazomicin (N=18) n (%) Colistin (N=21) n (%) TEAE 16 (88.9) 21 (100.0) Study Drug-related 5 (27.8) 9 (42.9) Led to Discontinuation of Study Drug 2 (11.1) 1 (4.8) SAE 9 (50.0) 17 (81.0) IV Study Drug-Related 1 (5.6) 4 (19.0) TEAEs Related to Renal Function Overall Pooled 6 (33.3) 11 (52.4) Study Drug Related 3 (16.7) 8 (38.1) Reduced drug-related AEs, SAEs, and AEs related to renal function in plazomicin group No study drug-related deaths or events of ototoxicity reported SAE, serious adverse event; TEAE, treatment-emergent adverse event 14
CARE Laboratory Parameters Associated with Renal Function Notable reduction in serum creatinine elevations in plazomicin arm Serum Creatinine (Safety Population) 1 Plazomicin (N = 18) n/n1 (%) Colistin (N = 21) n/n1 (%) 0.5 mg/dl increase any time on study (including on or post IV therapy) 2/12 (16.7) 8/16 (50.0) 0.5 mg/dl increase while on IV therapy 1/12 (8.3) 6/16 (37.5) Full recovery or improvement 2 1/1 3/6 1 Patients starting CRRT prior to baseline were excluded from the analysis, as were all post-baseline serum creatinine measurements collected after start of CRRT. 2 Full recovery defined as last post-baseline serum creatinine value <0.5 mg/dl above the baseline value. Improvement defined as last post-baseline serum creatinine value 0.3 mg/dl less than the peak serum creatinine but not <0.5 mg/dl above the baseline value. 15
FDA Actions Related to Plazomicin on June 25, 2018 EPIC Supported approval in patients for treatment of cuti, including pyelonephritis, who have limited or no alternative treatment options CARE Complete Response Letter (CRL) by the FDA for bloodstream infection We intend to meet with the FDA to determine whether there is a feasible resolution to address the CRL 16
ZEMDRI Market Opportunity 17
ZEMDRI Label and Favorable Administration Supports Attractive Commercial Opportunity Product Profile In-vitro activity against MDR Enterobacteriaceae, including ESBLproducing and CRE Opportunity Growing MDR Threat Significant unmet need Large and growing patient population Only once-daily aminoglycoside approved for cuti Evidence in patients with concomitant bacteremia and with aminoglycoside resistant organisms Inpatient cuti Carbapenem-sparing opportunity Focus on high risk population with recurrent cuti Once daily 30-minute IV Outpatient Convenient dosing Hospital avoidance or earlier patient discharge 18
There is a Significant Market in the U.S. for Treatment of CRE and ESBL Infections in the Inpatient Setting Opportunity in 2017 2017 Total Inpatient Gram-Negative Infections ~6 Million (US) ~40% cuti Enterobacteriaceae ~1.5% CRE Rate ~15% ESBL Rate Inpatient CRE ~90 K Patients Inpatient ESBL+ cuti ~360 K Patients Estimated annual US inpatient market opportunity: ~450 K Addressable Inpatients Sources: Decision Resources 2017, Arlington Medical Resources, primary literature, CDC & ECDC, TSN Surveillance Network, TEST Surveillance Database, and company internal analysis 19
CRE Cases Significant Growth in Confirmed CRE Cases in the U.S. with Approximately 70K to 80K Cases in 2016 and Trending Upwards 90,000 U.S. National Projection of CRE Cases Achaogen company analyses 80,000 70,000 60,000 50,000 40,000 30,000 20,000 10,000 0 2009 2010 2011 2012 2013 2014 2015 2016 Literature-based projection EHR-based projection CRE Population Projected to Double in Next 5 Years Sources: Literature-based projection: Literature review combined with surveillance network data EHR-based projection: Analysis of Cerner Health Facts EHR database from ~200 hospitals with national projection by Boston Health Economics (BHE) using hospital census data by IMS (HCOS); Schneider, Patel, Zillberberg, Society for Healthcare Epidemiology in America (SHEA), March 2017 20
Outpatient Setting Represents a Sizable Opportunity for ZEMDRI Given Convenient Once-Daily 30 Minute Infusion Decreases burden on healthcare providers and patients Hospital vs Non-Hospital Use of Other IV Antibiotics Hospital Non-Hospital Potential to reduce length of hospital stay 30-50% of ZEMDRI use may be in the outpatient setting based on other IV antibiotics 27% 26% 31% 31% 73% 74% 69% 69% 47% 48% 53% 52% Sources: IQVIA DDD data Jun 2017 to May 2018 21
ZEMDRI Launch Readiness 22
Available soon in the United States Visit ZEMDRI.com for full prescribing information including BOXED WARNINGS 23
ZEMDRI Launch: How We Will Succeed Focus on Launch Differentiated Class Experienced Hospital Team OPAT Opportunity Planning and Preparation Company focused on MDR gram negative space Organization built for launch Non betalactam Broad in-vitro coverage of resistance mechanisms Strong data package Sales team with deep ID and hospital experience - collectively launched 20 antibiotics Strategic fit for the outpatient setting Once-daily 30 minute infusion Susceptibility testing available early Focus on training and being trusted credible partners 24
Pipeline 25
C-Scape Executive Summary High Unmet Need Oral antibiotic to treat infections due to ESBL- producing Enterobacteriaceae - WHO: Critical Priority 1 Pathogen - CDC: Serious Public Health Threat Innovative Oral Antibacterial Attractive Risk Profile Combination of previously approved compounds (ceftibuten + clavulanate), potent activity against ESBL- producing isolates - Awarded QIDP status; eligible for streamlined development Higher probability of clinical and regulatory success given history of use of individual components - Compelling commercial opportunity based on at least 8 years of US exclusivity Development Underway Initial Phase 1 results positive; additional development underway, including a planned Phase 1 clinical pharmacology trial 26
C-Scape is a Uniquely Potent β-lactam / β-lactamase Inhibitor Combination of Ceftibuten and Clavulanate Organism ESBL Enzyme Amoxicillin-Clavulanate MIC (µg/ml) Ciprofloxacin MIC (µg/ml) C-Scape MIC (µg/ml) E. coli CTX-M-15,TEM-1 16 0.03 0.5 E. coli CTX-M-15,TEM-1 8 >4 0.5 E. coli CTX-M-14 8 0.03 0.5 K. pneumoniae SHV-5,TEM-1 8 0.25 0.12 K. pneumoniae SHV WT,CTX-M-15, OXA-1/30-like 16 1 0.5 K. pneumoniae SHV-11,SHV-12,TEM-1 8 >4 0.25 K. pneumoniae SHV-30 8 0.12 0.25 P. mirabilis CTX-M-15-like,TEM WT 2 0.03 0.03 P. mirabilis CTX-M-14-like,TEM WT 8 4 0.03 P. mirabilis None 0.5 >4 <0.015 P. mirabilis None 1 0.03 <0.015 E. coli None 8 >4 0.25 K. pneumoniae None 2 >4 0.06 C-Scape combination of ceftibuten and clavulanate demonstrated higher potency and favorable PK properties compared to all other oral cephalosporins evaluated MIC >2 MIC 1-2 MIC <1 JMI Laboratories, Inc. Achaogen Data on File MIC, minimal inhibitory concentration 27
Antibody Small Molecule Research is a Key Differentiator for Achaogen Lead with Science Leverage complementary modalities to pursue the right targets that impact significant public health needs Small Molecules Antibiotics focus Team Renowned expertise Significant experience Proven results Antibodies Well validated targets for antibiotics and other therapeutic areas Program Description Discovery C-Scape Novel Aminoglycoside Novel Beta-Lactam Vascular Leak Bactericidal mab Oral BL/BLI Combination IV Antibiotic Oral/IV Antibiotic IV Monoclonal Antibody IV Monoclonal Antibody Candidate Selection Early Dev Current Partners Applied for funding Leverage Nondilutive Funding / Partners NaV 1.7 for pain mab for pain IV Monoclonal Antibody IV Monoclonal Antibody 28
Corporate Profile 29
Patient Care is at the Center of Everything We Do Dedicated and deployed Medical Scientists team Data dissemination at medical meetings and through publications Medical information and pharmacovigilance infrastructure Achaogen s Commitment to Patients Investigator initiated research program Independent medical education program Active role in shaping policy around AMR Champion of antibiotic stewardship AMR: Antimicrobial resistance 30
Financial Snapshot $144 million in cash, cash equivalents, short-term investments at 3/31/18 Additional restricted cash of $7.8 million associated with Gates Foundation partnership at 3/31/18 Funding partnerships BARDA non-dilutive funding: $124.4 million (plazomicin) BARDA non-dilutive funding: up to $18 million (C-Scape) Gates Foundation grant and equity funding: up to $20.5 million (antibody) CARB-X non-dilutive funding: up to $12 million (novel aminoglycoside) $50 million loan agreement with Silicon Valley Bank 31
2017 Significant Progress Strong Execution Plazomicin NDA Accepted with Priority Review C-Scape Phase 1 Results Plazomicin MAA Submission ZEMDRI Commercial Launch Plazomicin NDA Submission Plazomicin FDA Action June 25 Plazomicin Advisory Committee 2018 Milestones with Potential to Drive Value for Patients and Shareholders 32