8-K

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, DC 20549

FORM 8-K

CURRENT REPORT

Pursuant to Section 13 or 15(d)

of The Securities Exchange Act of 1934

Date of Report (Date of earliest event reported):

March 15, 2018

Pfenex Inc.

(Exact name of registrant as specified in its charter)

Delaware	001-36540	27-1356759
(State or other jurisdiction of incorporation)	(Commission File Number)	(IRS Employer Identification No.)

10790 Roselle Street

San Diego, CA 92121

(Address of principal executive offices, including zip code)

(858) 352-4400

(Registrant’s telephone number, including area code)

Not Applicable

(Former name or former address, if changed since last report.)

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions (see General Instruction A.2. below):

☐ Written communications pursuant to Rule 425 under the Securities Act (17 CFR 230.425)

☐ Soliciting material pursuant to Rule 14a-12 under the Exchange Act (17 CFR 240.14a-12)

☐ Pre-commencement communications pursuant to Rule 14d-2(b) under the Exchange Act (17 CFR 240.14d-2(b))

☐ Pre-commencement communications pursuant to Rule 13e-4(c) under the Exchange Act (17 CFR 240.13e-4(c))

Indicate by check mark whether the registrant is an emerging growth company as defined in Rule 405 of the Securities Act of 1933 (17 CFR §230.405) or Rule 12b-2 of the Securities Exchange Act of 1934 (17 CFR §240.12b-2).

Emerging growth company  ☒

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act.  ☐

Item 2.02 Results of Operations and Financial Condition.

On March 15, 2018, Pfenex Inc. (the “Company”) issued a press release reporting its financial results for the fourth quarter and full year ended December 31, 2017. A copy of the press release is furnished herewith as Exhibit 99.1 to this Current Report on Form 8-K.

The information referenced under Item 2.02 (including Exhibit 99.1 referenced in Item 9.01 below) of this Current Report shall not be deemed to be “filed” for purposes of Section 18 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), or otherwise subject to the liabilities of that Section, nor shall it be deemed incorporated by reference in any filing under the Securities Act of 1933, as amended, or under the Exchange Act, whether made before or after the date hereof, except as expressly set forth by specific reference in such filing to this Current Report.

Item 7.01 Regulation FD Disclosure.

A copy of a slide presentation that the Company intends to present to investors is attached to this Current Report on Form 8-K as Exhibit 99.2 and is incorporated herein solely for purposes of this Item 7.01 disclosure.

The information referenced under Item 7.01 (including Exhibit 99.2 referenced in Item 9.01 below) of this Current Report shall not be deemed to be “filed” for purposes of Section 18 of the Exchange Act, or otherwise subject to the liabilities of that Section, nor shall it be deemed incorporated by reference in any filing under the Securities Act of 1933, as amended, or under the Exchange Act, whether made before or after the date hereof, except as expressly set forth by specific reference in such filing to this Current Report. This Current Report shall not be deemed an admission as to the materiality of any information in the Current Report that is required to be disclosed solely by Regulation FD.

Item 9.01 Financial Statements and Exhibits.

(d) Exhibits

Exhibit No.	Description
99.1	Press Release dated March 15, 2018.
99.2	Pfenex Inc. Investor Presentation

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned hereunto duly authorized.

		PFENEX INC.
Date: March 15, 2018	By:	/s/ Susan A. Knudson
		Susan A. Knudson
		Chief Financial Officer

-2-

EX-99.1

Exhibit 99.1

FOR IMMEDIATE RELEASE

Pfenex Reports Fourth Quarter and Full Year 2017 Results and Provides Business Update

SAN DIEGO, March 15, 2018 —Pfenex Inc. (NYSE American: PFNX) is a clinical-stage development and licensing biotechnology company focused on leveraging its Pfenex Expression Technology^® to improve protein therapies for unmet patient needs. Using the patented Pfenex Expression Technology^® platform, the Company has created an advanced pipeline of therapeutic equivalents, vaccines, biologics and biosimilars. Today Pfenex Inc. reported financial results for the fourth quarter and full year ended December 31, 2017 and provided a business update.

“Throughout 2017 we made considerable progress in advancing our lead product candidates as well as achieving substantial development milestones on our partnered programs,” said Eef Schimmelpennink, chief executive officer of Pfenex. “I joined Pfenex in August as the company’s chief executive officer because I saw a company with a unique and validated protein expression platform, a broad differentiated portfolio and a very talented team, but, was in need of change. From day-one the team and I focused on defining our priorities and setting a new course. We ended the year with a clear and concise strategic focus that leverages the strength of the Pfenex Expression Technology^® platform through the development of our own key assets in our pipeline, while selectively collaborating with strong partners. Pfenex is at a transformational point in our development, and I look forward to leading the team and continuing to build Pfenex into an industry success.” 

Business Updates and 2017 Highlights

PF708 therapeutic equivalent to Forteo^® (teriparatide). The Company completed the last patient visit in mid-February 2018 from its on-going PF708-301 trial which compares the effects of PF708 and Forteo in osteoporosis patients. The Company expects top-line immunogenicity data results in the second quarter of 2018. Pfenex believes that results from its PF708-301 trial, along with the bioequivalence findings from its PF708-101 trial in healthy subjects announced previously, should satisfy the clinical filing requirements for PF708. Pfenex expects to submit the new drug application (NDA) to the FDA in the third quarter of 2018, with a potential commercial launch possible in the US as early as the third quarter of 2019 upon expiration of the relevant patents and subject to receipt of US FDA marketing authorization.

Jazz Collaboration Agreement. In December 2017, Pfenex announced that under the amended collaboration agreement with Jazz Pharmaceuticals, Pfenex will be eligible to receive an additional $43.5 million in amendment fee and development milestone payments bringing the total value of payments and potential payments associated with the collaboration to $224.5 million. Upon signing the amended and restated agreement, Pfenex received a total of $18.5 million, consisting of an upfront payment of $5.0 million and a payment of $13.5 million for development achievement. Pfenex may also be eligible to receive tiered royalties on worldwide sales of any products resulting from the collaboration at rates reduced from those under the 2016 agreement. Finally, in the third quarter of 2017, we completed a process development milestone associated with this collaboration.

Px563L and RPA563. The development of the Company’s novel anthrax vaccine candidates is funded through an advanced development contract with the Department of Health and Human Services through the Biomedical Advanced Research and Development Authority (BARDA) valued at up to approximately $143.5 million. In January of 2017, BARDA exercised additional phases of the development contract, allowing for the continuing development of both Px563L and RPA563. In the second quarter of 2017, Pfenex completed its long-term follow-up of the Phase 1 study subjects, and the results showed no change to the interim safety or immunogenicity results. In October 2017, Pfenex completed a meeting with the FDA in which the Agency provided guidance for the proposed clinical development and licensure plans for post-exposure prophylaxis indication. Over the course of 2017, the Company continued to collect favorable stability data for both products. Potential next milestones in 2018 are triggering of analytical and non-clinical animal study options leading to potential Phase 2 study in 2019, subject in each case to continued funding by BARDA.

Financial Highlights for the Fourth Quarter and Full Year 2017

Total Revenue increased to $17.9 million in the three-month period ended December 31, 2017 compared to $5.5 million in same period in 2016. The increase in the three month period was due primarily to development achievements related to the Jazz collaboration. Total revenue decreased to $28.8 million in the year ended December 31, 2017 compared to $60.2 million in 2016. The year over year decrease in revenue was primarily due to the termination of the development and license agreement with Pfizer in the third quarter of 2016, which accelerated the recognition of revenue that had been previously deferred. In addition, in 2016 Pfenex recognized revenue of $4.9 million attributable to amortization of a development and license fee. The decrease in revenue was partially offset by $21.5 million of revenue recognized in 2017 from Jazz for development achievement and achievement of certain development milestones, development services and amortization of license fees.

Cost of revenue increased to $1.7 million in the three-month period ended December 31, 2017 compared to $1.3 million in same period in 2016. The change was due primarily to a net increase in costs for the Company’s proprietary novel vaccine program Px563L, which is funded by BARDA. Cost of revenue decreased to $5.2 million in the year ended December 31, 2017 compared to $5.3 million in 2016. The change was primarily due to a net decrease of costs for the Company’s proprietary novel vaccine program Px563L, which is funded by BARDA.

Research and development expenses decreased to $7.2 million in the three-month period ended December 31, 2017 compared to $10.7 million in same period in 2016. The decrease was primarily due to the Company’s decision to pause the Company’s development activities on certain product candidates. Research and development expenses decreased to $31.9 million in the year ended December 31, 2017 compared to $32.4 million in 2016. The decrease was primarily due to the Company’s decision to pause the Company’s development activities on certain product candidates. The decrease was partially offset by increased costs related to clinical trials for PF708, which began in the first quarter of 2017, and research and development expenses of hematology/oncology products related to the Company’s collaboration with Jazz, including PF743, a recombinant crisantaspase, and PF745, a recombinant crisantaspase with half-life extension technology, as well as other biosimilar product candidates.

Selling, general and administration expenses decreased to $3.7 million in the three-month period ended December 31, 2017 compared to $4.4 million in same period in 2016. This decrease in costs was

primarily due to the departure of the Company’s former CFO during the fourth quarter of 2017. In addition, in the fourth quarter of 2016, Pfenex incurred costs associated with the Audit Committee’s investigation. Selling, general and administration expenses increased to $17.7 million in the year ended December 31, 2017 compared to $17.3 million in 2016. The year over year increase was primarily due to costs incurred in connection with the separation of former officers.

Cash and cash equivalents as of December 31, 2017 was $57.7 million. Pfenex believes it has sufficient cash to meet the Company’s anticipated cash needs for at least the next 12 months. The Company also believes it has sufficient cash resources to fund all necessary activities leading up to and including the submission of a new drug application (NDA) for PF708 to the FDA.

Cautionary Note Regarding Forward-Looking Statement –

This press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. Forward-looking statements generally relate to future events or Pfenex’s future financial or operating performance. In some cases, you can identify forward-looking statements because they contain words such as “may,” “will,” “should,” “expects,” “plans,” “anticipates,” “could,” “intends,” “target,” “projects,” “contemplates,” “believes,” “estimates,” “predicts,” “potential” or “continue” or the negative of these words or other similar terms or expressions that concern Pfenex’s expectations, strategy, plans or intentions. Forward-looking statements in this press release include, but are not limited to, statements regarding the future potential of Pfenex’s product candidates and the company in general, including future plans to advance, develop, manufacture and commercialize its product candidates; Pfenex’s expectation to receive data from the PF708 clinical program in second quarter of 2018 and its expectation to submit an NDA in the third quarter of 2018, and the possibility of the potential commercial US launch of PF708 in the third quarter of 2019; Pfenex’s expectations with respect to the sufficiency of its cash resources; Pfenex’s expectations regarding the timing of the release of additional clinical trial data for its product candidates; Pfenex’s expectations regarding the timing and advancement of clinical trials and studies and the types of future clinical trials and studies for its product candidates, including PF708 and Px563L/RPA563; Pfenex’s expectations regarding the sufficiency of its clinical trials to satisfy regulatory requirements; Pfenex’s expectation for potential partnership opportunities for its product candidates; expectations with regard to future milestone and royalty payments from Pfenex’s collaboration with Jazz Pharmaceuticals; Pfenex’s expectations regarding potential payments from BARDA; Pfenex’s expectation that it will potentially initiate a phase 2 study for Px563L/RPA563 in 2019; and Pfenex’s future projections related to fluctuations and increases in revenue and expenses, including increases in research and development costs as Pfenex advances its product candidates. Pfenex’s expectations and beliefs regarding these matters may not materialize, and actual results in future periods are subject to risks and uncertainties that could cause actual results to differ materially from those projected. Actual results may differ materially from those indicated by these forward-looking statements as a result of the uncertainties inherent in the clinical drug development process, including, without limitation, Pfenex’s ability to successfully demonstrate the efficacy and safety of its product candidates; the pre-clinical and clinical results for its product candidates, which may not support further development of product candidates or may require Pfenex to conduct additional clinical trials or modify ongoing clinical trials or regulatory pathways; challenges related to commencement, patient enrollment, completion, and analysis of clinical trials; difficulties in achieving and demonstrating biosimilarity in formulations; Pfenex’s ability to manage operating expenses; Pfenex’s ability to obtain additional funding to support its business activities and establish and maintain strategic business alliances and new business initiatives; Pfenex’s dependence on

third parties for development, manufacture, marketing, sales and distribution of products; unexpected expenditures; and difficulties in obtaining and maintaining intellectual property protection for its product candidates. Information on these and additional risks, uncertainties, and other information affecting Pfenex’s business and operating results is contained in Pfenex’s Annual Report on Form 10-K for the period ended December 31, 2017 and in its other filings with the Securities and Exchange Commission. The forward-looking statements in this press release are based on information available to Pfenex as of the date hereof, and Pfenex disclaims any obligation to update any forward-looking statements, except as required by law.

Pfenex investors and others should note that we announce material information to the public about the Company through a variety of means, including our website (http://www.pfenex.com/), our investor relations website (http://pfenex.investorroom.com/), press releases, SEC filings, public conference calls, corporate Twitter account (https://twitter.com/pfenex), Facebook page (https://www.facebook.com/Pfenex-Inc-105908276167776/timeline/), and LinkedIn page (https://www.linkedin.com/company/pfenex-inc) in order to achieve broad, non-exclusionary distribution of information to the public and to comply with our disclosure obligations under Regulation FD. We encourage our investors and others to monitor and review the information we make public in these locations as such information could be deemed to be material information. Please note that this list may be updated from time to time.

About Pfenex Inc.

We are a clinical-stage development and licensing biotechnology company focused on leveraging our Pfenex Expression Technology^® to improve protein therapies for unmet patient needs. Using the patented Pfenex Expression Technology platform, we have created an advanced pipeline of therapeutic equivalents, vaccines, biologics and biosimilars. Our lead product candidates are PF708, a therapeutic equivalent candidate to Forteo^® (teriparatide) for the treatment of osteoporosis, and our novel anthrax vaccine candidates, Px563L and RPA563, funded through an advanced development contract with the U.S. government. In addition, we are developing hematology/oncology products, including PF743, a recombinant crisantaspase, and PF745, a recombinant crisantaspase with half-life extension technology, in collaboration with Jazz Pharmaceuticals. Furthermore, our pipeline includes biosimilar candidates to Lucentis^® and Neulasta^®.

Company Contact:

Susan A. Knudson

Chief Financial Officer

(858) 352-4324

sknudson@pfenex.com

PFENEX INC.

Consolidated Statements of Operations

	Three Months Ended December 31,					Twelve Months Ended December 31,
(in thousands, except per share data)	2017		2016			2017			2016
Revenue	$	17,909	$	5,471		$	28,780		$	60,194
Cost of revenue		1,675		1,312			5,156			5,313
Gross profit		16,234		4,159			23,624			54,881
Operating expense
Selling, general and administrative		3,701		4,405			17,674			17,340
Research and development		7,217		10,655			31,925			32,418
Total operating expense		10,918		15,060			49,599			49,758
(Loss) income from operations		5,316		(10,901	)		(25,975	)		5,123
Other income, net		2		51			119			149
Net (loss) income before income taxes		5,318		(10,850	)		(25,856	)		5,272
Income tax benefit		172		210			172			209
Net (loss) income	$	5,490	$	(10,640	)	$	(25,684	)	$	5,481
Net (loss) income per common share
Basic	$	0.23	$	(0.45	)	$	(1.09	)	$	0.23
Diluted	$	0.23	$	(0.45	)	$	(1.09	)	$	0.23
Weighted-average common shares used to compute net (loss) income per share
Basic		23,548		23,424			23,503			23,389
Diluted		23,697		23,424			23,503			23,688

PFENEX INC.

Consolidated Balance Sheets

	December 31, 2017			December 31, 2016
	(in thousands)
Assets
Current assets
Cash and cash equivalents	$	57,664		$	81,501
Restricted cash		200			—
Accounts and unbilled receivables, net		1,306			2,822
Income tax receivable		638			717
Other current assets		1,705			1,878
Total current assets		61,513			86,918
Property and equipment, net		7,397			5,246
Other long term assets		133			80
Intangible assets, net		4,771			5,301
Goodwill		5,577			5,577
Total assets	$	79,391		$	103,122
Liabilities and Stockholders’ Equity
Current liabilities
Accounts payable	$	1,905		$	1,284
Accrued liabilities		8,913			9,358
Current portion of deferred revenue		7,421			6,516
Current portion of capital lease obligations		228			54
Total current liabilities		18,467			17,212
Deferred revenue, less current portion		2,742			5,739
Capital lease obligations, less current portion		419			26
Total liabilities		21,628			22,977
Commitments and contingencies
Stockholders’ equity
Preferred stock, $0.001 par value, 10,000,000 shares authorized; no shares issued and outstanding		—			—
Common stock, $0.001 par value, 200,000,000 shares authorized; 23,548,280 and 23,429,501 shares issued and outstanding at December 31, 2017 and December 31, 2016, respectively		24			24
Additional paid-in capital		219,446			216,144
Accumulated deficit		(161,707	)		(136,023	)
Total stockholders’ equity		57,763			80,145
Total liabilities and stockholders’ equity	$	79,391		$	103,122

EX-99.2

NYSE American: PFNX Exhibit 99.2

This presentation, including the accompanying oral 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 future potential of Pfenex's product candidates, including future plans to advance, develop, manufacture and commercialize its product candidates; potential market opportunities for Pfenex’s product candidates; Pfenex's expectation to receive data from the PF708 clinical program in the second quarter of 2018, its expectation to submit an NDA for PF708 in the third quarter of 2018, and the earliest potential commercial US launch of PF708 in the third quarter of 2019; Pfenex’s belief in its cash position to support key development milestones and that it has more than twelve months of cash runway; the expected patent expiration timelines for Lucentis, Forteo, and other branded reference drugs; developments and projections relating to competitors and the industry, including support of the US administration for development of medical countermeasures; expected milestones for Px563L/RPA563, including the timing of the potential Phase 2 study initiation in 2019; the potential procurement contract for Px563L/RPA563 if within ten years of approval; expectations with regard to future milestone and royalty payments from Pfenex’s collaboration with Jazz Pharmaceuticals and that Pfenex is on track to meet key 2018 development milestones under the Jazz collaboration; expectations with respect to Pfenex’s ability to receive future payments under its government contracts; Pfenex’s expectations regarding the use of abbreviated regulatory pathways for the approval of its product candidates, including use of the 505(b)(2) regulatory pathway for PF708 and the 351(k) pathway for PF529; Pfenex's expectations regarding the timing and advancement of clinical trials and the types of future clinical trials for its product candidates; Pfenex's expectation for potential strategic partnership opportunities to maximize value for advancement of PF582, PF529, and its other product candidates; and Pfenex’s belief that that its teriparatide product does not infringe the ’334 patent. 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 Pfenex’s results and expectations to differ materially from those expressed in forward-looking statements include, without limitation, Pfenex’s need for additional funds to support its operations; its success being dependent on PF708, Px563L/RPA563, and its other product candidates; Pfenex’s reliance on its collaboration partner’s performance over which Pfenex does not have control; failure to achieve favorable results in later clinical trials for PF708, Px563L/RPA563, or its other product candidates or receive regulatory approval; delays in its clinical trials or in enrollment of patients in its clinical trials; failure to market PF708, Px563L, or its other product candidates due to the existence of intellectual property protection owned or controlled by a third party and directed to PF708, Px563L/RPA563, or its other product candidates; PF708, Px563L/RPA563 and its 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; Pfenex’s ability to enforce its 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. Pfenex has not received marketing approval for any product candidates, nor has Pfenex launched any products, and there is no certainty that any marketing approvals will be obtained, products launched, or as to the timelines on which they will occur. Further, even if Pfenex obtains marketing approval, Pfenex may be subject to direct legal challenges by the manufacturers of reference products, and Pfenex could be delayed or prevented from launching its product candidates, including PF708, as a result of court orders or as a result of the time necessary to resolve such challenges. Forward-looking statements represent Pfenex’s management’s beliefs and assumptions only as of our March 15, 2018 press release announcing results for the quarter and year ended December 31, 2017. You should read Pfenex’s Annual Report on Form 10-K for the year ended December 31, 2017, including the Risk Factors set forth therein, and its subsequent reports filed with the SEC, including the Risk Factors set forth therein, completely and with the understanding that Pfenex’s actual future results may be materially different from what Pfenex expects. Except as required by law, Pfenex assumes 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. Safe Harbor Statement Pfenex

Clinical stage development and licensing biotechnology company focused on leveraging its Pfenex Expression Technology® to improve protein therapies for unmet patient needs Advanced pipeline of therapeutic equivalents, vaccines, biologics and biosimilars Key pipeline products drive significant near term catalysts and address a >$10B market Seasoned management with extensive competencies from early R&D to regulatory filing, commercialization and partnership management Cash position that supports 2018 key milestones and >12 months runway Overview Pfenex

Pfenex Expression Technology® Platform based on Pseudomonas fluorescens Proprietary Platform 60+ partnerships, including 12 of 15 top pharma companies, resulting in multiple existing royalty-bearing partnerships plus broad wholly-owned portfolio Validated Scalable Therapeutic equivalents, vaccines, antibody fragments, peptides, biosimilars, biobetters and other non-glycosylated proteins Cost Effective Reduced manufacturing requirements drive competitive COGS IP Protected Broad intellectual property protection for platform and products with 22 issued US patents plus substantial know-how and trade secrets Key Differentiating Advantages >80% success rate where other previously-used systems failed Success Rate Rapid, high-quality, high-yield production and analysis of difficult-to-produce proteins Robust

Proprietary Platform Pfenex Expression Technology® Platform based on Pseudomonas fluorescens Robust Analytics State of the art analytical capability ensures high quality & targeted process optimization 3 Advanced Strain Engineering 1 Accelerated Development 2 Integrated and highly automated development approach enables rapid and predictable development Thousands of unique components can be seamlessly integrated to enable strain engineering for protein production Discards traditional, linear and iterative approach, adopts parallel, high throughput method for microbial strain development Ptac 1 lacO RBS RBS lacO Ptac 2 Secretion Leader Secretion Leader RE RE Gene 1 Gene 2 Bi-directional Terminator Synthesized DNA Fragment

Products in Development Pipeline Highlights Existing USG THIRD-PARTY Anthrax Vaccine Contract 5 Years - $911MM3 $1.7B Reference drug 2017 Global sales2 $3.3B $4.5B $0.2B PF7081 Teriparatide (Forteo®) PF582 Ranibizumab (Lucentis®) PF529 Pegfilgrastim (Neulasta®) PF690 Pegaspargase (Oncaspar®) PF743 Recombinant crisantaspase PF745 Recombinant crisantaspase + HLE Preclinical Phase 1 Phase 2 PX563L Adjuvanted Anthrax Vaccine RPA563 Non-Adjuvanted Anthrax Vaccine FULLY FUNDED BY US GOVERNMENT POTENTIAL Procurement REGULATORY submission Initial | CONFIRMATORY Us fda biosimilar Initial advisory meeting Preclinical Analytical Similarity Comparative clinical study

Focused Execution for 2018 Focus on and deliver key programs 1 Selectively expand and maximize our Pfenex Expression Technology® based partnered portfolio 2 Drive development and commercial partnerships 3 Targeted and lean execution 4 Strong base for success Anticipated Key Milestones PF708 (teriparatide equivalent) Q2’18: Immunogenicity study results Q3’18: NDA filing Q3’19: Earliest projected commercial US launch Jazz partnership Continuous advancement of development milestones PX563L/RPA563 (Anthrax vaccine) Potential Phase 2 study initiation 2019 subject to continued funding by BARDA

Strong Financial Position Financials Shares Outstanding 23.6 million as of December 31, 2017 Total Cash $57.7 million as of December 31, 2017 Runway Cash position that supports key 2018 milestones and >12 months runway

Evert (Eef) Schimmelpennink (Aug 2017) CEO, President, Director and Secretary Patrick K. Lucy Chief Business Officer Hubert Chen Chief Medical & Scientific Officer Senior Management Board of Directors Experienced Management New and Established Leadership Aligned to Drive Growth John Taylor Dennis Fenton Philip Schneider Robin Campbell Mayda Mercado Vice President, Quality Susan Knudson (Feb 2018) Chief Financial Officer Jason Grenfell-Gardner (May 2017) Sigurdur Olafsson (May 2017)

Products in Development

Forteo® (teriparatide) rDNA protein and pen combination product Indicated for treatment of high fracture risk osteoporosis 2017 global sales of $1.7B of reference drug4 Pfenex achieved: bioequivalence in healthy subjects high titer protein production competitive cost of goods functionally equivalent pen device Plasma Teriparatide (pg/mL) Products in Development PF708: Therapeutic Equivalent Candidate to Forteo® Mean ± Standard Deviation Time (hr) Bioequivalence results in healthy subjects

Phase 3 osteoporosis trial nearing completion N = 181, randomized 1:1 PF708 and Forteo® Primary endpoint immunogenicity Secondary endpoints pharmacokinetics, bone mineral density and bone turnover markers Phase 3 PK profiles show comparability between PF708 and Forteo® Complements Phase 1 bioequivalence results in healthy subjects Products in Development PF708: Therapeutic Equivalent Candidate to Forteo® Mean ± Standard Deviation Comparable PK results in osteoporosis patients Osteoporosis study design

Products in Development PF708: Therapeutic Equivalent Candidate to Forteo® Pfenex PF708 PF708 (teriparatide [rDNA] injection) Key upcoming program milestones: Primary endpoint of immunogenicity anticipated in Q2’18 505(b)(2) NDA filing expected Q3’18 Earliest projected commercial US launch Q3’19 Strong IP strategy that is expected to support launch at market formation Latest expiry of Orange Book listed teriparatide method of treatment, formulation and/or API patent expected in August 2019 in the US5 Clear commercially succinct pathway with or without A/B rating

Products in Development Orange Book listed patents for Forteo, teriparatide: Formulation Patents US6770623, US7144861, US7550434 (exp 08Dec18) Method of Treatment patents US6977077, US7351414, US7163684 (exp 19Aug19) Device Patent US7517334 (exp 25Mar25) The Pfenex teriparatide product launch is planned after expiry of the listed Formulation and Method of Treatment patents. 2020 2018 2019 Formulation Patent Family Expiry US6770623, US7144861, US7550434 Dec 8 Method Of Treatment Family expiry US6977077, US7351414, US7163684 Aug 19 Q3’18 Anticipated Pfenex NDA Filing Q3’19 Earliest Possible Commercial Launch of Pfenex teriparatide Product

Pfenex granted Jazz worldwide rights to develop and commercialize multiple Pfenex Expression Platform based hematology/oncology product candidates PF743 – recombinant crisantaspase PF745 – recombinant crisantaspase with half-life extension technology Key program highlights: Up to $224.5MM in upfront and potential milestone payments Tiered royalties on net sales $13.5MM development achievement and $5.0MM upfront payment received Q4’17 On target to meet key 2018 development milestones Products in Development Jazz Pharmaceuticals/Pfenex Partnership

Awarded BARDA contract in August 2015 Key program highlights: US Government funds up to $143.5MM of advanced development Potential procurement contract if within 10 years of FDA approval US administration has demonstrated strong support for development of medical countermeasures Current sole sourced contract is valued at close to $1B for a 5 year supply6 Products in Development Px563L/RPA563: Next Generation Anthrax Vaccine Candidates

Anthrax recombinant Protective Antigen (rPA) vaccine candidates: Demonstrated long term stability data from showing maintenance of high purity at 5°C at 40 months Phase 1a Day 70 analysis demonstrated that Px563L and RPA563 were well-tolerated and afforded immunogenicity protection with fewer doses than the currently licensed product Next milestones are triggering of analytical and non-clinical animal study options leading to potential Phase 2 study in 2019 subject to continued funding by BARDA Products in Development Px563L/RPA563: Next Generation Anthrax Vaccine Candidates Toxin Neutralizing Antibody NF50 Results Toxin Neutralizing Antibody NF50 (Geometric Mean Titer ± 95% Confidence Intervals) Time (Day) Time (Day) RPA563 Px563L REGULATORY THRESHOLD nf50 ≥ 0.56

Lucentis® (ranibizumab) main indication neovascular (wet) age-related macular degeneration Global Lucentis® market was $3.3 billion in 20177 Latest known composition of matter expected patent expiry: USA 2020; EU 20228 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® Considering strategic partnership opportunities to advance program and maximize value Pipeline Products PF582: Biosimilar to Lucentis® Best Corrected Visual Acuity Score ± SD PF582 Lucentis

Neulasta® (pegfilgrastim) is indicated for the prevention of febrile neutropenia in patients receiving cytotoxic chemotherapy Neulasta® global sales in 2017: $4.5 billion9 Production process developed and extensive analytical comparability to reference product completed Successfully completed a Biosimilar Initial Advisory Meeting(BIAM) US FDA feedback for PF529 supports the feasibility of development under the 351(k) biosimilar pathway  Considering strategic partnership opportunities to advance program and maximize value Pipeline Products PF529: Biosimilar Candidate to Neulasta®

Proven success developing complex therapeutic proteins with Pfenex Expression Technology® platform Proven Platform Near-term Catalysts Runway PF708 immunogenicity study results Q2’18 and NDA submission Q3’18; Continuous advancement of development milestones in Jazz partnership programs; Potential Phase 2 Anthrax vaccine study initiation 2019 subject to continued funding by BARDA Cash position that supports key 2018 milestones and >12 months runway Strong base for success Positioned well to drive value $ Attractive Portfolio Differentiated portfolio of therapeutic equivalents, vaccines, biologics and biosimilars Scalable Technology Opportunity to select additional partnered and wholly owned products for development up to various stages in cycle

References 1. Being developed via the 505(b)(2) pathway in the United States 2 Based on publicly available 2017 sales data for the third party branded pharmaceutical company 3 https://www.sec.gov/Archives/edgar/data/1367644/000136764416000084/form8kearningsq3q2016.htm 4 Eli Lilly Q4’17 and Full Year 17 Earnings Release dated January 31, 2018 5 Forteo® teriparatide patent, U.S. patent no. 7,351,414 B2; 6,977,077; and 7,163,684 6 https://www.sec.gov/Archives/edgar/data/1367644/000136764416000084/form8kearningsq3q2016.htm 7 Roche Finance Report 2017 and Novartis Annual Report 2017 8 GaBI Online, http://www.gabionline.net/Biosimilars/General/Biosimilars-of-ranibizumab 9 Amgen Annual Report 2017

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