This Amendment No. 4 (the “Amendment”) amends and supplements the
Solicitation/Recommendation Statement of Schedule 14D-9 (as amended or supplemented from time to time, the “Schedule 14D-9”) filed by Pfenex Inc., a
Delaware corporation (“Pfenex” or the “Company”), with the United States Securities Exchange Commission (the “SEC”) on August 31, 2020, relating to the tender offer (the
“Offer”) by Pelican Acquisition Sub, Inc., a Delaware corporation (“Acquisition Sub”) and a wholly owned subsidiary of Ligand Pharmaceuticals Incorporated, a Delaware corporation (“Ligand”), to
purchase all of the outstanding shares of common stock of Pfenex, par value $0.001 per share (the “Shares”), for a purchase price of (i) $12.00 per Share, in cash (the “Cash Portion”), and (ii) a non-transferrable contractual contingent value right per Share (a “CVR”), pursuant to the Contingent Value Rights Agreement (as it may be amended from time to time, the “CVR
Agreement”), to receive a contingent payment of $2.00 in cash upon the achievement of a specified milestone as set forth in the CVR Agreement (the “CVR Portion, and together with the Cash Portion, the “Offer
Price”), without interest, subject to any required tax withholding and upon the terms and subject to the conditions set forth in Acquisition Sub’s Offer to Purchase, dated August 31, 2020 (the “Offer to
Purchase”), and in the related Letter of Transmittal (“Letter of Transmittal”), which, together with the Offer to Purchase and other related materials, as each may be amended, supplemented, or otherwise modified from time
to time in accordance with the Agreement and Plan of Merger, dated as of August 10, 2020, by and among Ligand, Acquisition Sub, and Pfenex (the “Merger Agreement”), constitute the “Offer.” The Offer is
described in the Tender Offer Statement on Schedule TO (as amended or supplemented from time to time, the “Schedule TO”) filed by Ligand and Acquisition Sub filed with the SEC on August 31, 2020. The Offer to Purchase and the
Letter of Transmittal are filed as Exhibits (a)(1)(A) and (a)(1)(B), respectively, to the Schedule 14D-9 and are incorporated herein by reference.
Except to the extent specifically provided in this Amendment, the information set forth in the Schedule 14D-9 remains
unchanged. Capitalized terms used herein but not otherwise defined shall have the meanings ascribed to them in the Schedule 14D-9. This Amendment is being filed to reflect certain updates as set forth below.
Item 8 of the Schedule 14D-9 is hereby amended as follows:
Item 8. Additional Information.
Following the section entitled “Item 8. Additional Information—Legal Proceedings” and before the section entitled “Item 8. Additional
Information—Cautionary Statement Regarding Forward-Looking Statements” a new section is added as follows:
Expiration of the Offer.
At midnight, New York City time, on September 29, 2020, the Offer expired. Ligand, Acquisition Sub and Pfenex were advised by the depositary
agent for the Offer, that as of the expiration of the Offer, a total of 24,744,327 Shares (not including 2,847,227 Shares tendered by notice of guaranteed delivery for which Shares have not yet been delivered in satisfaction of such guarantee),
representing approximately 72% of the Company’s then-outstanding Shares, had been validly tendered (and not validly withdrawn) pursuant to the Offer. The number of Shares validly tendered and not validly withdrawn pursuant to the Offer
satisfied the minimum tender condition set forth in the Merger Agreement, and all other conditions to the Offer were satisfied or waived. Immediately after the expiration of the Offer, Acquisition Sub irrevocably accepted for payment all Shares that
were validly tendered and not validly withdrawn prior to the expiration of the Offer and will promptly pay for all such Shares.