Exhibit 4.12

COMMON STOCK WARRANT

NEITHER
THIS WARRANT NOR THE SECURITIES ISSUABLE UPON EXERCISE OF THIS WARRANT HAVE BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED. NO SALE OR DISPOSITION MAY BE EFFECTED EXCEPT
IN COMPLIANCE WITH RULE 144 UNDER SAID ACT OR WITHOUT AN EFFECTIVE REGISTRATION STATEMENT RELATED THERETO OR AN OPINION OF COUNSEL FOR THE HOLDER, REASONABLY SATISFACTORY TO THE COMPANY, THAT SUCH
REGISTRATION IS NOT REQUIRED UNDER THE ACT OR RECEIPT OF A NO-ACTION LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION.

WARRANT TO PURCHASE154,639SHARES OF COMMON STOCK

Dated:March 14, 2008

THIS
CERTIFIES THAT, for value received, Oxford Finance Corporation, ("Holder") is entitled to subscribe for and purchase154,639shares
of the fully paid and non-assessable Common Stock ("the Shares") of Metabasis Therapeutics, Inc., a Delaware corporation (the "Company"), at the Warrant Price (as hereinafter
defined), subject to the provisions and upon the terms and conditions
hereinafter set forth. As used herein, the term "Common Stock" shall mean the Company's presently authorized Common Stock, and any stock into which such Common Stock may hereafter be exchanged.

1.Warrant Price.The Warrant Price shall initially be $1.94per
share, subject to adjustment as provided in Section 6 below.

2.Conditions to Exercise.The purchase right represented by this Warrant may be exercised at any time, or from
time to time, in whole or in part during the term commencing on the date hereof and ending



provided, however, that in the event of an "Acquisition" as defined in Section 3(e)(iv), this Warrant shall terminate at an earlier date pursuant
to the terms of Section 3(e)(i)-(iii), as appropriate.

3.Method of Exercise; Payment; Issuance of Shares; Issuance of New Warrant.



1

---





X

=

Y (A-B)A






2

---





4.Representations and Warranties of Holder and Restrictions on Transfer Imposed by the Securities Act of 1933.



3

---





| |  |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
| |  | -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| |  | THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, AND MAY NOT BE TRANSFERRED UNLESS COVERED BY AN EFFECTIVE REGISTRATION STATEMENT UNDER SAID ACT, A "NO ACTION" LETTER FROM THE
SECURITIES AND EXCHANGE COMMISSION WITH RESPECT TO SUCH TRANSFER, A TRANSFER MEETING THE REQUIREMENTS OF RULE 144 OF THE SECURITIES AND EXCHANGE COMMISSION, OR (IF REASONABLY REQUIRED BY THE COMPANY) AN OPINION OF COUNSEL REASONABLY SATISFACTORY TO
THE ISSUER TO THE EFFECT THAT ANY SUCH TRANSFER IS EXEMPT FROM SUCH REGISTRATION.



4

---





5.Condition of Transfer or Exercise of Warrant.It shall be a condition to any transfer or exercise of this
Warrant that at the time of such transfer or exercise, the Holder shall provide the Company with a representation in writing that the Holder or transferee is acquiring this Warrant and the shares of
Common Stock to be issued upon exercise hereof, for investment purposes only and not with a view to any sale or distribution, or will provide the Company with a statement of pertinent facts covering
any proposed distribution. As a further condition to any transfer of this Warrant or any or all of the shares of Common Stock issuable upon exercise of this Warrant, other than a transfer registered
under the Act, the Company must have received a legal opinion, in form and substance reasonably satisfactory to the Company and its counsel, reciting the pertinent circumstances surrounding the
proposed transfer and stating that such transfer is exempt from the registration and prospectus delivery requirements of the Act. Each certificate evidencing the shares issued upon exercise of the
Warrant or upon any transfer of the shares (other than a transfer registered under the Act or any subsequent transfer of shares so registered) shall, at the Company's option, contain a legend in form
and substance satisfactory to the Company and its counsel, restricting the transfer of the shares to sales or other dispositions exempt from the requirements of the Act.

As
further condition to each transfer, the Holder shall surrender this Warrant to the Company and the transferee shall receive and accept a Warrant, of like tenor and date, executed by
the Company.

6.Stock Fully Paid; Reservation of Shares.All Shares, which may be issued upon the exercise of the rights
represented by this Warrant, will, upon issuance, be fully paid and non-assessable, and free from all taxes, liens, and charges with respect to the issue thereof other than any such taxes,
liens or changes created by or imposed upon the Holder through no action by the Company. During the period within which the rights represented by this Warrant may be exercised, the Company will at all
times have authorized, and reserved for issuance upon exercise of the purchase rights evidenced by this Warrant, a sufficient number of shares of its Common Stock to provide for the exercise of the
rights represented by this Warrant.

7.Adjustment for Certain Events.In the event of changes in the outstanding Common Stock by reason of stock
dividends, split-ups, recapitalizations, reclassifications, mergers, consolidations, combinations or exchanges of shares, separations, reorganizations, liquidations, or the like, the
number and class of shares available under the Warrant in the aggregate and the Warrant Price shall be correspondingly adjusted, as appropriate, by the Board of Directors of the Company. The
adjustment shall be such as will give the Holder of this Warrant upon exercise for the same aggregate Warrant Price the total number, class and kind of shares as it would have owned had the Warrant
been exercised prior to the event and had it continued to hold such shares until after the event requiring adjustment.

8.Notice of Adjustments.Whenever any Warrant Price shall be adjusted pursuant to Section 7 hereof, the
Company shall prepare a certificate signed by its chief financial officer setting forth, in

5

---



reasonable
detail, the event requiring the adjustment, the amount of the adjustment, the method by which such adjustment was calculated, and the Warrant Price and number of shares issuable upon
exercise of the Warrant after giving effect to such adjustment, and shall cause copies of such certificate to be mailed (by certified or registered mail, return receipt required, postage prepaid)
within 30 days of such adjustment to the Holder of this Warrant as set forth in Section 18 hereof.

9."Market Stand-Off" Agreement.Holder hereby agrees that for a period of up to 180 days (or
such longer period after the expiration of such 180-day period, as the underwriters or the Company shall request in order to facilitate compliance with NASD Rule 2711 or NYSE Member
Rule 472 or any successor or similar rule or regulation) following the effective date of any registration statement of the Company covering common stock (or other securities) to be sold on its
behalf of the Company in an underwritten public offering, it will not, to the extent requested by the Company and any underwriter, sell or otherwise transfer or dispose of (other than to designees or
transferees who agree to be similarly bound) any of the Shares at any time during such period except common stock included in such registration; provided, however, that all officers and directors of
the Company who hold securities of the Company or options to acquire securities of the Company and all other persons with registration rights enter into similar agreements.

10.Transferability of Warrant.This Warrant is transferable on the books of the Company at its principal office
by the registered Holder hereof upon surrender of this Warrant properly endorsed, subject to compliance with Section 5 and applicable federal and state securities laws. The Company shall issue
and deliver to the transferee a new Warrant representing the Warrant so transferred. Upon any partial transfer, the Company will issue and deliver to Holder a new Warrant with respect to the Warrant
not so transferred. Holder shall not have any right to transfer any portion of this Warrant to any direct competitor of the Company.

11.No Fractional Shares.No fractional share of Common Stock will be issued in connection with any exercise
hereunder, but in lieu of such fractional share the Company shall make a cash payment therefor upon the basis of the Warrant Price then in effect.

12.Charges, Taxes and Expenses.Issuance of certificates for shares of Common Stock upon the exercise of this
Warrant shall be made without charge to the Holder for any United States or state of the United States documentary stamp tax or other incidental expense with respect to the issuance of such
certificate, all of which taxes and expenses shall be paid by the Company, and such certificates shall be issued in the name of the Holder.

13.No Shareholder Rights Until Exercise.This Warrant does not entitle the Holder hereof to any voting rights
or other rights as a shareholder of the Company prior to the exercise hereof.

14.Registry of Warrant.The Company shall maintain a registry showing the name and address of the registered
Holder of this Warrant. This Warrant may be surrendered for exchange or exercise, in accordance with its terms, at such office or agency of the Company, and the Company and Holder shall be entitled to
rely in all respects, prior to written notice to the contrary, upon such registry.

15.Loss, Theft, Destruction or Mutilation of Warrant.Upon receipt by the Company of evidence reasonably
satisfactory to it of the loss, theft, destruction or mutilation of this Warrant, and, in the case of loss, theft, or destruction, of indemnity reasonably satisfactory to it, and, if mutilated, upon
surrender and cancellation of this Warrant, the Company will execute and deliver a new Warrant, having terms and conditions substantially identical to this Warrant, in lieu hereof.

16.Miscellaneous.



6

---





17.No Impairment.Except and to the extent as waived or consented to by the Holder, the Company will not, by
amendment of its Certificate of Incorporation or through any reorganization, transfer of assets, consolidation, merger, dissolution, issue or sale of securities or any other voluntary action, avoid or
seek to avoid the observance or performance of any of the terms to be observed or performed hereunder by the Company, but will at all times in good faith assist in the carrying out of all the
provisions of this Warrant and in the taking of all such action as may be necessary or appropriate in order to protect the exercise rights of the Holder against impairment.

18.Addresses.Any notice required or permitted hereunder shall be in writing and shall be mailed by overnight
courier, registered or certified mail, return receipt required, and postage pre-paid, or otherwise delivered by hand or by messenger, addressed as set forth below, or at such other address
as the Company or the Holder hereof shall have furnished to the other party.

If to the Company:

Metabasis Therapeutics, Inc.11119 North Torrey Pines RoadLa Jolla, CA 92037Attn: Chief Financial OfficerIf to the Holder:

Oxford Finance Corporation133 N. Fairfax StreetAlexandria, VA 22314Attn: Timothy A. Lex, Chief Operating Officer


IN
WITNESS WHEREOF, the Company has caused this Warrant to be executed by its officers thereunto duly authorized.

Dated
as of March 14, 2008.

METABASIS
THERAPEUTICS, INC.

|By:    |  |  |  | 
|------ |  |  |  | 
|       |  |  |  | 
|Name:  |  |  |  | 
|       |  |  |  | 
|Title: |  |  |  | 
|       |  |  |  | 

7

---



NOTICE OF EXERCISE

|TO: |  |  |  | 
|--- |  |  |  | 
|    |  |  |  | 
|    |  |  |  | 
|    |  |  |  | 

1.     The
undersigned, Oxford Finance Corporation ("Holder") elects to acquire shares of the Common Stock of                        (the
"Company"), pursuant to the terms of the Stock
Purchase Warrant dated March 14,2008 (the "Warrant").

2.     The
Holder exercises its rights under the Warrant as set forth below:



3.     The
Holder surrenders the Warrant with this Notice of Exercise.

4.     The
Holder represents that it is acquiring the aforesaid shares of Common Stock for investment and not with a view to or for resale in connection with, distribution and
that the Holder has no present intention of distributing or reselling the shares.

5.     Please
issue a certificate representing the shares of Common Stock in the name of the Holder or in such other name as is specified below:

Name:Address:Taxpayer I.D.:


|
|

|       |  | Oxford Finance Corporation |  | 
|------ |  | -------------------------- |  | 
|By:    |  |                            |  | 
|       |  |                            |  | 
|Name:  |  |                            |  | 
|       |  |                            |  | 
|Title: |  |                            |  | 
|       |  |                            |  | 
|Date:  |  |                            |  | 
|       |  |                            |  | 

8

---



QuickLinks