FORWARD LOOKING STATEMENTS

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1 Jefferies 2014 Healthcare Conference November 19, 2014

2 FORWARD LOOKING STATEMENTS This presentation contains forward looking statements. Any statements contained herein which do not describe historical facts, including but not limited to, statements regarding: our future financial and operating results, including our 2014 guidance, peak year sales estimates for our products and product candidates and the projected CUBICIN U.S. revenue annualized run rate or greater than $1 Billion; the expected timing for commencing and completing clinical trials and for clinical trial data presentations, regulatory filings and responses for our products and product candidates; the expected timing for potential commercial launches of our product candidates; the therapeutic and commercial potential of our products and product candidates; our Phase 3 clinical data for ZERBAXA; our development plans for our product candidates; the expected retirement of our current CEO and the expected appointment of our new CEO and our new non executive Chair of the Board, and our Building Blocks of Growth five year goals through 2017, are forward looking statements which involve risks and uncertainties that could cause actual results to differ materially from those discussed in such forward looking statements. Such risks and uncertainties include: risks related to drug development and commercialization; our ability to achieve our short and long term goals, including as a result of our ability to continue to grow revenues from the sale of our products, generic and other competition, manufacturing issues, our ability to successfully develop, gain marketing approval for and commercially launch our product candidates for their planned indications and on their expected timelines, and our ability to discover, in license or acquire new products and product candidates; the strength of, and our ability to successfully obtain, maintain and enforce intellectual property protecting our products and product candidates; our ability to successfully develop, gain marketing approval for and commercially launch ZERBAXA and our other product candidates for their planned indications and on the timelines that we expect; our ability to discover, in license or acquire new products and product candidates; our ability to achieve and manage the growth in our business; regulatory developments in the United States and foreign countries, including the risk that regulatory authorities may not agree with our interpretation of the results from our clinical studies of ZERBAXA and SIVEXTRO, may not approve on a timely basis or at all, our marketing authorization applications for ZERBAXA and SIVEXTRO or may require additional data, analysis, information or further studies that may not be clinically feasible or financially practicable; any marketing approval for any of our product candidates may impose significant limitations on its use and additional post marketing requirements; competitive risks from current and future therapeutic alternatives to our products and product candidates, including generic competitors such as Teva, Hospira, Strides and Fresenius; additional clinical trials of our products and product candidates may produce negative or inconclusive results or may not be initiated or conducted in a timely manner; technical difficulties or excessive costs relating to the manufacture or supply of our products and product candidates, including our ability to work with, and the performance of our third party contract manufacturers that manufacture and supply our products and product candidates on our behalf; our ability to work with, and the performance of our third party contract research organizations that help us conduct our clinical trials; the risk that our planned leadership transition does not occur in the manner or on the time frame that we currently expect and those additional factors discussed in our most recent Annual Report on Form 10 K and subsequent Quarterly Reports on Form 10 Q filed with the Securities and Exchange Commission. We caution investors not to place considerable reliance on the forward looking statements contained in this presentation. These forward looking statements speak only as of the date of this presentation and we undertake no obligation to update or revise any of these statements. 2

3 USE OF NON GAAP FINANCIAL MEASURES Within this presentation, in order to provide greater transparency regarding Cubist s performance, we refer to certain non GAAP financial measures that involve adjustments to GAAP measures. Any non GAAP financial measures presented should not be considered an alternative to measures required by GAAP, should not be considered measures of Cubist s liquidity and are unlikely to be comparable to non GAAP information provided by other companies. Reconciliations between our non GAAP financial measures and GAAP financial measures are included on our web site at on the Investor Relations page. 3

4 Cubist Mission What sets us apart Through our highly differentiated products and culture, our mission is to be the global leader in transforming the lives of patients in the acute care / hospital environment. 4

5 Addressing the Global Public Health Threat of Infections Caused by Resistant Bacteria Cubist is Focused on Fighting Serious & Life threatening Pathogens International Commission on Antimicrobial Resistance was recently announced by UK Prime Minister David Cameron. Will look broadly at the economic issues surrounding antimicrobial resistance. Cubist is participating in the World Health Organization s Strategic and Technical Advisory Group for Antimicrobial Resistance, as well as the Innovative Medicines Initiative s work in this area across Europe. 5

6 Cubist History 1992 Cubist founded with focus on developing novel antibiotics 2005 Achieved $100M net revenue for CUBICIN (U.S.) 2006 FDA approved expanded label for CUBICIN (SAB/IE) CUBICIN launch in Europe 2013 Cubist acquires Trius and Optimer 2010 CUBICIN has been used to treat 1 million patients NASDAQ: CBST Initial Public Offering 2003 CUBICIN launch in US (csssi label) 2007 First profitable year 2009 Cubist acquires Calixa 2011 Cubist acquires Adolor 2014 SIVEXTRO launch in US (ABSSSI label) 6

7 Cubist Annual Total Net Revenues We Estimate Peak Year Sales of CUBICIN Will Surpass $1B in the U.S. >2,100,000 Patients Treated with CUBICIN (estimated) as of 09/30/14 $1,200 $1,000 CAGR 36% ( ) $926.4 $1,054.4 $800 $754.0 $600 $562.1 $636.4 $400 $200 $ $433.6 $294.6 $194.7 $68.1 $120.6 $ CUBICIN U.S. Net Revenues Other Net Revenues 7

8 4 Marketed Products in the U.S. 8

9 Cubist Product and Pipeline Candidates Therapy / Candidate Phase 1 Phase 2 Phase 3 Filing Market Milestones/Highlights CUBICIN (daptomycin for injection) ENTEREG (alvimopan) DIFICID (fidaxomicin) SIVEXTRO (tedizolid phosphate) ABSSSI + SIVEXTRO (tedizolid phosphate) HABP/VABP* ZERBAXA TM (ceftolozane/tazobactam for injection) cuti /ciai* ZERBAXA TM (ceftolozane/tazobactam for injection) HABP/VABP* Surotomycin CDAD* Enrollment underway US: PDUFA December 21, 2014 EU: MAA filed August 22, 2014 Screening underway; expect FPI 4Q14 Phase 3; data expected mid 2015 Bevenopran OIC* CB 618 Beta lactamase inhibitor* *Potential indications sought, pending outcomes of clinical trials and regulatory applications/approvals. + Approved in the U.S. for acute bacterial skin and skin structure infections (ABSSSI); in Europe the Marketing Authorization Application filed for complicated skin and soft tissue infections (cssti) is under review. Information as of October 21, 2014 Long term safety trial data expected 4Q14 Regulatory strategy in discussion with FDA 9

10 Cubist Moving Forward Michael Bonney As of January 2015 Non Executive Chair Board of Directors Robert Perez As of January 2015 President & Chief Executive Officer 10

11 U.S. Launch of SIVEXTRO In the first quarter we ve had a couple dozen hospital formulary approvals, including some large academic centers on the East and West Coast. SIVEXTRO has had good initial uptake, particularly for use outside the hospital facilitated by AccessSIVEXTRO TM, our patient support program. SIVEXTRO profile has been received favorably once daily, short, 6 day course is seen as differentiator. 11

12 Globally, Majority of ICU Infections Are Due to Gram negative Bacteria 70% of infected patients have positive cultures; 62% are Gram negative Most common isolates include Pseudomonas aeruginosa, Escherichia coli, and Klebsiella pneumoniae Gram negative isolates (%) Pseudomonas spp. Escherichia coli Klebsiella spp. Acinetobacter spp. Enterobacter spp. Other Data from the Extended Prevalence of Infection in Intensive Care (EPIC II) Study, a global, 1 day point prevalence study of 13,796 patients from 1265 ICUs in 75 Vincent countries et in al. JAMA. Figures 2009;302: for Gram negative isolates (%) are calculated as % of all patients with Gram negative infections. 12

13 Pseudomonas aeruginosa resistance, 2012 a problem especially in South East Europe AMG NEM PTZ CAZ FQs MDR AMG, aminoglycoside; NEM, carbapenem; PTZ, piperacillin; CAZ, ceftazidime; FQ, fluoroquinolone; MDR, multi-drug resistant Percentage resistance <1% 25 to <50% 1 to <5% 50% 5 to <10% No data reported or <10 isolates 10 to <25% Source: resistance surveillance europe 2012.pdf 13

14 Resistance to 3rd generation cephalosporins (ESBL), 2012 Klebsiella pneumoniae Escherichia coli High proportions in several countries Increasing trends common Decreasing trends exceptional Percentage resistance <1% 1 to <5% 5 to <10% 10 to <25% 25 to <50% 50% No data reported or <10 isolates Not included Source: resistance surveillance europe 2012.pdf 14

15 Lead Pipeline Program under regulatory review in US and EU: FDA: PDUFA December 21,2014 EMA: MAA filed August 22,

16 3Q14 Total Net Revenue Growth of 16% GAAP (Unaudited) $350 $309.2 $300 $266.0 $250 In millions $200 $150 $100 $50 $0 3Q11 4Q11 1Q12 2Q12 3Q12 4Q12 1Q13 2Q13 3Q13 4Q13 1Q14 2Q14 3Q14 CUBICIN U.S. Net Revenues International Revenues Service Revenue DIFICID U.S. Net Revenues ENTEREG U.S. Net Revenues SIVEXTRO U.S. Net Revenues Other Revenues 16

17 3Q14: Top Line Growth, Strong Bottom Line and EPS Performance Strong top line, with double digit net revenue growth across portfolio Improved bottom line Non GAAP adjusted Operating Income of $99.1 Million, up by almost 90% vs. 3Q 2013 GAAP diluted EPS was 29 cents, compared with a loss of 50 cents in 3Q

18 2014 CUBIST GUIDANCE ($M)* As of October 21, 2014 Total Net Revenue $1,190 1,275 US Net CUBICIN $970 1,020 All Other Product Revenue $ Service and Other Revenue $15 20 Product Gross Margin (Non GAAP) (1) ~76 77% Operating Expenses (Non GAAP) (2) $ R&D (Including milestone payments) (3) $ SG&A (4) $ Adjusted Operating Income (Non GAAP) (5) $ Other Financials At December 31, 2014 Cash, Cash Equivalents, & Investments ~$700 Convertible Debt ~$1,030 (1) Excludes from GAAP Product Gross Margin the expected cost related to intangible asset amortization and inventory fair value step up. (2) Excludes from GAAP Operating Expenses the R&D and SG&A adjustments described below. (3) Excludes from GAAP R&D Expenses the expected acquisition related expenses, including restructuring. (4) Excludes from GAAP SG&A Expenses the expected acquisition related expenses, including restructuring. (5) Excludes from GAAP Operating Income expected contingent consideration, intangible asset amortization, inventory fair value step up and acquisition related expenses. * Excludes the impact of any future product acquisitions, future company acquisitions, or other potential one time events 18

19 BUILDING LONG TERM VALUE: BUILDING BLOCKS OF GROWTH ( ) $2 Billion in Global Revenue 4 Product Candidates in Late-Stage Clinical Trials $700 Million in Non-GAAP Adjusted Operating Income 19