Corporate Presentation March 2017

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1 Corporate Presentation March 2017

2 Safe Harbor Statement This presentation (the Presentation ) includes forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995, which are based on current expectations, estimates and projections based on information currently available to management. These forward-looking statements include, among others, statements regarding the timing of the initiation of our anticipated clinical trials and studies for Px563L and our other product candidates; expectations with regard to future milestone and royalty payments from our collaboration with Jazz Pharmaceuticals; potential market opportunities for PF582, PF708, PF529 and our other product candidates; developments and projections relating to competitors and the industry, including the rate and degree of market acceptance of biosimilars by stakeholders and physicians; the potential timing of our clinical trial results for PF708 and our other product candidates; the expected patent expiration timelines for Lucentis, Forteo, and other branded reference drugs; our expectations regarding the use of abbreviated regulatory pathways for the approval of our product candidates, including our use of the 505(b)(2) regulatory pathway for PF708; and expectations with regard to our potential to obtain a government procurement contract for Px563L if within ten years of FDA approval. Forward-looking statements are typically identified by words like believe, anticipate, could, should, estimate, expect, intend, plan, project, will, forecast, budget, pro forma, and similar terms. Factors that could cause the Company s results and expectations to differ materially from those expressed in forward-looking statements include, without limitation, our need for additional funds to support our operations; our success being dependent on PF582, PF708, and our other product candidates; our reliance on our collaboration partners performance over which we do not have control; failure to achieve favorable results in later clinical trials for PF582, PF708, or our other product candidates or receive regulatory approval; delays in our clinical trials or in enrollment of patients in our clinical trials; failure to market PF582, PF708, or our other product candidates due to the existence of intellectual property protection owned or controlled by a third party and directed to PF582, PF708, or our other product candidates; PF582, PF708, and our other product candidates may cause serious adverse side effects or have properties that delay or prevent regulatory approval or limit their commercial profile; if approved, risks associated with market acceptance, including pricing and reimbursement; our ability to enforce our intellectual property rights; adverse market conditions; and changes to laws and government regulations involving the labelling, approval process, funding and other matters affecting biosimilars, therapeutic equivalents to branded products and vaccines. Forward-looking statements represent our management s beliefs and assumptions only as of our March 15, 2017 press release announcing results for the quarter and year ended December 31, You should read our Annual Report on Form 10-K for the year ended December 31, 2016 and our subsequent reports filed with the SEC, including the Risk Factors set forth therein, completely and with the understanding that our actual future results may be materially different from what we expect. 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.

3 Corporate Overview & Investment Highlights Programs in our development pipeline include four programs in clinical development including three biosimilars and one vaccine PF708: Positive topline study results reported PF582: Phase 1b/2a completed PF708: Pivotal study initiated PF708: Immunogenicity study results anticipated PF582: Expected Lucentis patent expiry Q Q Q H H H H PF708 Px563L Px563L: Positive Phase 1 Day 70 analysis completed Jazz Pharmaceuticals partnership announced PF529: Regulatory feedback received Px563L: Consultation with BARDA PF708: PK study results anticipated Px563L: Potential phase 2 study initiation PF708: Expected Forteo patent expiry 3 PF582 PF529

4 Pfenex Pipeline PRECLINICAL/ BIOANALYTICAL CHARACTERIZATION COMPARATIVE CLINICAL STUDY TOTAL APPROX. SALES OF BRANDED REFERENCE DRUGS (2015) PF688 Certolizumab pegol biosimilar (Cimzia ) $1.2B* PF529 Pegfilgrastim biosimilar (Neulasta ) $4.7B* PF690 Pegaspargase biosimilar (Oncaspar ) $121MM** PF582 Ranibizumab biosimilar (Lucentis ) $3.6B* PF708 Teriparatide therapeutic equivalent to (Forteo ) $1.4B* $11 Billion HemOnc Products PF694 Peginterferon alpha-2a biosimilar (Pegasys ) $403MM** PF444 Human Growth Hormone biosimilar $3.5B*** $3.9 Billion PRE-CLINICAL PHASE 1 PHASE 2 Fully funded by US Government Px563L SDl rpa based Anthrax Vaccine 2nd Generation Px563L rpa based Anthrax Vaccine RPA563 rpa based Anthrax Vaccine 4 *Based on publicly available 2015 sales data for the branded pharmaceutical company. **Approximate 2015 global branded sales of third-party reference drug per IMS data accessed May 4, *** Approximate 2015 aggregate global branded sales of third-party growth hormone products per IMS data accessed May 4, 2016.

5 Pfenex Expression Technology Our unique Expression Technology allows for rapid, high quality production of therapeutics and vaccines and a revolutionary advancement in clinical technology. GOAL: HIGH QUALITY, HIGH TITER TRADITIONAL: TRIAL AND ERROR PRIMARY STRUCTURE Amino acids are the primary structures of a protein, linked together by peptide bonds, which form a polypeptide. Biosimilars are first compared at the polypeptide level. SECONDARY STRUCTURE Polypeptides are then coiled into a helix - this is the secondary structure that is compared for biosimilarity. 5 TERTIARY STRUCTURE These helixes of polypeptides then fold together in a specific manner. This resulting tertiary structure is then considered for biosimilarity. QUATERNARY STRUCTURE These polypeptide folds interact to form a functional protein. This is the quaternary structure considered for biosimilarity.

6 6 Biosimilars Market Landscape

7 Learning from the EU: US Biosimilars Gaining Momentum EU Biosimilar Product Reviews as of February 2017 US Biosimilar Product Reviews as of February Marketing Authorization Applications (MAA) submitted 7 accelerated Biologics License Applications (abla) submitted 34 MAAs reviewed 29 approved 17 MAAs under review 7 abla s reviewed 4 approved 66 programs in the Biosimilar Biologic Product Development (BPD) program The 351(k) pathway enables the expedited development of biosimilar products by minimizing the clinical testing requirement 2 Current US Biosimilar Pipeline Programs by Year 3 7

8 Biosimilars Expand Patient Access to Therapy Filgrastim Uptake in the EU 8

9 Stakeholders are Responding NOR-SWITCH Study: Physicians more comfortable switching patients to a biosimilar United Healthcare, Express Scripts, CVS Health have excluded Neupogen from their formulary in favor of its biosimilar Zarxio. Healthcare systems establishing biosimilars only tiers. (OPERS) 9 FirstWord Pharma Physician Views Poll, November 2016

10 10 Our Products in Development

11 PF582: Biosimilar to Lucentis Latest known composition of matter patent expiry: USA 2020; EU 2022 Phase 1b/2a first-in-human study completed: Met primary objective of demonstrating similar safety and tolerability between PF582 and Lucentis Demonstrated consistent pharmacological activity between PF582 and Lucentis Evaluating strategic options 11 Figure 1: No significant differences in best corrected visual acuity (BCVA) Figure 2: Comparable decreases in central retinal thickness Figure 3: Comparable immunogenicity (anti-drug antibody formation)

12 PF708: Therapeutic Equivalent Candidate to Forteo Forteo (teriparatide) indicated for treatment of high fracture risk osteoporosis Reference product produced via E. coli Forteo global sales in 2015: $1.4 billion 5 Expected section 505(b)(2) regulatory approval pathway for PF708 Latest expiry of Orange Book-listed teriparatide method of treatment, formulation and/or API patent expected in 2019 Pfenex has achieved high titer protein production; low cost of goods Completed bioequivalence in healthy subjects that met endpoints Pivotal immunogenicity/pharmacokinetic study in subjects with osteoporosis began at end of 2016 PK study results anticipated in second half of 2017 Immunogenicity study results anticipated in first half of 2018 Study Design Period 1 (1 Day) Washout (3 Days) Period 2 (1 Day) Sequence A PF708 PF708 Sequence B Forteo Forteo Results Dosing All 70 subjects completed the study Dosing 12

13 PF529: Potential Biosimilar to Neulasta Neulasta (pegfilgrastim) is indicated for the prevention of febrile neutropenia in patients receiving cytotoxic chemotherapy Neulasta global sales in 2015: $4.7 billion 6 Regulatory feedback for PF529 was received in 2016 and supports the feasibility of development under the 351(k) biosimilar pathway. Pfenex continues to evaluate the potential resource requirements and timeline for development. 13

14 Px563L: Next Generation Anthrax Vaccine Candidate In August 2015 awarded a BARDA contract of up to $143.5MM to fund advanced development Figure 1: Toxin Neutralizing Antibody NF 50 Results Anthrax recombinant Protective Antigen (rpa) vaccine candidates: Phase 1a Day 70 analysis demonstrated that Px563L was well-tolerated and conferred potentially superior protection after only 2 doses Potential procurement contract if within 10 years of FDA approval In addition to the base period, BARDA has exercised an additional two of the eight option periods effective January 2017, allowing for the continuing development of Px563L. The phase 2 study could initiate in 2018, provided the program continues to successfully advance with the support of BARDA. Table 1: Positive Day 70 Immunogenicity Results for Px563L 14 Regulatory Threshold For Post Exposure Prophylaxis Indication: For the percentage of subjects with TNA NF50 value 0.56, the lower limit of the 95% confidence interval should be 40%.

15 Jazz Pharmaceuticals/Pfenex Collaboration Agreement signed in July 2016 License and option agreement granting Jazz Pharmaceuticals worldwide rights to develop and commercialize multiple early stage hematology product candidates Partnership details: $181 MM in combined upfront and potential milestone payments including up to $41 MM non-sales related; tiered royalties on net sales Collaboration governed by Joint Development Committee with equal representation from each company Jazz obtains exclusive option to PF690, Pfenex s Pegaspargase biosimilar candidate to Oncaspar 15

16 Corporate Overview & Investment Highlights Programs in our development pipeline include four programs in clinical development including three biosimilars and one vaccine PF708: Positive topline study results reported PF582: Phase 1b/2a completed PF708: Pivotal study initiated PF708: Immunogenicity study results anticipated PF582: Expected Lucentis patent expiry Q Q Q H H H H PF708 Px563L: Positive Phase 1 Day 70 analysis completed Jazz Pharmaceuticals partnership announced PF529: Regulatory feedback received Px563L: Consultation with BARDA PF708: PK study results anticipated Px563L: Potential phase 2 study initiation PF708: Expected Forteo patent expiry Px563L 16 PF582 PF529

17 17 Appendix

18 Senior Management Patrick K. Lucy Interim CEO Chief Business Officer Hubert Chen M.D. Chief Medical Officer Patricia Lady M.B.A., CPA Chief Accounting Officer 18 Paul Wagner Ph.D., CFA Chief Financial Officer Mayda Mercado Vice President of Global Quality Steven S. Sandoval Chief Manufacturing Officer

19 Board of Directors William R. Rohn (Chairman) William R. Rohn joined the board of directors as the chairman in connection with Pfenex s initial public offering in July Most recently, Mr. Rohn served as Chief Operating Officer of Biogen Idec, the successor company to IDEC Pharmaceuticals, a biotechnology company, from 2003 until Robin D. Campbell, Ph.D. Dr. Robin D. Campbell joined the board of directors in September He has over 25 years of experience in pharmaceutical and biotechnology sales, marketing, product development and general management in both the U.S. and in international markets. Currently he serves as Chairman of the Board of Aptitude Medical Systems, an early stage company creating high performance aptamers for research, diagnostic and therapeutic use. Phillip M. Schneider, M.B.A. Phillip M. Schneider joined the board of directors in connection with Pfenex s initial public offering in July Most recently, Mr. Schneider held various positions with IDEC Pharmaceuticals Corporation, a biopharmaceutical company, from 1987 to 2003, including: Senior Vice President and Chief Financial Officer from 1997 to 2003; and Director of Finance and Administration from 1992 to John Taylor, J.D. John Taylor joined the board of directors in April He is the President and Principal of Compliance and Regulatory Affairs at Greenleaf Health LLC., and has over 24 years of experience working on food and drug related issues at the U.S. Food and Drug Administration (FDA) and in private industry. 19 Dennis Fenton, Ph.D. Dr. Dennis Fenton joined the board of directors in September 2015, deepening the manufacturing and product development expertise of our company. Dr. Fenton, an industry pioneer, has over three decades of experience in the biotechnology industry. Dr. Fenton retired after a lengthy and distinguished career with Amgen, where he held a variety of notable roles, including Executive Vice President, Operations.

20 The Pfenex Toolbox Our patent protected ability to enable rapid strain engineering for optimal protein production accelerates proof of concept, product development and long-term cost of goods advantage. Cell Model Our model enables 5,400,00+ opportunities for strain development. 20 Elements combined to generate >100 rapid cloning, off the shelf, expression vectors covered by our numerous issued/allowed patents* *As of March 7, 2016

21 References Biosimilars in the US: Progress and Promise DIA Biosimilars 2016 John Jenkins, M.D. Director Office of New Drugs Center for Drug Evaluation and Research October 27, 2016 BCC Research. Biologic Therapeutic Drugs: Technologies and Global Markets, Jan. 2015, p. 2. IMS Health, Shaping the biosimilars opportunity: A global perspective on the evolving biosimilars landscape. Dec. 2011, p. 6. Bayer Annual Report 2015, p Eli Lilly Annual Report 2015, p. 40. Amgen Annual Report 2015, p. 44 Medicines for Europe, Biosimilar Medicines: Did You Know? accessed Apr Generics and Biosimilars Initiative Journal, Saving Money in the European Healthcare Systems with Biosimilars, 2012, p Note: All trademarks mentioned herein are property of their respective owners.

22 INNOVATIVE SOLUTIONS FOR GLOBAL HEALTH Pfenex Inc. All rights reserved.