This Amendment No. 3 (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 3 of the Schedule 14D-9 is hereby amended as follows:
Item 3. Past Contacts, Transactions, Negotiations and Agreements.
On page 6, the paragraph under the heading “Item 3. Past Contacts, Transactions, Negotiations and Agreements—Arrangements with Directors and
Executive Officers of Pfenex—Interests of Certain Persons.” is hereby amended and restated in its entirety as follows:
The executive
officers of Pfenex and the members of the Board may have interests in the Offer, the Merger and the other transactions contemplated by the Merger Agreement that are different from, or in addition to, the interests of Pfenex’s stockholders,
generally. These interests may create potential conflicts of interest. Those interests include: (i) accelerated vesting and cash out of outstanding Company Options in connection with the Merger; (ii) in the case of executive officers,
enhanced severance benefits in the event of certain qualifying terminations of employment in connection with the closing of the Merger; and (iii) indemnification rights and benefits in their capacities as directors and officers of Pfenex. The
Board was aware of these interests and considered them, among other matters, in approving the Merger Agreement and the transactions contemplated thereby, as more fully discussed below in this “Item 3. Past Contacts, Transactions,
Negotiations and Agreements.” and “Item 4. The Solicitation or Recommendation—Recommendation of the Board.” For the avoidance of doubt, Ligand’s proposals or indications of interest did not address or mention
management retention programs.
Item 4 of the Schedule 14D-9 is hereby amended as follows:
Item 4. The Solicitation or Recommendation.
On page 16, the paragraph beginning with “On April 2, 2020,” under the heading “Item 4. The Solicitation or
Recommendation—Background of the Merger.” is hereby amended and restated as follows:
On April 2, 2020, Pfenex, as a result of a
conflict of interest with its existing financial advisor and in consultation with and at the direction of the Board, engaged a second financial advisor to assist with its existing strategy of exploring potential acquisitions. The existing financial
advisor was conflicted as a result of the fact that it was also representing a company that Pfenex was considering pursuing in an acquisition transaction. For the avoidance of doubt, neither of such financial advisors were, or were affiliated with,
William Blair.
On page 18, the paragraph beginning with “On May 15, 2020,” under the heading “Item 4. The Solicitation or
Recommendation—Background of the Merger.” is hereby amended and restated as follows:
On May 15, 2020, the Board held a special meeting,
which was attended by representatives of Wilson Sonsini. Mr. Schimmelpennink discussed with the other members of the Board the recent interactions with Ligand. Representatives of Wilson Sonsini provided the Board with a presentation of its
fiduciary duties in the context of its receipt of such offer. The Board engaged in a discussion of the financial terms of the offer from Ligand, along with the assumptions contained in the offer. The Board discussed whether the offer was
sufficiently attractive as to engage with Ligand, and compared the potential of engaging in such discussion—and ultimately selling Pfenex—with continuing to operate as a standalone entity. In particular, the Board discussed the impact of
the delay in receipt