Document:

<PAGE>
                                                                Exhibit 10.45

                            INDEMNIFICATION AGREEMENT

     THIS AGREEMENT is made and entered into this 27th day of July 2001 by and
between MICROCIDE PHARMACEUTICALS, INC., a Delaware corporation (the
"Corporation"), and DAVID SCHNELL ("Schnell").

                                    RECITALS

     WHEREAS, Schnell was formerly a director of the Corporation;

     WHEREAS, after resigning as a director of the Corporation, Schnell, in his
capacity as Member of Prospect Management Co., LLC, the General Partner of
Prospect Venture Partners L.P., and Member of Prospect Management Co. II, LLC,
the General Partner of Prospect Venture Partners II (collectively, "Prospect"),
has, on behalf of Prospect and other potential investors, proposed, arranged and
participated in negotiations for a $60,000,000 preferred stock financing and the
transactions contemplated thereby (the "Financing") for the Corporation; and

     WHEREAS, in order to induce Schnell, in his various capacities with
Prospect, and Prospect to participate in the Financing, the Corporation has
determined and agreed to enter into this Agreement with Schnell;

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

                                    AGREEMENT

     1. Indemnity of Schnell. Subject only to the exclusions set forth in
Section 2 hereof, the Corporation hereby agrees to hold harmless and indemnify
Schnell against any and all expenses (including attorneys' fees), witness fees,
damages, judgments, fines and amounts paid in settlement and any other amounts
that Schnell directly or indirectly suffers or incurs or may otherwise become
subject at any time and which arise directly or indirectly from or as a direct
or indirect result of, or are directly or indirectly connected with any claim or
claims made against or by him in connection with any threatened, pending or
completed action, suit or proceeding, whether civil, criminal, arbitrational,
administrative or investigative (including an action by or in the right of the
Corporation) to which Schnell is, was or at any time becomes a party, or is
threatened to be made a party, by reason of the fact that Schnell was a director
of the Corporation and/or, either in his various capacities with Prospect or
otherwise, proposed, arranged, negotiated and/or participated in the Financing.

     2. Limitations on Additional Indemnity. No indemnity pursuant to Section 1
hereof shall be paid by the Corporation:

          (a) on account of Schnell's conduct that is established by a final
     judgment as knowingly fraudulent or deliberately dishonest or that
     constituted willful misconduct;

          (b) for which payment is actually made to Schnell under a valid and
     collectible insurance policy or under a valid and enforceable indemnity
     clause, bylaw or agreement, except in respect of any excess beyond payment
     under such insurance, clause, bylaw or agreement;

<PAGE>

          (c) if indemnification is not lawful; or

          (d) in connection with any proceeding (or part thereof) initiated by
     Schnell, or any proceeding by Schnell against the Corporation or its
     directors, officers, employees or other agents, unless (i) such
     indemnification is expressly required to be made by law, (ii) the
     proceeding was authorized by the Board of Directors of the Corporation, or
     (iii) the proceeding is initiated pursuant to Section 7 hereof.

     3. Continuation of Indemnity. All agreements and obligations of the
Corporation contained herein shall continue so long as Schnell shall be subject
to any possible claim or threatened, pending or completed action, suit or
proceeding, whether civil, criminal, arbitrational, administrative or
investigative, by reason of the fact that Schnell was serving in the capacity
referred to in the recitals section of this Agreement.

     4. Partial Indemnification. Schnell shall be entitled under this Agreement
to indemnification by the Corporation for a portion of the expenses (including
attorneys' fees), witness fees, damages, judgments, fines and amounts paid in
settlement and any other amounts that Schnell directly or indirectly suffers or
incurs or may otherwise become subject at any time and which arise directly or
indirectly from or as a direct or indirect result of, or are directly or
indirectly connected with any action, suit or proceeding referred to in Section
1 hereof even if not entitled hereunder to indemnification for the total amount
thereof, and the Corporation shall indemnify Schnell for the portion thereof to
which Schnell is entitled.

     5. Notification and Defense of Claim. Not later than seven (7) business
days after receipt by Schnell of notice of the commencement of any action, suit
or proceeding, Schnell will, if a claim in respect thereof is to be made against
the Corporation under this Agreement, notify the Corporation of the commencement
thereof; but the omission so to notify the Corporation will not relieve it from
any liability which it may have to Schnell otherwise than under this Agreement.
With respect to any such action, suit or proceeding as to which Schnell notifies
the Corporation of the commencement thereof:

          (a) the Corporation will be entitled to participate therein at its own
     expense;

          (b) except as otherwise provided below, the Corporation may, at its
     option and jointly with any other indemnifying party similarly notified and
     electing to assume such defense, assume the defense thereof, with counsel
     reasonably satisfactory to Schnell. After notice from the Corporation to
     Schnell of its election to assume the defense thereof, the Corporation will
     not be liable to Schnell under this Agreement for any legal or other
     expenses subsequently incurred by Schnell in connection with the defense
     thereof except for reasonable costs of investigation or otherwise as
     provided below. Schnell shall have the right to employ separate counsel in
     such action, suit or proceeding but the fees and expenses of such counsel
     incurred after notice from the Corporation of its assumption of the defense
     thereof shall be at the expense of Schnell unless (i) the employment of
     counsel by Schnell has been authorized by the Corporation, (ii) Schnell
     shall have reasonably concluded, and so notified the Corporation, that
     there is an actual conflict of interest between the Corporation and Schnell
     in the conduct of the defense of such action or (iii) the Corporation shall
     not in fact have employed counsel to assume the defense of such action, in
     each of which cases the fees and expenses of Schnell's separate counsel
     shall be at the expense of the Corporation. The Corporation shall not be
     entitled to assume the defense of any action, suit or proceeding brought by
     or on behalf of the Corporation or as to which Schnell shall have made the
     conclusion provided for in clause (ii) above; and

                                        2

<PAGE>

          (c) the Corporation shall not be liable to indemnify Schnell under
     this Agreement for any amounts paid in settlement of any action or claim
     effected without its written consent, which shall not be unreasonably
     withheld. The Corporation shall be permitted to settle any action except
     that it shall not settle any action or claim in any manner which would
     impose any penalty or limitation on Schnell without Schnell's written
     consent, which may be given or withheld in Schnell's sole discretion.

     6. Expenses. The Corporation shall advance, prior to the final disposition
of any proceeding, promptly following request therefor, all expenses incurred by
Schnell in connection with such proceeding upon receipt of an undertaking by or
on behalf of Schnell to repay said amounts if it shall be determined ultimately
that Schnell is not entitled to be indemnified under the provisions of this
Agreement or otherwise.

     7. Enforcement. Any right to indemnification or advances granted by this
Agreement to Schnell shall be enforceable by or on behalf of Schnell in any
court of competent jurisdiction if (a) the claim for indemnification or advances
is denied, in whole or in part, or (b) no disposition of such claim is made
within ninety (90) days of request therefor. Schnell, in such enforcement
action, if successful in whole or in part, shall be entitled to be paid also the
expense of prosecuting his claim. It shall be a defense to any action for which
a claim for indemnification is made under Section 1 hereof (other than an action
brought to enforce a claim for expenses pursuant to Section 6 hereof, provided
that the required undertaking has been tendered to the Corporation) that Schnell
is not entitled to indemnification because of the limitations set forth in
Section 2 hereof. Neither the failure of the Corporation (including its Board of
Directors or its stockholders) to have made a determination prior to the
commencement of such enforcement action that indemnification of Schnell is
proper in the circumstances, nor an actual determination by the Corporation
(including its Board of Directors or its stockholders) that such indemnification
is improper shall be a defense to the action or create a presumption that
Schnell is not entitled to indemnification under this Agreement or otherwise.

     8. Subrogation. In the event of payment under this Agreement, the
Corporation shall be subrogated to the extent of such payment to all of the
rights of recovery of Schnell, who shall execute all documents required and
shall do all acts that may be necessary to secure such rights and to enable the
Corporation effectively to bring suit to enforce such rights.

     9. Non-Exclusivity of Rights. The rights conferred on Schnell by this
Agreement shall not be exclusive of any other right which Schnell may have or
hereafter acquire under any statute, provision of the Corporation's charter
documents, agreement, vote of stockholders or directors, or otherwise.

     10. Survival of Rights.

          (a) The rights conferred on Schnell by this Agreement shall inure to
     the benefit of Schnell's heirs, executors and administrators.

          (b) The Corporation shall require any successor (whether direct or
     indirect, by purchase, merger, consolidation or otherwise) to all or
     substantially all of the business or assets of the Corporation, expressly
     to assume and agree to perform this Agreement in the same manner and to the
     same extent that the Corporation would be required to perform if no such
     succession had taken place.

                                       3

<PAGE>

     11. Severability. Each of the provisions of this Agreement is a separate
and distinct agreement and independent of the others, so that if any provision
hereof shall be held to be invalid for any reason, such invalidity or
unenforceability shall not affect the validity or enforceability of the other
provisions hereof. Furthermore, if this Agreement shall be invalidated in its
entirety on any ground, then the Corporation shall nevertheless indemnify
Schnell to the fullest extent provided by any applicable law.

     12. Governing Law. This Agreement shall be interpreted and enforced in
accordance with the laws of the State of Delaware.

     13. Amendment and Termination. No amendment, modification, termination or
cancellation of this Agreement shall be effective unless in writing signed by
both parties hereto.

     14. Identical Counterparts. This Agreement may be executed in one or more
counterparts, each of which shall for all purposes be deemed to be an original
but all of which together shall constitute but one and the same Agreement. Only
one such counterpart need be produced to evidence the existence of this
Agreement.

     15. Headings. The headings of the sections of this Agreement are inserted
for convenience only and shall not be deemed to constitute part of this
Agreement or to affect the construction hereof.

     16. Notices. All notices, requests, demands and other communications
hereunder shall be in writing and shall be deemed to have been duly given upon
delivery if delivered by hand to the party to whom such communication was
directed or upon the third business day after the date on which such
communication was mailed if mailed by certified or registered mail with postage
prepaid:

          (a) If to Schnell, at the address indicated on the signature page
     hereof.

          (b) If to the Corporation, to:

              MICROCIDE PHARMACEUTICALS, INC.
              850 Maude Avenue
              Mountain View, California 94043

or to such other address as may have been furnished to Schnell by the
Corporation.

                                       4

<PAGE>

     17. This Agreement supercedes and terminates any previous agreement between
Schnell and the Corporation regarding the subject matter hereof.

                  [REMAINDER OF PAGE LEFT BLANK INTENTIONALLY.]

                                       5

<PAGE>

IN WITNESS WHEREOF, the parties hereto have executed this Agreement on and as of
the day and year first above written.

                                        MICROCIDE PHARMACEUTICALS, Inc.

                                        By:      /s/ John P. Walker
                                           ----------------------------
                                        Print Name:  John P. Walker
                                                    -------------------
                                        Title:       Chairman
                                              -------------------------

                                         /s/ David Schnell
                                        -------------------------------
                                             DAVID SCHNELL

                                        Address:  Prospect Management Co., LLC
                                                  ------------------------------
                                                  435 Taddio Street, Suite 200
                                                  ------------------------------
                                                  Palo Alto, CA 94301
                                                  ------------------------------

                                       6<PAGE>
                                                                Exhibit 10.46

                               SEVERANCE AGREEMENT
                                (Paul J. Mellett)

     THIS SEVERANCE AGREEMENT (this "Agreement") is entered into as of July 27,
                                     ---------
2001, by and between Paul J. Mellett (the "Employee") and MICROCIDE
                                           --------
PHARMACEUTICALS, INC., a Delaware corporation (the "Company").
                                                    -------

     WHEREAS, the Employee has an employment agreement (the "Prior Agreement")
                                                             ---------------
with The Althexis Company, Inc., a Delaware corporation, pursuant to which he
has certain rights and obligations thereunder; and

     WHEREAS, simultaneously with and contingent upon the termination of the
Prior Agreement, this Agreement shall become effective.

     NOW, THEREFORE, the parties hereto hereby agree as follows:

     1. Term of Agreement.
        -----------------

     This Agreement shall remain in effect from the date of the termination of
the Prior Agreement until the earlier of:

          (a) The date when the Employee's employment with the Company
     terminates for any reason not described in Section 6; or

          (b) The date when the Company has met all of its obligations under
     this Agreement following a Termination Event, as defined in Section 6,
     below.

     2. Definition of Change in Control.
        -------------------------------

     For all purposes under this Agreement, "Change in Control" shall mean (i) a
                                             -----------------
merger, reorganization or other transaction or series of related transactions
(other than financings) following which the shareholders of the Company do not
own a majority of the capital stock of the surviving corporation or (ii) the
sale of all or substantially all of the assets of the Company.

     3. Definition of Good Reason.
        -------------------------

     For all purposes under this Agreement, "Good Reason" shall mean that the
                                             -----------
Employee:

          (a) Has been demoted or has incurred a material reduction in his
     authority or responsibility as an employee of the Company, including
     (without limitation) a reduction or elimination of his authority to approve
     expenditures or to hire, promote, demote or terminate subordinates;

          (b) Has incurred a reduction in his total compensation (including
     benefits) as an employee of the Company, other than pursuant to a
     Company-wide reduction of total compensation (including benefits) for
     employees of the Company generally; or

<PAGE>

                                      -2-

          (c) Has been notified that his principal place of work as an employee
     of the Company will be relocated by a distance of 50 miles or more.

     4. Definition of Cause.
        -------------------

     For all purposes under this Agreement, "Cause", shall mean:
                                             -----
          (a) A willful act by the Employee which constitutes misconduct or
     fraud and which is injurious to the Company; provided, however, that no
                                                  --------  -------
     act, or failure to act, by the Employee shall be considered "willful"
                                                                  -------
     unless committed without good faith and without a reasonable belief that
     the act or omission was in the Company's best interest; or

          (b) Conviction of, or a plea of "guilty" or "no contest" to, a felony.
                                           ------      ----------

     The Board of Directors of the Company shall have sole discretion with
respect to whether any act or failure to act constitutes "Cause" for purposes of
this Agreement.

     5. Definition of Continuation Period.
        ---------------------------------

     For all purposes under this Agreement, "Continuation Period" shall mean the
                                             -------------------
period commencing on the date when the termination of the Employee's employment
under Section 6 is effective and ending on the earlier of:

          (a) The date twelve (12) months after the date when the employment
     termination was effective; or

          (b) The date of the Employee's death.

     6. Entitlement to Severance Pay and Benefits.
        -----------------------------------------

     The Employee shall be entitled to receive the severance pay described in
Section 7 (the "Severance Pay") and the benefits described in Section 8 from the
                -------------
Company if, and only if, one of the following events occurs (each a "Termination
                                                                     -----------
Event"):
-----

          (a) Within the first 12 month period after the occurrence of a Change
     in Control, the Employee voluntarily resigns his employment for Good
     Reason; or

          (b) Within the first 12 month period after the occurrence of a Change
     in Control, the Company terminates the Employee's employment for any reason
     other than Cause.

<PAGE>

                                      -3-

     7. Amount of Severance Pay.
        -----------------------

     During the Continuation Period, the Company shall pay the Employee
Severance Pay at an annual rate equal to the Employee's base compensation at the
annual rate in effect on the date when the termination of his employment with
the Company is effective. Such amount shall be paid pro-rata at periodic
intervals in accordance with the Company's standard payroll procedures.

     8. Other Benefits.
        --------------

          (a) Stock Options and Restricted Stock. All unvested stock options and
              ----------------------------------
     shares of restricted stock granted to Employee by the Company shall vest
     immediately upon the occurrence of a Termination Event. The
     post-termination exercise grace period under the Employee's stock options
     shall commence at the end of the Continuation Period. The Employee
     represents that he has consulted or will consult a tax adviser regarding
     the impact of this Subsection (a) on the tax treatment of incentive stock
     options and shares of restricted stock.

          (b) Group Insurance. At the commencement of the Continuation Period,
              ---------------
     the Employee (and, where applicable, his dependents) shall be entitled to
     convert his key employee long-term disability policy and group life
     insurance policy into individual policies pursuant to the terms of such
     policies. Should the Employee elect to convert either or both of such
     policies, the Company will pay the premiums for such policy or policies
     during the Continuation Period. At the commencement of the Continuation
     Period, the Employee shall be eligible to continue his group health
     continuation coverage under the Consolidated Omnibus Budget Reconciliation
     Act of 1986, and the Company will pay the premiums for such coverage during
     the Continuation Period. The foregoing notwithstanding, in the event that
     the Employee becomes eligible for comparable group insurance coverage in
     connection with new employment, the premium payments by the Company under
     this Subsection (b) shall terminate immediately.

          (c) Outplacement Services. Upon the occurrence of a Termination Event,
              ---------------------
     the Employee shall be entitled to reasonable outplacement services at the
     Company's expense. Such services shall be provided by a firm selected by
     the Employee from a list compiled by the Company and shall be limited to a
     period of six consecutive months.

     9. Limitation on Payments.
        ----------------------

          (a) Basic Rule. Any other provision of this Agreement notwithstanding,
              ----------
     the Company shall not be required to make any payment or property transfer
     to, or for the benefit of, the Employee (under this Agreement or otherwise)
     that would be nondeductible by the Company by reason of Section 280G of the
     Internal Revenue Code of 1986, as amended (the "Code"), or that would
                                                     ----
     subject the Employee to the excise tax described in Section 4999 of the
     Code. All calculations required by this Section 9 shall be performed by the
     independent auditors retained by the Company most recently prior to the
     Change in Control (the "Auditors"), based on information supplied by the
                             --------
     Company and the Employee, and shall be binding on the Company and the
     Employee. All fees and expenses of the Auditors shall be paid by the
     Company.

<PAGE>

                                      -4-

          (b) Reductions. If the amount of the aggregate payments or property
              ----------
     transfers to the Employee must be reduced under this Section 9, then the
     Employee shall direct in which order the payments or transfers are to be
     reduced, but no change in the timing of any payment or transfer shall be
     made without the Company's consent. As a result of uncertainty in the
     application of sections 280G and 4999 of the Code at the time of an initial
     determination by the Auditors hereunder, it is possible that a payment will
     have been made by the Company that should not have been made (an
     "Overpayment") or that an additional payment that will not have been made
      -----------
     by the Company could have been made (an "Underpayment"). In the event that
                                              ------------
     the Auditors, based upon the assertion of a deficiency by the Internal
     Revenue Service against the Company or the Employee that the Auditors
     believe has a high probability of success, determine that an Overpayment
     has been made, such Overpayment shall be treated for all purposes as a loan
     to the Employee that he shall repay to the Company, together with interest
     at the applicable federal rate specified in section 7872(f)(2) of the Code;
     provided, however, that no amount shall be payable by the Employee to the
     --------  -------
     Company if and to the extent that such payment would not reduce the amount
     that is nondeductible under section 280G of the Code or is subject to an
     excise tax under section 4999 of the Code. In the event that the Auditors
     determine that an Underpayment has occurred, such Underpayment shall
     promptly be paid or transferred by the Company to, or for the benefit of,
     the Employee, together with interest at the applicable federal rate
     specified in section 7872(f)(2) of the Code.

     10. Non-Solicitation.
         ----------------

     After the occurrence of a Termination Event, the Employee agrees that for a
period of two years from the date of the Termination Event (the
"Non-Solicitation Term") he will not directly or indirectly solicit for
 ---------------------
employment any employee of the Company who was employed by the Company at the
time of the occurrence of the Termination Event and remains in the employment of
the Company during the Non-Solicitation Term.

     11. Successors.
         ----------

          (a) Company's Successors. The Company shall require any successor
              --------------------
     (whether direct or indirect and whether by purchase, lease, merger,
     consolidation, liquidation or otherwise) to all or substantially all of the
     Company's business and/or assets, by an agreement in substance and form
     satisfactory to the Employee, to assume this Agreement and to agree
     expressly to perform this Agreement in the same manner and to the same
     extent as the Company would be required to perform it in the absence of a
     succession. For all purposes under this Agreement, the term "Company" shall
                                                                  -------
     include any successor to the Company's business and/or assets which
     executes and delivers the assumption agreement described in this Subsection
     (a) or which becomes bound by this Agreement by operation of law.

<PAGE>

                                      -5-

          (b) Employee's Successors. This Agreement and all rights of the
              ---------------------
     Employee hereunder shall inure to the benefit of, and be enforceable by,
     the Employee's personal or legal representatives, executors,
     administrators, successors, heirs, distributees, devisees and legatees.

     12. Miscellaneous Provisions.
         ------------------------

          (a) Notice. Notices and all other communications contemplated by this
              ------
     Agreement shall be in writing and shall be deemed to have been duly given
     when personally delivered or when mailed by U.S. registered or certified
     mail, return receipt requested and postage prepaid. In the case of the
     Employee, mailed notices shall be addressed to him at the home address
     which he most recently communicated to the Company in writing. In the case
     of the Company, mailed notices shall be addressed to its corporate
     headquarters, and all notices shall be directed to the attention of its
     Secretary.

          (b) Waiver. No provision of this Agreement shall be modified, waived
              ------
     or discharged unless the modification, waiver or discharge is agreed to in
     writing and signed by the Employee and by an authorized officer of the
     Company (other than the Employee). No waiver by either party of any breach
     of, or of compliance with, any condition or provision of this Agreement by
     the other party shall be considered a waiver of any other condition or
     provision or of the same condition or provision at another time.

          (c) Whole Agreement. No agreements, representations or understandings
              ---------------
     (whether oral or written and whether express or implied) which are not
     expressly set forth in this Agreement have been made or entered into by
     either party with respect to the subject matter hereof.

          (d) No Setoff; Withholding Taxes. There shall be no right of setoff or
              ----------------------------
     counterclaim, with respect to any claim, debt or obligation, against
     payments to the Employee under this Agreement. All payments made under this
     Agreement shall be subject to reduction to reflect taxes required to be
     withheld by law.

          (e) Choice of Law. The validity, interpretation, construction and
              -------------
     performance of this Agreement shall be governed by the laws of the
     Commonwealth of Massachusetts.

          (f) Severability. The invalidity or unenforceability of any provision
              ------------
     or provisions of this Agreement shall not affect the validity or
     enforceability of any other provision hereof, which shall remain in full
     force and effect.

          (g) Potential Pooling Transactions. In the event the Board determines
              ------------------------------
     that the acceleration of options pursuant to Sections 8(a) above would
     preclude accounting for a proposed business transaction involving a Change
     in Control as a "Pooling of Interests," but the Board otherwise desires to
     approve and account for such transaction as a "Pooling of Interests," the
     acceleration of options described in Sections 8(a) above shall be null and
     void, and the Company shall enter into a consulting agreement with the
     employee covering services and compensation to be determined by the parties
     at that time. Such agreement shall be for a period of three years and shall
     not be subject to earlier termination unless by mutual consent of the
     parties.

<PAGE>

                                      -6-

          (h) Arbitration. Except as otherwise provided in Section 9, any
              -----------
     dispute or controversy arising under or in connection with this Agreement
     shall be settled exclusively by arbitration in Boston, Massachusetts, in
     accordance with the rules of the American Arbitration Association then in
     effect. Judgment may be entered on the arbitrator's award in any court
     having jurisdiction. Punitive damages shall not be awarded.

          (i) No Assignment of Benefits. The rights of any person to payments or
              -------------------------
     benefits under this Agreement shall not be made subject to option or
     assignment, either by voluntary or involuntary assignment or by operation
     of law, including (without limitation) bankruptcy, garnishment, attachment,
     or other creditor's process, and any action in violation of this Subsection
     (i) shall be void.

          (j) Employment Taxes. All payments made pursuant to this Agreement
              ----------------
     will be subject to withholding of applicable income and employment taxes.

          (k) Counterparts. This Agreement may be executed in counterparts, each
              ------------
     of which shall be deemed an original, but all of which together will
     constitute one and the same instrument.

            [The remainder of this page is intentionally left blank]

<PAGE>

                                      Microcide Pharmaceuticals, Inc.

                                      By:  /s/ James E. Rurka
                                         -------------------------------------
                                           Name: James E. Rurka

                                           Title: President and Chief Executive
                                                  Officer

                                          /s/ Paul J. Mellett
                                         ---------------------------------------
                                              Paul J. Mellett

Source: [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00036-of-00352.parquet"}, [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00036-of-00352.parquet"}]]