Exhibit 10.47

CERTAIN MATERIAL (INDICATED BY AN ASTERISK) HAS BEEN OMITTED FROM THIS DOCUMENT
PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT. THE OMITTED MATERIAL HAS BEEN
FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

Execution Copy

SECOND AMENDMENT

TO AMENDED AND RESTATED SERVICES AND SUPPLY AGREEMENT

This SECOND AMENDMENT (this “Second Amendment”) dated as of December 17, 2012
(the “Second Amendment Effective Date”), is entered into among Biogen Idec MA
Inc. (“Biogen Idec”), Covella Pharmaceuticals, Inc. (a wholly owned subsidiary
of Santarus, “Covella”), and Santarus, Inc. (“Santarus”) (hereinafter
collectively, the “Parties”).

BACKGROUND

 

A. The Parties entered into that certain Amended and Restated Services and
Supply Agreement, dated as of September 10, 2010, as amended on November 4,
2011, among the Parties (as previously amended and supplemented and as may be
further amended and supplemented, the “Agreement”).

 

B. The Parties desire to amend the term of the Agreement and certain provisions
of the Agreement relating to the Storage Period for the Existing Inventory and
Master Cell Bank.

NOW THEREFORE, in consideration of the foregoing premises and the mutual
covenants herein contained, and for other good and valuable consideration, the
receipt and sufficiency of which are hereby acknowledged, the Parties hereby
agree as follows:

1. Defined terms. Capitalized terms not defined herein shall have the meanings
given to them in the Agreement.

2. Amendment to Section 2.3.1. Section 2.3.1 of the Agreement is hereby amended
to provide that the Storage Period shall be up to and including [***]. This
Section is further amended to provide that Santarus shall pay Biogen Idec a
total fee of $[***] for storage of [***] Material and [***] from the Second
Amendment Effective Date until expiration of the Storage Period (“Storage Fee”).
The Storage Fee shall be paid by Santarus to Biogen Idec in [***] installments
of $[***] each, beginning on [***] and [***] thereafter, and shall be paid to
Biogen Idec within thirty (30) days of Santarus’ receipt of an invoice from
Biogen Idec.

3. Amendment to Section 10.1. Section 10.1 of the Agreement is hereby amended
and restated in its entirety to read as follows:

10.1 The term of this Agreement shall commence as of the Effective Date and,
subject to earlier termination in accordance with this Section 10, shall
continue in force until the sixth (6th) anniversary of the Effective Date,
unless extended in writing by the mutual written agreement of the Parties.

 

 

*** Certain information on this page has been omitted and filed separately with
the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

--------------------------------------------------------------------------------

Execution Copy

 

4. General. Except as amended by this Second Amendment, the terms and conditions
of the Agreement shall remain in full force and effect.

5. Governing Law. This Second Amendment shall be governed by and construed in
accordance with the laws of California, without regard to the conflicts of law
principles that would provide for application of the law of a jurisdiction other
than California and excluding the United Nations Convention on Contracts for the
International Sales of Goods.

6. Entire Agreement. This Second Amendment, the Agreement and the exhibits,
schedules and addendums thereto, sets forth the entire agreement of the Parties
with respect to the subject matter contained herein, and may not be modified or
amended except by a written agreement executed by the Parties.

7. Enforceability. If any provision of this Second Amendment shall be found by a
court to be void, invalid or unenforceable, the same shall either be reformed to
comply with applicable law or stricken if not so conformable, so as not to
affect the validity or enforceability of this Second Amendment.

[remainder of page intentionally blank]

 

2

--------------------------------------------------------------------------------

Execution Copy

 

IN WITNESS WHEREOF, the Parties hereto have executed this Second Amendment
through their duly authorized representatives as of the date first set forth
above.

 

BIOGEN IDEC MA INC.     SANTARUS, INC. By:  

/s/John Cox

    By:  

/s/ Gerald T. Proehl

Name:   John Cox     Name:   Gerald T. Proehl Title:   Executive Vice President
    Title:   President and Chief Executive Officer COVELLA PHARMACEUTICALS, INC.
      By:  

/s/ Gerald T. Proehl

      Name:   Gerald T. Proehl       Title:   President      

[SIGNATURE PAGE TO SECOND AMENDMENT TO AMENDED AND RESTATED SERVICES AND SUPPLY
AGREEMENT]