Document:

exv10w2

Exhibit 10.2

ALNYLAM PHARMACEUTICALS, INC.

2009 STOCK INCENTIVE PLAN

1. Purpose

     The purpose of this 2009 Stock Incentive Plan (the “Plan”) of Alnylam Pharmaceuticals, Inc., a
Delaware corporation (the “Company”), is to advance the interests of the Company’s stockholders by
enhancing the Company’s ability to attract, retain and motivate persons who are expected to make
important contributions to the Company by providing such persons with equity ownership
opportunities and performance-based incentives that are intended to better align the interests of
such persons with those of the Company’s stockholders. Except where the context otherwise
requires, the term “Company” shall include any of the Company’s present or future parent or
subsidiary corporations as defined in Sections 424(e) or (f) of the Internal Revenue Code of 1986,
as amended, and any regulations promulgated thereunder (the “Code”) and any other business venture
(including, without limitation, joint venture or limited liability company) in which the Company
has a controlling interest, as determined by the Board of Directors of the Company (the “Board”).

2. Eligibility

     All of the Company’s employees, officers and directors are eligible to be granted options,
stock appreciation rights (“SARs”), restricted stock, restricted stock units (“RSUs”) and other
stock-based awards (each, an “Award”) under the Plan. Consultants and advisors to the Company (as
such terms are defined and interpreted for purposes of Form S-8 (or any successor form)) are also
eligible to be granted Awards. Each person who is granted an Award under the Plan is deemed a
“Participant.”

3. Administration and Delegation

     (a) Administration by Board of Directors. The Plan will be administered by the Board.
The Board shall have authority to grant Awards and to adopt, amend and repeal such administrative
rules, guidelines and practices relating to the Plan as it shall deem advisable. The Board may
construe and interpret the terms of the Plan and any Award agreements entered into under the Plan.
The Board may correct any defect, supply any omission or reconcile any inconsistency in the Plan or
any Award in the manner and to the extent it shall deem expedient to carry the Plan into effect and
it shall be the sole and final judge of such expediency. All decisions by the Board shall be made
in the Board’s sole discretion and shall be final and binding on all persons having or claiming any
interest in the Plan or in any Award.

     (b) Appointment of Committees. To the extent permitted by applicable law, the Board
may delegate any or all of its powers under the Plan to one or more committees or subcommittees of
the Board (a “Committee”). All references in the Plan to the “Board” shall mean the Board or a
Committee of the Board or the officers referred to in Section 3(c) to the extent that the Board’s
powers or authority under the Plan have been delegated to such Committee or officers.

 

 

     (c) Delegation to Officers. To the extent permitted by applicable law, the Board may
delegate to one or more officers of the Company the power to grant Options and other Awards that
constitute rights under Delaware law (subject to any limitations under the Plan) to employees or
officers of the Company or any of its present or future subsidiary corporations and to exercise
such other powers under the Plan as the Board may determine, provided that the Board shall fix the
terms of the Awards to be granted by such officers (including the exercise price of the Awards,
which may include a formula by which the exercise price will be determined) and the maximum number
of shares subject to such Awards that the officers may grant; provided further, however, that no
officer shall be authorized to grant Awards to any “executive officer” of the Company (as defined
by Rule 3b-7 under the Securities Exchange Act of 1934, as amended (the “Exchange Act”)) or to any
“officer” of the Company (as defined by Rule 16a-1 under the Exchange Act). The Board may not
delegate authority under this Section 3(c) to grant restricted stock, unless Delaware law then
permits such delegation.

     (d) Awards to Non-Employee Directors. Discretionary Awards to non-employee directors
will only be granted and administered by a Committee, all of the members of which are independent
as defined by Section 4200(a)(15) of the Nasdaq Marketplace Rules.

4. Stock Available for Awards

     (a) Number of Shares; Share Counting.

          (1) Authorized Number of Shares. Subject to adjustment under Section 10, Awards may
be made under the Plan for up to 2,200,000 shares of common stock, $0.01 par value per share, of
the Company (the “Common Stock”), any or all of which Awards may be in the form of Incentive Stock
Options. Shares issued under the Plan may consist in whole or in part of authorized but unissued
shares or treasury shares.

          (2) Fungible Share Pool. Subject to adjustment under Section 10, any Award that is
not a Full-Value Award shall be counted against the share limits specified in Sections 4(a)(1) and
4(b)(2) as one share for each share of Common Stock subject to such Award and any Award that is a
Full-Value Award shall be counted against the share limits specified in Sections 4(a)(1) and
4(b)(2) as 1.5 shares for each one share of Common Stock subject to such Full-Value Award.
“Full-Value Award” means any Restricted Stock Award or Other Stock-Based Award (each as defined
below). To the extent a share that was subject to an Award that counted as one share is returned
to the Plan pursuant to Section 4(a)(3), each applicable share reserve will be credited with one
share. To the extent that a share that was subject to a Full-Value Award that counted as 1.5
shares is returned to the Plan pursuant to Section 4(a)(3), each applicable share reserve will be
credited with 1.5 shares.

          (3) Share Counting. For purposes of counting the number of shares available for the
grant of Awards under the Plan and under the sublimits contained in Section 4(b)(2), (i) all shares
of Common Stock covered by independent SARs shall be counted against the number of shares available
for the grant of Awards; provided, however, that independent SARs that may be settled only in cash
shall not be so counted; (ii) if any Award (A) expires or is terminated, surrendered or canceled
without having been fully exercised or is forfeited in whole or in part (including as the result of
shares of Common Stock subject to such Award being repurchased by

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the Company at the original issuance price pursuant to a contractual repurchase right) or (B)
results in any Common Stock not being issued (including as a result of an independent SAR that was
settleable either in cash or in stock actually being settled in cash), the unused Common Stock
covered by such Award shall again be available for the grant of Awards; provided, however, in the
case of Incentive Stock Options (as hereinafter defined), the foregoing shall be subject to any
limitations under the Code; and provided further, in the case of independent SARs, that the full
number of shares subject to any stock-settled SAR shall be counted against the shares available
under the Plan and against the sublimits listed in the first clause of this Section in proportion
to the portion of the SAR actually exercised regardless of the number of shares actually used to
settle such SAR upon exercise; (iii) shares of Common Stock delivered (by actual delivery,
attestation, or net exercise) to the Company by a Participant to (A) purchase shares of Common
Stock upon the exercise of an Award or (B) satisfy tax withholding obligations (including shares
retained from the Award creating the tax obligation) shall not be added back to the number of
shares available for the future grant of Awards; and (iv) shares of Common Stock repurchased by the
Company on the open market using the proceeds from the exercise of an Award shall not increase the
number of shares available for future grant of Awards.

     (b) Sub-limits. Subject to adjustment under Section 10, the following sub-limits on
the number of shares subject to Awards shall apply:

          (1) Section 162(m) Per-Participant Limit. The maximum number of shares of Common
Stock with respect to which Awards may be granted to any Participant under the Plan shall be
500,000 per calendar year, except in the calendar year in which the Participant is hired by the
Company, in which case the maximum number of shares shall be 1,000,000. For purposes of the
foregoing limit, the combination of an Option in tandem with a SAR (as each is hereafter defined)
shall be treated as a single Award. The per Participant limit described in this Section 4(b)(1)
shall be construed and applied consistently with Section 162(m) of the Code or any successor
provision thereto, and the regulations thereunder (“Section 162(m)”).

          (2) Limit on Awards to Directors. Except for initial and annual grants provided under
Section 6, the maximum number of shares with respect to which Awards may be granted to directors
who are not employees of the Company at the time of grant shall be 5% of the maximum number of
authorized shares set forth in Section 4(a)(1).

     (c) Substitute Awards. In connection with a merger or consolidation of an entity with
the Company or the acquisition by the Company of property or stock of an entity, the Board may
grant awards in substitution for any options, stock or stock-based awards granted by such entity or
an affiliate thereof. Substitute Awards may be granted on such terms as the Board deems
appropriate in the circumstances, notwithstanding any limitations on Awards contained in the Plan.
Substitute Awards shall not count against the overall share limit set forth in Section 4(a)(1) or
any sublimits contained in the Plan, except as may be required by reason of Section 422 and related
provisions of the Code.

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5. Stock Options

     (a) General. The Board may grant options to purchase Common Stock (each, an “Option”)
and determine the number of shares of Common Stock to be covered by each Option, the exercise price
of each Option and the conditions and limitations applicable to the exercise of each Option,
including conditions relating to applicable federal or state securities laws, as it considers
necessary or advisable. An Option that is not intended to be an Incentive Stock Option (as
hereinafter defined) shall be designated a “Nonstatutory Stock Option”.

     (b) Incentive Stock Options. An Option that the Board intends to be an “incentive
stock option” as defined in Section 422 of the Code (an “Incentive Stock Option”) shall only be
granted to employees of Alnylam Pharmaceuticals, Inc., any of Alnylam Pharmaceuticals, Inc.’s
present or future parent or subsidiary corporations as defined in Sections 424(e) or (f) of the
Code, and any other entities the employees of which are eligible to receive Incentive Stock Options
under the Code, and shall be subject to and shall be construed consistently with the requirements
of Section 422 of the Code. The Company shall have no liability to a Participant, or any other
party, if an Option (or any part thereof) that is intended to be an Incentive Stock Option is not
an Incentive Stock Option or if the Company converts an Incentive Stock Option to a Nonstatutory
Stock Option.

     (c) Exercise Price. The Board shall establish the exercise price of each Option and
specify the exercise price in the applicable option agreement. The exercise price shall be not less
than 100% of the Fair Market Value (as defined below) on the date the Option is granted; provided
that if the Board approves the grant of an Option with an exercise price to be determined on a
future date, the exercise price shall be not less than 100% of the Fair Market Value on such future
date. “Fair Market Value” of a share of Common Stock for purposes of the Plan will be determined
as follows:

          (1) if the Common Stock trades on a national securities exchange, the closing sale price (for
the primary trading session) on the date of grant;

          (2) if the Common Stock does not trade on any such exchange, the average of the closing bid
and asked prices as reported by an authorized OTCBB market data vendor as listed on the OTCBB
website (otcbb.com) on the date of grant; or

          (3) if the Common Stock is not publicly traded, the Board will determine the Fair Market Value
for purposes of the Plan using any measure of value it determines to be appropriate (including, as
it considers appropriate, relying on appraisals) in a manner consistent with the valuation
principles under Section 409A of the Code, except as the Board or Committee may expressly determine
otherwise.

For any date that is not a trading day, the Fair Market Value of a share of Common Stock for such
date will be determined by using the closing sale price or average of the bid and asked prices, as
appropriate, for the immediately preceding trading day and with the timing in the formulas above
adjusted accordingly. The Board can substitute a particular time of day or other measure of
“closing sale price” or “bid and asked prices” if appropriate because of exchange or market
procedures or can, in its sole discretion, use weighted averages either on a daily basis or

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such longer period as complies with Section 409A of the Code. The Board has sole discretion to
determine the Fair Market Value for purposes of this Plan, and all Awards are conditioned on the
participants’ agreement that the Board’s determination is conclusive and binding even though others
might make a different determination.

     (d) Duration of Options. Each Option shall be exercisable at such times and subject
to such terms and conditions as the Board may specify in the applicable option agreement; provided,
however, that no Option will be granted for a term in excess of 10 years.

     (e) Exercise of Option. Options may be exercised by delivery to the Company of a
written notice of exercise signed by the proper person or by any other form of notice (including
electronic notice) approved by the Company, together with payment in full as specified in Section
5(f) for the number of shares for which the Option is exercised. Shares of Common Stock subject to
the Option will be delivered by the Company as soon as practicable following exercise.

     (f) Payment Upon Exercise. Common Stock purchased upon the exercise of an Option
granted under the Plan shall be paid for as follows:

          (1) in cash or by check, payable to the order of the Company;

          (2) except as may otherwise be provided in the applicable option agreement, by (i) delivery of
an irrevocable and unconditional undertaking by a creditworthy broker to deliver promptly to the
Company sufficient funds to pay the exercise price and any required tax withholding or (ii)
delivery by the Participant to the Company of a copy of irrevocable and unconditional instructions
to a creditworthy broker to deliver promptly to the Company cash or a check sufficient to pay the
exercise price and any required tax withholding;

          (3) to the extent provided for in the applicable option agreement or approved by the Board, in
its sole discretion, by delivery (either by actual delivery or attestation) of shares of Common
Stock owned by the Participant valued at their Fair Market Value, provided (i) such method of
payment is then permitted under applicable law, (ii) such Common Stock, if acquired directly from
the Company, was owned by the Participant for such minimum period of time, if any, as may be
established by the Board in its discretion and (iii) such Common Stock is not subject to any
repurchase, forfeiture, unfulfilled vesting or other similar requirements;

          (4) to the extent provided for in the applicable Nonstatutory Stock Option agreement or
approved by the Board in its sole discretion, by delivery of a notice of “net exercise” to the
Company, as a result of which the Participant would receive the number of shares of Common Stock
underlying the Option so exercised reduced by the number of shares of Common Stock equal to the
aggregate exercise price of the Option divided by the Fair Market Value on the date of exercise;

          (5) to the extent permitted by applicable law and provided for in the applicable Option
agreement or approved by the Board, in its sole discretion, by payment of such other lawful
consideration as the Board may determine; or

          (6) by any combination of the above permitted forms of payment.

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     (g) Limitation on Repricing. Unless such action is approved by the Company’s
stockholders: (1) no outstanding Option granted under the Plan may be amended to provide an
exercise price per share that is lower than the then-current exercise price per share of such
outstanding Option (other than adjustments pursuant to Section 10) and (2) the Board may not cancel
any outstanding option (whether or not granted under the Plan) and grant in substitution therefor
new Awards under the Plan covering the same or a different number of shares of Common Stock and
having an exercise price per share lower than the then-current exercise price per share of the
cancelled option.

6. Director Options

     (a) Initial Grant. Upon the commencement of service on the Board by any individual
who is not then an employee of the Company or any subsidiary of the Company, the Company shall
grant to such person a Nonstatutory Stock Option to purchase 30,000 shares of Common Stock (subject
to adjustment under Section 10).

     (b) Annual Grant. On the date of each annual meeting of stockholders of the Company,
the Company shall grant to each member of the Board who is both serving as a director of the
Company immediately prior to and immediately following such annual meeting and who is not then an
employee of the Company or any of its subsidiaries, a Nonstatutory Stock Option to purchase 15,000
shares of Common Stock (subject to adjustment under Section 10); provided, however, that a director
shall not be eligible to receive an option grant under this Section 6(b) until such director has
served on the Board for at least six months. In addition, on the date of each annual meeting of
stockholders of the Company, the Company shall grant a Nonstatutory Stock Option to purchase an
additional 10,000 shares of Common Stock (subject to adjustment under Section 10) to the Chairman
of the Audit Committee of the Board.

     (c) Terms of Director Options. Options granted under this Section 6 shall (i) have an
exercise price equal to the Fair Market Value on the date of grant, (ii) vest in full on the first
anniversary of the date of grant provided that the individual is serving on the Board on such date
(or, in the case of Options granted under Section 6(a), as to one-third of the shares subject to
the Option on each of the first, second and third anniversaries of the date of grant); provided
that no additional vesting shall take place after the Participant ceases to serve as a director and
further provided that the Board may provide for accelerated vesting in the case of death,
disability, change in control, attainment of mandatory retirement age or retirement, (iii) expire
on the earlier of 10 years from the date of grant or three months following cessation of service on
the Board and (iv) contain such other terms and conditions as the Board shall determine.

     (d) Board Discretion. The Board retains the specific authority to from time to time
increase or decrease the number of shares subject to Options granted under this Section 6, subject
to the limitation on the aggregate number of shares issuable to non-employee directors contained in
Section 4(b)(2). The Board also retains the specific authority to issue SARs, Restricted Stock
Awards or Other Stock-Based Awards in lieu of some or all of the Options otherwise issuable under
this Section 6, subject to the limitation on the aggregate number of shares issuable to
non-employee directors contained in Section 4(b)(2).

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7. Stock Appreciation Rights

     (a) General. The Board may grant Awards consisting of SARs entitling the holder, upon
exercise, to receive an amount of Common Stock or cash or a combination thereof (such form to be
determined by the Board) determined by reference to appreciation, from and after the date of grant,
in the Fair Market Value of a share of Common Stock over the measurement price established pursuant
to Section 7(c). The date as of which such appreciation is determined shall be the exercise date.

     (b) Grants. SARs may be granted in tandem with, or independently of, Options granted
under the Plan.

          (1) Tandem Awards. When SARs are expressly granted in tandem with Options, (i) the
SAR will be exercisable only at such time or times, and to the extent, that the related Option is
exercisable (except to the extent designated by the Board in connection with a Reorganization Event
and will be exercisable in accordance with the procedure required for exercise of the related
Option; (ii) the SAR will terminate and no longer be exercisable upon the termination or exercise
of the related Option, except to the extent designated by the Board in connection with a
Reorganization Event and except that a SAR granted with respect to less than the full number of
shares covered by an Option will not be reduced until the number of shares as to which the related
Option has been exercised or has terminated exceeds the number of shares not covered by the SAR;
(iii) the Option will terminate and no longer be exercisable upon the exercise of the related SAR;
and (iv) the SAR will be transferable only with the related Option.

          (2) Independent SARs. A SAR not expressly granted in tandem with an Option will
become exercisable at such time or times, and on such conditions, as the Board may specify in the
SAR Award.

     (c) Measurement Price. The Board shall establish the measurement price of each SAR
and specify it in the applicable SAR agreement. The measurement price shall not be less than 100%
of the Fair Market Value on the date the SAR is granted; provided that if the Board approves the
grant of a SAR with a measurement price to be determined on a future date, the measurement price
shall be not less than 100% of the Fair Market Value on such future date.

     (d) Duration of SARs. Each SAR shall be exercisable at such times and subject to such
terms and conditions as the Board may specify in the applicable SAR agreement; provided, however,
that no SAR will be granted with a term in excess of 10 years.

     (e) Exercise of SARs. SARs may be exercised by delivery to the Company of a written
notice of exercise signed by the proper person or by any other form of notice (including electronic
notice) approved by the Company, together with any other documents required by the Board.

     (f) Limitation on Repricing. Unless such action is approved by the Company’s
stockholders: (1) no outstanding SAR granted under the Plan may be amended to provide an exercise
price per share that is lower than the then-current exercise price per share of such outstanding
SAR (other than adjustments pursuant to Section 10) and (2) the Board may not cancel any
outstanding SAR (whether or not granted under the Plan) and grant in substitution

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therefor new Awards under the Plan covering the same or a different number of shares of Common
Stock and having an exercise price per share lower than the then-current exercise price per share
of the cancelled SAR.

8. Restricted Stock; Restricted Stock Units

     (a) General. The Board may grant Awards entitling recipients to acquire shares of
Common Stock (“Restricted Stock”), subject to the right of the Company to repurchase all or part of
such shares at their issue price or other stated or formula price (or to require forfeiture of such
shares if issued at no cost) from the recipient in the event that conditions specified by the Board
in the applicable Award are not satisfied prior to the end of the applicable restriction period or
periods established by the Board for such Award. Instead of granting Awards for Restricted Stock,
the Board may grant Awards entitling the recipient to receive shares of Common Stock or cash to be
delivered at the time such Award vests (“Restricted Stock Units”) (Restricted Stock and Restricted
Stock Units are each referred to herein as a “Restricted Stock Award”).

     (b) Terms and Conditions for All Restricted Stock Awards. The Board shall determine
the terms and conditions of a Restricted Stock Award, including the conditions for vesting and
repurchase (or forfeiture) and the issue price, if any. Restricted Stock Awards that vest solely
based on the passage of time shall be zero percent vested prior to the first anniversary of the
date of grant (or, in the case of Awards to non-employee directors, if earlier, the date of the
first annual meeting held after the date of grant), no more than one-third vested prior to the
second anniversary of the date of grant (or, in the case of Awards to non-employee directors, if
earlier, the date of the second annual meeting held after the date of grant), and no more than
two-thirds vested prior to the third anniversary of the date of grant (or, in the case of Awards to
non-employee directors, if earlier, the date of the third annual meeting held after the date of
grant). Restricted Stock Awards that do not vest solely based on the passage of time shall not
vest prior to the first anniversary of the date of grant (or, in the case of Awards to non-employee
directors, if earlier, the date of the first annual meeting held after the date of grant). The two
foregoing sentences shall not apply to (1) Performance Awards granted pursuant to Section 11(i) or
(2) Restricted Stock Awards granted, in the aggregate, for up to 10% of the maximum number of
authorized shares set forth in Section 4(a)(1). Notwithstanding any other provision of this Plan
(other than Section 11(i), if applicable), the Board may, in its discretion, either at the time a
Restricted Stock Award is made or at any time thereafter, waive its right to repurchase shares of
Common Stock (or waive the forfeiture thereof) or remove or modify any part or all of the
restrictions applicable to the Restricted Stock Award, provided that the Board may only exercise
such rights in the following extraordinary circumstances: death, disability or retirement of the
Participant, or a merger, consolidation, sale, reorganization, recapitalization, or change in
control of the Company.

     (c) Additional Provisions Relating to Restricted Stock.

          (1) Dividends. Participants holding shares of Restricted Stock will be entitled to
all ordinary cash dividends paid with respect to such shares, unless otherwise provided by the
Board. Unless otherwise provided by the Board, if any dividends or distributions are paid in
shares, or consist of a dividend or distribution to holders of Common Stock other than an

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ordinary cash dividend, the shares, cash or other property will be subject to the same
restrictions on transferability and forfeitability as the shares of Restricted Stock with respect
to which they were paid. Each dividend payment will be made no later than the end of the calendar
year in which the dividends are paid to shareholders of that class of stock or, if later, the 15th
day of the third month following the date the dividends are paid to shareholders of that class of
stock.

          (2) Stock Certificates. The Company may require that any stock certificates issued in
respect of shares of Restricted Stock shall be deposited in escrow by the Participant, together
with a stock power endorsed in blank, with the Company (or its designee). At the expiration of the
applicable restriction periods, the Company (or such designee) shall deliver the certificates no
longer subject to such restrictions to the Participant or if the Participant has died, to the
beneficiary designated, in a manner determined by the Board, by a Participant to receive amounts
due or exercise rights of the Participant in the event of the Participant’s death (the “Designated
Beneficiary”). In the absence of an effective designation by a Participant, “Designated
Beneficiary” shall mean the Participant’s estate.

     (d) Additional Provisions Relating to Restricted Stock Units.

          (1) Settlement. Upon the vesting of and/or lapsing of any other restrictions (i.e.,
settlement) with respect to each Restricted Stock Unit, the Participant shall be entitled to
receive from the Company one share of Common Stock or an amount of cash equal to the Fair Market
Value of one share of Common Stock, as provided in the applicable Award agreement. The Board may,
in its discretion, provide that settlement of Restricted Stock Units shall be deferred, on a
mandatory basis or at the election of the Participant in a manner that complies with Section 409A
of the Code.

          (2) Voting Rights. A Participant shall have no voting rights with respect to any
Restricted Stock Units.

          (3) Dividend Equivalents. To the extent provided by the Board, in its sole
discretion, a grant of Restricted Stock Units may provide Participants with the right to receive an
amount equal to any dividends or other distributions declared and paid on an equal number of
outstanding shares of Common Stock (“Dividend Equivalents”). Dividend Equivalents may be paid
currently or credited to an account for the Participants, may be settled in cash and/or shares of
Common Stock and may be subject to the same restrictions on transfer and forfeitability as the
Restricted Stock Units with respect to which paid, as determined by the Board in its sole
discretion, subject in each case to such terms and conditions as the Board shall establish, in each
case to be set forth in the applicable Award agreement.

9. Other Stock-Based Awards

     (a) General. Other Awards of shares of Common Stock, and other Awards that are valued
in whole or in part by reference to, or are otherwise based on, shares of Common Stock or other
property, may be granted hereunder to Participants (“Other Stock-Based-Awards”), including without
limitation Awards entitling recipients to receive shares of Common Stock to be delivered in the
future. Such Other Stock-Based Awards shall also be available as a form of payment in the
settlement of other Awards granted under the Plan or as payment in lieu of

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compensation to which a Participant is otherwise entitled. Other Stock-Based Awards may be
paid in shares of Common Stock or cash, as the Board shall determine.

     (b) Terms and Conditions. Subject to the provisions of the Plan, the Board shall
determine the terms and conditions of each Other Stock-Based Award , including any purchase price
applicable thereto. Other Stock-Based Awards that vest solely based on the passage of time shall
be zero percent vested prior to the first anniversary of the date of grant (or, in the case of
Awards to non-employee directors, if earlier, the date of the first annual meeting held after the
date of grant), no more than one-third vested prior to the second anniversary of the date of grant
(or, in the case of Awards to non-employee directors, if earlier, the date of the second annual
meeting held after the date of grant), and no more than two-thirds vested prior to the third
anniversary of the date of grant (or, in the case of Awards to non-employee directors, if earlier,
the date of the third annual meeting held after the date of grant). Other Stock-Based Awards that
do not vest solely based on the passage of time shall not vest prior to the first anniversary of
the date of grant (or, in the case of Awards to non-employee directors, if earlier, the date of the
first annual meeting held after the date of grant). The two foregoing sentences shall not apply to
(1) Performance Awards granted pursuant to Section 11(i) or (2) Other Stock-Based Awards granted,
in the aggregate, for up to 10% of the maximum number of authorized shares set forth in Section
4(a)(1). Notwithstanding any other provision of this Plan (other than Section 11(i), if
applicable), the Board may, in its discretion, either at the time an Other Stock-Based Award is
made or at any time thereafter, waive its right to repurchase shares of Common Stock (or waive the
forfeiture thereof) or remove or modify any part or all of the restrictions applicable to the Other
Stock-Based Award, provided that the Board may only exercise such rights in the following
extraordinary circumstances: death, disability or retirement of the Participant, or a merger,
consolidation, sale, reorganization, recapitalization, or change in control of the Company.

10. Adjustments for Changes in Common Stock and Certain Other Events

     (a) Changes in Capitalization. In the event of any stock split, reverse stock split,
stock dividend, recapitalization, combination of shares, reclassification of shares, spin-off or
other similar change in capitalization or event, or any dividend or distribution to holders of
Common Stock other than an ordinary cash dividend, (i) the number and class of securities available
under the Plan, (ii) the sub-limits, fungible pool and share counting rules set forth in Sections
4(a) and 4(b), (iii) the minimum vesting provisions of Restricted Stock Awards and Other
Stock-Based Awards set forth in Sections 8(b) and 9(b), (iv) the number and class of securities and
exercise price per share of each outstanding Option and each Option issuable under Section 6, (v)
the share- and per-share provisions and the measurement price of each SAR, (vi) the number of
shares subject to and the repurchase price per share subject to each outstanding Restricted Stock
Award and (vii) the share- and per-share-related provisions and the purchase price, if any, of each
outstanding Other Stock-Based Award, shall be equitably adjusted by the Company (or substituted
Awards may be made, if applicable) in the manner determined by the Board. Without limiting the
generality of the foregoing, in the event the Company effects a split of the Common Stock by means
of a stock dividend and the exercise price of and the number of shares subject to an outstanding
Option are adjusted as of the date of the distribution of the dividend (rather than as of the
record date for such dividend), then an optionee who exercises an Option between the record date
and the distribution date for such stock dividend

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shall be entitled to receive, on the distribution date, the stock dividend with respect to the
shares of Common Stock acquired upon such Option exercise, notwithstanding the fact that such
shares were not outstanding as of the close of business on the record date for such stock dividend.

     (b) Reorganization Events.

          (1) Definition. A “Reorganization Event” shall mean: (a) any merger or consolidation
of the Company with or into another entity as a result of which all of the Common Stock of the
Company is converted into or exchanged for the right to receive cash, securities or other property
or is cancelled, (b) any transfer or disposition of all of the Common Stock of the Company for
cash, securities or other property pursuant to a share exchange or other transaction or (c) any
liquidation or dissolution of the Company.

          (2) Consequences of a Reorganization Event on Awards Other than Restricted Stock
Awards. In connection with a Reorganization Event, the Board may take any one or more of the
following actions as to all or any (or any portion of) outstanding Awards other than Restricted
Stock Awards on such terms as the Board determines: (i) provide that Awards shall be assumed, or
substantially equivalent Awards shall be substituted, by the acquiring or succeeding corporation
(or an affiliate thereof), (ii) upon written notice to a Participant, provide that the
Participant’s unexercised Awards will terminate immediately prior to the consummation of such
Reorganization Event unless exercised by the Participant within a specified period following the
date of such notice, (iii) provide that outstanding Awards shall become exercisable, realizable, or
deliverable, or restrictions applicable to an Award shall lapse, in whole or in part prior to or
upon such Reorganization Event, (iv) in the event of a Reorganization Event under the terms of
which holders of Common Stock will receive upon consummation thereof a cash payment for each share
surrendered in the Reorganization Event (the “Acquisition Price”), make or provide for a cash
payment to a Participant equal to the excess, if any, of (A) the Acquisition Price times the
number of shares of Common Stock subject to the Participant’s Awards (to the extent the exercise
price does not exceed the Acquisition Price) over (B) the aggregate exercise price of all such
outstanding Awards and any applicable tax withholdings, in exchange for the termination of such
Awards, (v) provide that, in connection with a liquidation or dissolution of the Company, Awards
shall convert into the right to receive liquidation proceeds (if applicable, net of the exercise
price thereof and any applicable tax withholdings) and (vi) any combination of the foregoing. In
taking any of the actions permitted under this Section 10(b), the Board shall not be obligated by
the Plan to treat all Awards, all Awards held by a Participant, or all Awards of the same type,
identically.

          For purposes of clause (i) above, an Option shall be considered assumed if, following
consummation of the Reorganization Event, the Option confers the right to purchase, for each share
of Common Stock subject to the Option immediately prior to the consummation of the Reorganization
Event, the consideration (whether cash, securities or other property) received as a result of the
Reorganization Event by holders of Common Stock for each share of Common Stock held immediately
prior to the consummation of the Reorganization Event (and if holders were offered a choice of
consideration, the type of consideration chosen by the holders of a majority of the outstanding
shares of Common Stock); provided, however, that if the consideration received as a result of the
Reorganization Event is not solely common stock of the acquiring or succeeding corporation (or an
affiliate thereof), the Company may, with the consent

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of the acquiring or succeeding corporation, provide for the consideration to be received upon
the exercise of Options to consist solely of common stock of the acquiring or succeeding
corporation (or an affiliate thereof) equivalent in value (as determined by the Board) to the per
share consideration received by holders of outstanding shares of Common Stock as a result of the
Reorganization Event.

          (3) Consequences of a Reorganization Event on Restricted Stock Awards. Upon the
occurrence of a Reorganization Event other than a liquidation or dissolution of the Company, the
repurchase and other rights of the Company under each outstanding Restricted Stock Award shall
inure to the benefit of the Company’s successor and shall, unless the Board determines otherwise,
apply to the cash, securities or other property which the Common Stock was converted into or
exchanged for pursuant to such Reorganization Event in the same manner and to the same extent as
they applied to the Common Stock subject to such Restricted Stock Award; provided, however, that
the Board may provide for termination or deemed satisfaction of such repurchase or other rights
under the instrument evidencing any Restricted Stock Award or any other agreement between a
Participant and the Company, either initially or by amendment. Upon the occurrence of a
Reorganization Event involving the liquidation or dissolution of the Company, except to the extent
specifically provided to the contrary in the instrument evidencing any Restricted Stock Award or
any other agreement between a Participant and the Company, all restrictions and conditions on all
Restricted Stock Awards then outstanding shall automatically be deemed terminated or satisfied.

11. General Provisions Applicable to Awards

     (a) Transferability of Awards. Awards shall not be sold, assigned, transferred,
pledged or otherwise encumbered by the person to whom they are granted, either voluntarily or by
operation of law, except by will or the laws of descent and distribution or, other than in the case
of an Incentive Stock Option, pursuant to a qualified domestic relations order, and, during the
life of the Participant, shall be exercisable only by the Participant; provided, however, that the
Board may permit or provide in an Award for the gratuitous transfer of the Award by the Participant
to or for the benefit of any immediate family member, family trust or other entity established for
the benefit of the Participant and/or an immediate family member thereof if, with respect to such
proposed transferee, the Company would be eligible to use a Form S-8 for the registration of the
sale of the Common Stock subject to such Award under the Securities Act of 1933, as amended;
provided, further, that the Company shall not be required to recognize any such transfer until such
time as the Participant and such permitted transferee shall, as a condition to such transfer,
deliver to the Company a written instrument in form and substance satisfactory to the Company
confirming that such transferee shall be bound by all of the terms and conditions of the Award.
References to a Participant, to the extent relevant in the context, shall include references to
authorized transferees.

     (b) Documentation. Each Award shall be evidenced in such form (written, electronic or
otherwise) as the Board shall determine. Each Award may contain terms and conditions in addition
to those set forth in the Plan.

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     (c) Board Discretion. Except as otherwise provided by the Plan, each Award may be
made alone or in addition or in relation to any other Award. The terms of each Award need not be
identical, and the Board need not treat Participants uniformly.

     (d) Termination of Status. The Board shall determine the effect on an Award of the
disability, death, termination or other cessation of employment, authorized leave of absence or
other change in the employment or other status of a Participant and the extent to which, and the
period during which, the Participant, or the Participant’s legal representative, conservator,
guardian or Designated Beneficiary, may exercise rights under the Award.

     (e) Withholding. The Participant must satisfy all applicable federal, state, and
local or other income and employment tax withholding obligations before the Company will deliver
stock certificates or otherwise recognize ownership of Common Stock under an Award. The Company
may decide to satisfy the withholding obligations through additional withholding on salary or
wages. If the Company elects not to or cannot withhold from other compensation, the Participant
must pay the Company the full amount, if any, required for withholding or have a broker tender to
the Company cash equal to the withholding obligations. Payment of withholding obligations is due
before the Company will issue any shares on exercise or release from forfeiture of an Award or, if
the Company so requires, at the same time as is payment of the exercise price unless the Company
determines otherwise. If provided for in an Award or approved by the Board in its sole discretion,
a Participant may satisfy such tax obligations in whole or in part by delivery (either by actual
delivery or attestation) of shares of Common Stock, including shares retained from the Award
creating the tax obligation, valued at their Fair Market Value; provided, however, except as
otherwise provided by the Board, that the total tax withholding where stock is being used to
satisfy such tax obligations cannot exceed the Company’s minimum statutory withholding obligations
(based on minimum statutory withholding rates for federal and state tax purposes, including payroll
taxes, that are applicable to such supplemental taxable income). Shares used to satisfy tax
withholding requirements cannot be subject to any repurchase, forfeiture, unfulfilled vesting or
other similar requirements.

     (f) Amendment of Award. Except as otherwise provided in Sections 8(b) and 9(b) with
respect to the vesting of Restricted Stock Awards and Other Stock-Based Awards, Section 11(i) with
respect to Performance Awards or Section 12(d) with respect to actions requiring shareholder
approval, the Board may amend, modify or terminate any outstanding Award, including but not limited
to, substituting therefor another Award of the same or a different type, changing the date of
exercise or realization, and converting an Incentive Stock Option to a Nonstatutory Stock Option.
The Participant’s consent to such action shall be required unless (i) the Board determines that the
action, taking into account any related action, would not materially and adversely affect the
Participant’s rights under the Plan or (ii) the change is permitted under Section 10 hereof.

     (g) Conditions on Delivery of Stock. The Company will not be obligated to deliver any
shares of Common Stock pursuant to the Plan or to remove restrictions from shares previously
delivered under the Plan until (i) all conditions of the Award have been met or removed to the
satisfaction of the Company, (ii) in the opinion of the Company’s counsel, all other legal matters
in connection with the issuance and delivery of such shares have been satisfied, including any
applicable securities laws and any applicable stock exchange or stock

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market rules and regulations, and (iii) the Participant has executed and delivered to the
Company such representations or agreements as the Company may consider appropriate to satisfy the
requirements of any applicable laws, rules or regulations.

     (h) Acceleration. Except as otherwise provided in Sections 8(b), 9(b) and 11(i), the
Board may at any time provide that any Award shall become immediately exercisable in full or in
part, free of some or all restrictions or conditions, or otherwise realizable in full or in part,
as the case may be.

     (i) Performance Awards.

          (1) Grants. Restricted Stock Awards and Other Stock-Based Awards under the Plan may
be made subject to the achievement of performance goals pursuant to this Section 11(i)
(“Performance Awards”), subject to the limit in Section 4(b)(1) on shares covered by such grants.
Subject to Section 11(i)(4), no Performance Awards shall vest prior to the first anniversary of the
date of grant.

          (2) Committee. Grants of Performance Awards to any Covered Employee intended to
qualify as “performance-based compensation” under Section 162(m) (“Performance-Based Compensation”)
shall be made only by a Committee (or subcommittee of a Committee) comprised solely of two or more
directors eligible to serve on a committee making Awards qualifying as “performance-based
compensation” under Section 162(m). In the case of such Awards granted to Covered Employees,
references to the Board or to a Committee shall be treated as referring to such Committee or
subcommittee. “Covered Employee” shall mean any person who is, or whom the Committee, in its
discretion, determines may be, a “covered employee” under Section 162(m)(3) of the Code.

          (3) Performance Measures. For any Award that is intended to qualify as
Performance-Based Compensation, the Committee shall specify that the degree of granting and vesting
shall be subject to the achievement of one or more objective performance measures established by
the Committee, which shall be based on the relative or absolute attainment of specified levels of
one or any combination of the following: net income, earnings before or after discontinued
operations, interest, taxes, depreciation and/or amortization, operating profit before or after
discontinued operations and/or taxes, sales, sales growth, earnings growth, cash flow or cash
position, gross margins, stock price, market share, return on sales, assets, equity or investment,
improvement of financial ratings, achievement of balance sheet or income statement objectives,
total shareholder return, market penetration goals, unit volume, geographic business expansion
goals, drug discovery or other scientific goals, pre-clinical or clinical goals, organizational
goals, regulatory approvals, cost targets and goals relating to acquisitions, divestitures and/or
strategic partnerships.

          (4) Adjustments. Notwithstanding any provision of the Plan, with respect to any
Performance Award that is intended to qualify as Performance-Based Compensation, the Committee may
adjust downwards, but not upwards, the cash or number of Shares payable pursuant to such Award, and
the Committee may not waive the achievement of the applicable performance measures except in the
case of the death or disability of the Participant or a change in control of the Company.

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          (5) Other. The Committee shall have the power to impose such other restrictions on
Performance Awards as it may deem necessary or appropriate to ensure that such Awards satisfy all
requirements for Performance-Based Compensation.

12. Miscellaneous

     (a) No Right To Employment or Other Status. No person shall have any claim or right
to be granted an Award, and the grant of an Award shall not be construed as giving a Participant
the right to continued employment or any other relationship with the Company. The Company
expressly reserves the right at any time to dismiss or otherwise terminate its relationship with a
Participant free from any liability or claim under the Plan, except as expressly provided in the
applicable Award.

     (b) No Rights As Stockholder. Subject to the provisions of the applicable Award, no
Participant or Designated Beneficiary shall have any rights as a stockholder with respect to any
shares of Common Stock to be distributed with respect to an Award until becoming the record holder
of such shares.

     (c) Effective Date and Term of Plan. The Plan shall become effective on the date the
Plan is approved by the Company’s stockholders (the “Effective Date”). No Awards shall be granted
under the Plan after the expiration of 10 years from the Effective Date, but Awards previously
granted may extend beyond that date.

     (d) Amendment of Plan. The Board may amend, suspend or terminate the Plan or any
portion thereof at any time provided that (i) to the extent required by Section 162(m), no Award
granted to a Participant that is intended to comply with Section 162(m) after the date of such
amendment shall become exercisable, realizable or vested, as applicable to such Award, unless and
until the Company’s stockholders approve such amendment if required by Section 162(m) (including
the vote required under Section 162(m)); (ii) no amendment that would require stockholder approval
under the rules of the NASDAQ Stock Market (“NASDAQ”) may be made effective unless and until the
Company’s stockholders approve such amendment; and (iii) if the NASDAQ amends its corporate
governance rules so that such rules no longer require stockholder approval of “material amendments”
to equity compensation plans, then, from and after the effective date of such amendment to the
NASDAQ rules, no amendment to the Plan (A) materially increasing the number of shares authorized
under the Plan (other than pursuant to Sections 4(c) or 10), (B) expanding the types of Awards that
may be granted under the Plan, or (C) materially expanding the class of participants eligible to
participate in the Plan shall be effective unless and until the Company’s stockholders approve such
amendment. In addition, if at any time the approval of the Company’s stockholders is required as
to any other modification or amendment under Section 422 of the Code or any successor provision
with respect to Incentive Stock Options, the Board may not effect such modification or amendment
without such approval. Unless otherwise specified in the amendment, any amendment to the Plan
adopted in accordance with this Section 12(d) shall apply to, and be binding on the holders of, all
Awards outstanding under the Plan at the time the amendment is adopted, provided the Board
determines that such amendment does not materially and adversely affect the rights of Participants
under the Plan. No Award shall be made that is conditioned upon stockholder approval of any
amendment to the Plan.

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     (e) Authorization of Sub-Plans. The Board may from time to time establish one or more
sub-plans under the Plan for purposes of satisfying applicable securities or tax laws of various
jurisdictions. The Board shall establish such sub-plans by adopting supplements to the Plan
containing (i) such limitations on the Board’s discretion under the Plan as the Board deems
necessary or desirable or (ii) such additional terms and conditions not otherwise inconsistent with
the Plan as the Board shall deem necessary or desirable. All supplements adopted by the Board
shall be deemed to be part of the Plan, but each supplement shall apply only to Participants within
the affected jurisdiction and the Company shall not be required to provide copies of any supplement
to Participants in any jurisdiction which is not the subject of such supplement.

     (f) Non-U.S. Participants. Awards may be granted to Participants who are non-U.S.
citizens or residents employed outside the United States, or both, on such terms and conditions
different from those applicable to Awards to Participants employed in the United States as may, in
the judgment of the Board, be necessary or desirable in order to recognize differences in local law
or tax policy. The Board also may impose conditions on the exercise or vesting of Awards in order
to minimize the Board’s obligation with respect to tax equalization for Participants on assignments
outside their home country. The Board may approve such supplements to or amendments, restatements
or alternative versions of the Plan as it may consider necessary or appropriate for such purposes,
without thereby affecting the terms of this Plan as in effect for any other purpose, and the
Secretary or other appropriate officer of the Company may certify any such document as having been
approved and adopted in the same manner as this Plan.

     (g) Compliance with Section 409A of the Code. Except as provided in individual Award
agreements initially or by amendment, if and to the extent any portion of any payment, compensation
or other benefit provided to a Participant in connection with his or her employment termination is
determined to constitute “nonqualified deferred compensation” within the meaning of Section 409A of
the Code and the Participant is a specified employee as defined in Section 409A(a)(2)(B)(i) of the
Code, as determined by the Company in accordance with its procedures, by which determination the
Participant (through accepting the Award) agrees that he or she is bound, such portion of the
payment, compensation or other benefit shall not be paid before the day that is six months plus one
day after the date of “separation from service” (as determined under Section 409A of the Code) (the
“New Payment Date”), except as Section 409A of the Code may then permit. The aggregate of any
payments that otherwise would have been paid to the Participant during the period between the date
of separation from service and the New Payment Date shall be paid to the Participant in a lump sum
on such New Payment Date, and any remaining payments will be paid on their original schedule.

The Company makes no representations or warranty and shall have no liability to the Participant or
any other person if any provisions of or payments, compensation or other benefits under the Plan
are determined to constitute nonqualified deferred compensation subject to Section 409A of the Code
but do not to satisfy the conditions of that section.

     (h) Limitations on Liability. Notwithstanding any other provisions of the Plan, no
individual acting as a director, officer, other employee, or agent of the Company will be liable to
any Participant, former Participant, spouse, beneficiary, or any other person for any claim, loss,
liability, or expense incurred in connection with the Plan, nor will such individual be personally

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liable with respect to the Plan because of any contract or other instrument he or she executes
in his or her capacity as a director, officer, other employee, or agent of the Company. The
Company will indemnify and hold harmless each director, officer, other employee, or agent of the
Company to whom any duty or power relating to the administration or interpretation of the Plan has
been or will be delegated, against any cost or expense (including attorneys’ fees) or liability
(including any sum paid in settlement of a claim with the Board’s approval) arising out of any act
or omission to act concerning this Plan unless arising out of such person’s own fraud or bad faith.

     (i) Governing Law. The provisions of the Plan and all Awards made hereunder shall be
governed by and interpreted in accordance with the laws of the State of Delaware, excluding
choice-of-law principles of the law of such state that would require the application of the laws of
a jurisdiction other than such state.

-17-exv10w3

Exhibit 10.3

Execution Copy

Confidential Materials omitted and filed separately with the

Securities and Exchange Commission. Asterisks denote omissions.

AMENDED AND RESTATED

STRATEGIC COLLABORATION AND

LICENSE AGREEMENT

          This Amended and Restated Strategic Collaboration and License Agreement (the “Agreement”) is
executed this April 28, 2009 (the “Restatement Date”), between Isis Pharmaceuticals, Inc.,
a Delaware corporation having an address at 1896 Rutherford Road, Carlsbad, CA 92008 (“Isis”) and
Alnylam Pharmaceuticals, Inc., a Delaware corporation having an address
at 300 Third Street, Cambridge, Cambridge, MA 02142 (together with its wholly owned subsidiaries
Alnylam U.S., Inc., a Delaware corporation, and Alnylam Europe AG, a company organized under the
laws of Germany, “Alnylam”). Isis and Alnylam may be referred to herein as the “Parties,” or each
individually as a “Party.”

GUIDING PRINCIPLES

          Isis is the leader in RNA-based drug discovery, has created technology, intellectual property,
expertise, facilities and resources to discover and develop oligonucleotide drugs;

          Alnylam is the leader in RNAi therapeutics, has developed and acquired intellectual property,
expertise and technology in RNAi therapeutics, and is conducting research, drug discovery and
development focused on Double Stranded RNA drugs;

          Isis and Alnylam desire to create a long-term strategic relationship that will enhance the
positions of both companies in RNA-based drug discovery;

          Isis will continue to pursue RNA-based drug discovery technology very broadly including all
potential mechanisms of action. Isis will work with Alnylam as Isis’ primary means of
participating in the potential value of Double Stranded RNA Products, and will not enter into any
collaborations with Third Parties the primary purpose of which is to discover Double Stranded RNA
Products;

          Alnylam will focus on RNAi therapeutics and the use of Double Stranded RNA;

          Isis and Alnylam are parties to the Strategic Collaboration and License Agreement dated March
11, 2004 (as amended to date, the “Original Agreement”); and

          Isis and Alnylam now wish to amend and restate the Original Agreement primarily to expand the
Original Agreement by providing each other exclusive licenses to research, develop and
commercialize Single Stranded RNAi Products for a limited pool of gene targets, and co-exclusivity
in the field of Single Stranded RNAi Compounds.

     The objectives of the strategic relationship are to:

	•	 	Enhance the leadership of Alnylam in RNAi therapeutics.

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	•	 	Enhance the potential of Alnylam to develop Double Stranded RNA drugs.
	 
	•	 	Enhance the patent positions of each Party with respect to Double Stranded RNA drugs and
Single Stranded RNAi Products.
	 
	•	 	Provide Isis with a means for participating in the success of RNAi therapeutics.
	 
	•	 	Provide each party with exclusive rights to research, develop and commercialize Single
Stranded RNAi Products for a limited pool of gene targets, and provide each other
co-exclusivity in the field of Single Stranded RNAi Compounds.

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ARTICLE 1

DEFINITIONS; AMENDMENT AND RESTATEMENT

     1.1 Capitalized terms used herein and not defined elsewhere herein have the meanings set forth
in Exhibit 1.1.

     1.2 Effective as of the Restatement Date, this Agreement restates and supersedes the Original
Agreement as amended through the Restatement Date. The terms and conditions of the Original
Agreement shall apply for the period from the Effective Date until the Restatement Date unless
otherwise provided by this Agreement.

ARTICLE 2

EQUITY INVESTMENT

     2.1 In connection with the Original Agreement, Isis purchased from Alnylam 1,666,667 shares of
Series D Preferred Stock, at $6.00 per share (i.e., at an aggregate purchase price of $10,000,002).

ARTICLE 3

MANUFACTURING SERVICES RELATIONSHIP

     3.1 [Intentionally Deleted]

ARTICLE 4

COLLABORATIVE RESEARCH EFFORTS; PROTECTED TARGETS

     4.1 Research Management Committee.

          (a) To promote the success of the collaboration objectives and RNAi technology, the Parties
will establish a Research Management Committee (“RMC”), which will be comprised of equal numbers of
representatives of each of the Parties and will meet at least twice per calendar year, alternating
venues between the vicinities of Cambridge, Massachusetts and Carlsbad, California, to share
scientific direction and data, to coordinate basic research experiments, and to facilitate the
guiding principles of the collaboration.

          (b) Intellectual property representatives of each Party will be invited to participate in RMC
meetings and such meetings will provide a forum to discuss patent prosecution and enforcement
issues and to allocate responsibility for the filing and prosecution of any Joint Patents.

          (c) Through the RMC, the Parties will update one another regarding the progress of the
Research Program (as defined below), including a summary of the work

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each Party has performed thereunder; and regarding their respective Future Chemistry and Motif
and Mechanism Patents.

          (d) The RMC will establish a written clearance policy that will govern any publication or
presentation by a Party in which such Party proposes to include any previously undisclosed
information or intellectual property Controlled by the other Party.

          (e) The RMC and any subcommittees and working groups established by the RMC will dissolve at
the end of the Research Term. Upon termination of the RMC, the Parties will agree upon a strategy
to make decisions about the items in Sections 4.1 (b), (c), and (d).

     4.2 Single Stranded RNAi Collaboration. Subject to Alnylam’s early termination right
set forth in Section 14.4, during the 3 year period following the Restatement Date (the “Research
Term”), the Parties will collaborate in carrying out a research program focused on Single Stranded
RNAi Compounds (the “Research Program”). The Parties may extend the Research Term by mutual
written agreement.

          (a) Research Plan. The Research Program will be carried out in accordance with a
written research plan, including without limitation the Budget (as defined below), which research
plan shall be mutually agreed upon by the Parties (the “Research Plan”). The initial outline of
the Research Plan agreed to by the Parties as of the Restatement Date is hereby incorporated into
this Agreement by reference and is made a part of this Agreement; provided, within [**]
days of the Restatement Date, the Parties will complete and agree in writing on an initial Research
Plan, including without limitation an initial Budget, which is hereby incorporated into this
Agreement by reference and is made a part of this Agreement. The purpose of the Research Plan is
to detail the responsibilities and activities of Isis and Alnylam with respect to carrying out the
Research Program. The Research Plan will include a description of the specific activities to be
performed by the Parties in support of the Research Program, the allocation of Isis FTEs and
Alnylam FTEs to perform such activities, projected timelines for completion of such activities, and
an applicable budget (the “Budget”). The Budget for the Research Program must be mutually agreed
by the Parties and will be at least $3,000,000 per year during the Research Term, including without
limitation budgeted costs of Isis FTEs and Alnylam FTEs, and external costs. Beginning in 2010,
at least once during September of each year of the Research Term, the RMC will review the Research
Plan and will amend the Research Plan, as may be necessary, from time to time. In addition, each
Calendar Quarter the RMC will review the progress of the work under the Research Plan, including
spending against the Budget, and recommend adjustments to the Budget as necessary to support the
Research Plan. The Research Plan, including without limitation any Budget, may only be amended
with the written approval of the RMC. If the activities contemplated by the Research Plan at any
time do not justify the number of Isis FTEs allocated to the Research Program, the Parties will
work in good faith to mutually agree to modify the scope of the Research Plan or adjust the number
of Alnylam funded FTEs and related Budget; provided that the minimum Budget for the
Research Plan shall be as set forth in this Section 4.2(a). For clarity, Alnylam shall not be
required to agree to any Budget which exceeds $3,000,000 per year.

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          (b) Research Staffing. Subject to Alnylam’s obligations under Section 4.2(c), the
Research Plan will provide for (and Isis will supply) a minimum of [**] Isis FTEs per year during
the initial two-year period of the Research Term to perform activities in support of the Research
Program and a minimum of [**] Isis FTEs during the third year of the Research Program. Each Party
will supply the number of FTEs the Research Plan specifies that such Party will supply, and will
conduct the Research Program diligently and in good scientific manner, and in compliance with all
applicable good laboratory practices, and applicable legal requirements, to attempt to achieve
efficiently and expeditiously the objectives of the Research Program. Each Party will comply with
all Applicable Laws, in the performance of work under this Agreement.

          (c) Research Funding. Alnylam will fund 100% of the costs of conducting the Research
Program in accordance with the Research Plan (collectively, the “Research Costs”) to the extent
that such Research Costs are incurred under the Budget, including without limitation FTEs (whether
employed by Isis or Alnylam) plus any out-of-pocket expenses specified in the Research Plan. By
[**], 2009 with respect to the second Calendar Quarter of 2009 and thereafter within [**] Days
following [**] each Calendar Quarter, Alnylam will pay Isis [**] for the Alnylam-funded Isis FTEs
assigned to the Research Program for such Calendar Quarter (a prorated amount shall be payable for
any portion of a Calendar Quarter). With respect to any work to be performed in support of the
Research Program during the [**] days following the Restatement Date, if the Parties have not
agreed on an initial Research Plan, then Alnylam will make [**] payments for such work based on
[**] Isis FTEs. No later than [**] days following the end of each Calendar Quarter, Isis will
provide Alnylam with a report of the number of FTEs actually assigned to the Research Program with
a summary of the FTEs who performed under the Research Program (“Actual FTE Costs”) and a
reasonably detailed accounting of all other Research Costs actually incurred by Isis during such
Calendar Quarter (“Actual External Costs”). Alnylam shall not be responsible for any Research
Costs incurred by Isis that exceed the [**] amount in the Budget for the work specified in the
Research Plan to be conducted by Isis (“Excess Amount”), unless the RMC approves an amendment to
the Budget to include such Excess Amount. Similarly, (i) Alnylam will promptly provide Isis a
summary of the Alnylam FTEs who performed under the Research Program for a given Calendar Quarter
and a reasonably detailed accounting of all other Research Costs actually incurred by Alnylam
during such Calendar Quarter, and (ii) Research Costs incurred by Alnylam that exceed the total
amount in the Budget for the work specified in the Research Plan to be conducted by Alnylam will
not reduce the amounts committed in the Budget to fund Isis’ Research Costs. In addition, upon
reasonable request, each Party shall provide the other Party with reasonable documentation of
Research Costs incurred by such Party during the Research Term and shall grant the other Party
reasonable audit rights consistent with the terms set forth in Section 9.3 in connection with such
Research Costs.

          (d) Materials Transfer. In order to facilitate the Research Program, either Party may
provide to the other Party certain materials for use by the other Party in furtherance of the
Research Program. All such materials shall be used by the receiving Party in accordance with the
terms and conditions of this Agreement solely for purposes of performing its rights and obligations
under this Agreement and the Research Plan, and the receiving Party shall not transfer such
materials to any Third Party unless expressly

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contemplated by this Agreement or the Research Plan, or upon the written consent of the
supplying Party.

     4.3 Enabled Targets for Single Stranded RNAi.

          (a) Enabled Targets. Each Party will have a pool (with respect to either Party, an
“Enabled Target Pool”; with respect to Isis, the “Isis Enabled Target Pool”; and, with respect to
Alnylam, the “Alnylam Enabled Target Pool”) each containing [**] slots for which such Party can
designate certain Gene Targets against which such Party intends to research, develop and
commercialize a Single-Stranded RNAi Product (each such slot, an “Enabled Target Slot” and any Gene
Target occupying such a slot, an “Enabled Target”); provided, however, that, each time a
Party (the “Advancing Party”) designates as a Development Candidate a Single Stranded RNAi Product
Designed for one of such Advancing Party’s Enabled Targets, then (i) such Enabled Target will be
considered to have graduated from the Advancing Party’s Enabled Target Pool (a “Graduated Enabled
Target”), (ii) the Advancing Party will be permitted to designate a new Enabled Target to fill the
open Enabled Target Slot in the Advancing Party’s Enabled Target Pool, and (iii) so long as the
Advancing Party continues to maintain an Active Program for the applicable Single Stranded RNAi
Product Designed for the Graduated Enabled Target, such Graduated Enabled Target will remain an
Enabled Target of such Advancing Party hereunder. For purposes of clarity, except as set forth in
Sections 5.1(g)(i), 5.1(h)(i), 5.5, 6.6, 6.1(h)(i) and 6.1(i)(i), as applicable, neither Party may
research, develop or commercialize a Single Stranded RNAi Product other than a Single Stranded RNAi
Product Designed for one of such Party’s Enabled Targets.

          (b) Designating Enabled Targets. Within thirty (30) days following completion of
[**], the Parties will begin the process set forth below for selecting Enabled Targets for
inclusion in each Party’s Enabled Target Pool. For clarity, at no time may either Party designate
a Gene Target which is in the other Party’s Enabled Target Pool. Except as set forth in Section
4.3(e) below, the Parties will designate Enabled Targets by taking alternating turns (each Party’s
designation of a new Gene Target (a “Pick”) or affirmative election not to designate an Enabled
Target (a “Pass”) shall be considered a “Turn”; and each round in which Isis and Alnylam have each
Picked or Passed once shall be considered a “Round”) in one or more Rounds, as necessary. For each
Turn, a Party shall either Pick or Pass within five (5) Business Days (it being understood that if
a Party does not provide affirmative notice of a Pick or Pass within such five (5) Business
Day-period, then such Party shall be deemed to have “Passed” in such Turn). The Parties will
complete Rounds until the Parties have either (i) both filled all of their respective Enabled
Target Slots, or (ii) both elected to Pass in the same Round, thereby completing a Round (such
point being the end of a “Selection Session”, which Selection Session includes all of the Rounds
completed since the end of the last Selection Session (or, in the case of the first Selection
Session, all prior Rounds)). For purposes of clarity, either Party may, prior to Picking or
Passing in such Party’s Turn in any ongoing Round, remove any existing Gene Target(s) on its
Enabled Target List in accordance with Section 4.3(d) and use its Pick in such Turn to Pick a
different Gene Target as an Enabled Target on its Enabled Target List, subject to the [**] Enabled
Target Slot limitation. Either Party may initiate a new Selection Session at any time by providing
written notice to the other Party (such new Selection Session to begin on the

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first Business Day following the 30th day following such notice). For each new
Selection Session, the Party who gets to take the first Turn in the First Round will be determined
in accordance with Section 4.3(c) below.

          (c) Determining First Turn. Alnylam will take the first Turn in the first Round of
the first Selection Session. Thereafter:

               (i) If, immediately prior to the start of a Selection Session, one Party (the “Lopsided
Party”) has fewer Enabled Targets in its Enabled Target Pool than the number of Enabled Targets the
other Party has in such other Party’s Enabled Target Pool, then the Lopsided Party will take the
first Turn in the First Round. In such event (1) in each Turn the Lopsided Party makes a [**] that
is not a [**] the other Party [**] until both Parties have an [**] in their respective Enabled
Target Pools (and then subsequent Rounds in the Selection Session will continue in accordance with
Section 4.3(c)(iii) below with the other Party getting the first Pick in the first such subsequent
Round); and (2) if the Lopsided Party [**] or [**] in a Turn, the other Party may Pick or Pass (and
then any subsequent Rounds in the Selection Session will continue in accordance with Section
4.3(c)(iii) below).

               (ii) If there is no Lopsided Party immediately prior to the start of a Selection Session, then
the Party who was not the last Party to Pass in the prior Selection Session shall be the first
Party to take the first Turn in the first Round of such new Selection Session (and then any
subsequent Rounds in the Selection Session will continue in accordance with Section 4.3(c)(iii)
below).

               (iii) For any subsequent Rounds in a Selection Session, the Party who was not the
first Party to take a Turn in the most previous Round will have the first Turn in the next Round.

               (iv) The Parties have attached as Exhibit 4.3(c)(iv) examples of how the Parties intend this
Section 4.3(c) to operate.

          (d) Removing Enabled Targets. From time to time after the Restatement Date (except
during the 30-day period immediately preceding a Selection Session or when a Lopsided Party is
taking Turns under Section 4.3(c)(i)), each Party may remove a Gene Target from its Enabled Target
Pool upon written notice to the other Party (which removal will create an open Enabled Target
Slot). In addition, on an Enabled Target-by-Enabled Target basis, if the applicable Party has not
designated a Development Candidate comprising a Single Stranded RNAi Product Designed for the
applicable Enabled Target before the [**] year anniversary of the date such Party added the
applicable Enabled Target to such Party’s Enabled Target Pool, then such Gene Target will be
automatically removed from such Party’s Enabled Target Pool. Once a Party removes a Gene Target
from its Enabled Target Pool (whether voluntarily or by operation of this Section 4.3(d)), such
Gene Target shall no longer be deemed an Enabled Target hereunder and the removing Party will be
prevented from later adding such Gene Target to its Enabled Target Pool until [**] months have
passed from the date such Gene Target was removed.

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          (e) Isis Protected Targets. Notwithstanding the foregoing, Alnylam may not designate
as one of Alnylam’s Enabled Targets any of the Gene Targets identified as an Isis Protected Target
in the letter Isis issued to Alnylam on the Restatement Date (collectively, the “Isis Protected
Targets”).

               (i) With respect to any Isis Protected Target Isis identified as an Isis Protected Target on
the Restatement Date due to a contractual restriction that prevents or otherwise restricts Isis’
ability to grant a license to Alnylam under Sections 5.1(g) and 5.1(h) (each an “Isis Partnered
Excluded Target”), (1) Isis shall list in the above-reference letter such Isis Partnered Excluded
Targets separately such that they are clearly distinguished from other Isis Protected Targets, (2)
Isis shall diligently enforce the relevant terms governing Isis’ rights to clear any contractual
restrictions on such Isis Partnered Excluded Target, (3) once a particular contractual restriction
clears or expires on such Isis Partnered Excluded Target, such Gene Target will no longer be
considered an Isis Protected Target, such that Alnylam may then designate such Gene Target as one
of its Enabled Targets in accordance with the terms of this Agreement, and (4) when practical (but
at least every [**] months), Isis shall update the list of Isis Protected Targets to remove Gene
Targets that are no longer Isis Partnered Excluded Targets.

               (ii) For purposes of clarity, except as permitted under Sections 6.1(h)(i) and 6.1(i)(i), Isis
may not research, develop or commercialize a Single-Stranded RNAi Product Designed for any Isis
Protected Target unless such Isis Protected Target is designated as an Enabled Target by Isis
pursuant to Section 4.3(b) above or the remainder of this Section 4.3(e)(ii). Notwithstanding
anything in this Section 4.3 to the contrary, with respect to any Isis Partnered Excluded Target
for which the applicable contractual restriction has cleared or expired (each, a “Cleared Target”)
(A) Isis shall not have the right to designate such a Cleared Target as one of its Enabled Targets
until Isis has provided written notice to Alnylam of such clearance (as part of the regular updates
contemplated in Section 4.3(e)(i) above or otherwise) (such notice, a “Clearance Notice”), and (B)
in the first Selection Session following Alnylam’s Receipt of the applicable Clearance Notice with
respect to a particular Cleared Target, Isis may not Pick such Cleared Target as one of its Enabled
Targets until and unless Alnylam has had a full Turn in such Selection Session in which it could
Pick such Cleared Target as one of its Enabled Targets and does not elect to Pick such Cleared
Target. For example, if two Gene Targets become Cleared Targets (and Alnylam receives a Clearance
Notice related thereto) immediately prior to the start of a Selection Session and Isis has the
first Turn, (1) Isis may not Pick either such Cleared Target in its first Turn, (2) in Alnylam’s
next Turn, Alnylam could Pick either such Cleared Target, and (3) once Alnylam opts to Pick a Gene
Target (whether or not such Pick was for one of the two Cleared Targets) or Pass, Isis may then
pick either of the remaining two such Cleared Targets that it was prohibited from Picking in its
previous Turn.

          (f) Confidentiality. The fact that a Party has designated or removed a particular
Gene Target within its Enabled Target Pool is Confidential Information of such Party, subject to
the provisions of Article 12. Neither Party shall disclose such Confidential Information of the
other Party to any Third Party, including its Third Party collaborators, or use such Confidential
Information of the other Party to guide its own (or its Third Party collaborators’) decisions to
pursue particular Gene Targets, but either

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Party can use such Confidential Information to decline a Third Party’s request for a license
to such Gene Target. The Isis Protected Targets are Isis’ Confidential Information.

          (g) Review Designating Process. The Parties agree that on or about the three year
anniversary of the Restatement Date, if either Party deems appropriate, the Parties will, in good
faith, review the process for designating Enabled Targets for the purposes of improving the process
for the mutual benefit of both Parties, and if necessary, amend this Section 4.3, to effect such
improvements; provided, however, that either Party shall have the right to refuse any such changes
in its sole discretion.

ARTICLE 5

LICENSES GRANTED BY ISIS TO ALNYLAM; AND

CO-EXCLUSIVITY COVENANT

     5.1 License Grants. Subject to the terms and conditions of this Agreement, including,
but not limited to, the restrictions set forth in Section 5.3, Isis grants Alnylam the following
licenses:

          (a) Under Isis Current Motif and Mechanism Patents and Isis Current Chemistry Patents, a
license to research, develop, make, have made, use, import, offer to sell and sell Double Stranded
RNA and Double Stranded RNA Products.

          (b) Subject to the terms of Section 11.8, under Isis Future Motif and Mechanism Patents, Isis
Future Chemistry Patents and Isis’ rights in Joint Patents, a license to research, develop, make,
have made, use, import, offer to sell and sell Double Stranded RNA and Double Stranded RNA
Products.

          (c) Under the Isis Current Motif and Mechanism Patents and Isis Current Chemistry Patents, a
license to research, develop, make, have made, use, import, offer to sell and sell MicroRNA
Products.

          (d) Subject to the terms of Section 11.8, under the Isis Future Motif and Mechanism Patents
and Isis Future Chemistry Patents, a license to research, develop, make, have made, use, import,
offer to sell and sell MicroRNA Products.

          (e) A royalty-free, fully paid, license to practice any Know-How disclosed to Alnylam during
the performance of this Agreement, subject to the non-disclosure but not the non-use provisions
contained in Article 12.

          (f) A fully paid, royalty-free license under Isis Manufacturing Patents to research, develop,
make, have made, use and import Alnylam Products for Research Use.

          (g) Under the Isis Current Motif and Mechanism Patents and Isis Current Chemistry Patents, a
license to (i) research, develop, make, have made, use and import Single Stranded RNAi Compounds
and Single Stranded RNAi Products for Research

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Use, and (ii) research, develop, make, have made, use, import, offer to sell and sell Alnylam
Single Stranded RNAi Products.

          (h) Subject to the terms of Section 11.8, under Isis Future Motif and Mechanism Patents, Isis
Future Chemistry Patents and Isis’ rights in Joint Patents, a license to (i) research, develop,
make, have made, use and import Single Stranded RNAi Compounds and Single Stranded RNAi Products
for Research Use, and (ii) research, develop, make, have made, use, import, offer to sell and sell
Alnylam Single Stranded RNAi Products.

          (i) Under Isis’ rights in Research Program Patents, a royalty-free license for any and all
purposes, except to research, develop, make, have made, use, import, offer to sell or sell
any (1) oligonucleotides (or chemically modified oligonucleotide analogs) designed to work via the
RNase H 1 or 2 mechanism (including any oligonucleotide which has [**]), (2) Double Stranded RNA
Products, (3) MicroRNA Products, (4) Single Stranded RNAi Products, or (5) Isis Single Stranded
Products.

     5.2 License Exclusivity, Territory and Sublicenses.

          (a) Subject to the terms and conditions of this Agreement, including the restrictions set
forth in Section 5.3, the licenses from Isis to Alnylam granted in Sections 5.1(a) and (b) are
worldwide and co-exclusive (with Isis), with the exclusive right to grant Naked Sublicenses; the
licenses from Isis to Alnylam granted in Sections 5.1 (c), (d), (e), (f), (g)(i), (h)(i) and (i)
are worldwide and nonexclusive; and the licenses from Isis to Alnylam granted in Sections 5.1
(g)(ii) and (h)(ii) are worldwide and exclusive. Alnylam is not permitted to grant sublicenses
under the licenses granted in Sections 5.1(a) through 5.1(e), except that Alnylam is permitted to
grant (i) sublicenses in connection with a Bona Fide Drug Discovery Collaboration, (ii) sublicenses
in connection with a Development Collaboration, (iii) Naked Sublicenses and (iv) sublicenses under
the license granted in Section 5.1(e) in connection with the discovery, development or
commercialization of any product. Furthermore, Alnylam is not permitted to grant sublicenses under
the licenses granted in Section 5.1(f). Alnylam may grant sublicenses under Section 5.1(i),
subject to Section 7.7.

          (b) Alnylam may grant sublicenses under the licenses granted in Sections 5.1(g) and 5.1(h)
only to further the research, development or commercialization of an Alnylam Single Stranded RNAi
Product that Alnylam has performed on its own (or with Isis under the Research Plan) and [**] at
least [**]% of the work to discover and develop the Alnylam Single Stranded RNAi Product through
the [**] (or a date that is earlier than the [**] if requested by Alnylam and approved in writing
by Isis, such approval not to be unreasonably withheld).

          (c) Alnylam cannot sublicense its right to grant Naked Sublicenses under this Agreement except
that Alnylam may permit its sublicensees to grant further sublicenses in connection with a
sublicense to further the research, development or commercialization of an Alnylam Product.

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          (d) Notwithstanding the foregoing, (i) Alnylam acknowledged and permits the license Isis
granted [**], as amended through the Restatement Date, that granted [**] a nonexclusive license
under Isis Current Motif and Mechanism Patents and Isis Current Chemistry Patents for the
manufacture and sale of chemically modified oligonucleotides for [**] only and (ii) Isis may
continue to grant licenses to Third Parties for the purpose of manufacturing and selling
oligonucleotides; provided that, to the extent such licenses cover Double Stranded
RNA or Single Stranded RNAi Compounds, Isis will restrict such licenses to [**].

     5.3 Limitations on Licenses.

          (a) The licenses granted under Section 5.1 above are not intended to grant any rights to
Alnylam to practice the Isis Excluded Technology. If Alnylam wishes to license any Isis Excluded
Technology for which Isis has the right to grant a license or sublicense, Isis will negotiate in
good faith an appropriate license.

          (b) Notwithstanding the licenses granted to Alnylam under Section 5.1, Isis retains its rights
in the Isis Patent Rights and in the Joint Patents (i) exclusively for the Isis Reserved
DS-Targets, and (ii) exclusively for the Isis Encumbered Targets. Once a particular contractual
restriction expires on an Isis Encumbered Target, Alnylam’s licenses under Section 5.1 will no
longer be limited under this Section 5.3(b) for such target and such target shall no longer be an
Isis Encumbered Target. Isis will update the [**] (as defined in the letter agreement dated March
9, 2004 between Alnylam and Isis) provided to Alnylam prior to the Effective Date and subsequent
[**] provided to Alnylam from time to time to remove targets that are no longer Isis Encumbered
Targets promptly upon receipt of a written request from Alnylam to update such [**], but will not
be required to update such [**] more frequently than [**] a calendar quarter. In addition, the
licenses granted by Isis to Alnylam under each of Sections 5.1(g)(i) and 5.1(h)(i) do not include
the right to research, develop, make, have made, use, or import Single Stranded Compounds or Single
Stranded RNAi Products, in each case that are Designed for Isis’ Enabled Targets or the Isis
Protected Targets.

          (c) Licenses to Isis Patent Rights that are joint patents with Third Parties (i.e., invented
by one or more Isis inventors and one or more non-Isis inventors) are licensed subject to the
retained rights of any non-Isis inventors and their assignees and licensees. Any such retained
rights of non-Isis inventors and their assignees and licensees existing as of the Restatement Date
are set forth in Exhibit 5.3(c) attached hereto.

          (d) Licenses to Isis Patent Rights that are subject to contractual obligations between Isis
and Third Parties in effect as of the Restatement Date are licensed subject to the restrictions and
other terms described in Exhibit 5.3(d) attached hereto. Alnylam hereby agrees to comply, and to
cause its sublicensees to comply, with such restrictions and other terms.

     5.4 Alnylam Covenant Regarding Sublicensing of Isis Patent Rights. Alnylam shall use
good faith efforts to include sublicenses under the licenses under the Isis Patent Rights granted
to Alnylam in Sections 5.1(a) and 5.1(b) in any Third Party collaboration

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or license agreement in which Alnylam grants rights to develop and commercialize Double
Stranded RNA Products, unless the technology covered by such licensed Isis Patent Rights would not
reasonably be expected to advance the goals of such Third Party collaboration or license
relationship.

     5.5 Isis Covenant to Alnylam Regarding Co-Exclusivity for Single Stranded RNAi
Products. Isis hereby covenants to Alnylam, that, after the Restatement Date, Isis will not
itself, and will not grant to a Third Party a license under the Isis Current Motif and Mechanism
Patents, Isis Current Chemistry Patents, Isis Future Motif and Mechanism Patents, Isis Future
Chemistry Patents, the Co-Exclusive ssRNAi Patents, and/or Isis’ rights in any Joint Patents or
Research Program Patents to, research, develop, make, have made, use, import, offer to sell and
sell Single Stranded RNAi Compounds or Single Stranded RNAi Products, except Isis may (i) research,
develop, make, have made, use and import Single Stranded RNAi Compounds or Single Stranded RNAi
Products for [**], (ii) grant a license to Controlled Contractors to support work under the
Research Plan, (iii) grant a license to further the research, development or commercialization of
an Isis Single Stranded Product, (iv) grant a license to further the research, development or
commercialization of an Isis Single Stranded RNAi Product solely in conjunction with a permitted
sublicense by Isis under Section 6.3; and (v) continue to grant licenses to Third Parties for the
purpose of manufacturing and selling oligonucleotides; provided that, to the extent such
licenses cover Single Stranded RNAi Compounds, Isis will restrict such licenses to [**]. For
purposes of clarity, this Section 5.5 will not preclude Isis from (A) itself using the [**], or (B)
granting any Third Party a license under the [**].

ARTICLE 6

LICENSES GRANTED BY ALNYLAM TO ISIS; AND

CO-EXCLUSIVITY COVENANT

     6.1 License Grants. Subject to the terms and conditions of this Agreement, including,
but not limited to, the restrictions set forth in Section 6.5, Alnylam grants Isis the following
licenses:

          (a) A fully-paid, royalty-free, nonexclusive license under Alnylam Current Motif and Mechanism
Patents and Alnylam Current Chemistry Patents to research, develop, make, have made, use and import
Isis Products other than Isis Single Stranded RNAi Products for Research Use.

          (b) Subject to the terms of Section 11.8, a fully paid, royalty-free nonexclusive license
under Alnylam Future Motif and Mechanism Patents and Alnylam Future Chemistry Patents to research,
develop, make, have made, use and import Isis Products other than Isis Single Stranded RNAi
Products for Research Use.

          (c) A nonexclusive license under Alnylam Current Motif and Mechanism Patents and Alnylam
Current Chemistry Patents to research, develop, make, have made, use, import, offer to sell and
sell Isis Single Stranded Products.

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          (d) Subject to the terms of Section 11.8, a nonexclusive license under Alnylam Future Motif
and Mechanism Patents and Alnylam Future Chemistry Patents to research, develop, make, have made,
use, import, offer to sell and sell Isis Single Stranded Products.

          (e) Under the Alnylam Current Motif and Mechanism Patents and Alnylam Current Chemistry
Patents, a nonexclusive license to research, develop, make, have made, use, import, offer to sell
and sell MicroRNA Products.

          (f) Subject to the terms of Section 11.8, under the Alnylam Future Motif and Mechanism Patents
and Alnylam Future Chemistry Patents, a nonexclusive license to research, develop, make, have made,
use, import, offer to sell and sell MicroRNA Products.

          (g) A worldwide, royalty-free, fully paid, nonexclusive license to practice any Know-How
disclosed to Isis during the performance of this Agreement, subject to the non-disclosure but not
the non-use provisions contained in Article 12.

          (h) A worldwide license under the Alnylam Current Motif and Mechanism Patents and Alnylam
Current Chemistry Patents to (i) research, develop, make, have made, use and import Single Stranded
RNAi Compounds and Single Stranded RNAi Products for Research Use, and (ii) research, develop,
make, have made, use, import, offer to sell and sell Isis Single Stranded RNAi Products. The
license granted to Isis under the foregoing clause (i) shall be non-exclusive, and the license
granted to Isis under the foregoing clause (ii) shall be exclusive.

          (i) Subject to the terms of Section 11.8, a worldwide license under Alnylam Future Motif and
Mechanism Patents and Alnylam Future Chemistry Patents to (i) research, develop, make, have made,
use and import Single Stranded RNAi Compounds and Single Stranded RNAi Products for Research Use,
and (ii) research, develop, make, have made, use, import, offer to sell and sell Isis Single
Stranded RNAi Products. The license granted to Isis under the foregoing clause (i) shall be
non-exclusive, and the license granted to Isis under the foregoing clause (ii) shall be exclusive.

          (j) Under Alnylam’s rights in Research Program Patents, a royalty-free license for any and all
purposes, except to research, develop, make, have made, use, import, offer to sell or sell
any (1) oligonucleotides (or chemically modified oligonucleotide analogs) designed to work via the
RNase H 1 or 2 mechanism (including any oligonucleotide which has [**]), (2) Double Stranded RNA
Products, (3) MicroRNA Products, (4) Single Stranded RNAi Products, or (5) Isis Single Stranded
Product.

     6.2 License Option. For each Gene Target in the Isis DS-Target Pool (as further
described below) Alnylam grants Isis an option to obtain (on a Reserved DS-Target-by-Reserved
DS-Target basis), subject to the terms and conditions of this Agreement, including, but not limited
to, the restrictions set forth in Section 6.5, a non-exclusive license under (i) Alnylam Current
Motif and Mechanism Patents and Alnylam Current Chemistry Patents and (ii) subject to the terms of
Section 11.8, Alnylam Future

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Motif and Mechanism Patents, Alnylam Future Chemistry Patents and Alnylam’s rights in Joint
Patents, to research, develop, make, have made, use, import, offer for sale and sell Double
Stranded RNA Products that are Isis Products.

          (a) This option will expire on a Reserved DS-Target-by-Reserved DS-Target basis if Isis has
not paid Alnylam the option fee set forth in Section 8.1 below before the earlier of (i) the [**]
with respect to such Reserved DS-Target, (ii) the [**] anniversary of the date such Reserved
DS-Target [**] or the [**] anniversary of the date such Reserved DS-Target [**] with a Third Party
and Isis is contractually able to revoke such Third Party’s rights or (iii) the date [**] with
respect to such Reserved DS-Target.

          (b) For any Reserved DS-Target for which Isis obtains a license from Alnylam under this
Section 6.2, Isis will use Commercially Reasonable Efforts (either on its own or in an Antisense
Drug Discovery Program or Development Collaboration) to develop and commercialize Double Stranded
RNA Products that modulate such Reserved DS-Target.

     6.3 Sublicenses.

          (a) With respect to any license granted by Alnylam pursuant to Section 6.1(a), 6.1(b), or 6.2,
Isis may only grant a sublicense to a Third Party solely for (i) the purpose of enabling such Third
Party to collaborate with Isis in an Antisense Drug Discovery Program, or (ii) to develop and
commercialize an Isis Product in a Development Collaboration. With respect to any license granted
by Alnylam pursuant to Section 6.1(c), 6.1(d), 6.1(e), 6.1(f), 6.1(g), Isis may grant a sublicense
to a Third Party in connection with the discovery, development or commercialization of any product.
Isis may grant sublicenses under Section 6.1(j), subject to Section 8.5. With respect to the
licenses granted by Alnylam pursuant to Section 6.1(h) and 6.1(i), Isis may only grant a sublicense
to a Third Party to further the research, development or commercialization of an Isis Single
Stranded RNAi Product that Isis has performed on its own (or with Alnylam under the Research Plan)
and [**] at least [**]% of the work to discover and develop the Isis Single Stranded RNAi Product
through the [**] (or a date that is earlier than the [**] if requested by Isis and approved in
writing by Alnylam, such approval not to be unreasonably withheld).

          (b) Notwithstanding anything in this Agreement to the contrary, Isis may not enter into any
drug discovery collaboration the primary purpose of which is to discover Double Stranded RNA
Products and/or to develop Double Stranded RNA Products to any point up to the [**].

     6.4 DS-Target Pool.

          (a) Reserved DS-Target Slots. On the Effective Date, Isis will have a pool (the “Isis
DS-Target Pool”) containing up to [**] slots for which Isis can designate certain Gene Targets
solely for Antisense Drug Discovery Programs (each such slot, a “DS-Target Slot” and any Gene
Target occupying such a slot, a “Reserved DS-Target”); provided, however, that on January 1
of each year starting with January 1, 2007, Isis will gain the right to purchase one additional
DS-Target Slot by paying Alnylam $[**] per

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each additional DS-Target Slot. These rights are cumulative and, subject to Section 17.2(c)
do not expire during the License Term. Furthermore, in the event that Isis pays the $[**] license
option fee for a Reserved DS-Target pursuant to Section 8.1, such Reserved DS-Target will be
considered to have graduated from the Isis DS-Target Pool, and, subject to Section 6.4(e), Isis
will be permitted to designate a new Reserved DS-Target to fill the open DS-Target Slot in the Isis
DS-Target Pool. For purposes of clarity, except as permitted under Sections 6.1(h)(i) and
6.1(i)(i), Isis may not research, develop or commercialize Single Stranded RNAi Products for a
Reserved DS-Target unless such Reserved DS-Target is designated as an Enabled Target by Isis
pursuant to Section 4.3(a) above.

          (b) Initial Designations. The letter delivered by Isis to Alnylam on the Restatement
Date sets forth the Reserved DS-Targets as of the Restatement Date.

          (c) Removing/Adding DS-Targets. After the Restatement Date and no more than once in
any [**] period (a “Target Reallocation Period”), Isis may do any of the following:

(i) Remove a Gene Target from the Isis DS-Target Pool (which, following
such removal will create an open DS-Target Slot); or

(ii) Add a new Gene Target to any open DS-Target Slot (subject to the
procedures and provisions of Section 6.4(e).

          Notwithstanding the foregoing provisions of this Section 6.4(c), in any Target Reallocation
Period, Isis cannot remove a number of Reserved DS-Targets that exceeds the number calculated by
dividing the then current number of DS-Target Slots by [**] and rounding down to the nearest whole
number. For the purpose of the limitation described in the immediately preceding sentence,
removing a Gene Target from the Isis DS-Target Pool and then filling the open DS-Target Slot
created by such removal shall count as a single removal. Once Isis removes a Gene Target from the
Isis DS-Target Pool, Isis will be prevented from later adding such Gene Target to the Isis
DS-Target Pool until [**] have passed from the date Isis removed such Gene Target.

          (d) New Target Request. When Isis wishes to add a new Gene Target to occupy a vacant
DS-Target Slot, it will provide Alnylam with written notice (the “Request Notice”) of the Gene
Target it wishes to add (the “Proposed Reserved DS-Target”). The Request Notice will include the
gene name, and the NCBI accession number or nucleic acid sequence for the Proposed Reserved
DS-Target.

          (e) New Target Rejection/Approval. Within [**] of receipt of the Request Notice,
Alnylam will give Isis written notice if any of the criteria set forth below applied to such
Proposed Reserved DS-Target at the time of Alnylam’s receipt of the Request Notice. If, at such
time, the Proposed Reserved DS-Target is (i) subject to Alnylam’s own Active Program [**], (ii)
encumbered by a contractual obligation between Alnylam and a Third Party that would preclude
Alnylam from granting a license under Section 6.2 with respect to the Proposed Reserved DS-Target
or (iii) the subject of Alnylam’s good

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faith negotiations to enter into a contractual obligation within the [**] following receipt of
the Request Notice with a Third Party (as supported by a written request from such Third Party)
that would preclude Alnylam from granting a license under Section 6.2 with respect to the Proposed
Reserved DS-Target, then the Proposed Reserved DS-Target will be rejected and will not become a
Reserved DS-Target. If the Proposed Reserved DS-Target is not rejected under this subsection (e),
the Proposed Reserved DS-Target will become an Isis Reserved DS-Target. Alnylam will promptly
notify Isis in writing if a rejected Proposed Reserved DS-Target later becomes available to be
designated as a Reserved DS-Target.

          (f) [Intentionally Deleted].

          (g) Diligence on Rejected Targets. If (i) Alnylam rejects a Proposed Reserved
DS-Target under Section 6.4(e) above and (ii) Alnylam has [**] with respect to such rejected
Proposed Reserved DS-Target by the [**] anniversary of the date Alnylam rejected such Proposed
Reserved DS-Target if Alnylam is working on such target alone, or the [**] anniversary of the date
Alnylam rejected such Proposed Reserved DS-Target if such rejected Proposed Reserved DS-Target is
subject to a contractual obligation between Alnylam and a Third Party that would preclude Alnylam
from granting a license under Section 6.2 with respect to the rejected Proposed Reserved DS-Target
but Alnylam [**], then [**] such rejected Proposed Reserved DS-Target [**].

          (h) Diligence Obligations in Third Party Contractual Obligations. With the goal of
minimizing contractual encumbrances on Alnylam Patent Rights with respect to Gene Targets in the
absence of a reasonable intent to discover and develop products that modulate such Gene Targets by
Third Parties with which Alnylam enters into such contractual obligations, Alnylam intends to seek
reasonable diligence obligations from Third Parties in negotiating contracts between Alnylam and
such Third Parties that would constitute contractual obligations of Alnylam that would preclude
Alnylam from granting licenses to Isis under Section 6.2 with respect to Proposed Reserved
DS-Targets; or that would prevent Alnylam from granting Isis licenses with respect to Proposed
Reserved DS-Targets; provided that Isis hereby acknowledges that such diligence
obligations are often heavily negotiated in biotechnology license and collaboration agreements and
that this Section 6.4(h) shall not prevent Alnylam from entering into contracts between Alnylam and
Third Parties in accordance with Alnylam’s reasonable business judgment.

          (i) Confidentiality. The fact that Isis has designated or removed a particular Gene
Target within the Isis DS-Target Pool is Confidential Information of Isis, or that Alnylam has
rejected a particular Gene Target proposed for a DS-Target Slot or disallowed the redesignation of
a particular Gene Target is Confidential Information of Alnylam, subject to the provisions of
Article 12. Neither Party shall disclose such Confidential Information of the other Party to any
Third Party, including its Third Party collaborators, or use such Confidential Information of the
other Party to guide its own (or its Third Party collaborators’) decisions to pursue particular
Gene Targets, but Alnylam can use such Confidential Information of Isis to decline a Third Party’s
request for a license to such Gene Target.

     6.5 Limitations on Licenses.

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          (a) The licenses granted under Sections 6.1 and 6.2 above are not intended to grant any rights
to Isis to practice the Alnylam Excluded Technology. If Isis wishes to license any Alnylam
Excluded Technology for which Alnylam has the right to grant a sublicense, Alnylam will negotiate
in good faith an appropriate license.

          (b) Licenses to Alnylam Patent Rights that are joint patents with Third Parties (i.e.,
invented by one or more Alnylam inventors and one or more non-Alnylam inventors) are licensed
subject to the retained rights of any non-Alnylam inventors and their assignees and licensees.
There are no Alnylam Current Chemistry Patents or Alnylam Current Motif and Mechanism Patents
subject to such retained rights.

          (c) Licenses to Alnylam Patent Rights that are subject to contractual obligations between
Alnylam and Third Parties in effect as of the Effective Date are licensed subject to the
restrictions and other terms described in Exhibit 6.5(c) attached hereto. Isis hereby agrees to
comply, and to cause its sublicensees to comply, with such restrictions and other terms.

          (d) Notwithstanding anything to the contrary herein, the licenses to Alnylam Patent Rights
hereunder initially shall not include licenses to Patents licensed by Alnylam from Stanford
University under any agreement between Alnylam and Stanford University in effect as of the
Restatement Date; provided that if any such licensed Patents become issued Patents,
Isis shall have the option of expanding its licenses to Alnylam Patent Rights hereunder to include
such issued Patents by notifying Alnylam of such election and agreeing to pay to Alnylam, in
addition to all amounts otherwise payable to Alnylam hereunder (and without any right under Section
8.2 to reduce such otherwise payable amounts as a consequence of such additional payment amounts),
all amounts that (i) become payable by Alnylam to Stanford University as a result of such expansion
of Isis’ licenses and Isis’ (and its Affiliates’ and sublicensees’) exercise of its rights
thereunder and (ii) are described on Exhibit 6.5(d) attached hereto.

          (e) In addition, the licenses granted by Alnylam to Isis under each of Sections 6.1(h)(i),
6.1(i)(i) and 6.1(j) do not include the right to research, develop, make, have made, use, or import
Single Stranded RNAi Compounds or Single Stranded RNAi Products, in each case that are Designed for
Alnylam’s Enabled Targets.

     6.6 Alnylam Covenant to Isis Regarding Co-Exclusivity for Single Stranded RNAi
Products. Alnylam hereby covenants to Isis, that, after the Restatement Date, Alnylam will not
itself, and will not grant to a Third Party a license under the Alnylam Current Motif and Mechanism
Patents, Alnylam Current Chemistry Patents, Alnylam Future Motif and Mechanism Patents, Alnylam
Future Chemistry Patents, the Co-Exclusive ssRNAi Patents, and/or Alnylam’s rights in any Joint
Patents or Research Program Patents to, research, develop, make, have made, use, import, offer to
sell and sell Single Stranded RNAi Compounds or Single Stranded RNAi Products, except Alnylam may
(i) research, develop, make, have made, use or import Single Stranded RNAi Compounds or Single
Stranded RNAi Products for [**], (ii) grant a license to Controlled Contractors to support work
under the Research Plan, (iii) grant a license to further the research, development or
commercialization of an Alnylam Single Stranded RNAi Product solely in conjunction with a permitted
sublicense by Alnylam under

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Section 5.2; and (iv) continue to grant licenses to Third Parties for the purpose of
manufacturing and selling oligonucleotides; provided that, to the extent such licenses
cover Single Stranded RNAi Compounds, Alnylam will restrict such licenses to [**]. For purposes of
clarity, this Section 6.6 will not preclude Alnylam from (A) itself using the [**], or (B) granting
any Third Party a license under the [**].

ARTICLE 7

LICENSE FEES AND ROYALTIES PAYABLE TO ISIS

     7.1 License Fees.

          (a) In connection with the Original Agreement, Alnylam paid Isis an initial, irrevocable,
noncreditable and non-refundable license fee of $5,000,000.

          (b) Alnylam will pay Isis an additional, irrevocable, noncreditable and non-refundable license
fee of $11,000,000 within 5 Business Days following the Restatement Date.

     7.2 Royalties.

          (a) Subject to the terms and conditions of, and during the term of, this Agreement, Alnylam
will pay to Isis royalties on sales of Alnylam Double Stranded RNA Products by Alnylam, its
Affiliates or sublicensees (except Naked Sublicensees) equal to [**]% of Net Sales. Alnylam may
reduce the royalty due under this section by [**]% of any additional royalties that Alnylam owes to
Third Parties on such Alnylam Double Stranded RNA Product that arise from Alnylam acquiring access
to new technologies after the Effective Date; provided, however that (a) the royalty due
under this section can never be less than a floor of [**]% and (b) additional royalties arising as
the result of the addition, pursuant to Section 11.8, of Isis Future Chemistry Patents or Isis
Future Motif and Mechanism Patents to the Isis Patent Rights licensed to Alnylam cannot be used to
reduce the royalty.

          (b) Subject to the terms and conditions of, and during the term of, this Agreement, Alnylam
will pay to Isis royalties on sales of Alnylam Single Stranded RNAi Products by Alnylam, its
Affiliates or sublicensees equal to [**]% of Net Sales; provided, however, that if Alnylam
is the subject of an Acquisition, the royalty payable under this Section 7.2(b) on the Net Sales of
Alnylam Single Stranded RNAi Products after the date of such Acquisition will be [**]%.

     7.3 Research and Development Milestones.

          (a) Single Stranded Research Milestones. Alnylam, its Affiliates or sublicensees will pay to
Isis the following milestone payments within [**] after the first achievement of each of the
following events:

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	Milestone Event	 	Milestone Payment
	The earlier of (i) first In Vivo Efficacy in
Rodents and (ii) the 18-month anniversary of
the Restatement Date

	 	US$10,000,000
	First In Vivo Efficacy in NHP

	 	  US$  5,000,000  
	First Initiation of Phase I Trial

	 	  US$  5,000,000  

Alnylam shall have the right to prepay Isis any or all of the milestone payments set forth in this
Section 7.3(a) prior to achievement of the corresponding milestone event(s), in which event such
milestone event(s) shall be deemed to have been achieved as of the date of such early payment(s) by
Alnylam, and such early payments will be irrevocable, noncreditable and non-refundable. If Alnylam
decides to terminate this Agreement pursuant to Section 14.4, the terms of Section 14.4(d) shall
apply. For purposes of clarity, Alnylam does not have the right to prepay any of the milestones
set forth in Section 7.3(b) through 7.3(d) below.

          (b) Single Stranded Development Milestones. Alnylam, its Affiliates or sublicensees will pay
to Isis the following milestone payments for each Alnylam Single Stranded RNAi Product within [**]
after the first achievement of each of the following events:

	 	 	 
	Milestone Event	 	Milestone Payment*
	Initiation of Phase I Trial

	 	US$[**]
	Initiation of Phase III Trial

	 	US$[**]
	Filing NDA in U.S., EU or Japan

	 	US$[**]
	Marketing Approval in U.S., EU or Japan

	 	US$[**]

 

			
	*	 	If Alnylam is the subject of an Acquisition, any milestone payments under this Section 7.3(b)
that were not due before the date of such Acquisition will [**] in amount.

     Each milestone payment under this Section 7.3(b) will only be due on the [**] Alnylam Single
Stranded RNAi Product that modulates a particular Gene Target to trigger such milestone payment,
whether such milestone is achieved by Alnylam or an Affiliate or sublicensee of Alnylam.

          (c) Double Stranded Development Milestones. Alnylam, its Affiliates or sublicensees (except
Naked Sublicensees) will pay to Isis the following milestone payments for each Alnylam Double
Stranded RNA Product within [**] after the first achievement of each of the following events:

	 	 	 
	Milestone Event	 	Milestone Payment
	Initiation of Phase I Trial

	 	US$[**]
	Initiation of Phase III Trial

	 	US$[**]
	Filing NDA

	 	US$[**]
	Marketing Approval

	 	US$[**]

Each milestone payment under this Section 7.3(c) will only be due on the [**] Alnylam Double
Stranded RNA Product that modulates a particular Gene Target to trigger such milestone payment,
whether such milestone is achieved by Alnylam or an Affiliate or sublicensee of Alnylam.

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          (d) MicroRNA Milestone. Alnylam, its Affiliates or sublicensees will pay to Isis a milestone
payment of US$[**] for the [**] MicroRNA Product that is an Alnylam Product that modulates a
particular Gene Target within [**] after such MicroRNA Product reaches the initiation of [**], and
not for any other MicroRNA Product that is an Alnylam Product that modulates the particular Gene
Target.

     7.4 Sublicensing Revenue on Naked Sublicenses and Single Stranded Sublicenses.

          (a) With respect to Sublicense Revenue from each Naked Sublicense granted by Alnylam and its
Affiliates under this Agreement, Alnylam will pay Isis within [**] following receipt by Alnylam of
such Sublicense Revenue (i) fifty percent (50%) of all such Sublicense Revenue that does not
constitute royalty payments, and (ii) [**] percent ([**]%) of the amount that remains of the total
royalties received under such Naked Sublicense after Alnylam has paid the royalties that are due
from Alnylam to any Third Parties in connection with such Naked Sublicense.

          (b) Alnylam will pay Isis a percentage of Sublicense Revenue received by Alnylam and its
Affiliates pursuant to sublicenses (or right to obtain a sublicense) granted by Alnylam to a Third
Party as permitted by Section 5.2(b). Alnylam shall make such payment within [**] following
receipt by Alnylam of such Sublicense Revenue. Such percentage will be calculated based on the
year in which Alnylam executes such sublicense agreement, and whether or not Alnylam executes such
sublicense before or after the Product(s) that are the subject of such sublicense have met the [**]
under Section 7.3(b), using the following table:

For Single Stranded RNAi Products Alnylam Sublicenses Before [**]

	 	 	 	 	 	 	 	 	 	 	 
	Year
	 	2009-2011
	 	2012-2013
	 	2014-2015
	 	2016-2017
	 	2017+
	Applicable 

Percentage
	 	[**]%
	 	[**]%
	 	[**]%
	 	[**]%
	 	[**]%

For Single Stranded RNAi Products Alnylam Sublicenses [**] Such Products

	 	 	 	 	 	 	 	 	 
	Year
	 	2009-2012
	 	2013
	 	2014
	 	2015+
	Applicable 

Percentage
	 	[**]%
	 	[**]%
	 	[**]%
	 	[**]%

          (c) If Alnylam grants a sublicense (or right to obtain a sublicense) pursuant to which Alnylam
will be required to pay Isis Sublicense Revenue under Section 7.4(b), then, so long as Alnylam
pays Isis the applicable Sublicense Revenue when due, Alnylam [**] have to pay Isis [**] of the
milestones that become due under Section 7.3(b) after the execution of such sublicense solely with
respect to the Alnylam

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Single Stranded RNAi Product(s) that are being developed and commercialized under each such
sublicense.

          (d) Notwithstanding any of the foregoing, each of the applicable percentages set forth in the
tables above in Section 7.3(b) for any and all periods following the [**] anniversary of the
Restatement Date shall be recalculated by multiplying each such percentage by the fraction of X/Y,
where X is [**] and Y is the total number of Isis Partnered Excluded Targets for which contractual
restrictions have not expired or been cleared as of the [**] anniversary of the Restatement Date.
Such recalculation shall be made on the thirtieth (30th) day following the [**]
anniversary of the Restatement Date, provided, however, that (i) no recalculation shall be
made if the total number of Isis Partnered Excluded Targets for which contractual restrictions have
not expired or been cleared as of the [**] anniversary of the Restatement Date is less than or
equal to [**]; (ii) the applicable percentages, as so recalculated, shall apply only to all
sublicenses entered into between Alnylam and a Third Party following the [**] anniversary of the
Restatement Date; and (iii) this Section 7.4(d) shall not adjust the applicable percentages set
forth in the tables above in Section 7.3(b) as they apply to any sublicenses entered into between
Alnylam and a Third Party on or before the [**] anniversary of the Restatement Date.

     7.5 Technology Access Fees from Bona Fide Collaborations.

          (a) Alnylam will pay Isis a percentage of Technology Access Fees received by Alnylam and its
Affiliates pursuant to Bona Fide Drug Discovery Collaborations and Development Collaborations
entered into between Alnylam and a Third Party. Alnylam shall make such payment to Isis within
[**] following receipt by Alnylam of such Technology Access Fees. Such percentage will be
calculated based on the year in which Alnylam executes such Bona Fide Drug Discovery Collaboration
or Development Collaboration agreement using the following table:

	 	 	 	 	 	 	 	 	 
	Year
	 	2004/2005
	 	2006
	 	2007
	 	2008+
	Applicable 

Percentage
	 	[**]%
	 	[**]%
	 	[**]%
	 	[**]%

          However, Alnylam may credit any milestone payments made by Alnylam under Section
7.3(c) above with respect to an Alnylam Double Stranded RNA Product against any Technology Access
Fees that are later due under a Bona Fide Drug Discovery Collaboration or Development Collaboration
that involves the same Alnylam Double Stranded RNA Product that triggered such milestone payment.

          (b) Notwithstanding the foregoing, for any Bona Fide Drug Discovery Collaboration or
Development Collaboration agreement, Alnylam will pay Isis a minimum fee, payable upon the first
Alnylam Product other than a Single Stranded RNAi Product developed pursuant to such Bona Fide Drug
Discovery Collaboration agreement reaching [**] (in which event Alnylam shall pay Isis such minimum
fee within [**] following such initiation of [**]) or within [**] after the execution of such
Development Collaboration agreement, equal to the lesser of (i) $[**] or (ii) [**]% of the
Technology Access Fees from such collaboration; provided, however that Alnylam may credit
any

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amounts paid Isis pursuant to Section 7.5(a) above as the result of the same Bona Fide Drug
Discovery Collaboration or Development Collaboration agreement against this minimum fee with such
amounts credited only once, and provided further that if following such payment, additional
Technology Access Fees are owed to Isis for such Bona Fide Drug Discovery Collaboration or
Development Collaboration, the amounts paid under this Section 7.5(b) (after crediting of any
previous Technology Access Fees paid under Section 7.5(a) in accordance with the immediately
preceding proviso) will be creditable against such future Technology Access Fees.

     7.6 Allocation of Sublicense Income and Technology Access Fees. Each time Alnylam
enters a collaboration or license agreement (an “Isis IP Sublicense”) pursuant to which Alnylam
grants a sublicense under the Isis Patent Rights to a Third Party, the CEO of Isis and the CEO of
Alnylam will in mutually discuss and agree in writing upon: (a) if the Isis IP Sublicense only
relates Double Stranded RNA, a good faith determination as to whether such Isis IP Sublicense is a
Naked Sublicense or a Bona Fide Drug Discovery Collaboration or Development Collaboration; and (b)
if the Isis IP Sublicense relates to Double Stranded RNA and Alnylam Single Stranded RNAi
Product(s), a good faith allocation of the consideration received by Alnylam under such Isis IP
Sublicense between the consideration attributable to the components of such Isis IP Sublicense that
relate to (i) Double Stranded RNA and (ii) Alnylam Single Stranded RNAi Product(s). Within [**]
days following the execution of each Isis IP Sublicense, Alnylam, through its CEO, will provide
Isis’ CEO a reasonably detailed and accurate description of such Isis IP Sublicense for the purpose
of enabling the CEOs to perform the determination and allocation described in this Section 7.6.

     7.7 Revenue Sharing for Research Program Patents. Alnylam will pay Isis 50% of any
payments received by Alnylam and its Affiliates pursuant to licenses granted by Alnylam to a Third
Party under the Research Program Patents for any and all purposes, except to research,
develop, make, have made, use, import, offer to sell or sell any (1) oligonucleotides (or
chemically modified oligonucleotide analogs) designed to work via the RNase H 1 or 2 mechanism
(including any oligonucleotide which has [**]), (2) Double Stranded RNA Products, (3) MicroRNA
Products, (4) Single Stranded RNAi Products, or (5) Isis Single Stranded Product. Alnylam shall
make such payment to Isis within [**] following receipt by Alnylam of such payments.

ARTICLE 8

LICENSE FEES, SUBLICENSE REVENUE AND

ROYALTIES PAYABLE TO ALNYLAM

     8.1 Option Fee. For each Isis Reserved DS-Target for which Isis exercises its option
granted pursuant to Section 6.2, Isis will pay Alnylam an irrevocable, noncreditable and
non-refundable option fee of $[**] due upon the date of exercise. Isis may credit any $[**]
payment made under Section 6.4(a) for the DS-Target Slot occupied by such Reserved DS-Target
against this option fee. The option fee is only payable once per Gene Target.

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     8.2 Royalties.

          (a) Subject to the terms and conditions of, and during the term of, this Agreement, Isis will
pay to Alnylam royalties on sales of Double Stranded RNA Products that are Isis Products by Isis,
its Affiliates or sublicensees equal to [**]% of Net Sales. Isis may reduce the royalty due under
this section by [**]% of any additional royalties that Isis owes to Third Parties on such Double
Stranded RNA Products that are Isis Products that arise from Isis acquiring access to new
technologies after the Restatement Date; provided, however that (i) the royalty due under
this section can never be less than a floor of [**]%, (ii) additional royalties arising as the
result of the addition, pursuant Section 11.8, of Alnylam Future Chemistry Patents or Alnylam
Future Motif and Mechanism Patents to the Alnylam Patent Rights licensed to Isis, or as the result
of an expansion of Isis’ licenses pursuant to Section 6.5(d), cannot be used to reduce the royalty
and (iii) Isis shall not be entitled to reduce, pursuant to this sentence, its royalty obligation
to Alnylam below a royalty obligation equal to the lesser of (y) Alnylam’s aggregate royalty
obligations [**] existing as of the Effective Date [**] and (z) Alnylam’s aggregate royalty
obligations [**] as such obligations may be reduced from time to time after the Effective Date.

          (b) Subject to the terms and conditions of, and during the term of, this Agreement, Isis will
pay to Alnylam royalties on Net Sales of Isis Single Stranded RNAi Products by Isis, its Affiliates
or sublicensees equal to [**]% of Net Sales; provided, however, that if Isis is the
subject of an Acquisition, the royalty payable under this Section 8.2(b) on the Net Sales of Isis
Single Stranded RNAi Products following such Acquisition will be [**]%.

     8.3 Development Milestones.

          (a) Subject to Section 8.4, Isis, its Affiliates or sublicensees will pay to Alnylam the
following milestone payments for each Double Stranded RNA Product that is an Isis Product within
[**] after the first achievement of each of the following events:

	 	 	 
	Milestone Event	 	Milestone Payment
	Initiation of Phase I Trial

	 	US$[**]
	Initiation of Phase III Trial

	 	US$[**]
	Filing NDA

	 	US$[**]
	Marketing Approval

	 	US$[**]

Each milestone payment under this Section 8.3(a) will only be due on [**] Double Stranded RNA
Product that is an Isis Product that modulates a particular Gene Target to trigger such milestone
payment, whether such milestone is achieved by Isis or an Affiliate or sublicensee of Isis.

          (b) Isis, its Affiliates or sublicensees will pay to Alnylam a milestone payment of US$[**]
for the [**] Isis Single Stranded Product that is an Isis Product that modulates a particular Gene
Target within [**] after such Isis Single Stranded Product reaches the initiation of IND-Enabling
Studies, and not for any other Isis Single Stranded Product that modulates that particular Gene
Target.

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          (c) Isis, its Affiliates or sublicensees will pay to Alnylam a milestone payment of US$[**]
for the [**] MicroRNA Product that is an Isis Product that modulates a particular Gene Target
within [**] after such MicroRNA Product reaches the initiation of [**], and not for any other
MicroRNA Product that is an Isis Product that modulates the particular Gene Target.

     8.4 Sublicense Income on Single Stranded RNAi Sublicenses.

          (a) With respect to Sublicense Revenue from each sublicense (or right to obtain a sublicense)
related to an Isis Single Stranded RNAi Product granted by Isis and its Affiliates under this
Agreement after the Restatement Date, Isis will pay Alnylam, within [**] following receipt by Isis
of such Sublicense Revenue, a percentage of all such Sublicense Revenue that does not constitute
royalty payments. Such percentage will be calculated based on the year in which Isis executes such
sublicense agreement, and whether or not Alnylam has paid Isis the research funding and applicable
milestones under Section 4.2(c) and 7.3(a), using the following table:

	 	 	 	 	 	 	 
	 	 	 	 	 	 	Applicable
	Milestone Event	 	Percentage
	 	1	 	 	Sublicense executed after the Restatement Date
but before Alnylam pays Isis the $[**]
milestone under Section 7.3(a)

	 	[**]%
	 	2	 	 	Sublicense executed after Alnylam pays Isis
the $[**] milestone under Section 7.3(a) but
before the 3rd milestone event
described below

	 	[**]%
	 	3	 	 	Sublicense executed after Alnylam pays the
first 3 years of research funding under
Section 4.2(c) and the $[**] milestone for
First In Vivo Efficacy in NHP under Section
7.3(a)

	 	[**]%

          (b) In the event that Isis enters an Antisense Drug Discovery Program pursuant to which Isis
(i) grants a sublicense under the Alnylam Patent Rights to further develop and/or commercialize an
Isis Single Stranded RNAi Product, (ii) commits to discover and/or develop Double Stranded RNA
Products or single stranded oligonucleotides that are not Single Stranded RNAi Compounds, or (iii)
grants a license or sublicense to intellectual property which would not otherwise result in any
amounts becoming payable to Alnylam hereunder (an “Other Isis Sublicense”), then in determining the
applicable payment due from Isis to Alnylam in connection with such Antisense Drug Discovery
Program, the CEO of Isis and the CEO of Alnylam will mutually agree in writing upon a good faith
allocation of the consideration received by Isis under such Antisense Drug Discovery Program
between and among the consideration attributable to the components of such Antisense Drug Discovery
Program that qualify as (x) a sublicense to further develop and/or commercialize an Isis Single
Stranded Product, (y) a collaboration to discover and/or develop Double Stranded RNA Products or
single stranded oligonucleotides that are not Single Stranded RNAi Compounds, and (z) an Other Isis
Sublicense; and Isis will pay Alnylam Sublicense Income Fees under Section 8.4(a) in accordance
with such allocation. Within 30 days following the execution of each such transaction, Isis,
through its CEO, will provide Alnylam’s CEO a reasonably

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detailed and accurate description of such transaction for the purpose of enabling Alnylam’s
CEO to perform the allocation described in this Section 8.4(b).

     8.5 Revenue Sharing for Research Program Patents. Isis will pay Alnylam 50% of any
payments received by Isis and its Affiliates pursuant to licenses granted by Isis to a Third Party
under the Research Program Patents for any and all purposes, except to research, develop,
make, have made, use, import, offer to sell or sell any (1) oligonucleotides (or chemically
modified oligonucleotide analogs) designed to work via the RNase H 1 or 2 mechanism (including any
oligonucleotide which has [**]), (2) Double Stranded RNA Products, (3) MicroRNA Products, (4)
Single Stranded RNAi Products, or (5) Isis Single Stranded Product. Isis shall make such payment
to Alnylam within [**] following receipt by Isis of such payments.

ARTICLE 9

OTHER PAYMENT TERMS

     9.1 Payments. All payments by a Party under this Agreement will be made in United
States dollars by bank wire transfer in next day available funds to such bank account in the United
States designated in writing by Alnylam or Isis, from time to time. Royalties payable under
Sections 7.2 and 8.2 shall be payable on a quarterly basis within 45 days after the end of each
calendar quarter. The Party with such royalty obligation (the “Royalty-Paying Party”) shall
provide the other Party with a report setting forth (i) gross sales of Alnylam Products or Isis
Products, as applicable, by the Royalty-Paying Party, its Affiliates and sublicensees, (ii) all
deductions from such gross sales taken in calculating Net Sales, (iii) Net Sales of Alnylam
Products or Isis Products, as applicable, by the Royalty-Paying Party, its Affiliates and
sublicensees, (iv) royalties payable based on such Net Sales and (v) all other information relevant
to the calculation of such royalties, on a product-by-product and country-by-country basis, for
each calendar quarter within [**] after the end of such calendar quarter.

     9.2 Late Payments; Collections. In the event that any payment, including royalty,
milestone, Sublicense Revenue or Technology Access Fee payments, due hereunder is not made when
due, the payment will bear interest from the date due at the lesser of (i) 1.5% per month,
compounded monthly, or (ii) the highest rate permitted by law; provided, however, that in
no event will such rate exceed the maximum legal annual interest rate. If a Party disputes in
writing the amount of an invoice presented by the other Party within [**] of receipt of such
invoice, interest will only be due on the correct amount as later determined or agreed. The payment
of such interest will not limit a Party from exercising any other rights it may have as a
consequence of the lateness of any payment. In addition, each Party agrees to pay all external
costs of collection, including reasonable attorneys’ fees, incurred by the other Party in enforcing
the payment obligations after a due date has passed under this Agreement.

     9.3 Audit Rights.

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          (a) Upon the written request of Isis or Alnylam, as the case may be, and not more than once in
each calendar year, Isis or Alnylam will permit the other Party’s independent certified public
accountant to have access upon reasonable advance notice and during normal business hours to its
records as may be reasonably necessary to verify the accuracy of the royalty reports hereunder for
the current year and the preceding 2 years prior to the date of such request. The accounting firm
will disclose to the auditing Party only whether the royalty reports are correct or incorrect, the
specific details concerning any discrepancies, and the corrected amount of Net Sales and royalty
payments. No other information will be provided to the auditing Party. Once a Party has audited a
particular calendar year under this section, the Party will be precluded from subsequently auditing
such calendar year. In any sublicense granted by a Party under this Agreement, such Party will
endeavor to secure a similar audit right and if reasonably requested by the other Party will
enforce such audit right.

          (b) If such accounting firm concludes that additional royalties were owed during such period,
the delinquent Party will pay the additional royalties within 90 days of the date such Party
receives the accounting firm’s written report. The fees charged by such accounting firm will be
paid by the auditing Party unless the additional royalties, milestones or other payments owed by
the audited Party exceed 5% of the royalties, milestones or other payments paid for the time period
subject to the audit, in which case the audited Party will pay the reasonable fees and expenses
charged by the accounting firm.

          (c) Each Party will treat all financial information subject to review under this Section 9.3
or under any sublicense agreement in accordance with the confidentiality provisions of Article 12,
and will cause its accounting firm to enter into an acceptable confidentiality agreement obligating
such firm to retain all such financial information in confidence pursuant to such confidentiality
agreement.

     9.4 Taxes. If laws, rules or regulations require withholding of income taxes or other
taxes imposed upon payments set forth in Section 4.2(c) or Article 7 or 8, each Party will make
such withholding payments as required and subtract such withholding payments from the payments set
forth in Section 4.2(c) or Article 7 or 8. Each Party will submit appropriate proof of payment of
the withholding taxes to the other Party within a reasonable period of time. The Parties will
cooperate to obtain the appropriate tax clearance and/or recover any such withholdings if possible.

ARTICLE 10

ALNYLAM RIGHTS OF FIRST NEGOTIATION; PREFERRED LICENSEE

     10.1 Right of First Negotiation. Isis will notify Alnylam in writing once (i) Isis,
on its own with no subsequent rights to Third Parties, intends to initiate [**] for an Isis Product
that is a Double Stranded RNA Product or (ii) if a Third Party with which Isis has a Development
Collaboration or a collaboration on an [**] an Isis Double Stranded RNA Product before or during
clinical development or commercialization with no subsequent rights to Third Parties. Alnylam will
have [**] from the receipt of such

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notice to notify Isis in writing whether or not Alnylam wishes to negotiate with Isis
regarding the development and/or commercialization of such Isis Product. If Alnylam fails to
respond to Isis’ notice within the [**] or if Alnylam declines in writing to exercise its right of
first negotiation, then Isis will be free to develop and commercialize (either on its own or with a
Third Party) the Isis Product. If Alnylam wishes to negotiate a license or development or
commercialization rights in such Isis Product, the Parties will negotiate in good faith the terms
of the license or collaboration agreement. If, despite good faith negotiations, Alnylam and Isis
do not reach agreement within [**] from Alnylam’s exercise of its right of first negotiation, then
Isis will be free to develop and commercialize (either on its own or with a Third Party) the Isis
Product; provided that during the period prior to the latest of (x) the initiation
of [**] the Isis Product, (y) the [**] anniversary of the commencement of [**] for the Isis Product
or (z) in the case of an Isis Product [**] after the commencement of [**], the [**] anniversary of
Isis’ notice to Alnylam [**], Isis shall not enter into a license or collaboration agreement with a
Third Party for such Isis Product on terms (the “More Favorable Terms”) that are in the aggregate
materially more favorable to the Third Party than the terms on which Isis most recently offered in
writing to grant such rights to Alnylam without first offering the More Favorable Terms to Alnylam.

     10.2 Preferred Licensee. If, after the Effective Date, Alnylam grants to any Third
Party that is not a Major Pharmaceutical Company a license under the Alnylam Patent Rights to
develop and commercialize Double Stranded RNA Products, then if (a) either (i) the [**] terms of
such license are more favorable to the Third Party than the [**] terms hereunder with respect to
Isis Products are to Isis or (ii) the [**] covered by such license exceeds the [**] potentially
licensed to Isis hereunder for development and commercialization of Double Stranded RNA Products,
and (b) the roles to be played by Alnylam and such Third Party in the development and
commercialization of Double-Stranded RNA Products under such Third Party license, the nature of the
Gene Targets covered by such Third Party license and any other relevant terms of such Third Party
license do not collectively justify the conditions described in the preceding clauses (a)(i) and/or
(a)(ii), then Alnylam shall modify the terms of its licenses to Isis hereunder with respect to such
conditions so that they are reasonably equivalent to those granted to the Third Party.

ARTICLE 11

INTELLECTUAL PROPERTY

     11.1 Ownership of Inventions.

          (a) Each Party will solely own all inventions, technology, discoveries, or other proprietary
property (collectively, “Inventions”) that are made (as determined by U.S. rules of inventorship)
solely by employees of or consultants to that Party under this Agreement.

          (b) Isis and Alnylam will jointly hold title to all Inventions, whether or not patentable,
that are made (as determined by the U.S. rules of inventorship) jointly by employees of or
consultants to Isis and Alnylam, as well as to Patents filed thereon. Such

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Inventions will be “Joint Inventions,” and Patents claiming such Joint Inventions will be
“Joint Patents.” Isis and Alnylam will promptly provide each other with notice whenever a Joint
Invention is made. The Parties agree and acknowledge that, except insofar as this Agreement
provides otherwise, the default rights conferred on joint owners under US patent law, including the
right of each Party to independently practice, license and use a Joint Patent, will apply in
relation to the Joint Patents throughout the world as though US patent law applied worldwide.

          (c) The Parties agree, upon reasonable request, to execute any documents reasonably necessary
to effect and perfect each other’s ownership of any Invention.

     11.2 Filing and Prosecution of Isis and Alnylam Patent Rights.

          (a) Isis and Alnylam will work closely, through their interactions on the RMC to ensure that,
to the greatest degree permitted by United States and foreign patent laws, Patents for Inventions
relating to all aspects of Double Stranded RNA and/or Single Stranded RNAi Compounds or Single
Stranded RNAi Products are obtained and shared.

          (b) Except as set forth in Sections 11.2(f) and 11.2(g) below, Isis will be responsible for
preparing, filing, prosecuting, maintaining and taking such other actions as are reasonably
necessary or appropriate with respect to the Isis Patent Rights.

          (c) Except as set forth in Section 11.2(f) and 11.2(g) below, Alnylam will be responsible for
preparing, filing, prosecuting, maintaining and taking such other actions as are reasonably
necessary or appropriate with respect to the Alnylam Patent Rights.

          (d) Each Party will endeavor in good faith to coordinate its efforts with those of the other
Party to minimize or avoid interference with the prosecution of the other Party’s Patents. Neither
Party will initiate or participate in any opposition, reexamination, interference, litigation or
other proceeding for the purpose of narrowing or invalidating any claim in a Patent of the other
Party.

          (e) At either Party’s request, the other Party will keep the requesting Party continuously
informed of and provide documentation of all significant matters relating to the preparation,
filing, prosecution and maintenance of any designated Patent.

          (f) Alnylam will be responsible for preparing, filing, prosecuting, maintaining and taking
such other actions as are reasonably necessary or appropriate with respect to the Isis Special
Patents. If Alnylam elects not to file for or continue the prosecution (including any
interferences, oppositions, reissue proceedings and re-examinations) or maintenance of an Isis
Special Patent in any country, then, Alnylam will notify Isis promptly in writing of its intention
in sufficient time to enable Isis to meet any deadlines by which an action must be taken to
establish or preserve any such rights in such Patent in such country and Isis will have the right,
but not the obligation, to file for or continue the prosecution or maintenance of such Patent in
such country, and Alnylam will cooperate with Isis in regard thereto.

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          (g) Solely with respect to (i) Research Program Patents, or (ii) Patents licensed under this
Agreement that claim Inventions that primarily relate to Single Stranded RNAi Compounds, but, in
each case, excluding Joint Patents, the Party who Controls such Patent (the “Responsible Party”)
will be responsible for preparing, filing, prosecuting, maintaining and taking such other actions
as are reasonably necessary or appropriate with respect to such Patent. If the Responsible Party
decides to discontinue the preparation, filing, prosecution or maintenance of such a Patent, the
Responsible Party will notify the other Party at least [**] prior to any deadline that, if missed,
would materially prejudice the Patent, and the other Party will have the right, at such Party’s own
expense, to prepare, file, prosecute and maintain such Patent.

     11.3 Filing and Prosecution of Jointly Owned Patents.

          (a) The Research Management Committee will designate one of the Parties as being the
responsible Party for preparing, filing, prosecuting, maintaining and taking such other actions as
are reasonably necessary or appropriate with respect to any Joint Patent.

          (b) Each Party will keep the other Party continuously informed of all significant matters
relating to the preparation, filing, prosecution and maintenance of Joint Patents, and shall
provide the other Party with copies of any substantial prosecution papers within thirty days of
receipt.

     11.4 Costs and Expenses.

          (a) Except as set forth in Section 11.4(c) below, each Party will bear its own costs and
expenses in filing, prosecuting, maintaining and extending the Alnylam Patent Rights and Isis
Patent Rights, respectively.

          (b) Except as set forth in Section 11.4(c) below, the Parties will pay equal shares of all
costs and expenses in filing, prosecuting, maintaining and extending the Joint Patents.

          (c) Alnylam will bear [**]% of its own costs and expenses in filing, prosecuting, maintaining
and extending the Isis Special Patents. If Alnylam elects not to file for or continue the
prosecution (including any interferences, oppositions, reissue proceedings and re-examinations) or
maintenance of an Isis Special Patent in any country, and Isis assumes the continued prosecution of
such Isis Special Patent (as permitted by Section 11.2(f)) in such country, then the Parties will
[**] all of Isis’ costs and expenses in filing, prosecuting, maintaining and extending the Isis
Special Patent for which Isis assumed prosecution.

     11.5 Enforcement.

          (a) Each Party will promptly advise the other of any suspected or actual infringement of the
Isis Patent Rights, Alnylam Patent Rights, or Joint Patents by any person that reasonably affects
the other Party’s business. The notice shall set forth the facts of such infringement or
misappropriation in reasonable detail.

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          (b) Subject to subsections (c) and (h) below, Alnylam will have the sole and exclusive right,
in its sole discretion and at its expense, to assert and enforce any Isis Patent Rights, Alnylam
Patent Rights or Joint Patents against any party engaging in an unlicensed or unauthorized making,
having made, using, selling, offering for sale or importing of any allegedly infringing Double
Stranded RNA.

          (c) For any enforcement by Alnylam under subsection (b) above that includes Isis Patent Rights
covering a [**] chemical modification, Isis will actively participate in the planning and conduct
of such enforcement and will take the lead of such enforcement to the extent that the scope or
validity of any such Isis Patent Rights covering a [**] chemical modification is at risk.

          (d) Except as set forth in Sections 11.5(b) and (h),

               (i) Isis will have the sole and exclusive right, in its sole discretion and at its expense, to
assert and enforce any Isis Patent Rights;

               (ii) Alnylam will have the sole and exclusive right, in its sole discretion and at its
expense, to assert and enforce any Alnylam Patent Rights and the Isis Special Patent Rights; and

               (iii) The RMC will agree in advance on the enforcement of any Joint Patent and will apportion
enforcement responsibilities and recoveries amongst the parties.

          (e) The rights granted hereunder to Alnylam to enforce certain licensed in or jointly owned
Isis Patent Rights are further limited as described in Exhibit 5.3(d) attached hereto. The rights
granted hereunder to Isis to enforce certain licensed in or jointly owned Alnylam Patent Rights are
further limited as described in Exhibit 6.5(c) attached hereto.

          (f) The nonenforcing Party will have the right, at its own expense, to participate in the
conduct of the enforcement action and to be represented in such action by its own counsel.

          (g) The enforcing Party will not enter into any settlement that impacts the validity, scope or
interpretation of any claim of any Joint Patent or of any Patent of the nonenforcing Party without
prior written authorization of the nonenforcing Party.

          (h) If the Party with enforcement rights under section (b) or (d) above (the “Primary Party”)
fails to initiate proceedings against any actual or suspected infringement within [**] of receipt
of written request for enforcement from the other Party (the “Step-in Party”) and if the infringer
is directly competing with a Product (the “Affected Product”) of such Step-in Party, then (i) if
the license granted in this Agreement under which the Step-in Party is selling the Affected Product
is exclusive or co-exclusive, the Step-in Party will have the right to assert and enforce the
patents that are allegedly being infringed, or (ii) if the license granted in this Agreement under
which the Step-in Party is selling the Affected Product is non-exclusive, the Step-in Party will
have no obligation to pay royalties during the period for which the Primary Party fails to initiate
proceedings or

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take other action (including without limitation entering into a licensing arrangement) to
eliminate such infringement; provided that the provisions of the immediately preceding
clause (ii) shall not apply if the Primary Party elects to grant the Step-in Party enforcement
rights with respect to such infringement. The Primary Party will not grant a license to any such
infringing Third Party with respect to any directly competitive infringing product on terms
materially more favorable (milestones and royalties) than the terms of the license granted
hereunder to the Step-in Party or, solely with respect to the Affected Product, will adjust the
terms of such license so that they are not materially less favorable than the terms of the license
granted to the infringing Third Party. In addition, as a condition to the Step-in Party’s right
(under clause (i) of this Section 11.5(h)) to assert and enforce a Patent Controlled by the Primary
Party that is allegedly being infringed, the Step-in Party must also assert and enforce any
relevant Patents Controlled by such Step-in Party against the alleged infringer who is competing
with the Affected Product.

          (i) Except as otherwise agreed to by the Parties as part of a cost-sharing arrangement, any
recovery realized as a result of such litigation, after reimbursement of any reasonable litigation
expenses of Isis and Alnylam, shall be retained by the Party or Parties that brought and controlled
such litigation for purposes of this Agreement, except that any recovery realized as a result of
such litigation shall be treated as Net Sales of Isis Products or Net Sales of Alnylam Products and
distributed as such Net Sales would have been distributed.

     11.6 [Intentionally Deleted]

     11.7 Third Party Patents. The Parties will consult about the need to license any
patents Controlled by Third Parties that would be useful or necessary for either Party to research,
develop, make, have made, use, sell, offer for sale or import Double Stranded RNA Products or
Single Stranded RNAi Products. If it is agreed that there is a desire to obtain a license or to
acquire any such patent, the Parties will negotiate in good faith regarding (i) the share of the
financial obligations relating to the license or acquisition that each Party will bear; (ii) the
compensation of any acquisition costs incurred in connection with obtaining the Patent rights; and
(iii) an agreement by the Parties to abide by all terms of the agreement under which the patent
rights are granted.

     11.8 Future Licenses. If after the Effective Date, a Party (the “Controlling Party”)
later invents or acquires rights or title to an invention claimed by a Patent that (i) would be
included in the Isis Future Chemistry Patents or Isis Future Motif and Mechanism Patents if such
Party is Isis or in the Alnylam Future Chemistry Patents or Alnylam Future Motif and Mechanism
Patents if such Party is Alnylam (the “Additional Rights”) and (ii) carry financial or other
obligations, then the Controlling Party must promptly notify the non-Controlling Party of such
acquisition or invention. If the non-Controlling Party wishes to include such Additional Rights
under the licenses granted pursuant to Article 5 or 6, as applicable, the non-Controlling Party
will notify the Controlling Party of its desire to do so and will assume all financial and other
obligations to the Controlling Party’s licensors or collaborators, if any, arising from the grant
to the non-Controlling Party of such license. Any Additional Rights that do not carry financial or
other obligations shall be automatically included under the licenses granted pursuant to

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Article 5 or 6, as applicable. If a Party pays any upfront payments or similar acquisition
costs to access Additional Rights, the Parties will negotiate in good faith regarding sharing such
acquisition costs and payments. When acquiring or creating such Additional Rights, each Party will
endeavor in good faith to secure the right to sublicense such Additional Rights to the other Party.

ARTICLE 12

CONFIDENTIALITY

     12.1 Nondisclosure Obligation. All Confidential Information disclosed by one Party to
the other Party hereunder will be maintained in confidence by the receiving Party and will not be
disclosed to a Third Party or Affiliate or used for any purpose except as set forth below.

     12.2 Permitted Disclosures. Except as otherwise provided herein, a Party may disclose
Confidential Information received from the other Party:

          (a) to governmental or other regulatory agencies in order to obtain Patents or approval to
conduct clinical trials, or to gain Marketing Approval; provided that such disclosure may
be made only to the extent reasonably necessary to obtain such Patents or approvals;

          (b) to any adjudicative body as required by law, provided that prior to such disclosure, the
Party subject to such disclosure obligation (the “Notifying Party”) promptly notifies the other
Party of such requirement so that such other Party can seek a protective order, confidential
treatment or other appropriate remedy; and provided, further, that in the event that no such
protective order, confidential treatment or other remedy is obtained, or that such other Party
waives compliance with this section, the Notifying Party will furnish only that portion of the
other Party’s Confidential Information that it is advised by counsel it is legally required to
furnish;

          (c) to Affiliates, sublicensees, agents, consultants, and/or other Third Parties for the
development, manufacturing and/or marketing of Isis Products or Alnylam Products (or for such
parties to determine their interest in performing such activities) in accordance with this
Agreement on the condition that such Affiliates, sublicensees and Third Parties agree to be bound
by the confidentiality obligations contained in this Agreement;

          (d) if such disclosure is required by law or regulation (including without limitation by rules
or regulations of any securities exchange or NASDAQ), provided that prior to such
disclosure, the Notifying Party promptly notifies the other Party of such requirement so that such
other Party can seek a protective order, confidential treatment or other appropriate remedy; and
provided, further, that in the event that no such protective order, confidential treatment
or other remedy is obtained, or that such other Party waives compliance with this section, the
Notifying Party will furnish only that portion of the other Party’s Confidential Information that
it is advised by counsel it is legally required to furnish; or

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          (e) as necessary if embodied in products to develop and commercialize such products.

Either Party may disclose (i) a copy of this Agreement on a confidential basis to prospective
lenders and investors, (ii) a mutually agreed upon redacted copy of this Agreement on a
confidential basis to prospective collaborators and (iii) the terms of this Agreement as required
under applicable securities laws or regulations (including without limitation under rules or
regulations of any securities exchange or NASDAQ); provided, however, that, subject to
Section 6.4(i), Alnylam shall not disclose Isis’ past or current Reserved DS-Targets or past or
current Isis Protected Targets without the express prior written consent of Isis, and, subject to
Section 4.3(f), neither Party shall disclose the other Party’s past or current Enabled Targets
without the express prior written consent of the other Party.

     12.3 Announcements; Publicity.

     (a) Each Party understands that this Agreement is likely to be of significant interest to
investors, analysts and others, and that either Party therefore may make public announcements with
respect to this Agreement. The Parties agree that any such announcement will not contain
confidential business or technical information unless disclosure of confidential business or
technical information is required by law or regulation, in which case they will make reasonable
efforts to minimize such disclosure of confidential business or technical information to that
required by law or regulation. Each Party agrees to provide to the other Party a copy of any such
public announcement as soon as reasonably practicable under the circumstances prior to its
scheduled release. Except under extraordinary circumstances, each Party shall provide the other
with an advance copy of any press release at least two (2) business days prior to the scheduled
disclosure. The other Party shall have the right to expeditiously review and recommend changes to
any announcement regarding this Agreement or the subject matter of this Agreement, provided
that such right of review and recommendation shall only apply for the first time that specific
information is to be disclosed, and shall not apply to the subsequent disclosure of information
that (i) is substantially similar to a previously reviewed disclosure and (ii) in the context of
the subsequent disclosure, does not carry a substantially different qualitative message than that
carried by the previously reviewed disclosure. The Party whose press release has been reviewed
shall in good faith consider any changes that are timely recommended by the reviewing Party.

     (b) Each Party will (i) use reasonable, good faith efforts to provide the other Party with at
least 5 business days’ prior notice (which notice may be given orally to a senior executive officer
of the other Party) before such Party publicly announces the execution of a Naked Sublicense, Bona
Fide Drug Discovery Collaboration agreement or Development Collaboration agreement (or any material
amendments thereto) that could reasonably be expected to be of strategic or financial importance to
the other Party’s business and (ii) cooperate with the other Party to enable the other Party to
develop appropriate mutually beneficial public announcements regarding such transactions.

ARTICLE 13

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INDEMNIFICATION

     13.1 Indemnification by Alnylam. Alnylam will indemnify, defend and hold Isis and its
agents, employees, officers and directors (the “Isis Indemnitees”) harmless from and against any
and all liability, damage, loss, cost or expense (including reasonable attorneys’ fees) arising out
of Third Party claims or suits related to (a) Alnylam’s performance of its obligations under this
Agreement; (b) breach by Alnylam of its representations and warranties set forth in Article 15; or
(c) the discovery, development, manufacture, use, importation or commercialization (including
marketing and sale) of Alnylam Products.

     13.2 Indemnification by Isis. Isis will indemnify, defend and hold Alnylam and its
Affiliates and each of their respective agents, employees, officers and directors (the “Alnylam
Indemnitees”) harmless from and against any and all liability, damage, loss, cost or expense
(including reasonable attorneys’ fees) arising out of Third Party claims or suits related to (a)
Isis’ performance of its obligations under this Agreement; (b) breach by Isis of its
representations and warranties set forth in Article 15; or (c) the discovery, development,
manufacture, use, importation or commercialization (including marketing and sale) of Isis Products.

     13.3 Notification of Claims; Conditions to Indemnification Obligations. A Party
entitled to indemnification under this Article 13 shall (a) promptly notify the other Party as soon
as it becomes aware of a claim or action for which indemnification may be sought pursuant hereto,
(b) cooperate with the indemnifying Party in the defense of such claim or suit, and (c) permit the
indemnifying Party to control the defense of such claim or suit, including without limitation the
right to select defense counsel; provided that if the Party entitled to
indemnification fails to promptly notify the indemnifying Party pursuant to the foregoing clause
(a), the indemnifying Party shall only be relieved of its indemnification obligation to the extent
prejudiced by such failure. In no event, however, may the indemnifying Party compromise or settle
any claim or suit in a manner which admits fault or negligence on the part of the indemnified
Party, or which imposes obligations on the indemnified Party other than financial obligations that
are covered by the indemnifying Party’s indemnification obligation, without the prior written
consent of the indemnified Party. The indemnifying Party will have no liability under this Article
13 with respect to claims or suits settled or compromised without its prior written consent.

ARTICLE 14

TERM AND TERMINATION OF AGREEMENT

     14.1 Term and Termination of Agreement. This Agreement will be effective as of the
Restatement Date (unless otherwise expressly stated) and unless terminated earlier pursuant to
Sections 14.2 or 14.3 below, the term of this Agreement will continue in effect until expiration of
the License Term.

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     14.2 Termination upon Material Breach. This Agreement may be terminated upon written
notice by either Party to the other at any time during the term of this Agreement if the other
Party is in material breach of its obligations hereunder and has not cured such breach within 90
days after written notice requesting cure of the breach; provided, however, that (a) in the
event of a good faith dispute with respect to the existence of such a material breach, the 90-day
cure period will be stayed until such time as the dispute is resolved pursuant to Section 17.6
hereof, (b) so long as the breaching Party takes substantial steps to cure the breach promptly
after receiving notice of the breach from the non-breaching Party and thereafter diligently
prosecutes the cure to completion as soon as is practicable, the non-breaching Party may not
terminate this Agreement, and (c) any license granted under this Agreement with respect to an Isis
or Alnylam Product that has at least reached IND-Enabling Studies may not be terminated for a
material breach under this Section 14.2 (except for an uncured failure to make any undisputed
portion of any payment obligation under Article 7 or 8 with respect to such Isis or Alnylam
Product) to the extent such license is necessary to develop, make and have made, sell and import
such Isis or Alnylam Product.

     14.3 Termination upon Bankruptcy; Rights in Bankruptcy.

          (a) This Agreement may be terminated with written notice by either Party at any time during
the term of this Agreement upon the filing or institution of bankruptcy, reorganization,
liquidation or receivership proceedings by or against the other Party or upon an assignment of a
substantial portion of its assets for the benefit of creditors by the other Party; provided,
however, in the case of any involuntary bankruptcy proceeding such right to terminate will only
become effective if the Party consents to the involuntary bankruptcy or such proceeding is not
dismissed within 90 days of the filing thereof.

          (b) All rights and licenses granted under or pursuant to this Agreement by Isis or Alnylam
are, and will otherwise be deemed to be, for purposes of Section 365(n) of the U.S. Bankruptcy
Code, licenses of right to “intellectual property” as defined under Section 101 of the U.S.
Bankruptcy Code. The Parties agree that the Parties, as licensees of such rights under this
Agreement, will retain and may fully exercise all of their rights and elections under the U.S.
Bankruptcy Code. The Parties further agree that, in the event of the commencement of a bankruptcy
proceeding-by or against either Party under the U.S. Bankruptcy Code, the Party hereto which is not
a Party to such proceeding will be entitled to a complete duplicate of (or complete access to, as
appropriate) any such intellectual property and all embodiments of such intellectual property, and
same, if not already in their possession, will be promptly delivered to them (i) upon any such
commencement of a bankruptcy proceeding upon their written request therefore, unless the Party
subject to such proceeding elects to continue to perform all of its obligations under this
Agreement, or (ii) if not delivered under (i) above, following the rejection of this Agreement by
or on behalf of the Party subject to such proceeding upon written request therefore by the
non-subject Party.

     14.4 Alnylam’s Limited Right to Terminate the Research Program. Notwithstanding
Section 4.2, Alnylam may unilaterally elect to terminate the Research Program, by providing Isis a
written notice of such election (an “Early Termination Notice”) on or before 5:00 PM Pacific Time
on September 30, 2010. If Alnylam

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unilaterally terminates the Research Program (the “Early Collaboration Termination”) in
accordance with this Section 14.4, then, as of the date of the Early Termination Notice (the
“Collaboration Termination Date”):

          (a) each Party’s obligation to perform under the Research Program, and Alnylam’s obligation to
provide funding under the Research Program that was not payable on or before the Collaboration
Termination Date will automatically terminate;

          (b) Alnylam’s rights and Isis’ obligations under the licenses granted by Isis to Alnylam under
Section 5.1(g), 5.1(h) and 5.1(i), including any sublicenses granted by Alnylam thereunder, will
automatically terminate;

          (c) Solely with respect to the license granted to Isis under Section 6.1(i), the definition of
Alnylam Future Motif and Mechanism Patents, and Alnylam Future Chemistry Patents, will be fixed as
of the Collaboration Termination Date in accordance with Sections 12 and 13, respectively, of
Exhibit 1.1;

          (d) Alnylam will be relieved of its obligations to pay Isis any milestones, royalties and
sublicense income relating to Alnylam Single Stranded RNAi Products under Sections 7.2(b), 7.3(a),
7.3(b), and 7.4(b) that had not accrued by the Collaboration Termination Date, except that if the
Collaboration Termination Date is before the [**]-month anniversary of the Restatement Date and
before the [**] following the date Alnylam obtains the data that demonstrates the first In Vivo
Efficacy in Rodents, then Alnylam will not be obligated to pay the $[**] research milestone for the
first In Vivo Efficacy in Rodents set forth in Section 7.3(a); and

          (e) Isis will be relieved of its obligations under Sections 5.5 and 8.5, and its obligations
as a Responsible Party under Section 11.2(g).

     14.5 Accrued Rights and Surviving Obligations.

          (a) Expiration or termination of the Agreement will not relieve the Parties of any obligation
accruing prior to such expiration or termination, including, but not limited to, financial
obligations under Section 4.2(c) or Article 7 or 8. Sections 4.3(f), 6.4(i), 9.2, 9.3 and 11.1,
and Articles 1, 12, 13, 14 and 17 will survive expiration or termination of the Agreement.
Provisions concerning reporting requirements will continue in effect in accordance with any
applicable timetables set forth herein. Any expiration or early termination of this Agreement will
be without prejudice to the rights of either Party against the other accrued or accruing under this
Agreement prior to termination. No expiration of this Agreement will relieve a Party of its
obligation to pay milestones, royalties, or a percentage of Technology Access Fees or Sublicense
Revenue to the extent accrued prior to such expiration.

          (b) Except as set forth in Section 14.4.(b), the rights of any sublicensee under any permitted
sublicense granted in accordance with Section 5.2 or 6.3 will survive the termination of this
Agreement.

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ARTICLE 15

REPRESENTATIONS AND WARRANTIES; DISCLAIMER

     15.1 Representations and Warranties of the Parties. Each Party represents and
warrants to the other Party that, as of the Effective Date and the Restatement Date:

          (a) Such Party is duly organized and validly existing under the laws of the state of its
incorporation and has full corporate power and authority to enter into this Agreement and to carry
out the provisions hereof;

          (b) Such Party has taken all corporate action necessary to authorize the execution and
delivery of this Agreement and the performance of its obligations under this Agreement;

          (c) This Agreement is a legal and valid obligation of such Party, binding upon such Party and
enforceable against such Party in accordance with the terms of this Agreement. The execution,
delivery and performance of this Agreement by such Party does not conflict with any agreement,
instrument or understanding, oral or written, to which such Party is a Party or by which such Party
may be bound, and does not violate any law or regulation of any court, governmental body or
administrative or other agency having authority over such Party. All consents, approvals and
authorizations from all governmental authorities or other Third Parties required to be obtained by
such Party in connection with this Agreement have been obtained;

          (d) Such Party has sufficient right, power and authority to enter into this Agreement, to
perform its obligations under this Agreement and to grant the licenses granted hereunder.

     15.2 Disclaimers. THE PARTIES EXPRESSLY DISCLAIM ALL WARRANTIES, EXPRESS OR IMPLIED,
INCLUDING WITHOUT LIMITATION WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR
NON-INFRINGEMENT OF THIRD PARTY RIGHTS, UNLESS OTHERWISE EXPRESSLY PROVIDED IN THIS AGREEMENT.

ARTICLE 16

NOTICE

     16.1 Notice. All notices which are required or permitted hereunder will be in writing
and sufficient if delivered personally, sent by facsimile (and confirmed by telephone), sent by
nationally-recognized overnight courier or sent by registered or certified mail, postage prepaid,
return receipt requested, addressed as follows:

	 	 	 
	if to Isis, to:

	 	Isis Pharmaceuticals, Inc.
	 

	 	1896 Rutherford Road
	 

	 	Carlsbad, CA 92008
	 

	 	Attention: Chief Operating Officer

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	 	Fax No.: +1 (760) 603-4652
	 
	 	 
	with a copy to:

	 	Attention: General Counsel
	 

	 	Fax No.: +1 (760) 268-4922
	 
	 	 
	if to Alnylam, to:

	 	Alnylam Pharmaceuticals, Inc.
	 

	 	300 Third Street
	 

	 	Cambridge, MA 02142
	 

	 	Attention: VP Legal
	 

	 	Fax No.: +1 (617) 575-7315
	 
	 	 
	with a copy to:

	 	WilmerHale
	 

	 	60 State Street
	 

	 	Boston, Massachusetts 02109
	 

	 	Attention: Steven D. Singer, Esq.
	 

	 	Fax No.: +1 (617) 526-5000

or to such other address as the Party to whom notice is to be given may have furnished to the other
Party in writing in accordance herewith. Any such notice will be deemed to have been given when
delivered if personally delivered or sent by facsimile on a business day, on the business day after
dispatch if sent by nationally-recognized overnight courier and on the third business day following
the date of mailing if sent by mail.

ARTICLE 17

MISCELLANEOUS PROVISIONS

     17.1 Relationship of the Parties. It is expressly agreed that Isis and Alnylam will
be independent contractors and that the relationship between the two Parties will not constitute a
partnership, joint venture or agency. Neither Isis nor Alnylam will have the authority to make any
statements, representations or commitments of any kind, or to take any action, which will be
binding on the other, without the prior consent of the other Party.

     17.2 Successors and Assigns. Neither this Agreement nor any interest hereunder may be
assigned or otherwise transferred (whether by sale of stock, sale of assets or merger), nor, except
as expressly provided hereunder, may any right or obligations hereunder be assigned or transferred
by either Party without the prior written consent of the other Party; provided, however,
that a Party may, without such consent, assign this Agreement and its rights and obligations
hereunder to an Affiliate or in connection with an Acquisition. Notwithstanding the provisions of
this Section 17.2:

          (a) If Alnylam is the subject of an Acquisition and the entity surviving such Acquisition does
not maintain [**] that is substantially similar or greater [**] after the time of the Acquisition,
then (i) the limit on the [**] that Isis can [**] pursuant to Section 6.4(a) will [**], and (ii)
the exclusive right to grant Naked Sublicenses under Section 5.2 will [**].

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          (b) Additionally, if Alnylam is the subject of an Acquisition, (i) the royalties payable by
Alnylam with respect to Alnylam Single Stranded RNAi Products will be adjusted in accordance with
Section 7.2(b), (ii) the definition of Alnylam Future Motif and Mechanism Patents, and Alnylam
Future Chemistry Patents, will be fixed as of the date of such Acquisition in accordance with
Sections 13 and 12, respectively, of Exhibit 1.1, and (iii) [**].

          (c) If Isis is the subject of an Acquisition, (i) the entity surviving such Acquisition will
no longer [**] under Section 6.4(a), (ii) the number of [**] such Acquisition will be permitted to
[**] pursuant to Section 6.4(a) shall be limited to [**] per calendar year, (iii) the royalties
payable by Isis with respect to Isis Single Stranded RNAi Products will be adjusted in accordance
with Section 8.2(b), and (iv) the definition of Isis Future Motif and Mechanism Patents, and Isis
Future Chemistry Patents, will be fixed as of the date of such Acquisition in accordance with
Sections 57 and 58, respectively, of Exhibit 1.1.

          (d) Any permitted assignee will assume all obligations of its assignor under this Agreement.
Any attempted assignment not in accordance with this Section 17.2 will be void.

     17.3 Entire Agreement; Amendments. This Agreement contains the entire understanding
of the Parties with respect to the license, development and commercialization of Products
hereunder. All express or implied agreements and understandings, either oral or written, heretofore
made by the Parties on the same subject matter are expressly superseded by this Agreement. This
Agreement may be amended, or any term hereof modified, only by a written instrument duly executed
by both Parties hereto.

     17.4 Force Majeure. Neither Party will be held liable or responsible to the other
Party nor be deemed to have defaulted under or breached this Agreement for failure or delay in
fulfilling or performing any term of this Agreement when such failure or delay is caused by or
results from causes beyond the reasonable control of the affected Party including, without
limitation, embargoes, acts of war (whether war be declared or not), insurrections, riots, civil
commotions, acts of terrorism, strikes, lockouts or other labor disturbances, or acts of God. The
affected Party will notify the other Party of such force majeure circumstances as soon as
reasonably practical and will make every reasonable effort to mitigate the effects of such force
majeure circumstances.

     17.5 Applicable Law. The Agreement will be governed by and construed in accordance
with the laws of the State of Delaware without reference to any rules of conflict of laws.

     17.6 Dispute Resolution.

          (a) The Parties recognize that disputes may from time to time arise between the Parties during
the term of this Agreement. In the event of such a dispute, either Party, by written notice to the
other Party, may have such dispute referred to the Parties’ respective executive officers
designated below or their successors, for attempted

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resolution by good faith negotiations within 30 days after such notice is received. Said
designated officers are as follows:

	 	 	 
	For Isis:

	 	Chief Operating Officer
	For Alnylam:

	 	President and Chief Operating Officer

If the dispute is not resolved as provided above, the CEO of Isis and the CEO of Alnylam will meet
for attempted resolution by good faith negotiations within 15 days after the expiration of the
preceding 30 day period.

          (b) In the event the designated executive officers are not able to resolve such dispute during
such 15-day period, then any such dispute shall be resolved through binding arbitration under the
Commercial Arbitration Rules of the American Arbitration Association by a panel of three
arbitrators appointed in accordance with such rules. The Parties shall be entitled to the same
discovery as permitted under the U.S. Federal Rules of Civil Procedure; provided
that the panel shall be entitled in its discretion to grant a request from a Party for
expanded or more limited discovery. The award of the arbitrators shall be the sole and exclusive
remedy between the Parties regarding any such dispute. An award rendered in connection with an
arbitration pursuant to this Section 17.6 shall be final and binding upon the Parties and any
judgment upon such award may be entered and enforced in any court of competent jurisdiction. Any
arbitration pursuant to this Section 17.6 shall be conducted in San Diego, California if Alnylam
initiates the arbitration or in Boston, Massachusetts if Isis initiates the arbitration. Nothing
in this Section 17.6 shall be construed as limiting in any way the right of a Party to seek an
injunction or other equitable relief with respect to any actual or threatened breach of this
Agreement or to bring an action in aid of arbitration. Should any Party seek an injunction or
other equitable relief, or bring an action in aid of arbitration, then for purposes of determining
whether to grant such injunction or other equitable relief, or whether to issue any order in aid of
arbitration, the dispute underlying the request for such injunction or other equitable relief, or
action in aid of arbitration, may be heard by the court in which such action or proceeding is
brought.

     17.7 No Consequential Damages. IN NO EVENT WILL EITHER PARTY OR ANY OF ITS RESPECTIVE
AFFILIATES BE LIABLE TO THE OTHER PARTY OR ANY OF ITS AFFILIATES FOR SPECIAL, INDIRECT, INCIDENTAL
OR CONSEQUENTIAL DAMAGES, WHETHER IN CONTRACT, WARRANTY, TORT, NEGLIGENCE, STRICT LIABILITY OR
OTHERWISE, INCLUDING, BUT NOT LIMITED TO, LOSS OF PROFITS OR REVENUE, OR CLAIMS OF CUSTOMERS OF ANY
OF THEM OR OTHER THIRD PARTIES FOR SUCH OR OTHER DAMAGES.

     17.8 Captions. The captions to the several Articles and Sections hereof are not a
part of this Agreement, but are merely a convenience to assist in locating and reading the several
Articles and Sections hereof.

     17.9 Waiver. The waiver by either Party hereto of any right hereunder, or the failure
to perform, or a breach by the other Party will not be deemed a waiver of any

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other right hereunder or of any other breach or failure by said other Party whether of a
similar nature or otherwise.

     17.10 Compliance with Law. Nothing in this Agreement will be deemed to permit a Party
to export, re-export or otherwise transfer any Product sold under this Agreement without compliance
with applicable laws.

     17.11 Severability. In the event any one or more of the provisions contained in this
Agreement should be held invalid, illegal or unenforceable in any respect, the validity, legality
and enforceability of the remaining provisions contained herein will not in any way be affected or
impaired thereby, unless the absence of the invalidated provision(s) adversely affect the
substantive rights of the Parties. The Parties will in such an instance use their best efforts to
replace the invalid, illegal or unenforceable provision(s) with valid, legal and enforceable
provision(s) which, insofar as practical, maintains the balance of the rights and obligations of
the Parties under this Agreement.

     17.12 Waiver of Rule of Construction. Each Party has had the opportunity to consult
with counsel in connection with the review, drafting and negotiation of this Agreement.
Accordingly, the rule of construction that any ambiguity in this Agreement will be construed
against the drafting Party will not apply.

     17.13 Counterparts. This Agreement may be executed in two or more counterparts, each
of which will be deemed an original, but all of which together will constitute one and the same
instrument.

     17.14 Performance by Affiliates. To the extent that this Agreement imposes
obligations on Affiliates of a Party, such Party agrees to cause its Affiliates to perform such
obligations.

     17.15 No Implied License. Except as expressly provided in Sections 5.1, 6.1 and 6.2
of this Agreement, no Party will be deemed by estoppel or implication to have granted the other
Party any license or other right with respect to any intellectual property of such Party.

     .

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     IN WITNESS WHEREOF, the Parties have executed this Agreement as of the Restatement Date.

	 	 	 	 	 	 	 	 	 	 	 
	Isis Pharmaceuticals, Inc.	 	Alnylam Pharmaceuticals, Inc.
	 
	 	 	 	 	 	 	 	 	 	 
	By:	 	/s/ B. Lynne Parshall	 	By:	 	/s/ Barry Greene
	 	 	 	 	 	 	 
	 

	 	Name:
	 	B. Lynne Parshall
	 	 	 	Name:
	 	Barry Greene
	 

	 	Title:
	 	Chief Operating Officer
	 	 	 	Title:
	 	President & COO

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EXHIBIT 1.1

DEFINITIONS

	1.	 	“Acquisition” means any of the following events: (a) the acquisition by any Person or group,
other than a Person or group controlling such Party as of the Restatement Date, of “beneficial
ownership” (as defined in Rule 13d-3 under the United States Securities Exchange Act of 1934,
as amended), directly or indirectly, of fifty percent (50%) or more of the shares of such
Party’s voting stock; (b) the approval by the shareholders of such Party of a merger, share
exchange, reorganization, consolidation or similar transaction of such Party (a
“Transaction”), other than a Transaction which would result in the voting stock of such Party
outstanding immediately prior thereto continuing to represent (either by remaining outstanding
or by being converted into voting securities of the surviving entity) more than fifty percent
(50%) of the voting stock of such Party or such surviving entity immediately after such
Transaction; or (c) approval by the shareholders of such Party of a complete liquidation of
such Party or a sale or disposition of all or substantially all of the assets of such Party.
	 
	2.	 	“Active Program” means with respect to a Gene Target and a Party, any ongoing drug discovery,
development, or commercialization of a compound directed to such Gene Target being conducted
by such Party (whether on its own or through a sublicensee).
	 
	3.	 	“Actual FTE Costs” has the meaning set forth in Section 4.2(c).
	 
	4.	 	“Actual External Costs” has the meaning set forth in Section 4.2(c).
	 
	5.	 	“Advancing Party” has the meaning set forth in Section 4.3(a).
	 
	6.	 	“Affiliate” with respect to either Party means Person controlling, controlled by, or under
common control with such Party. For purposes of this definition, “control” refers to the
possession, directly or indirectly, of the power to direct the management or policies of a
Person, whether through the ownership of voting securities, by contract or otherwise, of a
Person. Notwithstanding the foregoing, Regulus Therapeutics Inc. will not be considered an
Affiliate of either Party.
	 
	7.	 	“Alnylam Current Chemistry Patents” means all Chemistry Patents Controlled by Alnylam as of
the Restatement Date, including without limitation the Patents listed on Schedule 1-7 attached
hereto, except Patents that constitute Alnylam Excluded Technology, or Co-Exclusive ssRNAi
Patents.
	 
	8.	 	“Alnylam Current Motif and Mechanism Patents” means all Motif and Mechanism Patents
Controlled by Alnylam as of the Restatement Date, including without limitation the Patents
listed on Schedule 1-8 attached hereto, except Patents that constitute Alnylam Excluded
Technology, or Co-Exclusive ssRNAi Patents.

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	9.	 	“Alnylam Double Stranded RNA Product” means a Double Stranded RNA Product discovered or
developed by Alnylam, its Affiliates or sublicensees, the manufacture, sale or use of which is
covered by a Valid Claim within the Isis Patent Rights.
	 
	10.	 	“Alnylam Enabled Target Pool” has the meaning set forth in Section 4.3(a).
	 
	11.	 	“Alnylam Excluded Technology” means inhibitors to specific genes or gene families,
manufacturing and analytical technologies, formulation and delivery technologies and the
specific technology listed on Schedule 1-10 attached hereto.
	 
	12.	 	“Alnylam Future Chemistry Patents” means all Chemistry Patents Controlled by Alnylam after
the Restatement Date and having an earliest priority date of no later than [**] or that is
necessary to practice a Patent licensed hereunder; provided, however that (a) for any
such Chemistry Patents that are acquired, licensed or invented that include financial or other
obligations to a Third Party, the provisions of Section 11.8 will govern whether such Patent
will be included as an Alnylam Future Chemistry Patent and (b) Alnylam Future Chemistry
Patents do not include Patents that constitute Alnylam Excluded Technology, or Co-Exclusive
ssRNAi Patents. Notwithstanding the foregoing, (i) in the event an Acquisition involving Isis
occurs before [**], the date “[**]” used in this definition will be automatically changed to
the date of such Acquisition; and (ii) in the event of an Early Collaboration Termination
under Section 14.4, solely with respect to the licenses granted to Isis under Section 6.1(i),
the date “[**]” used in this definition will be automatically changed to the Collaboration
Termination Date.
	 
	13.	 	“Alnylam Future Motif and Mechanism Patents” means all Motif and Mechanism Patents Controlled
by Alnylam after the Restatement Date and having an earliest priority date of no later than
[**] or that is necessary to practice a Patent licensed hereunder; provided, however
that (a) for any such Motif and Mechanism Patents that are acquired, licensed or invented that
include financial or other obligations to a Third Party, the provisions of Section 11.8 will
govern whether such Patent will be included as an Alnylam Future Motif and Mechanism Patent
and (b) Alnylam Future Motif and Mechanism Patents do not include Patents that constitute
Alnylam Excluded Technology, or Co-Exclusive ssRNAi Patents. Notwithstanding the foregoing,
(i) in the event an Acquisition involving Isis occurs before [**], the date “[**]” used in
this definition will be automatically changed to the date of such Acquisition, and (ii) in the
event of an Early Collaboration Termination under Section 14.4, solely with respect to the
licenses granted to Isis under Section 6.1(i), the date “[**]” used in this definition will be
automatically changed to the Collaboration Termination Date.
	 
	14.	 	“Alnylam Patent Rights” means Alnylam Current Motif and Mechanism Patents, Alnylam Future
Motif and Mechanism Patents, Alnylam Current Chemistry Patents and Alnylam Future Chemistry
Patents. For purposes of determining whether a royalty is payable by Isis under Section 8.2
in connection with the sale of an Isis Single Stranded RNAi Product, any Joint Patent, a Valid
Claim of

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	 	 	which covers the manufacture, use or sale of such Isis Single Stranded RNAi Product, will
be considered an Alnylam Patent Right.

	15.	 	“Alnylam Product” means an Alnylam Double Stranded RNA Product MicroRNA Product, or Alnylam
Single Stranded RNAi Product, discovered or developed by Alnylam, its Affiliates or
sublicensees, the manufacture, sale or use of which is covered by a Valid Claim within the
Isis Patent Rights.
	 
	16.	 	“Alnylam Single Stranded RNAi Product” means any Single Stranded RNAi Product Designed for an
Alnylam Enabled Target, the manufacture, sale or use of which is covered by a Valid Claim
within the Isis Patent Rights.
	 
	17.	 	“Antisense Drug Discovery Program” means an antisense drug discovery program that
investigates multiple different mechanisms of modulating a Gene Target to identify a drug
candidate, with a predominant emphasis on potential drug candidates that are single-stranded.
	 
	18.	 	“Applicable Laws” means all laws, statutes, rules, regulations, orders, judgments, or
ordinances having the effect of law of any federal, national, multinational, state,
provincial, county, city or other political subdivision.
	 
	19.	 	“Bona Fide Drug Discovery Collaboration” means a collaboration involving the discovery and
development of Double Stranded RNA Products, in which a Party plays an integral role in the
experimentation and an important, though not necessarily dominant or co-equal, role in the
decision-making, relating to the discovery and development of Double Stranded RNA Products
from the point in time at which the relevant Gene Target has been designated through the
initiation of [**]. A Bona Fide Drug Discovery Collaboration may continue beyond the
initiation of such [**]. For Isis Products that are Double Stranded RNA Products, a Bona Fide
Drug Discovery Collaboration must be an Antisense Drug Discovery Program. For each Party,
collaborations that do not include or involve Patents licensed from the other Party hereunder
shall not constitute Bona Fide Drug Discovery Collaborations. A Party’s experimentation
relating to the discovery and development of Double Stranded RNA Products that modulate a
relevant Gene Target prior to the commencement of a collaboration shall be deemed to have been
conducted in the course of the collaboration for purposes of determining whether the
collaboration is a Bona Fide Drug Discovery Collaboration. A series of related collaborations
and/or license agreements involving the discovery and development of Double Stranded RNA
Products with the same sublicensee or related sublicensees that includes a Bona Fide Drug
Discovery Collaboration agreement will be aggregated to constitute a single Bona Fide Drug
Discovery Collaboration.
	 
	20.	 	“Budget” has the meaning set forth in Section 4.2(a).
	 
	21.	 	“Business Day” means a weekday on which banking institutions in Boston, Massachusetts are
open for business. For purposes of clarity, a Business Day

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	 	 	shall not include any Saturday or Sunday or federal or Commonwealth of Massachusetts
holiday.
	 
	22.	 	“Calendar Quarter” means the respective periods of three (3) consecutive calendar months
ending on March 31, June 30, September 30 and December 31.
	 
	23.	 	“Chemistry Patent” means any Patent that covers (a) an oligomeric compound having a chemical
composition that differs from a native oligonucleotide composition or (b) any modification to
the base, sugar or internucleoside linkage of the oligomeric compound, and specifically, but
without limitation, includes covalently linked conjugates and other such moieties
	 
	24.	 	“Co-Exclusive ssRNAi Patents” means third party Patents in-licensed by both Alnylam and Isis
prior to [**] to the extent that such Patents Cover Single Stranded RNAi Compounds or Single
Stranded RNAi Products.
	 
	25.	 	“Collaboration Termination Date” has the meaning set forth in Section 14.4.
	 
	26.	 	“Commercially Reasonable Efforts” means the diligent efforts, expertise and resources
normally used by a Party to develop, manufacture and commercialize a product or compound owned
by it or to which it has rights, which is of similar market potential at a similar stage in
its development or product life, taking into account issues of safety, and efficacy, product
profile, difficulty in developing the product or compound, competitiveness of the marketplace
for the product, the proprietary position of the compound or product, the regulatory structure
involved, the potential total profitability of the applicable product(s) marketed or to be
marketed and other relevant factors affecting the cost, risk and timing of development and the
total potential reward to be obtained if a product is commercialized, but not less than
reasonably diligent efforts. In determining whether Commercially Reasonable Efforts have been
satisfied, the fact that a Party is required to pay the other Party a royalty or milestones
shall not be a factor weighed (i.e., a Party may not apply lesser resources or effort to a
Product because it must pay a royalty or milestones to the other Party).
	 
	27.	 	“Control” or “Controlled” means, with respect to any Patent or other intellectual property
right, possession of the right (whether by ownership, license or otherwise), to assign, or
grant a license, sublicense or other right to or under, such Patent or right as provided for
herein without violating the terms of any agreement or other arrangement with any Third Party.
	 
	28.	 	“Confidential Information” means information which is (a) of a confidential and proprietary
nature; and (b) not readily available to that Party’s competitors and which, if known by a
competitor of that Party, might lessen any competitive advantage of that Party or give such
competitor a competitive advantage.
	 
	 	 	Confidential Information includes, without limitation, (x) information that is proprietary
or confidential or which is treated by that Party as confidential and which relates either
directly or indirectly to the business of that Party regardless

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	 	 	of the form in which that information is constituted, and which is not lawfully in the
public domain; and (y) any confidential information in relation to Patents, technology,
know-how, or any improvements owned or Controlled by a Party hereto.

	 	 	Confidential Information will not include any information that the receiving Party can
establish by written records:

	 	(i)	 	was known by it prior to the receipt of Confidential Information from the disclosing
Party;
	 
	 	(ii)	 	was disclosed to the receiving Party by a Third Party having the right to do so;
	 
	 	(iii)	 	was, or subsequently became, in the public domain through no fault of the
receiving Party, its officers, directors, employees or agents; or
	 
	 	(iv)	 	was concurrently or subsequently developed by personnel of the receiving
Party without having had access to the disclosing Party’s Confidential Information.

	29.	 	“Controlled Contractor” means a Third Party contractor, such as a contract research
organization, contract employee, contract manufacturer, consultant and the like, who merely
conducts activities on behalf of a Party, is subject to such Party’s supervision and control,
and will not have any rights (other than non-exclusive rights) in any intellectual property
created in connection with such activities.
	 
	30.	 	“Designed for” means, when used in relation to a specified Gene Target, a Single Stranded
RNAi Compound that is [**] to [**] of the specified [**] via [**].
	 
	31.	 	“Development Candidate” means a Single Stranded RNAi Product for which [**] have commenced.
	 
	32.	 	“Development Collaboration” means a collaboration by either Party with a Third Party whose
purpose is the further development and/or commercialization of a Double Stranded RNA Product
or Single Stranded RNAi Product, as applicable, and that begins at or after the initiation of
IND-Enabling Studies for such Product. For each Party, collaborations that do not include or
involve Patents licensed from the other Party hereunder shall not constitute Development
Collaborations.
	 
	33.	 	“Double Stranded RNA” means a composition designed to act primarily through an RNAi mechanism
that is not a MicroRNA Construct and which consists of either (a) two separate oligomers of
native or chemically modified RNA that are hybridized to one another along a substantial
portion (greater than or equal to [**]%) of their lengths, or (b) a single oligomer of native
or chemically modified RNA that is hybridized to itself by self-complementary base-pairing
along a substantial portion (greater than or equal to [**]%) of its length to form a hairpin.

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	34.	 	“Double Stranded RNA Product” means a pharmaceutical composition that contains a Double
Stranded RNA.
	 
	35.	 	“Early Collaboration Termination” has the meaning set forth in Section 14.4.
	 
	36.	 	“Early Termination Notice” has the meaning set forth in Section 14.4.
	 
	37.	 	“Effective Date” means March 11, 2004.
	 
	38.	 	“Enabled Target” has the meaning set forth in Section 4.3(a).
	 
	39.	 	“Enabled Target Pool” has the meaning set forth in Section 4.3(a).
	 
	40.	 	“Enabled Target Slot” has the meaning set forth in Section 4.3(a).
	 
	41.	 	“FTE” means the equivalent of the work of one (1) employee working on a dedicated full time
basis for one (1) year (consisting of at least a total of [**] hours per year of dedicated
effort, excluding vacations and holidays) of work on or directly related to the Research Plan,
carried out by an Isis employee or an Alnylam employee, as the case may be. No one person
will be permitted to account for more than [**] hours of FTE contribution per year. Any
person who devotes less than [**] hours per year shall be treated as an FTE on a pro-rata
basis, based upon the actual number of hours worked divided by [**]. Scientific work
performed in the performance of the Research Program by an Isis FTE or Alnylam FTE may
include, but is not limited to, experimental laboratory work, recording and writing up
results, reviewing literature and references, and holding scientific discussions.
	 
	42.	 	“FTE Rate” means $[**] per FTE per year for the initial calendar year of the Research Term,
such FTE rate to be increased by the percentage increase in the Consumer Price Index — Urban
Wage Earners and Clerical Workers, US City Average, All Items, 1982-84 = 100, published by the
United States Department of Labor, Bureau of Labor Statistics (or its successor equivalent
index, the “CPI”) over the CPI as of June 30, 2009, starting as of the beginning of the 2nd
calendar year of the Research Term (i.e., beginning in 2010) and each calendar year thereafter
during the Research Term, provided that any such increase shall not exceed [**]% per
annum.
	 
	43.	 	“Gene Target” means a transcriptional unit of a gene, including any protein product of such
transcriptional unit, and including all splice variants.
	 
	44.	 	“Graduated Enabled Target” has the meaning set forth in Section 4.3(a).
	 
	45.	 	“In Vivo Efficacy in Rodents” means the first achievement by Alnylam or its sublicensees of
at least a [**]% nadir reduction of the mRNA of the intended Gene Target in an internal
organ(s), demonstrated in an independent rodent experiment and confirmed by [**], with an
unformulated, unconjugated Single

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	 	 	Stranded RNAi Compound administered subcutaneously as a [**] not to exceed [**] mg/kg. If
not achieved earlier, this milestone will be deemed to have occurred upon In Vivo Efficacy
in NHP.
	 
	46.	 	“In Vivo Efficacy in NHP” means the first achievement by Alnylam or its sublicensees of at
least a [**]% nadir reduction of the mRNA of the intended Gene Target in an internal organ(s),
demonstrated in an independent NHP experiment and confirmed by [**], with an unformulated,
unconjugated Single Stranded RNAi Compound administered subcutaneously at a [**] not to exceed
[**] mg/kg per week, with the nadir reduction seen and confirmed in [**] consecutive
administration cycles.
	 
	47.	 	“IND” means an Investigational New Drug Application or similar foreign application or
submission for approval to conduct human clinical investigations.
	 
	48.	 	“IND-Enabling Studies” means the pharmacokinetic and toxicology studies required to meet the
regulations for filing an IND.
	 
	49.	 	“Initiation of Phase I Trial” means the dosing of at least ten human subjects in the first
human clinical trial conducted and designed to evaluate safety of a product.
	 
	50.	 	“Initiation of Phase III Trial” means the dosing of the first patient in the first pivotal
human clinical trial the results of which could be used to establish safety and efficacy of a
Product as a basis for an application for marketing approval or that would otherwise satisfy
the requirements of 21 CFR 3 12.21I or its foreign equivalent.
	 
	51.	 	“Isis Current Chemistry Patents” means all Chemistry Patents Controlled by Isis as of the
Restatement Date, including without limitation the Patents listed on Schedule 1-51 attached
hereto, except Patents that constitute Isis Excluded Technology, or Co-Exclusive ssRNAi
Patents.
	 
	52.	 	“Isis Current Motif and Mechanism Patents” means all Motif and Mechanism Patents Controlled
by Isis as of the Restatement Date, including without limitation the Patents listed on
Schedule 1-52 attached hereto, except Patents that constitute Isis Excluded Technology, or
Co-Exclusive ssRNAi Patents.
	 
	53.	 	“Isis DS-Target Pool” has the meaning set forth in Section 6.4(a).
	 
	54.	 	“Isis Enabled Target Pool” has the meaning set forth in Section 4.3(a).
	 
	55.	 	“Isis Encumbered Target” means a Gene Target (a) to which Isis has a contractual obligation
to a Third Party existing as of the Restatement Date that precludes Isis from granting a
license under Section 5 with respect to such Gene Target and (b) that is identified and
described on a [**] (as defined in the letter agreement dated March 9, 2004 between Alnylam
and Isis). When and if such restrictions lapse a Gene Target will cease to be an Isis
Encumbered Target.

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	56.	 	“Isis Excluded Technology” means (a) RNase H mechanisms, RNase H motifs and RNase H
oligonucleotides when utilized in an RNase H mechanism, assays and methods thereof; (b)
modulators of specific genes, gene families or proteins; (c) manufacturing technologies; (d)
analytical technologies, kits and assays, including without limitation methods, systems and
compositions of matter for amplifying, quantifying, detecting, characterizing or identifying
nucleic acids or nonoligomeric ligands thereto; (e) formulation and delivery technologies; and
(f) the specific technology listed on Schedule 1-56 attached hereto.
	 
	57.	 	“Isis Future Motif and Mechanism Patents” means all Motif and Mechanism Patents Controlled by
Isis after the Restatement Date and having an earliest priority date of no later than [**] or
that is necessary to practice a Patent licensed hereunder; provided, however that (a)
for any such Motif and Mechanism Patents that are acquired, licensed or invented that include
financial or other obligations to a Third Party, the provisions of Section 11.8 will govern
whether such Patent will be included as an Isis Future Motif Mechanism Patent, and (b) Isis
Future Motif and Mechanism Patents do not include Patents that constitute Isis Excluded
Technology, or Co-Exclusive ssRNAi Patents. Notwithstanding the foregoing, in the event of an
Acquisition involving Alnylam, the date “[**]” used in this definition will be automatically
changed to the date of such Acquisition.
	 
	58.	 	“Isis Future Chemistry Patents” means the Chemistry Patents Controlled by Isis after the
Restatement Date and having an earliest priority date of no later than [**] or that is
necessary to practice a Patent licensed hereunder; provided, however that (a) for any
such Chemistry Patents that are acquired, licensed or invented that include financial or other
obligations to a Third Party, the provisions of Section 11.8 will govern whether such
Chemistry Patents will be included as an Isis Future Chemistry Patent, except Patents that
constitute Isis Excluded Technology and (b) Isis Future Chemistry Patents do not include
Patents that constitute Isis Excluded Technology, or Co-Exclusive ssRNAi Patents.
Notwithstanding the foregoing, in the event of an Acquisition involving Alnylam, the date
“[**]” used in this definition will be automatically changed to the date of such Acquisition.
	 
	59.	 	“Isis Manufacturing Patents” means the Patents specifically listed on Schedule 1-59 attached
hereto. The Parties may agree in writing from time to time to add additional Patents to
Schedule 1-59 attached hereto.
	 
	60.	 	“Isis Partnered Excluded Targets” has the meaning set forth in Section 4.3(e)(i).
	 
	61.	 	“Isis Patent Rights” means Isis Current Motif and Mechanism Patents, Isis Future Motif and
Mechanism Patents, Isis Current Chemistry Patents and Isis Future Chemistry Patents. For
purposes of determining whether a royalty is payable by Alnylam under Section 7.2 in
connection with the sale of an Alnylam Single Stranded RNAi Product, any Joint Patent, a Valid
Claim of which covers the manufacture, use or sale of such Alnylam Single Stranded RNAi
Product, will be considered an Isis Patent Right.

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	62.	 	“Isis Product” means any Isis Single Stranded Product, MicroRNA Product, Double Stranded RNA
Product or Isis Single Stranded RNAi Product, discovered or developed by Isis, its Affiliates
or sublicensees, the manufacture, sale or use of which is covered by a Valid Claim within the
Alnylam Patent Rights.
	 
	63.	 	“Isis Protected Targets” has the meaning set forth in Section 4.3(e).
	 
	64.	 	“Isis Single Stranded Product” means any single stranded oligomeric compound (a) that
hybridizes in whole or in part with a target RNA and modulates the Gene Target, (b) is not a
Double Stranded RNA or Double Stranded RNA Product and (c) the manufacture, sale or use of
which is covered by a Valid Claim within the Alnylam Patent Rights. For purposes of clarity,
an Isis Single Stranded Product shall not include Single Stranded RNAi Compounds, Single
Stranded RNAi Products and Isis Single Stranded RNAi Products.
	 
	65.	 	“Isis Single Stranded RNAi Product” means any Single Stranded RNAi Product Designed for an
Isis Enabled Target, the manufacture, sale or use of which is covered by a Valid Claim within
the Alnylam Patent Rights.
	 
	66.	 	“Isis Special Patents” means the Patents specifically listed on Schedule 1-66 attached
hereto. The Parties may mutually agree in writing from time to time to add additional Patents
to Schedule 1-66 attached hereto
	 
	67.	 	“Joint Invention” has the meaning set forth in Section 11.1(b).
	 
	68.	 	“Joint Patent” has the meaning set forth in Section 11.1(b).
	 
	69.	 	“Know-How” means all tangible or intangible know-how, discoveries, processes, formulas, data,
clinical and preclinical results, non-Patented Inventions, Inventions for which Patents are in
preparation, trade secrets, and any physical, chemical, or biological material or any
replication of any such material in whole or in part that are not otherwise covered by the
Isis Patent Rights or the Alnylam Patent Rights
	 
	70.	 	“License Term” means the period from the Restatement Date until the date of expiry of the
last to expire of the Patents licensed hereunder.
	 
	71.	 	“Major Pharmaceutical Company” means a Person that, together with all of its affiliated
Persons, had annual pharmaceutical product sales during the most recently completed calendar
year in excess of $[**].
	 
	72.	 	“Marketing Approval” means the act of a Regulatory Authority necessary for the marketing and
sale of the Product in a country or regulatory jurisdiction, including, without limitation,
the approval of the NDA by the FDA, EC Approval, and Japanese Approval.
	 
	73.	 	“MicroRNA Construct” is a construct having the chemical and physical description of a Double
Stranded RNA that is either (a) designed to target a precursor microRNA or a microRNA, thereby
to inhibit the production or

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	 	 	function of the microRNA, or (b) designed to function by mimicking the translational
repressor function of a naturally occurring microRNA, and which, in relation to its target
RNA, has been demonstrated in vitro and, to the extent reasonably feasible, in vivo, to
function solely as a translational repressor and not via cleavage of such target RNA.
	 
	74.	 	“MicroRNA Product” means a pharmaceutical product that contains a MicroRNA Construct.
	 
	75.	 	“Motif and Mechanism Patents” means any Patent that covers an oligomeric structure or
composition of matter, or any method of using or incorporating such oligomeric structure or
composition of matter in vitro or in vivo, including without limitation for therapeutic use,
in which target RNA levels are modulated by any mechanism other than RNase H.
	 
	76.	 	“Naked Sublicense” means a license for Double Stranded RNA that includes rights to the Isis
Patent Rights that is not a license in connection with (a) a Development Collaboration or (b)
a Bona Fide Drug Discovery Collaboration. A series of Naked Sublicenses to the same
sublicensee or related sublicensees will be aggregated to constitute a single Naked
Sublicense. For the avoidance of doubt, where this Agreement grants Alnylam exclusive rights
to grant Naked Sublicenses, such exclusive rights preclude Isis from granting licenses to the
Isis Patent Rights to Third Parties for Double Stranded RNA even though such license grants by
Isis would technically be license grants and not sublicense grants. Licenses that do not
include or involve rights to Isis Patents shall not constitute Naked Sublicenses.
	 
	77.	 	“Naked Sublicensee” means a Third Party that obtains a Naked Sublicense from Alnylam in
accordance with the terms of this Agreement.
	 
	78.	 	“NDA” means New Drug Application or similar application or submission for approval to market
and sell a new pharmaceutical product filed with or submitted to a Regulatory Authority.
	 
	79.	 	“Net Sales” will mean the gross invoice price of Products sold by Alnylam or Isis (as
applicable), their respective Affiliates and sublicensees (but with respect to Alnylam does
not include Naked Sublicensees) to a Third Party less the following items: (i) trade
discounts, credits or allowances, (ii) credits or allowances additionally granted upon
returns, rejections or recalls, (iii) freight, shipping and insurance charges, (iv) taxes,
duties or other governmental tariffs (other than income taxes) and (v) government-mandated
rebates and (vi) a reasonable reserve for bad debts. Except in the cases of Products used to
conduct clinical trials, reasonable amounts of Products used as marketing samples and Product
provided without charge for compassionate or similar uses, a Party, its Affiliates or
sublicensees will be treated as having sold Products for an amount equal to the fair market
value of Products if: (a) Products are used by such Party, its Affiliates or sublicensees
without charge or provision of invoice, or (b) Products are provided to a Third Party by such
Party, its Affiliates or sublicensees without

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	 	 	charge or provision of invoice and used by such third party.
	 
	 	 	Such amounts shall be determined from the books and records of Alnylam or Isis (as
applicable) and their respective Affiliates and sublicensees, maintained in accordance with
GAAP, consistently applied.
	 
	 	 	In the event the Product is sold as part of a Combination Product (as defined below), the
Net Sales from the Combination Product, for the purposes of determining royalty payments,
shall be determined by multiplying the Net Sales (as determined without reference to this
paragraph) of the Combination Product, during the applicable royalty reporting period, by
the fraction, A/A+B, where A is the average sale price of the Product when sold separately
in finished form and B is the average sale price of the other product(s) included in the
Combination Product when sold separately in finished form, in each case during the
applicable royalty reporting period or, if sales of both the Product and the other
product(s) did not occur in such period, then in the most recent royalty reporting period
in which sales of both occurred. In the event that such average sale price cannot be
determined for both the Product and all other products(s) included in the Combination
Product, Net Sales for the purposes of determining royalty payments shall be calculated by
multiplying the Net Sales of the Combination Product by the fraction of C/C+D where C is
the fair market value of the Product and D is the fair market value of all other product(s)
included in the Combination Product. As used above, the term “Combination Product” means
any pharmaceutical product which consists of a Product and other therapeutically active
pharmaceutical compound or any delivery technology that embodies substantial intellectual
property rights Controlled by the selling Party (e.g., a common syringe would not
constitute a delivery technology that embodies substantial intellectual property rights
Controlled by the selling Party, but an implantable delivery device such as a stent would
constitute such a delivery technology).
	 
	80.	 	“Other Alnylam Sublicense” has the meaning set forth in Section 7.6(a).
	 
	81.	 	“Other Isis Sublicense” has the meaning set forth in Section 8.4(b).
	 
	82.	 	“Patent” or “Patents” means (a) patent applications (including provisional applications and
applications for certificates of invention); (b) any patents issuing from such patent
applications (including certificates of invention); (c) all patents and patent applications
based on, corresponding to, or claiming the priority date(s) of any of the foregoing; (d) any
substitutions, extensions (including supplemental protection certificates), registrations,
confirmations, reissues, divisionals, continuations, continuations-in-part, re-examinations,
renewals and foreign counterparts thereof; and (e) all patents claiming overlapping priority
therefrom.
	 
	83.	 	“Person” means any person, organization, corporation or other business entity.
	 
	84.	 	“Product” means either an Alnylam Product or an Isis Product as the case may be.

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	85.	 	“Regulatory Authority” means any applicable government regulatory authority involved in
granting approvals for the marketing and/or pricing of a Product worldwide including, without
limitation, the United States Food and Drug Administration (“FDA”) and any successor
government authority having substantially the same function, and foreign equivalents thereof.
	 
	86.	 	“Research Costs” has the meaning set forth in Section 4.2(c).
	 
	87.	 	“Research Plan” has the meaning set forth in Section 4.2(a).
	 
	88.	 	“Research Program” has the meaning set forth in Section 4.2.
	 
	89.	 	“Research Program Patent” means any Patents that claim Inventions that were discovered by the
employees of either Party in the performance of the Research Program. For purposes of
clarity, Research Program Patents may also be Isis Future Motif and Mechanism Patents, Isis
Future Chemistry Patents, Alnylam Future Motif and Mechanism Patents, or Alnylam Future
Chemistry Patents.
	 
	90.	 	“Research Term” has the meaning set forth in Section 4.2.
	 
	91.	 	“Research Use” means discovering, developing and optimizing an Alnylam Product or an Isis
Product, as applicable, up to, but not including, [**], and/or conducting pilot manufacturing
studies of an Alnylam Product or an Isis Product, as applicable. Research Use may include
small pilot toxicology studies. With respect to Isis, Research Use does not include studies
[**] for potential drug targets, but does include studies [**] for development of Double
Stranded RNA Products or Single Stranded RNAi Products, as applicable, from among potential
targets for which a reasonable scientific basis exists for believing that such potential
targets are associated with a particular disease or condition.
	 
	92.	 	“Reserved DS-Target” has the meaning set forth in Section 6.4(a).
	 
	93.	 	“RMC” has the meaning set forth in Section 4.1(a).
	 
	94.	 	“Single Stranded RNAi Compound” means a single stranded chemically modified oligonucleotide
and/or analog designed to cause target mRNA cleavage via the RISC or RNAi mechanism. For
purposes of clarity, an ssRNAi compound does not include oligonucleotides (or chemically
modified oligonucleotide analogs) designed to work via other mechanisms such as (i) RNase H 1
or 2 (including any oligonucleotide which has [**]); (ii) alteration of splicing; (iii)
translation arrest (excluding RNAi-mediated repression of translation); (iv) alteration of
processing; (v) polyadenylation; (vi) capping; (vii) modulation of pre-mRNA processing of the
target mRNA; or (viii) oligonucleotides (or chemically modified oligonucleotide analogs)
designed to mimic a known naturally occurring microRNA.
	 
	 	 	Working via the RISC or RNAi mechanism means that the compound is capable

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	 	 	of, in an in vitro cell culture assay, causing cleavage of the target mRNA at the [**], as
evidenced for example by a [**] assay.

	95.	 	“Single Stranded RNAi Product” means a pharmaceutical composition that contains a Single
Stranded RNAi Compound.
	 
	96.	 	“Sublicense Revenue” means any payments that (1) with respect to Alnylam, Alnylam receives
from a sublicensee in consideration of a Naked Sublicense or a sublicense granted by Alnylam
as permitted by Section 5.2(b), or (2) with respect to Isis, Isis receives from a sublicensee
in consideration of a sublicense to further the research, development or commercialization of
an Isis Single Stranded RNAi Product, in each case including, but not limited to, license
fees, royalties, milestone payments, and license maintenance fees, but excluding: (i) payments
made in consideration of equity or debt securities of the applicable Party at fair market
value and (ii) payments specifically committed to reimburse the applicable Party for the
fully-burdened cost of research and development. If a Party receives any non-cash Sublicense
Revenue, such Party will pay the other Party, at the election of the Party who is entitled to
receive Sublicense Revenue payment, either (x) a cash payment equal to the fair market value
of the appropriate percentage of the Sublicense Revenue or (y) the in-kind portion, if
practicable, of the Sublicense Revenue.
	 
	97.	 	“Technology Access Fee” means any payments that Alnylam receives from granting a Third Party
access (through sublicense or otherwise) to the Isis Patent Rights as part of a Bona Fide
Collaboration or Development Collaboration agreement, including, but not limited to, (1)
license fees, (2) collaboration fees, (3) option fees, (4) payments made in consideration for
the issuance of equity or debt securities above fair market value, (5) payments made for
research and development support above Alnylam’s fully-burdened cost, but excluding the
following payments: (i) payments made in consideration for equity or debt securities of
Alnylam at fair market value, (ii) payments made in consideration for thirty-five percent
(35%) or more of Alnylam’s equity securities at fair market value plus a reasonable control
premium, (iii) payments specifically committed to reimburse Alnylam for the fully-burdened
cost of research and development, including without limitation the fully-burdened cost of
products transferred by Alnylam in connection with such research and development, (iv) [**]
(v) payments that are not milestones and that are associated with the sale of commercial
products, and (vi) payments that count as Sublicense Revenue under a Naked Sublicense subject
to Alnylam’s payment obligations to Isis under Section 7.4. If Alnylam receives any non-cash
Technology Access Fees, Alnylam will pay Isis, at Isis’ election, either (x) a cash payment
equal to the fair market value of Isis’ appropriate portion of the Technology Access Fee or
(y) the in-kind portion, if practicable, of the Technology Access Fee.
	 
	98.	 	“Third Party” means any party other than Isis or Alnylam and their respective Affiliates.

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	99.	 	“Valid Claim” means (i) an issued claim of an unexpired Patent that has not been withdrawn,
canceled or disclaimed, or held invalid or unenforceable by a court of competent jurisdiction
in an unappealed or unappealable decision, or (ii) a claim of a patent application which has
been pending for less than [**] years from the earliest priority date for such application.

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EXHIBIT 4.3(c)(iv)

Picking Mechanism Examples

Example A

In the initial round of Picking, the following will be the order (with total number of Enabled
Targets after Pick in parentheses):

Alnylam(1) — Isis(1) — Isis(2) — Alnylam(2) — Alnylam(3) —Isis(3) — Isis(4) —
Alnylam(4) . . .

Example B

If both Parties have an equal number of Enabled Targets (10, for this example) and the previous
round ended with an Alnylam Pass followed by an Isis Pass, the following will be the order (with
total number of Enabled Targets after Pick in parentheses):

Alnylam(11) — Isis(11) — Isis(12) — Alnylam(12) — Alnylam(13) —Isis(13) — Isis(14) —
Alnylam(14) . . .

Example C

If Alnylam has 10 Enabled Targets and Isis has 5 Enable Targets and there have been no Cleared
Targets since the previous Selection Section, the following will be the order (with total number of
Enabled Targets after Pick in parentheses) regardless of how the previous Round ended:

[**] . . .

Example D

If Alnylam has 10 Enabled Targets and Isis has 5 Enable Targets and there have been one or more
Cleared Targets since the previous Selection Section, the following will be the order (with total
number of Enabled Targets after Pick in parentheses) but Isis will not be entitled to Pick a
Cleared Target until it Picks its [**] Enabled Target (in italics below) regardless of how the
previous Round ended:

[**]

Example E1

If Isis has 10 Enabled Targets and Alnylam has 5 Enable Targets and there have been one or more
Cleared Targets since the previous Selection Section, the following will be the order (with total
number of Enabled Targets after Pick in parentheses) regardless of how the previous Round ended and
assuming that Alnylam does not Pick a Cleared Target until it Picks its [**] Enabled Target (in
italics below):

[**] . . .

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Example E2

If Isis has 10 Enabled Targets and Alnylam has 5 Enable Targets and there have been one or more
Cleared Targets since the previous Selection Section, the following will be the order (with total
number of Enabled Targets after Pick in parentheses) regardless of how the previous Round ended and
assuming that Alnylam Picks a Cleared Target with its [**] Enabled Target (in italics below), and
for clarity, Isis may pick a Cleared Target for its [**] Enabled Target (underlined below):

[**]

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Exhibit 5.3(c) Part I

Isis Third-Party Joint Patents Rights

     The following schedule is provided by Isis Pharmaceuticals, Inc. to Alnylam Pharmaceuticals,
Inc., in connection with the Strategic Collaboration and License Agreement between Alnylam and Isis
(the “Agreement”). Capitalized terms used but not otherwise defined herein have the meanings given
to such terms in the Agreement.

     This schedule and the information and disclosures contained in this schedule are intended only
to qualify and limit the licenses granted by Isis to Alnylam in the Agreement and do not expand in
any way the scope or effect of any such licenses.

Isis has cases with joint inventorship with the [**] following entities:

[**]

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Exhibit 5.3(c) Part II, Joint Patent Rights

	 	 	 	 	 	 	 	 	 	 	 	 	 
	Isis Docket Number	 	Country Name	 	Status	 	Patent Number	 	Grant Date	 	Title	 	3rd Party
	[**]
	 	[**]
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	Isis Docket Number	 	Country Name	 	Status	 	Patent Number	 	Grant Date	 	Title	 	3rd Party
	[**]
	 	[**]
	 	[**]
	 	 	 	 	 	[**]
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	[**]
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	[**]
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Exhibit 5.3(d)

Isis Encumbered Patent Rights

     The following schedule of encumbered Patents is provided by Isis Pharmaceuticals, Inc. to
Alnylam Pharmaceuticals, Inc., in connection with the Strategic Collaboration and License Agreement
between Alnylam and Isis (the “Agreement”). Capitalized terms used but not otherwise defined
herein have the meanings given to such terms in the Agreement.

     This schedule and the information and disclosures contained in this schedule are intended only
to qualify and limit the licenses granted by Isis to Alnylam in the Agreement and do not expand in
any way the scope or effect of any such licenses.

1. Merck

The Patents identified by Isis docket numbers [**] cover the incorporation of certain
Merck-proprietary [**].

The licenses from Isis to Alnylam with respect to these Patents are limited to the Isis Field. In
addition, Merck has a research license to practice these Patents in the Isis Field.

“Isis Field” means the use of [the Merck [**]] solely for the purposes of developing [**].

Reference is made to the discussion regarding Merck nucleosides on the Excluded Technology
schedule.

2. Gilead Sciences, Inc.

Gilead has retained exclusive rights in the Patents identified by a “Gilead” in the Third Party
column to make, have made, use, import, export or sell compounds and other subject matter claimed
within the scope of the patents which are [**].

In addition, Gilead has a non-exclusive, non-sublicensable, non-assignable license under such
Patents to make and use CodeBlocker Compounds and Oligonucleotide Delivery Systems for internal
research purposes, but not for any commercial purpose.

“Codeblocker Compound” means an oligonucleotide that binds directly to DNA or RNA within a cell on
a selective basis determined by the nucleotide sequence of the target DNA or RNA and exerts its
biological activity predominantly through binding to DNA or RNA to inhibit the transcription or
replication of the target DNA or RNA or binding to RNA to inhibit the translation, processing,
packaging or regulatory activity of the target RNA. A Codeblocker Compound may also have a
mechanism of action or biological activity other than one conferred through direct binding to RNA
or DNA provided that (i) the compound originally was designed to bind a target DNA or RNA and (ii)
the final compound or any compounds used to derive the final compound were not identified using

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selective purification and polymerase amplification in any fashion. An oligonucleotide, is [**].
An oligonucleotide includes RNA or DNA fragments, and may be composed of naturally occurring or
non-naturally occurring bases, sugars or intersugar linkages. An oligonucleotide may have [**].
Oligonucleotides may be made such that adjacent nucleoside or nucleoside fragments are linked
together by [**] linkages to form the [**] in the linkage.

“Oligonucleotide Delivery System” means any [**] which was developed by Gilead on or prior to [**],
and which (i) enhances the [**] of a Codeblocker Compound, (ii) selectively delivers a Codeblocker
compound to the intended [**], (iii) provides [**], or (iv) otherwise favorably alters the [**] so
as to enhance its pharmacological activity of clinical value. “Oligonucleotide Delivery System”
includes [**].

Glaxo Smith Kline has retained rights (originally granted from Gilead to GSK) in the Patents
identified by a “Gilead” in the Third Party column to (i) conduct research and development within
the GSK Field and (ii) make, have made, use, offer for sale, sell, supply and import within the GSK
Field any form or dosage of a GSK Codeblocker Compound and any GSK Codeblocker Delivery System used
in connection therewith.

GSK may grant sublicenses only (a) to affiliates, for any use within the GSK Field, and (b) to
non-affiliates only to the extent necessary to enable such sublicensee to make, have made, use,
offer for sale, sell, supply and import a GSK Codeblocker Compound developed by GSK or a research
or development collaborator of GSK during the term of such collaboration and for which GSK (alone
or in conjunction with a commercialization partner for such compound) has commenced or is prepared
to commence human clinical trials.

“GSK Field” means research with respect to, and the development and use of, GSK Codeblocker
Compounds for the diagnosis, prevention or treatment of conditions or diseases in humans.

“GSK Codeblocker Compound” means any material which (i) binds directly to DNA or RNA within a cell
on a selective basis determined by the nucleotide sequence of the target DNA or RNA and exerts its
biological activity predominantly through binding to DNA or RNA to inhibit the transcription or
replication of the target DNA or RNA or binding to RNA to inhibit the translation, processing,
packaging or regulatory activity of the target RNA, and (ii) is a molecule [**], and (iii) is not a
naturally occurring protein that binds to DNA to regulate transcription, or a peptide derived from
such a naturally occurring protein, and (iv) is [**], and (v) was not known by GSK prior to [**].

“GSK Codeblocker Delivery System” means any [**] which is developed by GSK or Gilead pursuant to
their Collaborative Research Agreement dated March 25, 1996, and which (i) [**] a GSK Codeblocker
Compound, (ii) [**] to the intended target [**], (iii) provides [**] a GSK Codeblocker Compound
from [**], or (iv) otherwise [**] a GSK Codeblocker Compound so as to [**].

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3. [**], Inc.

Alnylam cannot grant Naked Sublicenses with respect to the Patents identified by a “[**]” in the
Third Party column or the Patents listed on Annex 3. In addition, [**] has the first right to
defend and enforce such Patents if it is facing the greatest competitive threat from infringement.

Alnylam must notify Isis if it grants a sublicense of any kind to a Third Party with respect to
such Patents.

The [**] has the first right to defend and maintain the Patents with a docket number containing
“[**].”

Isis also has access to certain other [**] technology to the extent it is useful for Antisense
Products and Antisense Technology (both as defined in Annex 3). However, in addition to the
restrictions described above, this technology carries certain other use restrictions depending on
how the technology is characterized under the in-license agreement. We do not believe that such
technology will be useful to Alnylam, but have provided a description of the technology and its
related encumbrances on Annex 3 attached hereto.

4. Tullis Patents.

The Patents identified by a “Tullis” in the Third Party column can only be sublicensed in
combination with a product that (i) uses such Patents and (ii) employs as a material element other
Isis Patent Rights.

5. Amgen, GSK, Chiron and Pfizer.

Amgen, Inc., Glaxo Smith Kline, Chiron Corporation and Pfizer, Inc. each have a license to use some
or all of the Patents identified by a “TV” in the Third Party column for their own internal target
validation research.

6. Integrated DNA Technologies, Inc.

With respect to the Patents identified by an “IDT” in the Third Party column, Integrated DNA
Technologies, Inc. has a nonexclusive license to make, have made, use, import, offer to sell, sell
and have sold oligonucleotides and other related research products to the Academic Market.

“Academic Market” means end-users employed by and located at or in academic, university,
government, and other 501(c)(3) registered not-for-profit organizations; provided however that
specifically excluded from this definition shall be those end-users at such institutions whose
research is directly funded by a for-profit corporation for the purpose of drug discovery, drug
development, or target validation/gene functionalization wherein the funding corporation has a
specific legal interest or right to the data and information of the funded research

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7. TriLink Biotechnologies, Inc.

TriLink Biotechnologies, Inc. has a non-exclusive license to the Patents identified by a “TriLink”
in the Third Party column to (i) make, use, distribute and sell Licensed Products to purchasers who
have signed a form license agreement and (ii) have [**] in the manufacture of Licensed Products.

“Licensed Product” means [**]

	 	•	 	“Propyne” means any of the following [**]

[**]

8. Government Rights

Inventions claimed in US Patent Applications: [**] were funded in part by a Small Business
Innovation Research grant administered by the National Institutes of Health. Accordingly, the U.S.
Federal Government retains certain rights to those inventions.

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Annex 3

If the Patents marked with either a B1 or B2 restriction are [**] prevails in the [**] and [**] for
such Patents broadly cover [**], the licenses under such Patents are limited to discover, develop,
make, have made, use, sell, have sold, offer to sell, import and have imported Antisense Products
and to practice Antisense Technology; provided that the license will only extend to the issued
claims corresponding to the [**] and shall not extend to any other claim of such Patents.

The licenses under the Patents marked with an F restriction are limited (i) to discover, develop,
make, have made, use, sell, have sold, offer to sell, import and have imported Antisense Products
which contain modifications which have [**], (ii) to practice Antisense Technology using
oligonucleotides [**] in such oligonucleotides, and (iii) to discover, develop, make, have made,
use, sell, have sold, offer to sell, import and have imported Antisense Products which target genes
involved in [**].

The licenses under the Patents marked with a C or D restriction are limited to discover, develop,
make, have made, use, sell, have sold, offer to sell, import and have imported Antisense Products
and practice Antisense Technology, provided that neither such Antisense Products nor such Antisense
Technology use, or are used with, [**].

The licenses under the Patents marked with an A restriction are limited to discover, develop, make,
have made, use, sell, have sold, offer to sell, import and have imported Antisense Products and
practice Antisense Technology, provided that such Antisense Products and Antisense Technology use,
or are used with, the technology covered by the claims of such Patents solely for the [**] purposes
only.

The licenses under the Patents marked with an M restriction are limited to discover, develop, make,
have made, use, sell, have sold, offer to sell, import and have imported Antisense Products and
practice Antisense Technology, which Antisense Products and Antisense Technology primarily act
[**].

The licenses under the Patents marked with a K restriction are limited to discover, develop, make,
have made, use, sell, have sold, offer to sell, import and have imported Antisense Products and
practice Antisense Technology; provided, however, that such licenses will not extend to [**].

For purposes of this description:

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	•	 	Antisense Products means oligonucleotides or oligonucleotide analogs or mimics thereof
targeted to a specific sequence of RNA that hybridize to such sequence and through such
hybridization modulate the production of the targeted gene product. The term Antisense
Products shall not include Ribozymes.”
	 
	•	 	Antisense Technology means the use of any oligonucleotide or oligonucleotide analog or
mimic thereof targeted to a specific sequence of RNA that hybridizes to such sequence and
through such hybridization modulates the production of the targeted gene product. The
term Antisense Technology shall not include Ribozyme technology.
	 
	•	 	Ribozymes means oligonucleotides or oligonucleotide analogs or mimics containing a
catalytic core having a bulge or stem loop and regions flanking the catalytic core that
hybridize to a targeted RNA and modulate the targeted RNA by cleavage at a site next to a
specific ribonucleotide triplet by an oligonucleotide catalyzed transesterification
reaction.
	 
	•	 	Ribozyme Technology means the use of any oligonucleotides or oligonucleotide analogs or
mimics thereof containing a catalytic core having a bulge or stem loop and regions
flanking the catalytic core that hybridize to a targeted RNA and modulate the targeted RNA
by cleavage at a site next to a specific ribonucleotide triplet by an oligonucleotide
catalyzed transesterification reaction.

	 	 	 	 	 	 	 	 	 	 	 
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Exhibit 6.5(c)

Restrictions Imposed by Agreements Between Alnylam and Third Parties

 Executed Prior to the Effective Date 

Because of agreements in effect with Third Parties as of the Effective Date, the following
restrictions and other terms apply to Alnylam Patent Rights with respect to which Isis is granted a
license, or option to obtain a license, under this Agreement.

Rights Licensed from [**]

The rights licensed from [**] (“[**]”) relate to the “[**]” and “[**]” patents.

“[**] patent” means the pending patent applications listed in Schedule 1-5 with the following
case numbers: [**].

“[**] patent” means the pending patent applications listed in Schedule 1-5 with the following case
numbers, excluding claims [**] (case number [**]) and the equivalent claims in any patent
applications and patents resulting from this PCT application: [**].

The restrictions on, and other terms relating to, the rights available to Isis under the Agreement
are described in the following clauses excerpted from the Co-Exclusive License executed between
Alnylam and [**] on December 20, 2002.

     “ARTICLE 2 — GRANT OF RIGHTS

     2.4 Sublicenses

.... Immediately after the signature of each sublicense granted under this Agreement,
COMPANY shall provide [**] with a copy of the signed sublicense agreement, and COMPANY
shall confirm in writing to [**] that COMPANY shall be liable for payment of royalties on
NET SALES of the SUBLICENSEE in accordance with Sections 5.2 and 5.3.

     ARTICLE 4 — COMPANY DILIGENCE OBLIGATIONS AND REPORTS

     4.1 Activity Requirements

COMPANY shall use commercially reasonable efforts, and shall oblige its SUBLICENSEES to use
commercially reasonable efforts, to develop and to introduce into the commercial market
LICENSED PRODUCTS at the earliest practical date.

     4.2 Development Reports

Commencing with the beginning of 2003, COMPANY shall furnish, and shall oblige its
SUBLICENSEES to furnish to COMPANY for inclusion in its reports to [**], to [**] in
writing, within 30 (thirty) days after the end of each calendar quarter with COMPANY’s
standard R&D report, as provided to the investors pursuant to the Amended and Restated
Investor’s Rights Agreement Series B, on

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the progress of its efforts during the immediately preceding calendar quarter to develop
and commercialize LICENSED PRODUCTS for each indication and sub-indication within the
FIELD. The report shall also contain a discussion of intended R&D efforts for the calendar
quarter in which the report is submitted.

     4.4 Liability for SUBLICENSEES

If SUBLICENSEES of COMPANY develop, manufacture, use and/or sell LICENSED PRODUCTS under
the PATENT RIGHTS, COMPANY warrants and is liable towards [**] that the SUBLICENSEES
perform their sublicense agreement in accordance with this Agreement, and COMPANY shall be
responsible and liable for royalty payments and reports of the SUBLICENSEES.

     4.5 Effect of Failure

In the event that [**] determines that COMPANY or any of its SUBLICENSEES has failed to
fulfill any of its obligations under this Section 4, then [**] may treat such failure as a
material breach in accordance with Section 11.7.

     ARTICLE 5 — SHARES, Royalties and Payment Terms

     5.2 Running Royalties

COMPANY shall pay to [**] the following running royalties on NET SALES of therapeutic and
prophylactic LICENSED PRODUCTS by COMPANY and its SUBLICENSEES:

[[**]% ([**] percent) to [**]% ([**]%) of NET SALES depending on level of NET
SALES].

In the event that COMPANY or a SUBLICENSEE develops [**] LICENSED PRODUCTS, COMPANY shall
initiate negotiations with [**] at least 3 (three) months prior to the intended first
commercial sale of each [**] LICENSED PRODUCT. COMPANY and [**] shall negotiate in good
faith royalties on reasonable market terms for such [**] LICENSED PRODUCT.

.... Non-cash consideration shall not be accepted by COMPANY or any SUBLICENSEE for LICENSED
PRODUCTS without the prior written consent of [**].

     5.3 Royalty Stacking

     (a) Third Party Licenses

In the event COMPANY or a SUBLICENSEE takes, for objective commercial and/or legal reasons,
a license from any third party under any patent applications or patents that dominate the
PATENT RIGHTS or is dominated by the PATENT RIGHTS in order to develop, make, use, sell or
import any LICENSED PRODUCT [**], then COMPANY is allowed to deduct [**]% ([**] percent)
of any additional running royalties to be paid to such third party up to [**]% ([**]
percent) of the running royalties stated in Section 5.2, from the date COMPANY

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has to pay running royalties to such third party. However, the running royalties stated in
Section 5.2 shall not be reduced to less than a minimum of [**]% ([**] percent) of NET
SALES in any case.

For avoidance of doubt, if COMPANY or a SUBLICENSEE takes a license [**], COMPANY is in no
event allowed to deduct any license fees [**] from running royalties due to [**] under this
Agreement.

     (b) PATENT RIGHTS Coverage

In the event that (i) COMPANY or its SUBLICENSEES sell a LICENSED PRODUCT in a country
where no PATENT RIGHTS are issued and no patent applications that are part of the PATENT
RIGHTS are pending that have not been pending for less than [**] years after filing
national patent applications in the country in question, and (ii) such LICENSED PRODUCT is
manufactured in a country where PATENT RIGHTS are issued or patent applications that are
part of the PATENT RIGHTS are pending that have not been pending for more than [**] years
after filing national patent applications in the country in question, the royalties stated
in Section 5.2 will be reduced by [**]% ([**] percent) for such LICENSED PRODUCT, until the
expiration or abandonment of all issued patents and filed patent applications within the
PATENT RIGHTS in the country in which the LICENSED PRODUCT is manufactured.

     5.4 Reports

Within 30 (thirty) days of the end of each calendar half year, COMPANY shall deliver a
detailed report to [**] for the immediately preceding calendar half year showing at least
(i) the number of LICENSED PRODUCTS sold by COMPANY and its SUBLICENSEES in each country,
(ii) the gross price charged by COMPANY and its SUBLICENSEES for each LICENSED PRODUCTS in
each country, (iii) the calculation of NET SALES, and (iv) the resulting running royalties
due to [**] according to those figures. If no running royalties are due to [**], the report
shall so state.

     5.6 Bookkeeping and Auditing

COMPANY is obliged to keep, and shall oblige its SUBLICENSEES to keep, complete and
accurate books on any reports and payments due to [**] under this Agreement, which books
shall contain sufficient information to permit [**] to confirm the accuracy of any reports
and payments made to [**]. [**], or [**] appointed agents, is authorized to check the
books of COMPANY, and, upon [**] request, COMPANY, or agents appointed by [**] for COMPANY,
shall check the books of its SUBLICENSEES for [**]. The charges for such a check shall be
borne by [**]. In the event that such check reveals an underpayment in excess of 5% (five
percent), COMPANY shall bear the full cost of such check and shall remit any amounts due to
[**] within thirty days of receiving notice thereof from [**].

The right of auditing by [**] under this Section shall expire five years after each report
or payment has been made. Sublicenses granted by COMPANY shall

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provide that COMPANY shall have the right to check the books of its SUBLICENSEES according
to this Section 5.6.

     5.7 No Refund

All payments made by COMPANY or its SUBLICENSEES under this Agreement are nonrefundable and
noncreditable against each other.

     ARTICLE 6 — Patent Prosecution AND Infringement

     6.3 Infringement

COMPANY shall inform [**] promptly in writing of any alleged infringement of the PATENT
RIGHTS by a third party and of any available evidence thereof.

Subject to COMPANY’s right to join in the prosecution of infringements set forth below, the
OWNERS shall have the right, but not the obligation, to prosecute in their own discretion
and at their own expense, all infringements of the PATENT RIGHTS. The total cost of any
such sole infringement action shall be borne by the OWNERS, and the OWNERS shall keep any
recovery or damages derived therefrom. In any such infringement suits, COMPANY shall, at
the OWNERS’ expense, cooperate in all respects.

COMPANY shall have the right to join the OWNERS’ prosecution of any infringements of the
PATENT RIGHTS: In any such joint infringement suits, the OWNERS and COMPANY will cooperate
in all respects. The OWNERS and COMPANY will agree in good faith on the sharing of the
total cost of any such joint infringement action and the sharing of any recovery or damages
derived therefrom.

In the event that the OWNERS decide not to prosecute infringements of the PATENT RIGHTS,
neither solely nor jointly with COMPANY, [**] shall offer to COMPANY to prosecute any such
infringement in its own discretion and at its own expense. ... The OWNERS shall, at
COMPANY’S expense, cooperate. The total cost of any such sole infringement action shall be
borne by COMPANY, and COMPANY shall keep any recovery or damages derived therefrom.

In the event that COMPANY intends to make any arrangements with the infringer to settle
the infringement (such as sublicenses), and solely the OWNERS or the OWNERS jointly with
COMPANY have prosecuted the infringement, any such settlement needs the prior written
approval of [**], which shall not unreasonably be withheld; reasons to withheld include,
without limitation, that the settlement is financially disadvantageous for the OWNERS or
[**]. Any infringer to which COMPANY grants such sublicenses shall be a SUBLICENSEE under
this Agreement.

     ARTICLE 8 — CONFIDENTIALITY

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     8.2 Obligation for [**]

The content of this Agreement and any information marked confidential which is disclosed to
[**] under this Agreement by COMPANY or its SUBLICENSEES shall be treated confidential by
[**] during the TERM and for [**] years thereafter. [**] shall not use such information for
any purposes other than those necessary to directly further the purpose of this Agreement.
[**] may disclose such information to the OWNERS, provided however, that the OWNERS are
obliged to confidentiality to the same extent as [**].

The confidentiality obligation shall not apply to information which is (i) publicly
available or becomes publicly available through no fault of [**], or (ii) obtained by [**]
from another source without a duty of confidentiality, or (iii) demonstrably independently
developed or possessed by [**], or (iv) is required by law, regulation, accounting
principles or an order of a court or government agency to be disclosed.

     ARTICLE 10 — General Compliance with Laws

     10.2 Non-Use of OWNERS Names

Neither COMPANY nor its SUBLICENSEES shall use the name of [**] or any variation,
adaptation, or abbreviation thereof, or of any of its trustees, officers, faculty,
students, employees, or agents, or any trademark owned by any of the OWNERS, in any
promotional material or other public announcement or disclosure without the prior written
consent of the OWNERS or in the case of an individual, the consent of that individual. The
foregoing notwithstanding, without the consent of the OWNERS, COMPANY may state generally
that it is co-exclusively licensed by the OWNERS under the PATENT RIGHTS.

     ARTICLE 11 — EFFECTIVENESS AND TERMINATION

     11.5 Attack on PATENT RIGHTS

[**] shall have the right to terminate this Agreement immediately upon written notice to
COMPANY, if COMPANY attacks, or has attacked or supports an attack through a third party,
the validity of any of the PATENT RIGHTS. To the extent legally enforcable, sublicenses
granted by COMPANY shall provide that in the event the SUBLICENSEE attacks, or has attacked
or supports an attack through a third party, the validity of any of the PATENT RIGHTS,
COMPANY shall have the right to terminate the sublicense agreement immediately; upon
request of [**], COMPANY shall have the obligation to terminate such sublicense agreement.

     11.8 Effect of Termination

.... In no event shall termination of this Agreement release COMPANY or its SUBLICENSEES
from the obligation to pay any amounts that became due on or before the effective date of
termination. In the event that any license granted to COMPANY under this Agreement is terminated, any
sublicense under such license granted prior to termination of said license shall remain in
full fore and effect, provided that:

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(a) the SUBLICENSEE is not then in breach of its sublicense agreement, and

(b) the SUBLICENSEE agrees to be bound to [**] as licensor under the terms and conditions
of the sublicense agreement, provided that [**] shall have no other obligation than to
leave the sublicense granted by COMPANY in place.”

Rights Licensed from [**]

The rights licensed from [**] relate to the pending patent applications listed in Schedule 1-5 with
the following case numbers: [**].

The restrictions on, and other terms relating to, the rights available to Isis under the Agreement
are described in the following clauses excerpted from the agreement executed between Alnylam and
[**] on [**]. Articles 7, 8 and 9 of such agreement are included in these excerpts because clause
13.4 of such agreement states that “Any sublicense will expressly include the provisions of
Articles 7, 8, and 9 for the benefit of [**].”

     “7 ROYALTY REPORTS, PAYMENTS, AND ACCOUNTING

7.1 Quarterly Earned Royalty Payment and Report. Beginning with the first sale of a
Licensed Product, Alnylam will make written reports (even if there are no sales) and earned
royalty payments to [**] within thirty days after the end of each calendar quarter. This
report will be in the form of the report of Appendix B and will state the number,
description, and aggregate Net Sales of Licensed Product during the completed calendar
quarter, and resulting calculation pursuant to Section 6.3 of earned royalty payment due
[**] for the completed calendar quarter. With each report, Alnylam will include payment
due [**] of royalties for the completed calendar quarter.”

7.2 Termination Report. Alnylam will make a written report to [**] within ninety days
after the license expires under Section 3.2. Alnylam will continue to make reports after
the license has expired, until all Licensed Product produced under the license have been
sold or destroyed. Concurrent with the submittal of each post-termination report, Alnylam
will pay [**] all applicable royalties.

7.3 Accounting. Alnylam will keep and maintain records for a period of three years showing
the manufacture, sale, use, and other disposition of products sold or otherwise disposed of
under the license. Records will include general-ledger records showing cash receipts and
expenses, and records that include production records, customers, serial numbers, and
related information in sufficient detail to enable Alnylam to determine the royalties
payable under this Agreement.

7.4 Audit by [**]. Alnylam will permit an independent certified public accountant selected
by [**] and acceptable to Alnylam to examine Alnylam’s books and records from time to time
(but no more than one time a year) to the extent necessary to verify reports provided for
in Sections 7.1 and 7.2. [**] will pay for the cost of such audit, unless the results of
the audit reveal an

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underreporting of royalties due [**] of five percent or more, in which case, Alnylam will
pay the audit costs.

     8 NEGATION OF WARRANTIES

8.1 To the best of [**] OTL knowledge, [**] is the sole owner of Licensed Patent and has
the right to enter into this Agreement and to grant the rights and licenses set forth
herein.

8.2 Negation of Warranties. Nothing in this Agreement is construed as:

	 	(A)	 	[**] warranty or representation as to the validity or scope
of any Licensed Patent;
	 
	 	(B)	 	A warranty or representation that anything made, used, sold,
or otherwise disposed of under any license granted in this Agreement is or
will be free from infringement of patents, copyrights, and other rights of
third parties;
	 
	 	(C)	 	An obligation to bring suit against third parties for
infringement, except as described in Article 12;
	 
	 	(D)	 	Granting by implication, estoppel, or otherwise any licenses
or rights under patents or other rights of [**] or other persons other than
Licensed Patent, regardless of whether the patents or other rights are
dominant or subordinate to any Licensed Patent; or
	 
	 	(E)	 	An obligation to furnish any technology or technological
information.

8.3 No warranties. Except as expressly set forth in this Agreement, [**] makes no
representations and extends no warranties of any kind, either express or implied. There
are no express or implied warranties of merchantability or fitness for a particular
purpose, or that Licensed Product will not infringe any patent, copyright, trademark, or
other rights, or any other express or implied warranties.

8.4 Specific Exclusion. Nothing in this Agreement grants Alnylam any express or implied
license or right under or to [**] entitled [**] or any patent application corresponding
thereto.

     9 INDEMNITY

9.1 Indemnification. Alnylam will indemnify, hold harmless, and defend [**] and [**]
Hospitals and Clinics, and their respective trustees, officers, employees, students, and
agents against all claims for death, illness, personal injury, property damage, and
improper business practices arising out of the

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manufacture, use, sale, or other disposition of Invention, Licensed Patent, Licensed
Product, by Alnylam or any sublicensee, or their customers except to the extent such claims
are due to the gross negligence or willful misconduct of [**]. [**] agreed to promptly
notify Alnylam in writing of any such claim and Alnylam shall manage and control, at its
own expense, the defense of such claim and its settlement. Alnylam agrees not to settle
any such claim against [**] without [**] written consent where such settlement would
include any admission of liability on the part of [**], where the settlement would impose
any restriction on the conduct by [**] of any of its activities, or where the settlement
would not include an unconditional release of [**] from all liability for claims that are
the subject matter of such claim.

9.2 No Liability. Subject to Section 9.1, neither party will be liable to each other for
any loss profit, expectation, punitive or other indirect, special, consequential, or other
damages whatsoever, in connection with any claim arising out of or related to this
Agreement whether grounded in tort (including negligence), strict liability, contract, or
otherwise.

9.3 Workers’ Compensation. Alnylam will at all times comply, through insurance or
self-insurance, with all statutory workers’ compensation and employers’ liability
requirements covering all employees with respect to activities performed under this
Agreement.

9.4 Insurance. Alnylam will maintain, during the term of this Agreement, Comprehensive
General Liability Insurance, including Product Liability Insurance prior to
commercialization, with a reputable and financially secure insurance carrier to cover the
activities of Alnylam and its sublicensees. Upon initiation of human clinical trials of
Licensed Product, such insurance will provide minimum limits of liability of Five Million
Dollars and will include [**] and [**] Hospitals and Clinics, and their respective
trustees, directors, officers, employees, students, and agents as additional insureds.
Insurance will be written to cover claims incurred, discovered, manifested, or made during
or after the expiration of this Agreement and must be placed with carriers with ratings of
at least A- as rated by A.M. Best. Alnylam will furnish a Certificate of Insurance
evidencing primary coverage and additional insured requirements and requiring thirty (30)
days prior written notice of cancellation or material change to [**]. Alnylam will advise
[**], in writing, that it maintains excess liability coverage (following form) over primary
insurance for at least the minimum limits set forth above. All insurance of Alnylam will
be primary coverage; insurance of [**] and [**] Hospitals and Clinics will be excess and
noncontributory.

     12 INFRINGEMENT BY OTHERS: PROTECTION OF PATENTS

	 	12.1	 	Infringement Action.

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	 	(A)	 	The parties will promptly inform each other of any suspected
infringement of any Licensed Patent by a third party.
	 
	 	(B)	 	[**], Licensee and the other Co-Exclusive licensee will meet
to discuss the matter during the Co-Exclusive period of this Agreement.
	 
	 	(C)	 	If the Field-of-Use becomes Exclusive for Licensee, [**] and
Licensee will meet to discuss the matter during the Exclusive period of this
Agreement.
	 
	 	(D)	 	If [**] does not choose to institute suit against said third
party within sixty days of notification, then the suit may be brought in both
Licensee’s and the other Co-Exclusive licensee’s names, and [**] name if
necessary and the out-of-pocket costs thereof shall be borne equally by
Licensee and the other Co-Exclusive licensee and any recovery or settlement
shall be shared equally between Licensee and the other Co-Exclusive licensee.
In such situation, Licensee and the other Co-Exclusive licensee shall agree to
the manner in which they exercise control over such action and if either party
desires to also be represented by separate counsel of its own selection, the
fees for such counsel shall be paid by such party.
	 
	 	(E)	 	If both [**] and the other Co-Exclusive licensee, or [**] if
there is no other Co-Exclusive Licensee, choose not to institute suit against
said third party within sixty days of notification, then Licensee shall have
the right to institute suit in its own name or if necessary, in [**] name, to
enjoin such infringement. Licensee shall bear the entire cost of such
litigation and shall be entitled to retain the entire amount of any recovery
or settlement. However, any recovery in excess of litigation/settlement costs
will be considered Net Sales and Licensee will pay [**] royalties as indicated
in Article 6 hereof. [**] shall provide reasonable assistance to Licensee in
the prosecution of any such suit brought by Licensee, at Licensee’s expense.

     13 SUBLICENSING

	 	13.1	 	Permitted Sublicensing for Licensed Co-Exclusive Field of Use. Alnylam may
grant sublicenses in the Co-exclusive Licensed Field of Use during the Co-Exclusive
period:

	 	(A)	 	only in conjunction with intellectual property under
Alnylam’s control; and

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	 	(B)	 	only if Alnylam is developing or selling Licensed Products in
the Co-Exclusive Licensed Field of Use.

	 	13.2	 	Required Sublicensing for Licensed Co-Exclusive Field of Use.

	 	(A)	 	If Alnylam or its sublicensee(s) is unable or unwilling to
serve or develop a potential market or market territory for which there is a
willing sublicensee, Alnylam will, at [**] request, negotiate in good faith a
sublicense under the Licensed Patents, provided that the same request has been
made of the other Co-Exclusive licensee.
	 
	 	(B)	 	Bona fide business concerns of Alnylam will be considered in
any good faith negotiations for a sublicense under this Agreement and Alnylam
shall not be required to license/sublicense any other intellectual property to
such sublicensee.
	 
	 	(C)	 	If the other Co-Exclusive licensee itself or through its
sublicensees is already developing a product in the market or market territory
for which there is a willing sublicensee, Alnylam will not be required to
sublicense to such party.
	 
	 	(D)	 	In case that any other issue arises in the context of
Required Sublicensing, [**] will discuss and try to resolve such issue with
Alnylam in good faith.

	 	13.3	 	Sublicense Requirements. Any sublicense granted by Alnylam under this
Agreement will be subject and subordinate to terms and conditions of this Agreement,
except:

	 	(A)	 	Sublicense terms and conditions will reflect that any
sublicensee will not further sublicense, with the exception that sublicensee
may further sublicense rights under Licensed Patents only as needed or implied
in the course of distribution or performance of service as required for the
sale to an end user of Licensed Products; and
	 
	 	(B)	 	The earned royalty rate specified in the sublicense [**] in
this Agreement.

	 	13.4	 	Sublicenses Revert to [**]. Any sublicense will expressly include the
provisions of Articles 7, 8, and 9 for the benefit of [**]. If a sublicensee desires
that its sublicense survive the termination of this agreement, [**] agrees that the
sublicense will revert to [**] subject to the transfer of all obligations, including
the payment of royalties specified in the sublicense, to [**] or its designee, if this
Agreement is terminated.

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	 	13.5	 	Copy of Sublicenses. Alnylam will provide [**] in confidence a copy of all
relevant portions of any sublicenses granted pursuant to this Article 13.
	 
	 	13.6	 	Sharing of Sublicensing Income. In addition to the earned royalties defined
in Article 6, Alnylam will pay [**] percent ([**]%) of the amount received by Alnylam,
that is specifically attributable to the Licensed Patents, from a sublicensee in

	 	(A)	 	[**], and
	 
	 	(B)	 	[**] as defined in [**].

	 	13.7	 	Royalty-free Sublicenses. Alnylam may grant royalty-free or noncash
sublicenses or cross-licenses if Alnylam pays all royalties due [**] from
sublicensee’s Net Sales.”

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EXHIBIT 6.5(d)

DESCRIPTION OF POTENTIAL PASS-THROUGH AMOUNTS PAYABLE TO

STANFORD UNIVERSITY

The passages shown below are excerpted from the License Agreement between THE BOARD OF TRUSTEES OF
THE LELAND Stanford JUNIOR UNIVERSITY (“Stanford”) and Alnylam Pharmaceuticals, Inc. dated
September 17, 2003. These passages were selected to provide Isis with sufficient information to
understand its potential obligation to Stanford pursuant to Section 6.5(d) of the Agreement.

DEFINITIONS

	2.5	 	“Licensed Field of Use” means delivery of ex-vivo synthesized siRNA Molecules for research,
development and therapeutic uses (including a diagnostic necessary for development, sale or
reimbursement of a therapeutic Licensed Product). The Licensed Field of Use specifically
excludes delivery of any system producing in vivo expressed siRNAs for therapeutic use,
including but not limited to episomal and integrated vectors, and recombinant viruses.
	 
	2.7	 	“Co-Exclusive” means that, subject to Article 4, Stanford will only grant one further license
in the Licensed Territory in the Licensed Field of Use.

GRANT

	3.2	 	Co-Exclusivity. The license is Co-Exclusive, including the right to sublicense pursuant to
Article 13, in the Licensed Field of Use for a term beginning on the Effective Date, and
ending, on a country-by-country basis, on the expiration of the last to expire of Licensed
Patents.
	 
	3.4	 	Exclusivity.

	 	(A)	 	If the other Co-Licensee discontinues licensing this Field of Use, then the
Field of Use will become exclusive for Alnylam.
	 
	 	(B)	 	If the other Co-Licensee discontinues any other therapeutic license under
the Licensed Patents, Stanford shall so inform Alnylam and Alnylam shall have the
option to obtain an exclusive, worldwide sublicensable license to such therapeutic
field. The terms of any such license shall be negotiated in good faith by Stanford
and Alnylam. This option may be exercised by Alnylam by written notice to Stanford
at any time during a period of ninety (90) days after notification by Stanford.

ROYALTIES

	6.3	 	Earned Royalty. In addition, Alnylam will pay Stanford earned royalties on Net Sales as
follows:

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	 	(A)	 	[**]% of Net Sales for a Licensed Product subject to the following;
	 
	 	(B)	 	Such royalty payments shall be reduced up to [**]% (from [**]% of Net Sales
down to [**]% of Net Sales) by the amount of royalty paid to access additional
intellectual property necessary in order to sell Licensed Products (“Additional
Earned Royalties”).
	 
	 	(C)	 	Such royalty payments shall be reduced as follows:

	 	(1)	 	[**]% if Additional Earned Royalties are [**]% or less.
	 
	 	(2)	 	[**]% if Additional Earned Royalties are greater than [**]%
but less than [**]%.
	 
	 	(3)	 	[**]% if Additional Earned Royalties are equal to or greater
than [**]% but less than [**]%.
	 
	 	(4)	 	[**]% if Additional Earned Royalties are equal to or greater
than [**]% but less than [**]%.
	 
	 	(5)	 	[**]% if Additional Earned Royalties are equal to or higher
than [**]%.

	 	(D)	 	Only one royalty is due on each Licensed Product sold by Alnylam or its
sublicensees regardless of whether its manufacture, use, importation or sale are or
shall be covered by more than one patent or patent application included in Licensed
Patents under this Agreement, and no further royalties will be due for use of such
Licensed Product by Alnylam or its sublicensee’s customers.

	6.4	 	Creditable Payments. Creditable payments under this Agreement will be an offset to Alnylam
against each earned royalty payment which Alnylam would be required to pay under Section 0
until the entire credit is exhausted.
	 
	6.5	 	Milestone Payments.

	 	(A)	 	For the first Licensed Product, Alnylam will make the following payments
for the filing of an IND, intitiation of Phase II trial, initiation of Phase III
trial, and approval of New Drug Application or equivalent in the U.S. (“Milestone
Payments”):

	 	(1)	 	$[**] for filing of the first IND.
	 
	 	(2)	 	$[**] for initiation of the first Phase II trial.
	 
	 	(3)	 	$[**] for initiation of the first Phase III trial.
	 
	 	(4)	 	$[**] for approval of the first New Drug Application or
equivalent regulatory approval in the U.S..

	 	(B)	 	For the second Licensed Product, Alnylam will make the following Milestone
Payments:

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	 	(1)	 	$[**] for filing of the first IND.
	 
	 	(2)	 	$[**] for initiation of the first Phase II trial.
	 
	 	(3)	 	$[**] for initiation of the first Phase III trial.
	 
	 	(4)	 	$[**] for approval of the first New Drug Application or
equivalent regulatory approval in the U.S..

	 	(C)	 	For the third and every subsequent Licensed Product, Alnylam will make the
following Milestone Payments:

	 	(1)	 	$[**] for filing of the first IND.
	 
	 	(2)	 	$[**] for initiation of the first Phase II trial.
	 
	 	(3)	 	$[**] for initiation of the first Phase III trial.
	 
	 	(4)	 	$[**] for approval of the first New Drug Application or
equivalent regulatory approval in the U.S..

	 	(D)	 	Notwithstanding the above, at the time that Stanford receives a Milestone
Payment from Alnylam on behalf of a sublicensee under 13.6, the corresponding
Milestone Payment under this Section 6.5 will not be due.

	6.6	 	Obligation to Pay Royalties. If this Agreement is not terminated in accordance with other
provisions, Alnylam will be obligated to pay royalties on all Licensed Product that is either
sold or produced under the license granted in Article 3, whether or not the Licensed Product
is produced before the Effective Date of this Agreement or sold after the Licensed Patent has
expired.

13 SUBLICENSING

	13.1	 	Permitted Sublicensing for Licensed Co-Exclusive Field of Use. Alnylam may grant sublicenses
in the Co-exclusive Licensed Field of Use during the Co-Exclusive period:

	 	(A)	 	only in conjunction with intellectual property under Alnylam’s control; and
	 
	 	(B)	 	only if Alnylam is developing or selling Licensed Products in the
Co-Exclusive Licensed Field of Use.

	13.3	 	Sublicense Requirements. Any sublicense granted by Alnylam under this Agreement will be
subject and subordinate to terms and conditions of this Agreement, except:

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	 	(A)	 	Sublicense terms and conditions will reflect that any sublicensee will not
further sublicense, with the exception that sublicensee may further sublicense rights
under Licensed Patents only as needed or implied in the course of distribution or
performance of service as required for the sale to an end user of Licensed Products;
and
	 
	 	(B)	 	The earned royalty rate specified in the sublicense may be at different
rates than the rates in this Agreement.

	13.4	 	Sublicenses Revert to Stanford. Any sublicense will expressly include the provisions of
Articles 7, 8, and 9 for the benefit of Stanford [Note: these provisions are detailed in
Exhibit 6.5(c)]. If a sublicensee desires that its sublicense survive the termination of this
agreement, Stanford agrees that the sublicense will revert to Stanford subject to the transfer
of all obligations, including the payment of royalties specified in the sublicense, to
Stanford or its designee, if this Agreement is terminated.
	 
	13.5	 	Copy of Sublicenses. Alnylam will provide Stanford in confidence a copy of all relevant
portions of any sublicenses granted pursuant to this Article 13.
	 
	13.6	 	Sharing of Sublicensing Income. In addition to the earned royalties defined in Article 6,
Alnylam will pay Stanford [**] percent ([**]%) of the amount received by Alnylam, that is
specifically attributable to the Licensed Patents, from a sublicensee in

	 	(A)	 	up-front license fees, and
	 
	 	(B)	 	clinical Milestone Payments as defined in Article 6.5.

	13.7	 	Royalty-free Sublicenses. Alnylam may grant royalty-free or noncash sublicenses or
cross-licenses if Alnylam pays all royalties due Stanford from sublicensee’s Net Sales.

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EXHIBIT 8.2(c)

DESCRIPTION OF ALNYLAM ROYALTY OBLIGATIONS TO [**] EXISTING AS OF THE EFFECTIVE DATE

As of the Effective Date, Alnylam has the following royalty obligations to [**] (“[**]”):

Alnylam is obligated to pay [**] running royalties on NET SALES (as defined in Alnylam’s agreements
with [**]) of therapeutic and prophylactic LICENSED PRODUCTS (as defined in Alnylam’s agreements
with [**]) by Alnylam and its SUBLICENSEES (as defined in Alnylam’s agreements with [**]) that
range from [**]% ([**] percent) to [**]% ([**] percent) of NET SALES, depending on the level of NET
SALES. Royalties payable by Alnylam to [**] are subject to the following Royalty Stacking
provision:

“5.3 Royalty Stacking

(a) Third Party Licenses

In the event COMPANY or a SUBLICENSEE takes, for objective commercial and/or legal reasons, a
license from any third party under any patent applications or patents that dominate the PATENT
RIGHTS or is dominated by the PATENT RIGHTS in order to develop, make, use, sell or import any
LICENSED PRODUCT (explicitly excluding, without limitation, any third party patents and patent
applications for formulation, stabilization and delivery), then COMPANY is allowed to deduct [**]%
([**] percent) of any additional running royalties to be paid to such third party up to [**]% ([**]
percent) of the running royalties stated in Section 5.2, from the date COMPANY has to pay running
royalties to such third party. However, the running royalties stated in Section 5.2 shall not be
reduced to less than a minimum of [**]% ([**] percent) of NET SALES in any case.

For avoidance of doubt, if COMPANY or a SUBLICENSEE takes a license to a third party target,
COMPANY is in no event allowed to deduct any license fees for such target from running royalties
due to [**] under this Agreement.”

Because Alnylam’s right to reduce its royalty obligations to [**] pursuant to the foregoing royalty
stacking provision is not co-extensive with Isis’ right to reduce its royalty obligations to
Alnylam pursuant to Section 8.2 of this Agreement, Isis’ right to reduce its royalty obligations to
Alnylam pursuant to Section 8.2 of this Agreement is limited, pursuant to Section 8.2(c) of this
Agreement, to the extent necessary to ensure that Isis’ royalty obligations to Alnylam are never
less than Alnylam’s royalty obligations to [**] with respect to sales by Isis, its Affiliates and
its sublicensees of any Isis Product.

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Schedule 1-7

Alnylam Current Chemistry Patents

Alnylam Current Chemistry Patents include all claims of the patents and patent applications listed
below that do not claim inhibitors to specific genes or gene families.

	 	 	 	 	 	 	 	 	 	 	 
	 	 	Filing	 	 	 	 	 	 	 	 
	Case No.	 	Date	 	Country	 	Serial No.	 	Status	 	Title
	[**]
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	 	[**]

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Schedule 1-8

Alnylam Current Motif and Mechanism Patents

Alnylam Current Motif and Mechanism Patents include all claims of the patents and patent
applications listed below that do not claim inhibitors to specific genes or gene families.

	 	 	 	 	 	 	 	 	 	 	 
	 	 	Filing	 	 	 	 	 	 	 	 
	Case No.	 	Date	 	Country	 	Serial No.	 	Status	 	Title
	[**]
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	 	 	Filing	 	 	 	 	 	 	 	 
	Case No.	 	Date	 	Country	 	Serial No.	 	Status	 	Title
	[**]
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	 	 	Filing	 	 	 	 	 	 	 	 
	Case No.	 	Date	 	Country	 	Serial No.	 	Status	 	Title
	[**]
	 	[**]
	 	[**]
	 	[**]
	 	[**]
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	 	[**]	 	 

 

			
	[**]†	 	 Note that Alnylam’s license to this series of patent applications specifically excludes
claims [**] and the equivalent claims in any patent applications and patents resulting from
this PCT application. The application contains claims relating to [**]. The claims excluded
from Alnylam’s license are those that [**].
	 
	*	 	Subject to the provisions of section 6.5(d).

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Schedule 1-10

Alnylam Excluded Technology

	 	1.	 	All Patent rights licensed to Alnylam under the license agreements between [**] dated
[**], and between [**] and Alnylam dated [**].
	 
	 	2.	 	All Patent rights licensed to Alnylam under the license agreement between [**] and
Alnylam dated [**].
	 
	 	3.	 	All Patent rights licensed to Alnylam under the license agreement between [**] and
Alnylam dated [**].

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Schedule 1-51 (Updated April 28, 2009)

Isis Current Chemistry Patents

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	Patent	 	 	 	 	 	 	 	 
	Docket Number	 	Country	 	Status	 	Serial Number	 	Filing Date	 	Number	 	Grant Date	 	Title	 	3rd party	 	3rd Party

Confidential materials omitted and filed separately with the Securities and Exchange Commission. A
total of 41 pages have been omitted pursuant to a request for confidential treatment.

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Schedule 1-52 (Updated April 28, 2009)

Isis Current Motif and Mechanism Patents

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	Patent	 	 	 	 	 	 	 	 
	Docket Number	 	Country	 	Status	 	Serial Number	 	Filing Date	 	Number	 	Grant Date	 	Title	 	3rd party	 	3rd Party

Confidential materials omitted and filed separately with the Securities and Exchange Commission. A
total of 15 pages have been omitted pursuant to a request for confidential treatment.

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Schedule 1-56

Excluded Technology

          The following schedule of Excluded Technology is provided by Isis Pharmaceuticals, Inc. to
Alnylam Pharmaceuticals, Inc., in connection with the Strategic Collaboration and License Agreement
between Alnylam and Isis (the “Agreement”). Capitalized terms used but not otherwise defined
herein have the meanings given to such terms in the Agreement.

          This schedule and the information and disclosures contained in this schedule are intended only
to qualify and limit the licenses granted by Isis to Alnylam in the Agreement and do not expand in
any way the scope or effect of any such licenses.

          In the event of a conflict between this schedule of Excluded Technology and any other schedule
or terms of the Agreement, this schedule will govern.

	 	1.	 	Intellectual property covering:

	 	•	 	RNA processing, including modulation of [**]
	 
	 	•	 	PNA chemistry licensed or acquired from (i) [**];
	 
	 	•	 	[**] chemistry licensed or acquired from [**];
	 
	 	•	 	[**] a Gene Target.

	 	2.	 	[**]/4’-Thio Chemistry.

     4’-thio chemistries including patents licensed in from [**]

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     In addition, the following Patents in-licensed from the [**] are excluded:

	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	Patent	 	 	 	 
	Isis Docket Number	 	Country	 	Status	 	Number	 	Granted Date	 	Title
	[**]
	 	[**]
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	 	[**]

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	 	 	 	 	 	 	Patent	 	 	 	 
	Isis Docket Number	 	Country	 	Status	 	Number	 	Granted Date	 	Title
	[**]
	 	[**]
	 	[**]
	 	[**]
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	 	[**]

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	 	 	 	 	 	 	Patent	 	 	 	 
	Isis Docket Number	 	Country	 	Status	 	Number	 	Granted Date	 	Title
	[**]
	 	[**]
	 	[**]
	 	[**]
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	[**]
	 	[**]
	 	[**]
	 	 	 	 	 	[**]

	 	3.	 	Gen-Probe and NIH. (A)

The following Patents in-licensed from Gen-Probe Inc. and the National Institute of Health are
excluded:

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U.S. Patent No. [**] entitled: [**];

U.S. Patent No. [**] entitled: [**]; and

U.S. Patent No. [**] entitled: [**]

	 	4.	 	McGill University (B)

In addition to certain manufacturing technology excluded by definition, the following Patents
in-licensed from McGill University are excluded:

	 	 	 	 	 	 	 
	Isis Docket Number	 	Country	 	Status	 	Title
	[**]
	 	[**]
	 	[**]
	 	[**]
	[**]
	 	[**]
	 	[**]
	 	[**]

	 	5.	 	[**] (B)

The following Patents in-licensed from the [**] are excluded:

[**] Patent No. [**] entitled [**];

[**] Patent Application [**] entitled “[**];

[**] Patent Application [**] entitled [**]; and

[**] Patent No. [**] entitled [**].

	 	6.	 	Walder Patents (B)

The Walder Patents are excluded. “Walder Patents” means and includes [**]. Patent Nos. [**];
[**] Patent No. [**], and [**] Patent Application No. [**] (allowed).

	 	7.	 	Merck Nucleoside

Single nucleosides, nucleotides or monomers claimed in Patents filed as of the Effective Date
which are prosecuted by Merck and Co. are excluded. However if such Patents are necessary for
Alnylam to practice the licenses granted under Section 5.1 with respect to a specific Alnylam
Product, then Isis will include such necessary Patents in the licenses granted under Section
5.1.

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Isis believes the agreement under which Isis received a license to the [**] Patents listed
below [**].

	 	 	 	 	 	 	 	 	 	 	 
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	 	 	 	 	 	 	Patent	 	Grant	 	 
	Isis Docket Number	 	Country	 	Status	 	Number	 	Date	 	Title
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	 	9.	 	Carnegie Institution of Washington.

Isis is not granting Alnylam any sublicense under the License Agreement dated January 28, 2005
between Isis and Carnegie Institution of Washington.

	 	10.	 	Garching Innovation GmbH.

Isis is not granting Alnylam any sublicense under the Co-Exclusive License Agreement dated
October 18, 2004 among Isis, Alnylam and Garching Innovation GmbH.

 

			
	(A)	 	Isis cannot sublicense the technologies marked with this footnote.
	 
	(B)	 	Although, Isis can sublicense the technologies marked with this footnote, such a
sublicense carries additional financial and other obligations. Isis is willing to
negotiate a separate sublicense agreement for these technologies.

Schedule 1-59

Isis Manufacturing Patents

The Parties have not yet agreed to a specific list of Manufacturing Patents as of the date of the
Addendum Transmittal. However, the Parties agree to work together to develop a list of
Manufacturing Patents by [**].

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Schedule 1-66

Isis Special Patents

	 	 	 	 	 	 	 	 	 	 	 
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	Docket Number	 	Country	 	Status	 	Number	 	Date	 	Title
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