<PAGE>
                                                                   EXHIBIT 10.47


February 27, 2004


Re:   ACCELERATION BENEFITS AGREEMENT

Dear Emile:

This letter will memorialize our agreement (the "Agreement") as to certain
acceleration benefits to which you will be entitled upon termination of your
employment by Epimmune Inc. (the "Company") under the circumstances described in
this Agreement.

We agree that you are employed by the Company as an "at-will" employee and that
either you or the Company has the right at any time to terminate your employment
with the Company, with or without cause or advance notice, for any reason or for
no reason.

For purposes of this Agreement, the following terms will have the meanings set
forth below:

      "BENEFIT" means any benefit received or to be received by you pursuant to
      this Agreement.

      "CAUSE" means (i) willful misconduct by you including, but not limited to,
      dishonesty which materially and adversely reflects upon your ability to
      perform your duties for the Company, (ii) your conviction of, or the entry
      of a pleading of guilty or nolo contendere by you to, any crime involving
      moral turpitude or any felony, (iii) fraud, embezzlement or theft against
      the Company, (iv) a material breach by you of any material provision of
      the Proprietary Information and Inventions Agreement between you and the
      Company, or (v) your willful and habitual failure to attend to your duties
      as assigned by the Board of Directors or officers of the Company to whom
      you report and, in the case of clauses (iv) and (v) above, which breach,
      misconduct or non-performance is not cured by you within thirty (30) days
      after you receive written notice from the Company of such breach,
      misconduct or non-performance.

      "CHANGE IN CONTROL" means (i) a dissolution or liquidation of the Company;
      (ii) a sale or other disposition of all or substantially all of the assets
      of the Company; (iii) a merger or consolidation in which the Company is
      not the surviving corporation and in which beneficial ownership of
      securities of the Company representing at least fifty percent (50%) of the
      combined voting power entitled to vote in the election of Directors has
      changed; (iv) an acquisition by any person, entity or group within the
      meaning of Section 13(d) or 14(d) of the Securities Exchange Act, or any
      comparable successor provisions (excluding any employee benefit plan, or
      related trust, sponsored or maintained by the Company or subsidiary of the
      Company or other entity controlled by the Company) of the beneficial
      ownership (within the meaning of Rule 13d-3 promulgated under the Exchange
      Act, or comparable successor rule) of securities of the Company
      representing at least fifty percent


                                       1
<PAGE>
      (50%) of the combined voting power entitled to vote in the election of
      Directors.

      "COMPANY" for the purposes of this Agreement shall include the Company's
      successor if a Change in Control occurs.

      "GOOD REASON" means termination by you of your employment with the Company
      upon not less than thirty (30) days' prior written notice to the Company
      (to allow the Company to remedy any basis for Good Reason termination) as
      a result of (i) a substantial diminution in the scope of your duties and
      authority within the Company which results in the assignment of duties and
      responsibilities of materially lesser status, dignity and character than
      your duties and responsibilities on the date of execution of this
      Agreement, which is not the result of your failure to attend to and/or
      successfully complete your duties and responsibilities, (ii) any reduction
      in your base salary as initially set forth herein or as may be increased
      from time to time, or (iii) relocation of your office, without your
      consent, to a location that is more than thirty (30) miles from the
      Company's current corporate headquarters.

If, within 365 days following the occurrence of a Change in Control, your
employment is terminated by the Company without Cause or you voluntarily
terminate your employment for Good Reason, then with respect to any Company
stock options granted to you after December 9, 2003, the vesting and
exercisability of such stock options will be immediately accelerated as to 100%
of the then unvested shares subject to such stock options, so that all such
unvested shares will be immediately vested and exercisable as of the date of
your termination.

In the event that any Benefit provided for in this Agreement would (i)
constitute "parachute payments" within the meaning of Section 280G of the
Internal Revenue Code of 1986, as amended (the "Code"), and (ii) but for this
subsection would be subject to the excise tax imposed by Section 4999 of the
Code (the "Excise Tax"), then, the Benefit to which you are entitled pursuant to
this Agreement shall be either:

   (a)  Provided to you in full, or

   (b)  Provided  to you at such  lesser  extent  that  would  result  in no
   portion of the Benefit being subject to the Excise Tax,

whichever of the foregoing amounts, when taking into account applicable federal,
state, local and foreign income and employment taxes, the Excise Tax, and any
other applicable taxes, results in the receipt by you, on an after tax basis, of
the greatest amount of the Benefit, notwithstanding that all or some portion of
the Benefit may be taxable under the Excise Tax. Unless you and the Company
otherwise agree in writing, any determination required under this subsection
shall be made in writing in good faith by an accountant selected by you. In the
event of a reduction of the Benefit under this Agreement or otherwise provided
to you, you shall be given the choice of which to reduce. For purposes of making
the calculations required by this subsection, the accountant that you select may
make reasonable assumptions and approximations concerning applicable taxes and
may rely on reasonable, good faith interpretations concerning the application of
the Code, and other applicable legal authority. You and the Company shall
furnish your accountant such information and documents as he may reasonably
request in order to make a determination under this subsection.


                                       2
<PAGE>
This Agreement may be changed or terminated only upon the mutual written consent
of the Company and you. Nothing in this Agreement will prevent or limit your
continuing or future participation in any benefit, bonus, incentive or other
plans, programs, policies or practices provided by the Company and for which you
may otherwise qualify, nor will anything herein limit or otherwise affect such
rights as you may have under any stock option or other agreements with the
Company.

If either party hereto brings any action to enforce such party's rights
hereunder, the prevailing party in any such action will be entitled to recover
such party's reasonable attorneys' fees and costs incurred in connection with
such action.

This Agreement constitutes the entire agreement between you and the Company. It
is entered into without reliance on any promise or representation other than
those expressly contained herein. All questions concerning the construction,
validity and interpretation of this Agreement will be governed by the law of the
State of California.

Very truly yours,

EPIMMUNE INC.

/s/ Robert De Vaere
--------------------------------------
Robert De Vaere
Chief Financial Officer

Agreed and Accepted:



/s/ Emile Loria
--------------------------------------
Dr. Emile Loria

Dated:  February 27, 2004


                                       3