Document:

exv10w1

Exhibit 10.1

BIOCRYST PHARMACEUTICALS, INC.

STOCK INCENTIVE PLAN

(AS AMENDED AND RESTATED FEBRUARY 17, 2011)

ARTICLE ONE

GENERAL PROVISIONS

     I. PURPOSES OF THE PLAN

          A. This Stock Incentive Plan (the “Plan”), formerly the “BioCryst Pharmaceuticals, Inc. 1991
Stock Option Plan,” is intended to promote the interests of BioCryst Pharmaceuticals, Inc., a
Delaware corporation (the “Company”), by providing a method whereby (i) key employees (including
officers and directors) of the Company (or its parent or subsidiary corporations) who are
responsible for the management, growth and financial success of the Company (or any parent or
subsidiary corporations), (ii) non-employee members of the board of directors of the Company (the
“Board”) (or of any parent or subsidiary corporations) and (iii) consultants and other independent
contractors who provide valuable services to the Company (or any parent or subsidiary corporations)
may be offered the opportunity to acquire a proprietary interest, or otherwise increase their
proprietary interest, in the Company as an incentive for them to remain in the service of the
Company (or any parent or subsidiary corporations).

          B. For purposes of the Plan, the following provisions shall be applicable in determining the
parent and subsidiary corporations of the Company:

               (i) Any corporation (other than the Company) in an unbroken chain of corporations ending with
the Company shall be considered to be a parent corporation of the Company, provided each such
corporation in the unbroken chain (other than the Company) owns, at the time of the determination,
stock possessing fifty percent (50%) or more of the total combined voting power of all classes of
stock in one of the other corporations in such chain.

               (ii) Each corporation (other than the Company) in an unbroken chain of corporations beginning
with the Company shall be considered to be a subsidiary of the Company, provided each such
corporation (other than the last corporation) in the unbroken chain owns, at the time of the
determination, stock possessing fifty percent (50%) or more of the total combined voting power of
all classes of stock in one of the other corporations in such chain.

          C. The Plan, as hereby amended and restated, was approved and adopted by the Board on February
17, 2011 in order to increase by 1,600,000 the number of shares of the Company’s common stock, par
value $0.01 per share (the “Common Stock”), that may be issued pursuant to the Plan. The Board’s
adoption of the share increase was approved by the Company’s stockholders at the Company’s 2011
Annual Stockholders Meeting held on May 12, 2011.

     II. STRUCTURE OF THE PLAN

          A. The Plan shall be divided into three separate equity programs:

 

 

          (i) the Discretionary Option Grant Program specified in Article Two, pursuant to which
eligible persons may, at the discretion of the Plan Administrator, be granted options to
purchase shares of Common Stock,

          (ii) the Stock Issuance Program specified in Article Three, pursuant to which eligible
persons may, at the discretion of the Plan Administrator, be issued shares of Common Stock
directly, either through immediate purchase of such shares or as compensation for services
rendered to the Company (or any parent or subsidiary), and

          (iii) the Automatic Option Grant Program specified in Article Four, pursuant to which
non-employee members of the Board will automatically receive option grants to purchase
shares of Common Stock.

          B. Unless the context clearly indicates otherwise, the provisions of Articles One and Five of
the Plan shall apply to all equity programs under the Plan and shall accordingly govern the
interests of all individuals under the Plan.

     III. ADMINISTRATION OF THE PLAN

          A. A committee of two (2) or more non-employee Board members appointed by the Board (the
“Primary Committee”) shall have sole and exclusive authority to administer the Discretionary Option
Grant and Stock Issuance Programs with respect to Section 16 Insiders. For purposes of this
Section, a Section 16 Insider shall mean an officer or director of the Company subject to the
short-swing profit liabilities of Section 16 of the Securities Exchange Act of 1934 (the “1934
Act”).

          B. Administration of the Discretionary Option Grant and Stock Issuance Programs with respect
to all other persons eligible to participate in the programs may, at the Board’s discretion, be
vested in the Primary Committee, another committee of one (1) or more Board members appointed by
the Board (the “Secondary Committee”), or the Board may retain the power to administer those
programs with respect to all such persons.

          C. Members of the Primary Committee and any Secondary Committee shall serve for such period of
time as the Board may determine and shall be subject to removal by the Board at any time.

          D. Each Plan Administrator (whether the Primary Committee, the Board or the Secondary
Committee) shall, within the scope of its administrative functions under the Plan, have full power
and authority (subject to the express provisions of the Plan) to establish such rules and
regulations as it may deem appropriate for the proper administration of the Discretionary Option
Grant and Stock Issuance Programs and to make such determinations under, and issue interpretations
of, the provisions of such programs and any outstanding options or stock issuances thereunder as it
may deem necessary or advisable. Decisions of the Plan Administrator within the scope of its
administrative authority under the Plan shall be final and binding on all parties.

          E. Service on the Primary Committee or the Secondary Committee shall constitute service as a
Board member, and members of each such committee shall accordingly be

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entitled to full indemnification and reimbursement as Board members for their service on such
committee. No member of the Primary Committee or Secondary Committee shall be liable for any act
of omission made in good faith with respect to the Plan or any option grants or stock issuances
under the Plan.

          F. Administration of the Automatic Option Grant Program shall be self-executing in accordance
with the express terms and conditions of Article Four, and no Plan Administrator shall exercise any
discretionary functions under that program.

     IV. ELIGIBILITY

          A. The persons eligible to participate in the Discretionary Option Grant and Stock Issuance
Programs shall be limited to the following:

               (i) officers and other key employees of the Company (or its parent or subsidiary corporations)
who render services which contribute to the management, growth and financial success of the Company
(or its parent or subsidiary corporations);

               (ii) individuals who are consultants or independent advisors and who provide valuable services
to the Company (or its parent or subsidiary corporations); and

               (iii) non-employee members of the Board (or of the board of directors of parent or subsidiary
corporations).

          B. Only Board members who are not employees of the Company (or any parent or subsidiary) shall
be eligible to receive automatic option grants pursuant to the Automatic Option Grant Program
specified in Article Four.

          C. The Plan Administrator shall, within the scope of its administrative jurisdiction under the
Plan, have full power and authority to determine (i) whether to grant options in accordance with
the Discretionary Option Grant Program or to effect stock issuances in accordance with the Stock
Issuance Program, (ii) which eligible persons are to receive option grants under the Discretionary
Option Grant Program, the time or times when such option grants are to be made, the number of
shares to be covered by each such grant, the status of the granted option as either an incentive
stock option (“Incentive Option”) which satisfies the requirements of Section 422 of the Internal
Revenue Code of 1986, as amended (the “Code”) or a non-statutory option not intended to meet such
requirements, the time or times when each such option is to become exercisable, the vesting
schedule (if any) applicable to the option shares and the maximum term for which such option is to
remain outstanding, and (iii) which eligible persons are to receive stock issuances under the Stock
Issuance Program, the time or times when such issuances are to be made, the number of shares to be
issued to each participant, the vesting schedule (if any) applicable to the shares and the
consideration for such shares.

     V. STOCK SUBJECT TO THE PLAN

          A. Shares of the Company’s Common Stock shall be available for issuance under the Plan and
shall be drawn from either the Company’s authorized but unissued shares of Common Stock or from
reacquired shares of Common Stock, including shares repurchased by

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the Company on the open market. The maximum number of shares of Common Stock which may be
issued over the term of the Plan, as amended and restated, shall not exceed 12,460,000 shares,
subject to adjustment from time to time in accordance with the provisions of this Section V. The
total number of shares available under the Plan as of March 24, 2011 is 10,333,704. This amount
includes: 8,733,704 shares reserved for awards already issued; 522,842 shares of Common Stock
available for future issuance under the Plan; and the increase of 1,600,000 shares of Common Stock
authorized by the Board and approved by the Company’s stockholders at the 2011 Annual Stockholders
Meeting.

          B. In no event shall the number of shares of Common Stock for which any one individual
participating in the Plan may receive options, separately exercisable stock appreciation rights and
direct stock issuances exceed 1,500,000 shares of Common Stock in the aggregate. For purposes of
such limitation, however, no stock options granted prior to the date the Common Stock was first
registered under Section 12 of the 1934 Act (the “Section 12(g) Registration Date”) shall be taken
into account.

          C. Should an outstanding option under this Plan expire or terminate for any reason prior to
exercise in full, the shares subject to the portion of the option not so exercised shall be
available for subsequent option grant or direct stock issuances under the Plan. Unvested shares
issued under the Plan and subsequently repurchased by the Company, at the original issue price paid
per share, pursuant to the Company’s repurchase rights under the Plan, or shares underlying
terminated share right awards, shall be added back to the number of shares of Common Stock reserved
for issuance under the Plan and shall accordingly be available for reissuance through one or more
subsequent option grants or direct stock issuances under the Plan. However, should the exercise
price of an outstanding option under the Plan be paid with shares of Common Stock or should shares
of Common Stock otherwise issuable under the Plan be withheld by the Company in satisfaction of the
withholding taxes incurred in connection with the exercise of an outstanding option or the vesting
of a direct stock issuance under the Plan, then the number of shares of Common Stock available for
issuance under the Plan shall be reduced by the gross number of shares for which the option is
exercised or which vest under the direct stock issuance, and not by the net number of shares of
Common Stock actually issued to the holder of such option or stock issuance. Shares of Common
Stock subject to any option surrendered for an appreciation distribution under Section IV of
Article Two or Section IV of Article Four shall not be available for subsequent issuance under the
Plan.

          D. In the event any change is made to the Common Stock issuable under the Plan by reason of
any stock split, stock dividend, recapitalization, combination of shares, exchange of shares or
other change affecting the outstanding Common Stock as a class without receipt of consideration,
then appropriate adjustments shall be made to (i) the maximum number and/or class of securities
issuable under the Plan, (ii) the maximum number and/or class of securities for which any one
individual participating in the Plan may be granted stock options, separately exercisable stock
appreciation rights, and direct stock issuances under the Plan from and after the Section 12(g)
Registration Date, (iii) the number and/or class of securities and price per share in effect under
each outstanding option under the Plan, (iv) the number and/or class of securities in effect under
each outstanding direct stock issuance under the Plan, and (v) the number and/or class of
securities for which automatic option grants are subsequently to be made per non-employee Board
member under the Automatic Option Grant Program. The purpose of

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such adjustments shall be to preclude the enlargement or dilution of rights and benefits under
the Plan.

          E. The fair market value per share of Common Stock on any relevant date under the Plan shall
be determined in accordance with the following provisions:

               (i) If the Common Stock is not at the time listed or admitted to trading on any national
securities exchange but is traded in the over-the-counter market, the fair market value shall be
the mean between the highest bid and lowest asked prices (or, if such information is available, the
closing selling price) per share of Common Stock on the date in question in the over-the-counter
market, as such prices are reported by the National Association of Securities Dealers through the
Nasdaq National Market, the Nasdaq Global Select Market or any successor system. If there are no
reported bid and asked prices (or closing selling price) for the Common Stock on the date in
question, then the mean between the highest bid price and lowest asked price (or the closing
selling price) on the last preceding date for which such quotations exist shall be determinative of
fair market value.

               (ii) If the Common Stock is at the time listed or admitted to trading on any national
securities exchange, then the fair market value shall be the closing selling price per share of
Common Stock on the date in question on the securities exchange determined by the Plan
Administrator to be the primary market for the Common Stock, as such price is officially quoted in
the composite tape of transactions on such exchange. If there is no reported sale of Common Stock
on the exchange on the date in question, then the fair market value shall be the closing selling
price on the exchange on the last preceding date for which such quotation exists.

               (iii) If the Common Stock is at the time neither listed nor admitted to trading on any
securities exchange nor traded in the over-the-counter market, then the fair market value shall be
determined by the Plan Administrator after taking into account such factors as the Plan
Administrator shall deem appropriate.

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ARTICLE TWO

DISCRETIONARY OPTION GRANT PROGRAM

     I. TERMS AND CONDITIONS OF OPTIONS

          Options granted pursuant to this Article Two shall be authorized by action of the Plan
Administrator and may, at the Plan Administrator’s discretion, be either Incentive Options or
non-statutory options. Individuals who are not Employees may only be granted non-statutory options
under this Article Two. Each option granted shall be evidenced by one or more instruments in the
form approved by the Plan Administrator. Each such instrument shall, however, comply with the
terms and conditions specified below, and each instrument evidencing an Incentive Option shall, in
addition, be subject to the applicable provisions of Section II of this Article Two.

          A. Option Price.

               1. The option price per share shall be fixed by the Plan Administrator. In no event,
however, shall the option price per share be less than one hundred percent (100%) of the
fair market value per share of Common Stock on the date of the option grant.

               2. The option price shall become immediately due upon exercise of the option and
shall, subject to the provisions of Section IV of this Article Two and the instrument
evidencing the grant, be payable as follows:

                    (i) full payment in cash or check drawn to the Company’s order;

                    (ii) full payment in shares of Common Stock held by the optionee for the requisite period
necessary to avoid a charge to the Company’s earnings for financial reporting purposes and valued
at fair market value on the Exercise Date (as such term is defined below);

                    (iii) full payment through a combination of shares of Common Stock held by the optionee for
the requisite period necessary to avoid a charge to the Company’s earnings for financial reporting
purposes and valued at fair market value on the Exercise Date and cash or cash equivalent; or

                    (iv) full payment through a broker-dealer sale and remittance procedure pursuant to which the
optionee (I) shall provide irrevocable written instructions to a designated brokerage firm to
effect the immediate sale of the purchased shares and remit to the Company, out of the sale
proceeds available on the settlement date, sufficient funds to cover the aggregate option price
payable for the purchased shares plus all applicable Federal and State income and employment taxes
required to be withheld by the Company in connection with such purchase and (II) shall provide
written directives to the Company to deliver the certificates for the purchased shares directly to
such brokerage firm in order to complete the sale transaction.

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     For purposes of this subparagraph 2, the Exercise Date shall be the date on which written
notice of the option exercise is delivered to the Company. Except to the extent the sale and
remittance procedure is utilized in connection with the exercise of the option, payment of the
option price for the purchased shares must accompany such notice.

          B. Term and Exercise of Options.

               Each option granted under this Article Two shall be exercisable at such time or times, during
such period, and for such number of shares as shall be determined by the Plan Administrator and set
forth in the instrument evidencing the option grant. No such option, however, shall have a maximum
term in excess of ten (10) years from the grant date. During the lifetime of the optionee, the
option, together with any stock appreciation rights pertaining to such option, shall be exercisable
only by the optionee and shall not be assignable or transferable by the optionee except for a
transfer of the option by will or by the laws of descent and distribution following the optionee’s
death. However, the Plan Administrator shall have the discretion to provide that a non-statutory
option may, in connection with the optionee’s estate plan, be assigned in whole or in part during
the optionee’s lifetime either as (i) as a gift to one or more members of optionee’s immediate
family, to a trust in which optionee and/or one or more such family members hold more than fifty
percent (50%) of the beneficial interest or an entity in which more than fifty percent (50%) of the
voting interests are owned by optionee and/or one or more such family members, or (ii) pursuant to
a domestic relations order. The assigned portion shall be exercisable only by the person or
persons who acquire a proprietary interest in the option pursuant to such assignment. The terms
applicable to the assigned portion shall be the same as those in effect for this option immediately
prior to such assignment and shall be set forth in such documents issued to the assignee as the
Plan Administrator may deem appropriate.

          C. Termination of Service.

               1. Except to the extent otherwise provided pursuant to Section V of this Article Two,
the following provisions shall govern the exercise period applicable to any options held by
the optionee at the time of cessation of Service or death.

               (i) Should the optionee cease to remain in Service for any reason other than death or
permanent disability, then the period for which each outstanding option held by such optionee is to
remain exercisable shall be limited to the three (3)-month period following the date of such
cessation of Service. However, should optionee die during the three (3)-month period following his
or her cessation of Service, the personal representative of the optionee’s estate or the person or
persons to whom the option is transferred pursuant to the optionee’s will or in accordance with the
laws of descent and distribution shall have a twelve (12)-month period following the date of the
optionee’s death during which to exercise such option.

               (ii) In the event such Service terminates by reason of permanent disability (as defined in
Section 22(e)(3) of the Internal Revenue Code), then the period for which each outstanding option
held by the optionee is to remain exercisable shall be limited to the twelve (12)-month period
following the date of such cessation of Service.

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               (iii) Should the optionee, after completing five (5) full years of Service, die while in
Service, then the exercisability of each of his or her outstanding options shall automatically
accelerate so that each such option shall become fully exercisable with respect to the total number
of shares of Common Stock at the time subject to such option and may be exercised for all or any
portion of such shares. The personal representative of the optionee’s estate or the person or
persons to whom the option is transferred pursuant to the optionee’s will or in accordance with the
laws of descent and distribution shall have a twelve (12)-month period following the date of the
optionee’s death during which to exercise such option.

               (iv) In the event such Service terminates by reason of death prior to the optionee obtaining
five (5) full years of Service, then the period for which each outstanding vested option held by
the optionee at the time of death shall be exercisable by the optionee’s estate or the person or
persons to whom the option is transferred pursuant to the optionee’s will shall be limited to the
twelve (12)-month period following the date of the optionee’s death.

               (v) Under no circumstances, however, shall any such option be exercisable after the specified
expiration date of the option term.

               (vi) Each such option shall, during such limited exercise period, be exercisable for any or
all of the shares for which the option is exercisable on the date of the optionee’s cessation of
Service. Upon the expiration of such limited exercise period or (if earlier) upon the expiration
of the option term, the option shall terminate and cease to be exercisable. However, each
outstanding option shall immediately terminate and cease to remain outstanding, at the time of the
optionee’s cessation of Service, with respect to any shares for which the option is not otherwise
at that time exercisable or in which the optionee is not otherwise vested.

               (vii) Should (i) the optionee’s Service be terminated for misconduct (including, but not
limited to, any act of dishonesty, willful misconduct, fraud or embezzlement) or (ii) the optionee
make any unauthorized use or disclosure of confidential information or trade secrets of the Company
or its parent or subsidiary corporations, then in any such event all outstanding options held by
the optionee under this Article Two shall terminate immediately and cease to be exercisable.

               2. The Plan Administrator shall have complete discretion, exercisable either at the
time the option is granted or at any time while the option remains outstanding, to permit
one or more options held by the optionee under this Article Two to be exercised, during the
limited period of exercisability provided under subparagraph 1 above, not only with respect
to the number of shares for which each such option is exercisable at the time of the
optionee’s cessation of Service but also with respect to one or more subsequent
installments of purchasable shares for which the option would otherwise have become
exercisable had such cessation of Service not occurred.

               3. For purposes of the foregoing provisions of this Section I.C (and for all other
purposes under the Plan):

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               (i) The optionee shall be deemed to remain in the Service of the Company for so long as such
individual renders services on a periodic basis to the Company (or any parent or subsidiary
corporation) in the capacity of an Employee, a non-employee member of the board of directors or an
independent consultant or advisor, unless the agreement evidencing the applicable option grant
specifically states otherwise.

               (ii) The optionee shall be considered to be an Employee for so long as such individual remains
in the employ of the Company or one or more of its parent or subsidiary corporations, subject to
the control and direction of the employer entity not only as to the work to be performed but also
as to the manner and method of performance.

          D. Stockholder Rights.

               An optionee shall have no stockholder rights with respect to any shares covered by the option
until such individual shall have exercised the option and paid the option price for the purchased
shares.

          E. Repurchase Rights.

               The shares of Common Stock acquired upon the exercise of options granted under this Article
Two may be subject to repurchase by the Company in accordance with the following provisions:

               1. The Plan Administrator shall have the discretion to grant options which are exercisable for
unvested shares of Common Stock under this Article Two. Should the optionee cease Service while
holding such unvested shares, the Company shall have the right to repurchase any or all those
unvested shares at the option price paid per share. The terms and conditions upon which such
repurchase right shall be exercisable (including the period and procedure for exercise and the
appropriate vesting schedule for the purchased shares) shall be established by the Plan
Administrator and set forth in the instrument evidencing such repurchase right.

               2. All of the Company’s outstanding repurchase rights shall automatically terminate, and all
shares subject to such terminated rights shall immediately vest in full, upon the occurrence of any
Corporate Transaction under Section III of this Article Two, except to the extent: (i) any such
repurchase right is expressly assigned to the successor corporation (or parent thereof) in
connection with the Corporate Transaction or (ii) such termination is precluded by other
limitations imposed by the Plan Administrator at the time the repurchase right is issued.

               3. The Plan Administrator shall have the discretionary authority, exercisable either before or
after the optionee’s cessation of Service, to cancel the Company’s outstanding repurchase rights
with respect to one or more shares purchased or purchasable by the optionee under this
Discretionary Option Grant Program and thereby accelerate the vesting of such shares in whole or in
part at any time.

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     II. INCENTIVE OPTIONS

          The terms and conditions specified below shall be applicable to all Incentive Options granted
under this Article Two. Incentive Options may only be granted to individuals who are Employees of
the Company. Options which are specifically designated as “non-statutory” options when issued
under the Plan shall not be subject to such terms and conditions.

          A. Dollar Limitation. The aggregate fair market value (determined as of the
respective date or dates of grant) of the Common Stock for which one or more options granted to any
Employee under this Plan (or any other option plan of the Company or its parent or subsidiary
corporations) may for the first time become exercisable as incentive stock options under the
Federal tax laws during any one calendar year shall not exceed the sum of One Hundred Thousand
Dollars ($100,000). To the extent the Employee holds two or more such options which become
exercisable for the first time in the same calendar year, the foregoing limitation on the
exercisability of such options as incentive stock options under the Federal tax laws shall be
applied on the basis of the order in which such options are granted. Should the number of shares
of Common Stock for which any Incentive Option first becomes exercisable in any calendar year
exceed the applicable One Hundred Thousand Dollar ($100,000) limitation, then that option may
nevertheless be exercised in such calendar year for the excess number of shares as a non-statutory
option under the Federal tax laws.

          B. 10% Stockholder. If any individual to whom an Incentive Option is granted is the
owner of stock (as determined under Section 424(d) of the Internal Revenue Code) possessing 10% or
more of the total combined voting power of all classes of stock of the Company or any one of its
parent or subsidiary corporations, then the option price per share shall not be less than one
hundred and ten percent (110%) of the fair market value per share of Common Stock on the grant
date, and the option term shall not exceed five (5) years, measured from the grant date.

          C. Termination of Employment. Any portion of an Incentive Option that remains
outstanding (by reason of the optionee remaining in the Service of the Company, pursuant to the
Plan Administrator’s exercise of discretion under Section V of this Article Two, or otherwise) more
than 3 months following the date an optionee ceases to be an Employee of the Company shall
thereafter be exercisable as a non-statutory option under federal tax laws.

          Except as modified by the preceding provisions of this Section II, the provisions of Articles
One, Two and Five of the Plan shall apply to all Incentive Options granted hereunder.

     III. CORPORATE TRANSACTIONS/CHANGES IN CONTROL

          A. In the event of any of the following stockholder-approved transactions (a “Corporate
Transaction”):

               (1) a merger or consolidation in which the Company is not the surviving entity, except for a
transaction the principal purpose of which is to change the State of the Company’s incorporation,

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               (2) the sale, transfer or other disposition of all or substantially all of the assets of the
Company in liquidation or dissolution of the Company, or

               (3) any reverse merger in which the Company is the surviving entity but in which securities
possessing more than fifty percent (50%) of the total combined voting power of the Company’s
outstanding securities are transferred to a person or persons different from the persons holding
those securities immediately prior to such merger,

then the exercisability of each option outstanding under this Article Two shall automatically
accelerate so that each such option shall, immediately prior to the specified effective date for
the Corporate Transaction, become fully exercisable with respect to the total number of shares of
Common Stock at the time subject to such option and may be exercised for all or any portion of such
shares. However, an outstanding option under this Article Two shall not so accelerate if and to
the extent the acceleration of such option is subject to other limitations imposed by the Plan
Administrator at the time of grant, unless the Plan Administrator, in its discretion, later
determines to waive such limitations.

          B. Immediately after the consummation of the Corporate Transaction, all outstanding options
under this Article Two shall terminate and cease to be outstanding, except to the extent assumed by
the successor corporation or its parent company. The Plan Administrator shall have complete
discretion to provide, on such terms and conditions as it sees fit, for a cash payment to be made
to any optionee on account of any option terminated in accordance with this paragraph, in an amount
equal to the excess (if any) of (A) the fair market value of the shares subject to the option as of
the date of the Corporate Transaction, over (B) the aggregate exercise price of the option.

          C. Each outstanding option under this Article Two which is assumed in connection with the
Corporate Transaction or is otherwise to continue in effect shall be appropriately adjusted,
immediately after such Corporate Transaction, to apply and pertain to the number and class of
securities which would have been issued to the option holder, in consummation of such Corporate
Transaction, had such person exercised the option immediately prior to such Corporate Transaction.
Appropriate adjustments shall also be made to the option price payable per share, provided
the aggregate option price payable for such securities shall remain the same. In addition, the
class and number of securities available for issuance under the Plan following the consummation of
the Corporate Transaction shall be appropriately adjusted.

          D. The grant of options under this Article Two shall in no way affect the right of the Company
to adjust, reclassify, reorganize or otherwise change its capital or business structure or to
merge, consolidate, dissolve, liquidate or sell or transfer all or any part of its business or
assets.

          E. The exercisability of each outstanding option under this Article Two shall automatically
accelerate, and the Company’s outstanding repurchase rights under this Article Two shall
immediately terminate upon the occurrence of a Change in Control.

          F. For purposes of this Section III (and for all other purposes under the Plan), a Change in
Control shall be deemed to occur in the event:

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          (1) any person or related group of persons (other than the Company or a person that
directly or indirectly controls, is controlled by, or is under common control with, the
Company) directly or indirectly acquires beneficial ownership (within the meaning of Rule
13d-3 of the 1934 Act) of securities possessing more than fifty percent (50%) of the total
combined voting power of the Company’s outstanding securities pursuant to a tender or
exchange offer made directly to the Company’s stockholders; or

          (2) there is a change in the composition of the Board over a period of twenty-four (24)
consecutive months or less such that a majority of the Board members (rounded up to the next
whole number) ceases, by reason of one or more contested elections for Board membership, to
be comprised of individuals who either (A) have been Board members continuously since the
beginning of such period or (B) have been elected or nominated for election as Board members
during such period by at least two-thirds of the Board members described in clause (A) who
were still in office at the time such election or nomination was approved by the Board.

          G. All options accelerated in connection with the Change in Control shall remain fully
exercisable until the expiration or sooner termination of the option term.

          H. The portion of any Incentive Option accelerated under this Section III in connection with a
Corporate Transaction or Change in Control shall remain exercisable as an incentive stock option
under the Federal tax laws only to the extent the dollar limitation of Section II of this Article
Two is not exceeded. To the extent such dollar limitation is exceeded, the accelerated portion of
such option shall be exercisable as a non-statutory option under the Federal tax laws.

     IV. STOCK APPRECIATION RIGHTS

          A. Provided and only if the Plan Administrator determines in its discretion to implement the
stock appreciation right provisions of this Section IV, one or more optionees may be granted the
right, exercisable upon such terms and conditions as the Plan Administrator may establish, to
surrender all or part of an unexercised option granted under this Article Two in exchange for a
distribution from the Company in an amount equal to the excess of (i) the fair market value (on the
option surrender date) of the number of shares in which the optionee is at the time vested under
the surrendered option (or surrendered portion thereof) over (ii) the aggregate option price
payable for such vested shares. The distribution may be made in shares of Common Stock valued at
fair market value on the option surrender date, in cash, or partly in shares and partly in cash, as
the Plan Administrator shall determine in its sole discretion.

          B. The shares of Common Stock subject to any option surrendered for an appreciation
distribution pursuant to this Section IV shall not be available for subsequent option grant under
the Plan.

     V. EXTENSION OF EXERCISE PERIOD

          The Plan Administrator shall have full power and authority, exercisable either at the time the
option is granted or at any time while the option remains outstanding, to extend the

12

 

period of time for which any option granted under this Article Two is to remain exercisable
following the optionee’s cessation of Service or death from the limited period in effect under
Section I.C.1 of Article Two to such greater period of time as the Plan Administrator shall deem
appropriate; provided, however, that in no event shall such option be exercisable after the
specified expiration date of the option term.

ARTICLE THREE

STOCK ISSUANCE PROGRAM

     I. STOCK ISSUANCE TERMS

Shares of Common Stock may be issued under the Stock Issuance Program through direct and immediate
issuances without any intervening option grants. Each such stock issuance shall be evidenced by a
Stock Issuance Agreement which complies with the terms specified below. Shares of Common Stock may
also be issued under the Stock Issuance Program pursuant to share right awards which entitle the
recipients to receive shares upon the attainment of designated Service and/or performance goals.

          A. Purchase Price.

               1. The purchase price per share shall be fixed by the Plan Administrator, but shall
not be less than one hundred percent (100%) of the fair market value per share of Common
Stock on the issuance date.

               2. Shares of Common Stock may be issued under the Stock Issuance Program for any of
the following items of consideration which the Plan Administrator may deem appropriate in
each individual instance:

	 	(i)	 	cash or check made payable to the Company, or
	 
	 	(ii)	 	services rendered to the Company
(or any parent or subsidiary).

          B. Vesting Provisions.

               1. The Plan Administrator may issue shares of Common Stock under the Stock Issuance
Program which are fully and immediately vested upon issuance or which are to vest in one or
more installments over the participant’s period of Service or upon attainment of specified
performance objectives. Alternatively, the Plan Administrator may issue share right awards
under the Stock Issuance Program which shall entitle the recipient to receive a specified
number of shares of Common Stock upon the attainment of one or more Service and/or
performance goals established by the Plan Administrator. Upon the attainment of such
Service and/or performance goals, fully-vested shares of Common Stock shall be issued in
satisfaction of those share right awards.

               2. Any new, substituted or additional securities or other property (including money
paid other than as a regular cash dividend) issued by reason of

13

 

any stock dividend, stock split, recapitalization, combination of shares, exchange of
shares or other change affecting the outstanding Common Stock as a class without the
Company’s receipt of consideration, shall be issued or set aside with respect to the shares
of unvested Common Stock granted to a participant or subject to a participant’s share right
award, subject to (i) the same vesting requirements applicable to the participant’s
unvested shares of Common Stock or share rights award, and (ii) such escrow arrangements as
the Plan Administrator shall deem appropriate.

               3. The participant shall have full stockholder rights with respect to any shares of
Common Stock issued to the participant under the Stock Issuance Program, whether or not the
participant’s interest in those shares is vested. Accordingly, the participant shall have
the right to vote such shares and to receive any regular cash dividends paid on such
shares.

               4. The participant shall not have any stockholders rights with respect to any shares
of Common Stock subject to a share right award. However, the Plan Administrator may provide
for a participant to receive one or more dividend equivalents with respect to such shares,
entitling the participant to all regular cash dividends payable on the shares of Common
Stock underlying the share right award, which amounts shall be (i) subject to the same
vesting requirements applicable to the shares of Common Stock underlying the share rights
award, and (ii) payable upon issuance of the shares to which such dividend equivalents
relate.

               5. Should the participant cease to remain in Service while holding one or more
unvested shares of Common Stock issued under the Stock Issuance Program or should the
performance objectives not be attained with respect to one or more such unvested shares of
Common Stock, then those shares shall be immediately surrendered to the Company for
cancellation, and the participant shall have no further stockholder rights with respect to
those shares. To the extent the surrendered shares were previously issued to the
participant for consideration paid in cash, the Company shall repay to the participant the
cash consideration paid for the surrendered shares.

               6. The Plan Administrator may in its discretion waive the surrender and cancellation
of one or more unvested shares of Common Stock which would otherwise occur upon the
cessation of the Participant’s Service or the non-attainment of the performance objectives
applicable to those shares. Such waiver shall result in the immediate vesting of the
participant’s interest in the shares of Common Stock as to which the waiver applies. Such
waiver may be effected at any time, whether before or after the participant’s cessation of
Service or the attainment or non-attainment of the applicable performance objectives.

               7. Outstanding share right awards under the Stock Issuance Program shall automatically
terminate, and no shares of Common Stock shall actually be issued in satisfaction of those
awards, if the Service and/or performance goals established for such awards are not
attained. The Plan Administrator, however, shall have the discretionary authority to issue
shares of Common Stock in satisfaction of one or more outstanding share right awards as to
which the designated Service and/or performance

14

 

goals are not attained. Such authority may be exercised at any time, whether before or
after the participant’s cessation of Service or the attainment or non-attainment of the
applicable performance objectives.

     II. CORPORATE TRANSACTION/CHANGE IN CONTROL

          A. All of the Company’s outstanding repurchase rights under the Stock Issuance Program shall
terminate automatically, and all the shares of Common Stock subject to those terminated rights
shall immediately vest in full, in the event of any Corporate Transaction, except to the extent (i)
those repurchase rights are to be assigned to the successor corporation (or parent thereof) in
connection with the such Corporate Transaction, or (ii) such accelerated vesting is precluded by
other limitations imposed in the Stock Issuance Agreement, unless the Plan Administrator determines
to waive such limitations.

          B. Each repurchase right which is assigned in connection with (or is otherwise to continue in
effect after) a Corporate Transaction shall be appropriately adjusted such that it shall apply and
pertain to the number and class of securities issued to the participant in consummation of the
Corporate Transaction with respect to the shares granted to participant under this Article Three.

          C. All of the Company’s outstanding repurchase rights under the Stock Issuance Program shall
automatically terminate, and all shares of Common Stock subject to those terminated rights shall
immediately vest, in the event of any Change in Control.

          D. All shares of Common Stock underlying outstanding share right awards issued under the Stock
Issuance Program shall vest, and all of the shares of Common Stock subject to such share right
awards shall be issued to participants, immediately prior to the consummation of any Corporate
Transaction or Change in Control.

     III. SHARE ESCROW / LEGENDS

          Unvested shares may, in the Plan Administrator’s discretion, be held in escrow by the Company
until the participant’s interest in such shares vests or may be issued directly to the participant
with restrictive legends on the certificates evidencing those unvested shares.

15

 

ARTICLE FOUR

AUTOMATIC OPTION GRANT PROGRAM

     I. ELIGIBILITY.

          The individuals eligible to receive automatic option grants pursuant to the provisions of this
Article Four shall be (i) those individuals who, after the effective date of this amendment and
restatement, first become non-employee Board members, whether through appointment by the Board,
election by the Company’s stockholders, or by continuing to serve as a Board member after ceasing
to be employed by the Company, and (ii) those individuals already serving as non-employee Board
members on the effective date of this amendment and restatement. As used herein, a “non-employee”
Board member is any Board member who is not employed by the Company on the date in question.

     II. TERMS AND CONDITIONS OF AUTOMATIC OPTION GRANTS

          A. Grants. Option grants shall be made under this Article Four as follows:

               1. Each individual who first becomes a non-employee Board member on or after the
effective date of this amendment and restatement shall automatically be granted at such
time a non-statutory stock option under the terms and conditions of this Article Four, to
purchase a number shares of Common Stock equal to the product of (i) 25,000, and (ii) a
fraction, the numerator of which is the number of months (rounded to the nearest whole
number) remaining between the date such Board member first became a non-employee Board
member and the Company’s next scheduled Annual Stockholders Meeting, and the denominator of
which is 12.

               2. Immediately following each Annual Stockholders Meeting of the Company, each
individual who is then serving as a non-employee Board member (except for those
individuals first elected to serve as non-employee Board members at such meeting), shall
automatically be granted a non-statutory stock option under this Article Four to acquire
15,000 shares of Common Stock.

          B. Exercise Price. The exercise price per share of each automatic option grant made
under this Article Four shall be equal to one hundred percent (100%) of the fair market value per
share of Common Stock on the automatic grant date.

          C. Payment. The exercise price shall be payable in one of the alternative forms
specified below:

               (1) payment in cash or check made payable to the Company’s order; or

               (2) full payment in shares of Common Stock held for the requisite period necessary to avoid a
charge to the Company’s reported earnings and valued at fair market value on the Exercise Date (as
such term is defined below); or

16

 

               (3) full payment in a combination of shares of Common Stock held for the requisite period
necessary to avoid a charge to the Company’s reported earnings and valued at fair market value on
the Exercise Date and cash or check payable to the Company’s order; or

               (4) full payment through a sale and remittance procedure pursuant to which the non-employee
Board member (I) shall provide irrevocable written instructions to a designated brokerage firm to
effect the immediate sale of the purchased shares and remit to the Company, out of the sale
proceeds available on the settlement date, sufficient funds to cover the aggregate exercise price
payable for the purchased shares and shall (II) concurrently provide written directives to the
Company to deliver the certificates for the purchased shares directly to such brokerage firm in
order to complete the sale transaction.

     For purposes of this subparagraph C, the Exercise Date shall be the date on which written
notice of the option exercise is delivered to the Company. Except to the extent the sale and
remittance procedure specified above is utilized for the exercise of the option, payment of the
option price for the purchased shares must accompany the exercise notice.

          D. Option Term. Each automatic grant under this Article Four shall have a term of ten
(10) years measured from the automatic grant date.

          E. Exercisability.

               1. Each initial automatic grant made pursuant to Section II.A.1 of this Article Four
shall vest and become exercisable over the period extending from the date of grant to the
scheduled date of the next Annual Stockholders Meeting following the grant. A pro rata
portion of such automatic grant shall vest on the last day of each calendar month following
the date of grant, with the final portion vesting on the scheduled date of such Annual
Stockholders Meeting.

               2. Each 15,000 share automatic grant made pursuant to Section II.A.2 of this Article
Four shall vest and become exercisable for 1/12th of the option shares upon the optionee’s
completion of each month of Board service over the twelve (12)-month period measured from
the automatic grant date.

          F. Non-Transferability. During the lifetime of the optionee, each automatic option
grant, together with the limited stock appreciation right pertaining to such option, shall be
exercisable only by the optionee, except to the extent such option or the limited stock
appreciation right is assigned or transferred (i) by will or by the laws of descent and
distribution following the optionee’s death, or (ii) during optionee’s lifetime either (A) as a
gift in connection with the optionee’s estate plan to one or more members of optionee’s immediate
family, to a trust in which optionee and/or one or more such family members hold more than fifty
percent (50%) of the beneficial interest or to an entity in which more than fifty percent (50%) of
the voting interests are owned by optionee and/or one or more such family members, or (B) pursuant
to a domestic relations order. The portion of any option assigned or transferred during optionee’s
lifetime shall be exercisable only by the person or persons who acquire a proprietary interest in
the option pursuant to such assignment. The terms applicable to the assigned portion shall be the
same as those in effect for this option immediately prior to such assignment and shall

17

 

be set forth in such documents issued to the assignee as the Plan Administrator may deem
appropriate.

          G. Cessation of Board Service.

               1. Should the optionee cease to serve as a Board member for any reason while holding
one or more automatic option grants under this Article Four, then such optionee shall have
the remainder of the ten (10) year term of each such option in which to exercise each such
option for any or all of the shares of Common Stock for which the option is exercisable at
the time of such cessation of Board service. Each such option shall immediately terminate
and cease to be outstanding, at the time of such cessation of Board service, with respect
to any shares for which the option is not otherwise at that time exercisable. Upon the
expiration of the ten (10)-year option term, the automatic grant shall terminate and cease
to be outstanding in its entirety. Upon the death of the optionee, whether before or after
cessation of Board service, any option held by optionee at the time of optionee’s death may
be exercised, for any or all of the shares of Common Stock for which the option was
exercisable at the time of cessation of Board service by the optionee and which have not
been theretofore exercised by the optionee, by the personal representative of the
optionee’s estate or by the person or persons to whom the option is transferred pursuant to
the optionee’s will or in accordance with the laws of descent and distribution. Any such
exercise must occur during the reminder of the ten (10) year term of such option.

               H. Stockholder Rights. The holder of an automatic option grant under this Article
Four shall have none of the rights of a stockholder with respect to any shares subject to such
option until such individual shall have exercised the option and paid the exercise price for the
purchased shares.

     III. CORPORATE TRANSACTIONS/CHANGES IN CONTROL

          A. In the event of a Corporate Transaction, the exercisability of each option outstanding
under this Article Four shall automatically accelerate so that each such option shall, immediately
prior to the specified effective date for the Corporate Transaction, become fully exercisable with
respect to the total number of shares of Common Stock at the time subject to such option and may be
exercised for all or any portion of such shares.

          B. Immediately after the consummation of the Corporate Transaction, all outstanding options
under this Article Four shall terminate and cease to be outstanding, except to the extent assumed
by the successor corporation or its parent company. If so provided by the terms of the Corporate
Transaction, the optionee shall receive a cash payment on account of any option terminated in
accordance with this paragraph, in an amount equal to the excess (if any) of (A) the fair market
value of the shares subject to the option as valued pursuant to the Corporate Transaction over (B)
the aggregate exercise price of the option.

          C. Each outstanding option under this Article Four which is assumed in connection with the
Corporate Transaction or is otherwise to continue in effect shall be appropriately adjusted,
immediately after such Corporate Transaction, to apply and pertain to the

18

 

number and class of securities which would have been issued to the option holder, in
consummation of such Corporate Transaction, had such person exercised the option immediately prior
to such Corporate Transaction. Appropriate adjustments shall also be made to the option price
payable per share, provided the aggregate option price payable for such securities shall
remain the same.

          D. In connection with any Change in Control, the exercisability of each option grant
outstanding at the time under this Article Four shall automatically accelerate so that each such
option shall, immediately prior to the specified effective date for the Change in Control, become
fully exercisable with respect to the total number of shares of Common Stock at the time subject to
such option and may be exercised for all or any portion of such shares.

          E. The automatic grant of options under this Article Four shall in no way affect the right of
the Company to adjust, reclassify, reorganize or otherwise change its capital or business structure
or to merge, consolidate, dissolve, liquidate or sell or transfer all or any part of its business
or assets.

     IV. STOCK APPRECIATION RIGHTS

          A. With respect to options granted under the Automatic Option Grant Program prior to March 7,
2006:

               1. Upon the occurrence of a Hostile Take-Over, the optionee shall have a thirty
(30)-day period in which to surrender to the Company each option held by him or her under
this Article Four. The optionee shall in return be entitled to a cash distribution from
the Company in an amount equal to the excess of (i) the Take-Over Price of the shares of
Common Stock at the time subject to each surrendered option (whether or not the option is
then exercisable for those shares) over (ii) the aggregate exercise price payable for such
shares. The cash distribution shall be made within five (5) days following the date the
option is surrendered to the Company, and neither the approval of the Plan Administrator
nor the consent of the Board shall be required in connection with the option surrender and
cash distribution. Any unsurrendered portion of the option shall continue to remain
outstanding and become exercisable in accordance with the terms of the instrument
evidencing such grant. This limited stock appreciation right shall in all events terminate
upon the expiration or sooner termination of the option term and may not be assigned or
transferred by the optionee.

               2. For purposes of Article Four, the following definitions shall be in effect:

                    (i) A Hostile Take-Over shall be deemed to occur in the event any person or related group of
persons (other than the Company or a person that directly or indirectly controls, is controlled by,
or is under common control with, the Company) directly or indirectly acquires beneficial ownership
(within the meaning of Rule 13d-3 of the 1934 Act, as amended) of securities possessing more than
fifty percent (50%) of the total combined voting power of the Company’s outstanding securities
pursuant to a tender or exchange offer made

19

 

directly to the Company’s stockholders which the Board does not recommend such stockholders to
accept.

                    (ii) The Take-Over Price per share shall be deemed to be equal to the fair market value per
share on the option surrender date.

          B. With respect to each option granted under the Automatic Option Grant Program on and after
March 7, 2006, each optionee shall have the right to surrender all or part of the option (to the
extent not then exercised) in exchange for a distribution from the Company in an amount equal to
the excess of (i) the fair market value (on the option surrender date) of the number of shares in
which the optionee is at the time vested under the surrendered option (or surrendered portion
thereof) over (ii) the aggregate option price payable for such vested shares. The distribution
shall be made in shares of Common Stock valued at fair market value on the option surrender date.

          C. The shares of Common Stock subject to any option surrendered for an appreciation
distribution pursuant to this Section IV shall not be available for subsequent option grant under
the Plan.

ARTICLE FIVE

MISCELLANEOUS

     I. AMENDMENT OF THE PLAN

          The Board shall have complete and exclusive power and authority to amend or modify the Plan in
any or all respects whatsoever. However, no such amendment or modification shall, without the
consent of the holders, adversely affect rights and obligations with respect to options at the time
outstanding under the Plan. In addition, certain amendments may require stockholder approval
pursuant to applicable laws or regulations.

     II. TAX WITHHOLDING

          A. The Company’s obligation to deliver shares or cash upon the exercise of stock options or
stock appreciation rights or upon the grant or vesting of direct stock issuances under the Plan
shall be subject to the satisfaction of all applicable Federal, State and local income and
employment tax withholding requirements.

          B. The Plan Administrator may, in its discretion and upon such terms and conditions as it may
deem appropriate, provide any or all holders of outstanding options or stock issuances under the
Plan (other than the automatic option grants under Article Four) with the election to have the
Company withhold, from the shares of Common Stock otherwise issuable upon the exercise or vesting
of such awards, a whole number of such shares with an aggregate fair market value equal to the
minimum amount necessary to satisfy the Federal, State and local income and employment tax
withholdings (the “Taxes”) incurred in connection with the

20

 

acquisition or vesting of such shares. In lieu of such direct withholding, one or more
participants may also be granted the right to deliver whole shares of Common Stock to the Company
in satisfaction of such Taxes. Any withheld or delivered shares shall be valued at their fair
market value on the applicable determination date for such Taxes.

     III. EFFECTIVE DATE AND TERM OF PLAN

          A. The Plan, as amended and restated, shall be effective on the date specified in the Board of
Directors resolution adopting the Plan. Except as provided below, each option issued and
outstanding under the Plan immediately prior to such effective date shall continue to be governed
solely by the terms and conditions of the agreement evidencing such grant, and nothing in this
restatement of the Plan shall be deemed to affect or otherwise modify the rights or obligations of
the holders of such options with respect to their acquisition of shares of Common Stock thereunder.
The Plan Administrator shall, however, have full power and authority, under such circumstances as
the Plan Administrator may deem appropriate (but in accordance with Section I of this Article
Five), to extend one or more features of this amendment and restatement to any options outstanding
on the effective date.

          B. Unless sooner terminated in accordance with the other provisions of this Plan, the Plan
shall terminate upon the earlier of (i) March 6, 2016 or (ii) the date on which all shares
available for issuance under the Plan shall have been issued or cancelled pursuant to the exercise,
surrender or cash-out of the options granted hereunder. If the date of termination is determined
under clause (i) above, then any options or stock issuances outstanding on such date shall continue
to have force and effect in accordance with the provisions of the agreements evidencing those
awards.

          C. Options may be granted with respect to a number of shares of Common Stock in excess of the
number of shares at the time available for issuance under the Plan, provided each granted
option is not to become exercisable, in whole or in part, at any time prior to stockholder approval
of an amendment authorizing a sufficient increase in the number of shares issuable under the Plan.

     IV. USE OF PROCEEDS

          Any cash proceeds received by the Company from the sale of shares pursuant to options or stock
issuances granted under the Plan shall be used for general corporate purposes.

     V. REGULATORY APPROVALS

          A. The implementation of the Plan, the granting of any option hereunder, and the issuance of
stock (i) upon the exercise or surrender of any option or (ii) under the Stock Issuance Program
shall be subject to the procurement by the Company of all approvals and permits required by
regulatory authorities having jurisdiction over the Plan, the options granted under it and the
stock issued pursuant to it.

          B. No shares of Common Stock or other assets shall be issued or delivered under the Plan
unless and until there shall have been compliance with all applicable requirements of Federal and
state securities laws, including (to the extent required) the filing and effectiveness

21

 

of the Form S-8 registration statement for the shares of Common Stock issuable under the Plan,
and all applicable listing requirements of any stock exchange (or the Nasdaq National Market, the
Nasdaq Global Select Market or any successor system, if applicable) on which Common Stock is then
trading.

     VI. NO EMPLOYMENT/SERVICE RIGHTS

          Neither the action of the Company in establishing or restating the Plan, nor any action taken
by the Plan Administrator hereunder, nor any provision of the Plan shall be construed so as to
grant any individual the right to remain in the employ or service of the Company (or any parent or
subsidiary corporation) for any period of specific duration, and the Company (or any parent or
subsidiary corporation retaining the services of such individual) may terminate such individual’s
employment or service at any time and for any reason, with or without cause.

     VII. MISCELLANEOUS PROVISIONS

          A. Except to the extent otherwise expressly provided in the Plan, the right to acquire Common
Stock or other assets under the Plan may not be assigned, encumbered or otherwise transferred by
any participant.

          B. The provisions of the Plan relating to the exercise of options and the issuance and/or
vesting of shares shall be governed by the laws of the State of Alabama without resort to that
state’s conflict-of-laws provisions, as such laws are applied to contracts entered into and
performed in such State.

22Exhibit 4.1

Exhibit 4.1

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF
1933, AS AMENDED (THE “ACT”), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AND PURSUANT TO THE
PROVISIONS OF ARTICLE 5 BELOW, MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR
HYPOTHECATED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND APPLICABLE STATE SECURITIES LAW OR, IN
THE OPINION OF LEGAL COUNSEL IN FORM AND SUBSTANCE SATISFACTORY TO THE ISSUER OF THESE SECURITIES,
SUCH OFFER, SALE OR TRANSFER, PLEDGE OR HYPOTHECATION IS EXEMPT FROM REGISTRATION.

WARRANT TO PURCHASE STOCK

Company: Alimera Sciences, Inc., a Delaware corporation

Number of Shares: As set forth below

Class of Stock: Common Stock, $0.01 par value per share

Warrant Price: $11.00 per share, subject to adjustment

Issue Date: May 16, 2011

Expiration Date: May 16, 2021

			
	Credit Facility:	 	This Warrant is issued in connection with that certain
First Loan Modification Agreement of even date herewith
among Midcap Funding III, LLC, Silicon Valley Bank, and
the Company, which amends certain provisions of that
certain Loan and Security Agreement, dated as of October
14, 2010, among Midcap Funding III, LLC, Silicon Valley
Bank, and the Company (as amended and in effect from time
to time, the “Loan Agreement”).

THIS WARRANT CERTIFIES THAT, for good and valuable consideration, MIDCAP FUNDING III, LLC
(Midcap Funding III, LLC, together with any successor or permitted assignee or transferee of this
Warrant or of any shares issued upon exercise hereof, is referred to hereinafter as “Holder”) is
entitled to purchase the number of fully paid and non-assessable shares (the “Shares”) of the
above-stated Class of Stock (the “Class”) of the above-named company (the “Company”) at the
above-stated Warrant Price per Share, all as set forth above and as adjusted pursuant to Article 2
of this Warrant, subject to the provisions and upon the terms and conditions set forth in this
Warrant.

A. Number of Shares. If, but only if, the balance of the Term B Loan (as defined in the
Loan Agreement) is advanced pursuant to the Loan Agreement by Holder (or its affiliate) to the
Company, then, upon such advance, this Warrant automatically shall become exercisable for such
number of Shares as shall equal (a) 199,500, divided by (b) the Warrant Price in effect on and as
of the date of such advance, and subject to adjustment thereafter from time to time in accordance
with the provisions of this Warrant..

 

 

 

ARTICLE 1. EXERCISE.

1.1 Method of Exercise. Holder may exercise this Warrant by delivering the original
of this Warrant together with a duly executed Notice of Exercise in substantially the form attached
as Appendix 1 to the principal office of the Company. Unless Holder is exercising the conversion
right set forth in Article 1.2, Holder shall also deliver to the Company a check, wire transfer (to
an account designated by the Company), or other form of payment acceptable to the Company for the
aggregate Warrant Price for the Shares being purchased.

1.2 Conversion Right. In lieu of exercising this Warrant as specified in Article 1.1,
Holder may from time to time convert this Warrant, in whole or in part, into a number of Shares
determined by dividing (a) the aggregate fair market value of the Shares or other securities
otherwise issuable upon exercise of this Warrant minus the aggregate Warrant Price of such Shares
by (b) the fair market value of one Share. The fair market value of the Shares shall be determined
pursuant to Article 1.3.

1.3 Fair Market Value. If shares of the Class are then publicly listed or quoted on
one or more securities exchanges, inter-dealer quotation systems or over-the-counter markets, the
fair market value of a Share shall be the closing price of a share of the Class reported on the
principal such exchange, system or market for the business day immediately before Holder delivers
this Warrant together with its Notice of Exercise to the Company. If shares of the Class are not
then publicly listed or quoted on one or more securities exchanges, inter-dealer quotation systems
or over-the-counter markets, then the Board of Directors of the Company shall determine the fair
market value of a Share in its reasonable good faith judgment.

1.4 Delivery of Certificate and New Warrant. Promptly after Holder exercises or
converts this Warrant and, if applicable, the Company receives payment of the aggregate Warrant
Price, the Company shall deliver to Holder certificates for the Shares acquired and, if this
Warrant has not been fully exercised or converted and has not expired, a new warrant of like tenor
representing the Shares not so acquired.

1.5 Replacement of Warrants. On receipt of evidence reasonably satisfactory to the
Company of the loss, theft, destruction or mutilation of this Warrant and, in the case of loss,
theft or destruction, on delivery of an indemnity agreement reasonably satisfactory in form and
amount to the Company or, in the case of mutilation, on surrender and cancellation of this Warrant,
the Company shall execute and deliver, in lieu of this Warrant, a new warrant of like tenor.

1.6 Treatment of Warrant Upon Acquisition of Company.

1.6.1 “Acquisition”. For the purpose of this Warrant, “Acquisition” means any sale,
exclusive license, or other disposition of all or substantially all of the assets of the Company,
or any reorganization, consolidation, merger or sale of outstanding equity securities of the
Company where the holders of the Company’s outstanding voting equity securities as of immediately
before the transaction beneficially own less than a majority of the outstanding voting equity
securities of the surviving or successor entity as of immediately after the transaction.

 

2

 

1.6.2 Treatment of Warrant at
Acquisition.

A) Upon the written request of the Company, Holder agrees that, in the event of an Acquisition in
which the sole consideration is cash, either (a) Holder shall exercise its conversion or purchase
right under this Warrant and such exercise will be deemed effective immediately prior to the
consummation of such Acquisition or (b) if Holder elects not to exercise the Warrant, this Warrant
will expire upon the consummation of such Acquisition. The Company shall provide the Holder with
written notice of its request relating to the foregoing (together with such reasonable information
as the Holder may request in connection with such contemplated Acquisition giving rise to such
notice), which is to be delivered to Holder not less than ten (10) days prior to the closing of the
proposed Acquisition.

B) Upon the written request of the Company, Holder agrees that, in the event of an Acquisition that
is an “arms length” sale of all or substantially all of the Company’s assets (and only its assets)
to a third party that is not an Affiliate (as defined below) of the Company (a “True Asset Sale”),
either (a) Holder shall exercise its conversion or purchase right under this Warrant and such
exercise will be deemed effective immediately prior to the consummation of such Acquisition or (b)
if Holder elects not to exercise the Warrant, this Warrant will continue until the Expiration Date
if the Company continues as a going concern following the closing of any such True Asset Sale. The
Company shall provide the Holder with written notice of its request relating to the foregoing
(together with such reasonable information as the Holder may request in connection with such
contemplated Acquisition giving rise to such notice), which is to be delivered to Holder not less
than ten (10) days prior to the closing of the proposed Acquisition.

C) Upon the closing of any Acquisition other than those particularly described in subsections (A)
and (B) above, the successor entity shall assume the obligations of this Warrant, and this Warrant
shall be exercisable for the same securities, cash, and property as would be payable for the Shares
issuable upon exercise of the unexercised portion of this Warrant as if such Shares were
outstanding on the record date for the Acquisition and subsequent closing. The Warrant Price and/or
number of Shares shall be adjusted accordingly.

As used in this Article 1.6, “Affiliate” shall mean any person or entity that owns or
controls directly or indirectly ten percent (10%) or more of the stock of Company, any person or
entity that controls or is controlled by or is under common control with such persons or entities,
and each of such person’s or entity’s officers, directors, joint venturers or partners, as
applicable.

ARTICLE 2. ADJUSTMENTS TO THE SHARES.

2.1 Stock Dividends, Splits, Etc. If the Company declares or pays a dividend on the
outstanding shares of the Class payable in common stock or other securities, then upon exercise of
this Warrant, for each Share acquired, Holder shall receive, without cost to Holder, the total
number and kind of securities to which Holder would have been entitled had Holder owned the Shares
of record as of the date the dividend occurred. If the Company subdivides the outstanding shares
of the Class by reclassification or otherwise into a greater number of shares, the number of Shares
purchasable hereunder shall be proportionately increased and the Warrant Price shall be
proportionately decreased. If the outstanding shares of the Class are combined or consolidated, by
reclassification or otherwise, into a lesser number of shares, the Warrant Price shall be proportionately increased and the number of Shares shall be
proportionately decreased.

 

3

 

2.2 Reclassification, Exchange, Combinations or Substitution. Upon any
reclassification, exchange, substitution, recapitalization, reorganization or other event affecting
the outstanding shares of the Class, Holder shall be entitled to receive, upon exercise or
conversion of this Warrant, the number and kind of securities and property that Holder would have
received for the Shares if this Warrant had been exercised in full immediately before such
reclassification, exchange, substitution, recapitalization, reorganization or other event, at an
aggregate Warrant Price not exceeding the aggregate Warrant Price in effect as of immediately prior
thereto. The Company or its successor shall promptly issue to Holder a certificate pursuant to
Article 2.6 hereof setting forth the number, class and series or other designation of such new
securities or other property issuable upon exercise or conversion of this Warrant as a result of
such reclassification, exchange, substitution, recapitalization, reorganization or other event.
The provisions of this Article 2.2 shall similarly apply to successive reclassifications,
exchanges, substitutions, recapitalizations, reorganizations and other events.

2.3 [Intentionally Omitted].

2.4 No Impairment. The Company shall not, by amendment of its Certificate of
Incorporation or through a reorganization, transfer of assets, consolidation, merger, dissolution,
issue, or sale of securities or any other voluntary action, avoid or seek to avoid the observance
or performance of any of the terms to be observed or performed under this Warrant by the Company,
but shall at all times in good faith assist in carrying out of all the provisions of this Article 2
and in taking all such action as may be necessary or appropriate to protect Holder’s rights under
this Article against impairment. For the avoidance of doubt, an amendment of the Company’s
Certificate of Incorporation that does not impact the rights of the Holder to be granted upon
exercise of this Warrant in a manner differently than the rights of all other holders of the Class
in their capacity as such shall not be deemed an impairment for the purposes of this Warrant.

2.5 Fractional Shares. No fractional Shares shall be issuable upon exercise or
conversion of the Warrant and the number of Shares to be issued shall be rounded down to the
nearest whole Share. If a fractional share interest arises upon any exercise or conversion of the
Warrant, the Company shall eliminate such fractional share interest by paying Holder the amount
computed by multiplying the fractional interest by the fair market value of a full Share.

2.6 Certificate as to Adjustments. Upon each adjustment of the Warrant Price, Class
and/or number of Shares, the Company shall promptly notify Holder in writing, and, at the Company’s
expense, promptly compute such adjustment, and furnish Holder with a certificate of its Chief
Financial Officer setting forth such adjustment and the facts upon which such adjustment is based.
The Company shall, upon written request, furnish Holder a certificate setting forth the Warrant
Price, Class and number of Shares in effect upon the date thereof and the series of adjustments
leading to such Warrant Price, Class and number of Shares.

 

4

 

ARTICLE 3. REPRESENTATIONS AND COVENANTS OF THE COMPANY.

3.1 Representations and Warranties. The Company represents and warrants to, and
agrees with, the Holder as follows:

(a) All Shares which may be issued upon the exercise of the purchase right represented by this
Warrant shall, upon issuance, be duly authorized, validly issued, fully paid and non-assessable,
and free of any liens and encumbrances except for restrictions on transfer provided for herein or
under applicable federal and state securities laws.

3.2 Notice of Certain Events. If the Company proposes at any time (a) to declare any
dividend or distribution upon the outstanding shares of the Class, whether in cash, property,
stock, or other securities and whether or not a regular cash dividend; (b) to offer for
subscription or sale pro rata to the holders of the outstanding shares of the Class any additional
shares of any class or series of the Company’s stock; (c) to effect any reclassification,
reorganization or recapitalization of the shares of the Class; (d) to effect an Acquisition or to
liquidate, dissolve or wind up; or (e) offer holders of registration rights the opportunity to
participate in an underwritten public offering of the Company’s securities for cash, then, in
connection with each such event, the Company shall give Holder: (1) at least 10 days prior written
notice of the date on which a record will be taken for such dividend, distribution, or subscription
rights (and specifying the date on which the holders of shares of the Class will be entitled
thereto) or for determining rights to vote, if any, in respect of the matters referred to in (c)
and (d) above; (2) in the case of the matters referred to in (c) and (d) above at least 10 days
prior written notice of the date when the same will take place (and specifying the date on which
the holders of shares of the Class will be entitled to exchange their shares for the securities or
other property deliverable upon the occurrence of such event); and (3) in the case of the matter
referred to in (e) above, the same notice as is given to the holders of such registration rights.

3.3 Registration Under Securities Act of 1933, as amended. The Company agrees that
the Shares shall have the same incidental, or “Piggyback,” and S-3 registration rights that the
holders of registrable securities have under the Company’s Investor Rights Agreement. The
provisions set forth in the Company’s Investor Rights Agreement relating to the above in effect as
of the Issue Date may not be amended, modified or waived without the prior written consent of
Holder unless such amendment, modification or waiver affects the rights associated with the Shares
in the same manner as such amendment, modification, or waiver affects the rights associated with
all other registrable securities under such Agreement.

3.4 No Shareholder Rights. Except as provided in this Warrant, Holder will not have
any rights as a shareholder of the Company until the exercise of this Warrant.

3.5 Certain Information. Subject to the provisions of Section 12.9 of the Loan
Agreement, the Company agrees to provide Holder at any time and from time to time with such
information as Holder may reasonably request for purposes of Holder’s compliance with regulatory,
accounting and reporting requirements applicable to Holder.

 

5

 

ARTICLE 4. REPRESENTATIONS, WARRANTIES OF THE HOLDER. The Holder represents and warrants
to the Company as follows:

4.1 Purchase for Own Account. This Warrant and the securities to be acquired upon
exercise of this Warrant by Holder will be acquired for investment for Holder’s account, not as a
nominee or agent, and not with a view to the public resale or distribution within the meaning of
the Act. Holder also represents that it has not been formed for the specific purpose of acquiring
this Warrant or the Shares.

4.2 Disclosure of Information. Holder has received or has had full access to all the
information it considers necessary or appropriate to make an informed investment decision with
respect to the acquisition of this Warrant and its underlying securities. Holder further has had
an opportunity to ask questions and receive answers from the Company regarding the terms and
conditions of the offering of this Warrant and its underlying securities and to obtain additional
information (to the extent the Company possessed such information or could acquire it without
unreasonable effort or expense) necessary to verify any information furnished to Holder or to which
Holder has access.

4.3 Investment Experience. Holder understands that the purchase of this Warrant and
its underlying securities involves substantial risk. Holder has experience as an investor in
securities of companies in the development stage and acknowledges that Holder can bear the economic
risk of such Holder’s investment in this Warrant and its underlying securities and has such
knowledge and experience in financial or business matters that Holder is capable of evaluating the
merits and risks of its investment in this Warrant and its underlying securities and/or has a
preexisting personal or business relationship with the Company and certain of its officers,
directors or controlling persons of a nature and duration that enables Holder to be aware of the
character, business acumen and financial circumstances of such persons.

4.4 Accredited Investor Status. Holder is an “accredited investor” within the meaning
of Regulation D promulgated under the Act.

4.5 The Act. Holder understands that this Warrant and the Shares issuable upon
exercise or conversion hereof have not been registered under the Act in reliance upon a specific
exemption therefrom, which exemption depends upon, among other things, the bona fide nature of the
Holder’s investment intent as expressed herein. Holder understands that this Warrant and the
Shares issued upon any exercise or conversion hereof must be held indefinitely unless subsequently
registered under the Act and qualified under applicable state securities laws, or unless exemption
from such registration and qualification are otherwise available.

ARTICLE 5. MISCELLANEOUS.

5.1 Term: This Warrant is exercisable in whole or in part at any time and from time
to time on or before the Expiration Date. 

 

6

 

5.2 Legends. This Warrant and the Shares shall be imprinted with a legend in
substantially the following form:

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED
UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR THE SECURITIES LAWS OF ANY STATE
AND, EXCEPT AND PURSUANT TO THE PROVISIONS OF ARTICLE 5 OF THAT CERTAIN WARRANT TO
PURCHASE STOCK ISSUED BY THE COMPANY TO MIDCAP FUNDING III, LLC DATED
AS OF MAY___, 2011 MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED
OR HYPOTHECATED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND APPLICABLE
STATE SECURITIES LAW OR, IN THE OPINION OF LEGAL COUNSEL IN FORM AND
SUBSTANCE SATISFACTORY TO THE ISSUER OF THESE SECURITIES, SUCH OFFER, SALE
OR TRANSFER, PLEDGE OR HYPOTHECATION IS EXEMPT FROM REGISTRATION.

5.3 Compliance with Securities Laws on Transfer. This Warrant and/or the Shares
issued upon exercise or conversion of this Warrant may not be transferred or assigned in whole or
in part without compliance with applicable federal and state securities laws by the transferor and
the transferee (including, without limitation, the delivery of investment representation letters
and legal opinions reasonably satisfactory to the Company, as reasonably requested by the Company).
The Company shall not require Holder to provide an opinion of counsel if the transfer is to an
affiliate of Holder, provided that such affiliate is an “accredited investor” as defined in
Regulation D promulgated under the Act.

5.4 Transfer Procedure. Subject to the provisions of Article 5.3 and upon providing
the Company with written notice, Holder may transfer all or part of this Warrant or the Shares
issuable upon exercise of this Warrant to any transferee, provided, however, in connection with any
such transfer, Holder will give the Company notice of the portion of the Warrant being transferred
with the name, address and taxpayer identification number of the transferee and Holder will
surrender this Warrant to the Company for reissuance to the transferee(s) (and Holder if
applicable). The foregoing provisions of this Article 5.4 shall not apply to a public sale of any
Shares issued on exercise or conversion of this Warrant pursuant to the provisions of Rule 144
promulgated under the Act.

5.5 Notices. All notices and other communications from the Company to the Holder, or
vice versa, shall be deemed delivered and effective when given personally or mailed by first-class
registered or certified mail, postage prepaid (or on the first business day after transmission by
facsimile), at such address as may have been furnished to the Company or Holder, as the case may
be, in writing by the Company or such holder from time to time. All notices to Holder shall be
addressed as follows until the Company receives notice of a change of address in connection with a
transfer or otherwise:

Midcap Funding III, LLC

7735 Old Georgetown Road, Suite 400

Bethesda, Maryland 20814

Attention: Portfolio Management- Life Sciences

Telephone: 301-760-7600

Facsimile: 301-941-1450

 

7

 

Notice to the Company shall be addressed as follows until Holder receives notice of a change
in address:

Alimera Sciences, Inc.

Attn: Richard S. Eiswirth, Jr.

6120 Windward Parkway, Suite 290

Alpharetta, Georgia 30005

Telephone: 678-527-1750

Facsimile: 678-990-5744

5.6 Waiver. This Warrant and any term hereof may be changed, waived, discharged or
terminated only by an instrument in writing signed by the party against which enforcement of such
change, waiver, discharge or termination is sought.

5.7 Attorney’s Fees. In the event of any dispute between the parties concerning the
terms and provisions of this Warrant, the party prevailing in such dispute shall be entitled to
collect from the other party all costs incurred in such dispute, including reasonable attorneys’
fees.

5.8 Automatic Conversion upon Expiration. In the event that, upon the Expiration
Date, the fair market value of one Share (or other security issuable upon the exercise hereof) as
determined in accordance with Article 1.3 above is greater than the Warrant Price in effect on such
date, then this Warrant shall automatically be deemed on and as of such date to be converted
pursuant to Article 1.2 above as to all Shares (or such other securities) for which it shall not
previously have been exercised or converted, and the Company shall promptly deliver a certificate
representing the Shares (or such other securities) issued upon such conversion to Holder.

5.9 Counterparts. This Warrant may be executed in counterparts, all of which together
shall constitute one and the same agreement.

 

8

 

5.10 Governing Law. This Warrant shall be governed by and construed in accordance
with State of Delaware without giving effect to its principles regarding conflicts of law.

	 	 	 	 
	“COMPANY”	 
	 
	 	 	 
	By:

	 	/s/ Richard S. Eiswirth, Jr.	 
	 

	 	 	 
	Name:

	 	Richard S. Eiswirth, Jr.	 
	 

	 	(Print)	 
	Title:

	 	Chief Operating Officer and
Chief Financial Officer	 
	 
	 	 	 
	“HOLDER”	 
	 
	 	 	 
	MIDCAP FUNDING III, LLC	 
	 
	 	 	 
	By:
	 	/s/ Luis Viera	 
	 

	 	 	 
	Name:
	 	Luis Viera	 
	 

	 	 	 
	 

	 	(Print)	 
	Title:
	 	Managing Director	 

 

9

 

APPENDIX 1

NOTICE OF EXERCISE

1. Holder elects to purchase
 _____ 
shares of the Common Stock of Alimera Sciences, Inc.
pursuant to the terms of the attached Warrant, and tenders payment of the purchase price of the
shares in full.

[or]

1. Holder elects to convert the attached Warrant into Shares/cash [strike one] in the manner
specified in the Warrant. This conversion is exercised for
 _____ 
of the Shares
covered by the Warrant.

[Strike paragraph that does not apply.]

2. Please issue a certificate or certificates representing the Shares in the name specified
below:

	 	 	 	 	 
	 

	 	 

	 	 
	 

	 	Holders Name	 	 
	 
	 	 	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	 	 	 
	 

	 	     (Address)	 	 

3. By its execution below and for the benefit of the Company, Holder hereby restates each of
the representations and warranties in Article 4 of the Warrant as of the date hereof.

	 	 	 	 	 	 	 
	 	 	HOLDER:	 	 
	 
	 	 	 	 	 	 
	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	 	 	 

	 	 
	 

	 	Name:	 	 	 	 
	 

	 	 	 	 	 	 
	 

	 	Title:	 	 	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	(Date):	 	 	 	 
	 

	 	 	 	 	 	 

 

10

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