Pfenex Inc. San Diego, CA NYSE MKT: PFNX

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1 Pfenex Inc. San Diego, CA NYSE MKT: PFNX

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; expectations with respect to our ability to receive future payments under our government contracts; our expectation to update the status of our strategic review for PF582 in Q3; potential market opportunities for PF582, PF708, PF529, PF690 and our other product candidates; developments and projections relating to competitors and the industry; 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 the 351(k) pathway for PF529; our expectations with regard to our potential to obtain a government procurement contract for Px563L if within ten years of FDA approval; expected milestones for Px563L; and the expected NDA filing for PF708. 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 May 8, 2017 press release announcing results for the quarter ended March 31, You should read our Annual Report on Form 10-K for the year ended December 31, 2016, our Quarterly Report on Form 10-Q for the quarter ended March 31, 2017 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 Pfenex Overview 65 full time employees (15 PhDs/MDs)* 47,000 square feet of lab and office space with 17,000 square feet housing state of the art molecular biology, fermentation, purification, analytical and pilot plant capabilities* Recently added Jason Grenfell-Gardner (Chairman) and Sigurdur (Siggi) Olafsson to Board of Directors Anticipate NDA filing on PF708 teriparatide, a therapeutic equivalent candidate to Forteo, in 2H Up to $181M partnership with Jazz Pharmaceuticals to develop hematology/oncology products Up to $143.5M contract with the US government to develop a next generation anthrax vaccine Proprietary Production Platform enables robust pipeline of product candidates 3 *As of June 14, 2017

4 Corporate Overview & Investment Highlights Programs in our development pipeline include four programs in clinical development including three biosimilar candidates and one vaccine candidate PF708: Positive topline study results reported PF582: Phase 1/2 completed PF708: Pivotal study initiated PF708: Immunogenicity study results anticipated PF708: Expected NDA Filing PF582: Expected Lucentis patent expiry in US Q Q Q H H H H Jazz Pharmaceuticals partnership announced PF708 - teriparatide Px563L Anthrax vaccine Px563L: Positive Phase 1 Day 70 analysis completed PF529: Regulatory feedback received Px563L: Consultation with BARDA PF708: PK study results anticipated Px563L: Potential phase 2 study initiation PF708: Expected Forteo patent expiry (with respect to API, MOT and/or formulation patents in US) 4 PF582 - ranibizumab PF529 - pegfilgrastim

5 Pfenex Pipeline Highlights PreclinicalPRECLINICAL/ Analytical BIOANALYTICAL Similarity CHARACTERIZATION US FDA Biosimilar Initial Advisory Meeting Comparative Clinical Study Initial I Pivotal 2016 Sales of Third Party Branded Reference Product PF708 teriparatide (Forteo ) 1 $1.5B 2 Wholly Owned PF582 ranibizumab (Lucentis ) PF529 pegfilgrastim (Neulasta ) $3.2B 2 $4.6B 2 ~$9.5B 1 Being developed via the 505(b)(2) pathway in the United States 2 Based on publicly available 2016 sales data for the third party branded pharmaceutical company. 3 Approximate 2016 global branded sales of third-party reference drug per IMS data accessed June 5, FullyFunded By US Government PF690 pegaspargase (Oncaspar ) Multiple HemOnc Products Preclinical Phase 1 Phase 2 Px563L Adjuvanted Anthrax Vaccine RPA563 Non-Adjuvanted Anthrax Vaccine $188M 3

6 Pfenex Expression Technology Platform Our proprietary protein production platform allows for rapid, high quality production and analysis of therapeutics and vaccines. 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. 6 Thousands of parallel experiments enables accelerated development 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.

7 7 Biosimilars Market Landscape

8 FDA and EMA Biosimilars Guidance: Focus Is on Analytical Similarity Biological Characterization Analytical Characterization Novel Drugs Phase 3 Phase 1/2 Biosimilars Biological Characterization Analytical Characterization Pharmacodynamics, Immunogenicity Pharmacokinetics 8

9 Globally Biosimilars Are Gaining Momentum EU Biosimilar Product Reviews as of June Marketing Authorization Applications (MAA) submitted US Biosimilar Product Reviews as of June accelerated Biologics License Applications (abla) submitted 40 MAAs reviewed 29 approved 17 MAAs under review 10 abla s reviewed* 5 approved 66+ programs in the FDA Biosimilar Biological Product Development program 9 Recent Sandoz v. Amgen US Supreme Court decision not requiring approval prior to 180-day notice of commercial marketing a clear win for biosimilar developers *estimated

10 10 Pfenex Products in Development

11 PF708: Therapeutic Equivalent Candidate to Forteo Forteo (teriparatide) indicated for treatment of high fracture risk osteoporosis Forteo global sales in 2016: $1.5 billion 5 Expected via Section 505(b)(2) regulatory approval pathway Latest expiry of Orange Book-listed teriparatide method of treatment, formulation and/or API patent expected in 2019 in US Pfenex has achieved high titer protein production; low cost of goods Completed bioequivalence in healthy subjects that met all endpoints Pivotal immunogenicity/pharmacokinetic study in subjects with osteoporosis began at end of 2016 and ongoing PF708 (teriparatide [rdna] injection 11 Key Upcoming Expected Milestones: PK study results anticipated in second half of 2017 Immunogenicity study results anticipated in first half of 2018 NDA Filing 2H 2018

12 PF708: Therapeutic Equivalent Candidate to Forteo - Bioequivalence Study Results Period 1 (1 Day) Washout (3 Days) Period 2 (1 Day) Sequence A PF708 PF708 Study Design Sequence B Forteo Forteo Dosing All 70 subjects completed the study Dosing Study Results 12

13 PF582: Biosimilar to Lucentis Latest known composition of matter expected patent expiry: USA 2020; EU 2022 Phase 1/2 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 Phase 1/2 Study Design: 13 Currently evaluating strategic options

14 PF582: Biosimilar to Lucentis Figure 1: No significant differences in best corrected visual acuity (BCVA) Figure 2: Comparable decreases in central retinal thickness Key Upcoming Expected Milestones: We expect to update the status of our strategic review in Q3 14 Figure 3: Comparable immunogenicity (anti-drug antibody formation)

15 PF529:Biosimilar Candidate to Neulasta Neulasta (pegfilgrastim) is indicated for the prevention of febrile neutropenia in patients receiving cytotoxic chemotherapy Neulasta global sales in 2016: $4.6 billion US FDA feedback for PF529 was received in Q supporting the feasibility of development under the 351(k) biosimilar pathway. Pfenex continues to evaluate the potential resource requirements and timeline for development. 15

16 Px563L/RPA563: Next Generation Anthrax Vaccine Candidates 16 Awarded a BARDA contract of up to $143.5MM to fund advanced development in August 2015 Anthrax recombinant Protective Antigen (rpa) vaccine candidates: Demonstrated long term stability data from our toxicology lot showing greater than 90% purity at 5 C at 40 months. 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 two of the eight option periods effective January 2017 Next Expected Milestones: Option Period 1 in support of confirmatory study for product specific correlate of protection The Phase 2 study could initiate in 2018, provided the program continues to successfully advance with the support of BARDA.

17 Px563L/RPA563: Next Generation Anthrax Vaccine Candidates Figure 1: Toxin Neutralizing Antibody NF 50 Results Table 1: Positive Day 70 Immunogenicity Results for Px563L 17 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%.

18 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: Up to $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 18

19 Corporate Overview & Investment Highlights Programs in our development pipeline include four programs in clinical development including three biosimilar candidates and one vaccine candidate PF708: Positive topline study results reported PF582: Phase 1/2 completed PF708: Pivotal study initiated PF708: Immunogenicity study results anticipated PF708: Expected NDA Filing PF582: Expected Lucentis patent expiry in US Q Q Q H H H H Jazz Pharmaceuticals partnership announced PF708 - teriparatide Px563L Anthrax vaccine Px563L: Positive Phase 1 Day 70 analysis completed PF529: Regulatory feedback received Px563L: Consultation with BARDA PF708: PK study results anticipated Px563L: Potential phase 2 study initiation PF708: Expected Forteo patent expiry (with respect to API, MOT and/or formulation patents in US) 19 PF582 - ranibizumab PF529 - pegfilgrastim

20 INNOVATIVE SOLUTIONS FOR GLOBAL HEALTH 2017 Pfenex Inc. All rights reserved.

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, 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 European Medicines Agency, European Public Assessment Report (EPAR) for Human Medicines, Biosimilars. Amgen 10K Annual Report. Biosimilars, The Regulatory Framework, Peter Richardson, EMA, February 8, Biosimilars, FDA Update, Joe Franklin, JD PhD, Center for Drug Evaluation & Research, FDA, May 4, Approved and Pending Biosimilar Applications, Mintz Levin, August Note: All trademarks mentioned herein are property of their respective owners.