Pfenex Inc.San Diego, CANYSE MKT: PFNX

This presentation (the “Presentation”) includes forward-looking statements within the meaning of the Private Securities LitigationReform Act of 1995, which are based on current expectations, estimates and projections based on information currently available tomanagement. These forward-looking statements include, among others, statements regarding the timing of the initiation of ouranticipated clinical trials and studies for Px563L and our other product candidates; expectations with regard to future milestone androyalty payments from our collaboration with Jazz Pharmaceuticals; expectations with respect to our ability to receive future paymentsunder our government contracts; our expectation to update the status of our strategic review for PF582 in Q3; potential marketopportunities for PF582, PF708, PF529, PF690 and our other product candidates; developments and projections relating tocompetitors and the industry; the potential timing of our clinical trial results for PF708 and our other product candidates; the expectedpatent expiration timelines for Lucentis, Forteo, and other branded reference drugs; our expectations regarding the use of abbreviatedregulatory pathways for the approval of our product candidates, including our use of the 505(b)(2) regulatory pathway for PF708 andthe 351(k) pathway for PF529; our expectations with regard to our potential to obtain a government procurement contract for Px563Lif within ten years of FDA approval; expected milestones for Px563L; and the expected NDA filing for PF708. Forward-lookingstatements 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 andexpectations to differ materially from those expressed in forward-looking statements include, without limitation, our need foradditional funds to support our operations; our success being dependent on PF582, PF708, and our other product candidates; ourreliance on our collaboration partners’ performance over which we do not have control; failure to achieve favorable results in laterclinical trials for PF582, PF708, or our other product candidates or receive regulatory approval; delays in our clinical trials or inenrollment of patients in our clinical trials; failure to market PF582, PF708, or our other product candidates due to the existence ofintellectual 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 preventregulatory approval or limit their commercial profile; if approved, risks associated with market acceptance, including pricing andreimbursement; our ability to enforce our intellectual property rights; adverse market conditions; and changes to laws andgovernment regulations involving the labelling, approval process, funding and other matters affecting biosimilars, therapeuticequivalents to branded products and vaccines. Forward-looking statements represent our management’s beliefs and assumptions onlyas of our May 8, 2017 press release announcing results for the quarter ended March 31, 2017. You should read our Annual Report onForm 10-K for the year ended December 31, 2016, our Quarterly Report on Form 10-Q for the quarter ended March 31, 2017 and oursubsequent reports filed with the SEC, including the Risk Factors set forth therein, completely and with the understanding that ouractual future results may be materially different from what we expect. Except as required by law, we assume no obligation to updatethese forward-looking statements publicly, or to update the reasons why actual results could differ materially from those anticipatedin the forward-looking statements, even if new information becomes available in the future.

Safe Harbor Statement

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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 2018. • 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

*As of June 14, 2017

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Programs in our development pipeline include four programs in clinical development including three biosimilar candidates and one vaccine candidate

Corporate Overview & Investment Highlights

Q2 2016 Q3 2016 Q4 2016 1H 2017 2H 2017 1H 2018 2H 2018 2019 2020

PF708: Positive topline study results reported

Jazz Pharmaceuticals

partnership announced

PF582: Phase 1/2 completed

Px563L: Positive Phase 1 Day 70analysis completed

PF708: Pivotal study initiated

PF529: Regulatory feedback received PF708: Expected

Forteo® patent expiry(with respect to API, MOT and/or formulation patents in US)

PF582: ExpectedLucentis®

patent expiry in US

Px563L: Consultation with BARDA

PF708 - teriparatide

Px563L – Anthrax vaccine

PF582 - ranibizumab

PF529 - pegfilgrastim

PF708: PK study results anticipated

PF708: Immunogenicity study results anticipated

Px563L: Potential phase 2

study initiation

PF708: Expected NDA Filing

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Pfenex Pipeline Highlights

PRECLINICAL/ BIOANALYTICAL CHARACTERIZATION

Preclinical Analytical Similarity US FDA BiosimilarInitial Advisory

Meeting

Comparative Clinical Study

Initial I Pivotal

2016 Sales of Third Party Branded Reference

Product

FullyFunded ByUS Government

Preclinical Phase 1 Phase 2

Px563L – Adjuvanted Anthrax Vaccine

RPA563 – Non-Adjuvanted Anthrax Vaccine

~$9.5B

1 Being developed via the 505(b)(2) pathway in the United States2 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, 2017.

PF582 – ranibizumab (Lucentis®)

PF529 – pegfilgrastim (Neulasta®)

Multiple HemOnc Products

$1.5B2

$3.2B2

$4.6B2

PF690 –pegaspargase (Oncaspar®)

$188M3

Wholly Owned

PF708 – teriparatide (Forteo®)1…………………………………………………

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Our proprietary protein production platform allows for rapid, high quality production and analysis of therapeutics and vaccines.

Pfenex Expression Technology Platform

TRADITIONAL: TRIAL AND ERROR

GOAL:HIGH QUALITY,HIGH TITER 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 STRUCTUREPolypeptides are then coiled into a helix - this is the secondary structure that is compared for biosimilarity.

TERTIARY STRUCTUREThese helixes of polypeptides then fold together in a specific manner. This resulting tertiary structure is then considered for biosimilarity.

QUATERNARY STRUCTUREThese polypeptide folds interact to form a functional protein. This is the quaternary structure considered for biosimilarity.

Thousands of parallel experiments enables accelerated development

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Biosimilars Market Landscape

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FDA and EMA Biosimilars Guidance: Focus Is on Analytical Similarity

Phase 3

Phase 1/2

BiologicalCharacterization

AnalyticalCharacterization

Novel Drugs

Analytical Characterization

BiologicalCharacterization

Pharmacokinetics

Pharmacodynamics,Immunogenicity

Biosimilars

Globally Biosimilars Are Gaining Momentum

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EU Biosimilar Product Reviews as of June 2017

57 Marketing Authorization Applications (MAA) submitted

17 MAAs under review

40 MAAs reviewed

29 approved

14 accelerated Biologics License Applications (aBLA) submitted

66+ programs in the FDA

Biosimilar Biological Product

Development program

10 aBLA’sreviewed*

5 approved

US Biosimilar Product Reviews as of June 2017

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

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Pfenex Products in Development

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• Forteo® (teriparatide) indicated for treatment of high fracture risk osteoporosis• Forteo global sales in 2016: $1.5 billion5

• 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

• 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

PF708: Therapeutic Equivalent Candidate to Forteo®

PF708 (teriparatide [rDNA] injection

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PF708: Therapeutic Equivalent Candidate to Forteo® - Bioequivalence Study Results

PF708

Forteo

PF708

Forteo

Sequence A

Sequence B

Period 1 (1 Day)

Washout (3 Days)

Period 2 (1 Day)

Dosing Dosing

• All 70 subjects completed the study

Study Design

Study Results

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• 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:

PF582: Biosimilar to Lucentis®

• Currently evaluating strategic options

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PF582: Biosimilar to Lucentis®

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)

Key Upcoming Expected Milestones:• We expect to update the status of

our strategic review in Q3

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• 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 Q4 2016 supporting the feasibility of development under the 351(k) biosimilar pathway.

• Pfenex continues to evaluate the potential resource requirements and timeline for development.

PF529:Biosimilar Candidate to Neulasta®

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• 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.

Px563L/RPA563: Next Generation Anthrax Vaccine Candidates

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Px563L/RPA563: Next Generation Anthrax Vaccine Candidates

Figure 1: Toxin Neutralizing Antibody NF50 Results

Table 1: Positive Day 70 Immunogenicity Results for Px563L

• 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%.

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• 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®

Jazz Pharmaceuticals/Pfenex Collaboration

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Programs in our development pipeline include four programs in clinical development including three biosimilar candidates and one vaccine candidate

Corporate Overview & Investment Highlights

Q2 2016 Q3 2016 Q4 2016 1H 2017 2H 2017 1H 2018 2H 2018 2019 2020

PF708: Positive topline study results reported

Jazz Pharmaceuticals

partnership announced

PF582: Phase 1/2 completed

Px563L: Positive Phase 1 Day 70analysis completed

PF708: Pivotal study initiated

PF529: Regulatory feedback received PF708: Expected

Forteo® patent expiry(with respect to API, MOT and/or formulation patents in US)

PF582: ExpectedLucentis®

patent expiry in US

Px563L: Consultation with BARDA

PF708 - teriparatide

Px563L – Anthrax vaccine

PF582 - ranibizumab

PF529 - pegfilgrastim

PF708: PK study results anticipated

PF708: Immunogenicity study results anticipated

Px563L: Potential phase 2

study initiation

PF708: Expected NDA Filing

© 2017 Pfenex Inc. All rights reserved.

INNOVATIVE SOLUTIONS FOR GLOBAL HEALTH

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• 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. 156.• Eli Lilly Annual Report 2015, p. 40.• Amgen Annual Report 2015, p. 44.• Medicines for Europe, “Biosimilar Medicines: Did You Know?” accessed Apr. 2016.• Generics and Biosimilars Initiative Journal, “Saving Money in the European Healthcare Systems with

Biosimilars,” 2012, p. 124.• 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, 2017.• Biosimilars, FDA Update, Joe Franklin, JD PhD, Center for Drug Evaluation & Research, FDA, May 4, 2017.• Approved and Pending Biosimilar Applications, Mintz Levin, August 2016.

References

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