Registration Rights Agreement



 






Exhibit 10.3




AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT




     This Amended and Restated Registration Rights Agreement (this “Agreement”) dated as of
February 1, 2005, is by and among Triad Pharmaceuticals, Inc., a Delaware corporation (the
“Corporation”), the holders of capital stock of the Corporation that are parties to the
Original Registration Rights Agreement (as defined below) (the “Existing Stockholders”),
the “Purchasers” specified in the Series F Purchase Agreement (as defined below) (the
“Purchasers” and, collectively, with the Existing Stockholders, the “Investors”),
Tufts University, a Massachusetts not-for-profit corporation (“Tufts”), William Bachovchin
(“Bachovchin”) and Christopher Kiritsy (“Kiritsy”).



     WHEREAS, the Corporation, the Existing Stockholders, Tufts and Bachovchin are parties to a
Registration Rights Agreement dated as of September 8, 1999, as amended (the “Original
Registration Rights Agreement”);



     WHEREAS, Kiritsy has been granted, and may in the future be granted, one or more options to
purchase shares of common stock, par value $.001 per share (“Common Stock”), of the
Corporation;



     WHEREAS, concurrently herewith, the Corporation and the Purchasers are entering into a Series
F Preferred Stock Purchase Agreement of even date herewith (the “Series F Purchase
Agreement”), pursuant to which the Corporation has agreed to issue and sell to the Purchasers,
and the Purchasers have agreed to purchase from the Corporation, shares of Series F Preferred
Stock, $.10 par value per share, of the Corporation, on the terms and subject to the conditions
therein (such financing, the “Series F Financing”);



     WHEREAS, in connection with the Series F Financing, (i) the Corporation, (ii) Tufts, (iii)
Bachovchin, and (iv) the Existing Stockholders executing this Agreement, who collectively hold a
majority in voting power of the outstanding of shares of Registrable Securities (as defined by the
Original Registration Rights Agreement), acting in accordance with Section 20.2 of the Original
Registration Rights Agreement, hereby desire to amend and restate the Original Registration Rights
Agreement in its entirety as set forth herein;



     NOW, THEREFORE, in consideration of the mutual covenants contained herein, and for other
valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties
hereto hereby agree that the Original Registration Rights Agreement shall be, and hereby is,
amended and restated in its entirety as follows:



     1. Definitions. As used in this Agreement, the following terms shall have the
following meanings:



          1.1 The term “Exchange Act” means the Securities Exchange Act of 1934, as amended;



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          1.2 The term “Holder” means any Investor, Tufts, Bachovchin, Kiritsy and any other
person or entity holding Registrable Securities to whom the registration rights granted in this
Agreement have been transferred pursuant to Section 15 hereof;



          1.3 The term “Information” shall have the meaning set forth in Section 4.8;



          1.4 The term “Inspectors” shall have the meaning set forth in Section 4.8;



          1.5 The term “Investor Counsel” shall mean one counsel selected by a majority in
voting power of the selling Holders in each applicable registration;



          1.6 The term “Preferred Stock” means, collectively, the Series A Convertible Preferred
Stock, Series B Convertible Preferred Stock, Series C Convertible Preferred Stock, Series D
Convertible Preferred Stock, Series E Convertible Preferred Stock and Series F Convertible
Preferred Stock, $.10 par value per share, of the Corporation held by the Investors or their
transferees in accordance with this Agreement;



          1.7 The term “Records” shall have the meaning set forth in Section 4.8;



          1.8 The terms “register,” “registered,” and “registration” refer to a
registration effected by preparing and filing a registration statement in compliance with the
Securities Act and the declaration or ordering of effectiveness of such registration statement;



          1.9 The term “Registrable Securities” means: (1) the Common Stock issuable upon
conversion of the Preferred Stock; (2) Common Stock purchased by an Investor pursuant to Section 4
of the Stockholders Agreement (as defined below), or Common Stock for or into which New Securities
(as therein defined) purchased by the Investor pursuant to such Section 4 may be exercised,
exchanged or converted; (3) Common Stock held by Tufts; (4) Common Stock held by Bachovchin,
including Common Stock issued to Bachovchin pursuant to the exercise of stock options heretofore or
hereafter granted to Bachovchin; (5) Common Stock held by Kiritsy pursuant to the exercise of stock
options heretofore or hereafter granted to Kiritsy; and (6) any Common Stock of the Corporation
issued as a dividend or other distribution with respect to, or in exchange or in replacement of,
such Preferred Stock or Common Stock. Registrable Securities shall cease to be Registrable
Securities (i) when they have been sold pursuant to an effective registration statement under the
Securities Act or (ii) when they have been sold pursuant to Rule 144, promulgated under the
Securities Act;



          1.10 The term “SEC” means the Securities and Exchange Commission;



          1.11 The term “Securities Act” means the Securities Act of 1933, as amended; and



          1.12 The term “Stockholders Agreement” refers to that certain Stockholders Agreement
dated as of the date hereof by and among the Corporation, Bachovchin and certain other stockholders
of the Corporation.



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     In addition, for purposes of all calculations and notices hereunder, and of all provisions of
this Agreement, where the context permits, a holder of the Preferred Stock shall be deemed the
Holder of such securities and such securities shall be deemed outstanding Registrable Securities
hereunder. The foregoing notwithstanding, nothing in this Agreement shall require the Corporation
actually to register any shares of the Preferred Stock.



     2. Request for Registration. If at any time after the earlier of (i) one hundred
twenty (120) days after any registration statement covering a public offering of securities of the
Corporation under the Securities Act having become effective and (ii) the fourth anniversary of the
date of this Agreement, the Corporation shall receive a written request (specifying that it is
being made pursuant to this Section 2) from the Holder or Holders of at least twenty-five percent
(25%) of the then outstanding Registrable Securities (and, solely for purposes of calculating such
percentages (and not for any other purpose) any shares of Common Stock issued either to Bachovchin
or to Kiritsy pursuant to the exercise of stock options heretofore or hereafter granted either to
Bachovchin or to Kiritsy shall be excluded from the definition of Registrable Securities) that the
Corporation file a registration statement under the Securities Act, or a similar document pursuant
to any other statute then in effect corresponding to the Securities Act, covering the registration
of at least the lesser of (i) at least twenty-five percent (25%) of the then outstanding
Registrable Securities or (ii) the number of Registrable Securities having an aggregate expected
offering price to the public of at least $5,000,000, then the Corporation shall promptly notify all
other Holders of such request and shall use its best efforts to cause all Registrable Securities
that Holders have requested be registered to be registered under the Securities Act; provided, that
if the request hereunder is for an initial public offering, the reasonably anticipated aggregate
price to the public of such initial public offering, including all securities to be sold by the
Corporation and all shares of Registrable Stock as to which registration shall have been requested,
shall be greater than $10,000,000, and the managing underwriter (or co-managing underwriter) of
such offering shall be an underwriter with a national reputation for serving as managing
underwriter for initial public offerings selected by the Corporation and reasonably acceptable to a
majority of the Holders of the Registrable Securities being sold in such offering.



     Notwithstanding the foregoing: (a) the Corporation shall not be obligated to effect a
registration pursuant to this Section 2 during the period starting with the date sixty (60) days
prior to the Corporation’s estimated date of filing of, and ending on a date one hundred twenty
(120) days following the effective date of, a registration statement pertaining to an underwritten
public offering of securities for the account of the Corporation, provided that the Corporation is
actively employing in good faith its best efforts to cause such registration statement to become
effective and that the Corporation’s estimate of the date of filing such registration statement is
made in good faith; (b) the Corporation shall not be obligated to effect a registration pursuant to
this Section 2 one hundred twenty (120) days after the effective date of a prior registration
effected pursuant to this Section 2; (c) if the Corporation shall furnish to the Holders a
certificate signed by the President of the Corporation stating that in the good faith judgment of
the Board of Directors it would be seriously detrimental to the Corporation or its stockholders for
a registration statement to be filed in the near future, then the Corporation’s obligation to use
its best efforts to file a registration statement shall be deferred for a period not to exceed
three (3)



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months and (d) unless the Holders agree to bear the costs of any special audit, the
Corporation may postpone a registration pursuant to this Section 2 for such period of time as may
be necessary to permit the use of regular audited year end figures with supplemental short period
figures, provided that such postponement shall not exceed three (3) months, after which time the
Corporation shall bear the cost of any such special audit as may still be required.



     The Corporation shall not be obligated to effect more than three (3) registrations pursuant to
this Section 2. Any request for registration under this Section 2 must be for a firm commitment
underwritten public offering to be managed by an underwriter or underwriters of recognized national
standing selected by the Corporation and reasonably acceptable to a majority of the Holders of the
Registrable Securities being sold in such offering.



     At any time before a registration statement filed pursuant to this Section 2 becomes
effective, the Holders of a majority of Registrable Securities included in such registration
statement may request that the Corporation withdraw or not file such registration statement. In
that event, unless such request of withdrawal was caused by, or made in response to, a material
adverse effect or a similar event related to the business, properties, condition, operations or
prospects of the Corporation not known (without imputing the knowledge of any other person to such
Holders) by the Holders initiating such request at the time their request was made, or other
material facts not known to such Holders at the time their request was made, the Holders shall be
deemed to have used one of their registration rights under this Section 2; provided, that
the Holders shall not be deemed to have used one of their registration rights under this Section 2
if the Holders of the Registrable Securities included in such registration statement agree to
reimburse the Corporation for its reasonable out-of-pocket expenses in connection with such
withdrawn registration statement.



     3. Corporation Registration. Subject to Section 8 of this Agreement, if at any time,
or from time to time, the Corporation determines to register any of its Common Stock under the
Securities Act in connection with the public offering of such securities for its own account or for
the accounts of other stockholders, solely for cash on a form that would also permit the
registration of the Registrable Securities (other than on Form S-4, S-8 or any successor forms
thereto) the Corporation shall, each such time, promptly give each Holder written notice of such
determination. Upon the written request of any Holder given within thirty (30) days after mailing
of any such notice by the Corporation, the Corporation shall use, subject to the limitations set
forth in Section 8.1, its best efforts to cause to be registered under the Securities Act all of
the Registrable Securities that each such Holder has requested be registered. Notwithstanding the
foregoing, no such notice need be given of any determination by the Corporation to register any of
its Common Stock on Form S-3 (or any successor form thereto) under the Securities Act in connection
with any re-offering or re-sale of such securities by a stockholder who or which received such
securities in connection with any merger, acquisition, consolidation or similar transaction
involving the Corporation and the Corporation shall not be under any obligation hereunder to
include in any such registration the Registrable Securities of any Holder.



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     4. Obligations of the Corporation. Whenever required under Section 2, 3 or 11 to use
its best efforts to effect the registration of any Registrable Securities, the Corporation shall,
as expeditiously as reasonably possible:



          4.1 Use its best efforts to prepare and file with the SEC a registration statement on any form
for which the Corporation then qualifies or which counsel for the Corporation shall deem
appropriate and which form shall be available for the sale of the Registrable Securities to be
registered thereunder in accordance with the intended method of distribution thereof, and use its
best efforts to cause such filed registration statement to become and remain effective until all of
such Registrable Securities have been disposed of, provided, however, that in connection with any
proposed registration intended to permit an offering of securities from time to time (also known as
a “shelf registration”), except for such a registration pursuant to Section 11, the
Corporation shall in no event be obligated to cause any such registration to remain effective for
more than one hundred eighty (180) days;



          4.2 Furnish, at least five business days before filing a registration statement that registers
such Registrable Securities, to each selling Holder, to each underwriter, if any, of the
Registrable Securities covered by such registration statement and to the Investor Counsel
copies of such registration statement as proposed to be filed, and thereafter furnish to such
selling Holder, underwriter, if any, and Investor Counsel such number of copies of such
registration statement, each amendment and supplement thereto (in each case including all exhibits
thereto and documents incorporated by reference therein), the prospectus included in such
registration statement (including each preliminary prospectus), any amendment or supplement thereto
and such other documents as such selling Holder, underwriter or Investor Counsel may reasonably
request in order to facilitate the disposition of the Registrable Securities owned by such selling
Holder (it being understood that such five-business-day period need not apply to successive drafts
of the same document proposed to be filed so long as such successive drafts are supplied to the
Investors’ Counsel in advance of the proposed filing by a period of time that is customary and
reasonable under the circumstances);



          4.3 Prepare and file with the SEC such amendments and supplements to such registration
statement and the prospectus used in connection therewith as may be necessary to keep such
registration statement effective until all of such Registrable Securities have been disposed of
(subject to the limitation for shelf registrations in Section 4.1) and to comply with the
provisions of the Securities Act with respect to the sale or other disposition of such Registrable
Securities;



          4.4 Notify in writing the Investor Counsel (i) of the receipt by the Corporation of any
comments by the SEC with respect to such registration statement or prospectus or any amendment or
supplement thereto or any request by the SEC for the amending or supplementing thereof or for
additional information with respect thereto, (ii) of the receipt by the Corporation of any
notification with respect to the issuance by the SEC of any stop order suspending the effectiveness
of such registration statement or prospectus or any amendment or supplement thereto or the
initiation or threatening of any proceeding for that purpose and (iii) of the receipt



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by the Corporation of any notification with respect to the suspension of the qualification of
such Registrable Securities for sale in any jurisdiction or the initiation or threatening of any
proceeding for such purposes;



          4.5 Use its best efforts to register or qualify the Registrable Securities covered by such
registration statement under such other securities or blue sky laws of such domestic and foreign
jurisdictions as the selling Holders reasonably request and do any and all other acts and things
which may be reasonably necessary or advisable to enable the selling Holders to consummate the
disposition in such jurisdictions of the Registrable Securities owned by the selling Holders;
provided, however, that the Corporation will not be required to qualify generally
to do business, subject itself to general taxation or consent to general service of process in any
jurisdiction where it would not otherwise be required to do so but for this Section 4.5;



          4.6 Furnish to the selling Holders and the underwriters, if any, such number of copies of a
summary prospectus, if any, or other prospectus, including a preliminary prospectus, in conformity
with the requirements of the Securities Act, and such other documents as such selling Holders may
reasonably request in order to facilitate the public sale or other disposition of such Registrable
Securities;



          4.7 Notify the selling Holders, the underwriters, if any, and the Investor Counsel on a timely
basis at any time when, to the Corporation’s knowledge, a prospectus relating to such Registrable
Securities, including any documents incorporated by reference therein, includes an untrue statement
of a material fact or omits to state a material fact required to be stated therein or necessary to
make the statements therein not misleading in light of the circumstances then existing and, at the
request of the selling Holders prepare and furnish to such selling Holders a reasonable number of
copies of a supplement to or an amendment of such prospectus as may be necessary so that, as
thereafter delivered to the offerees of such shares, such prospectus shall not include an untrue
statement of a material fact or omit to state a material fact required to be stated therein or
necessary to make the statements therein not misleading in light of the circumstances then
existing;



          4.8 Make available upon reasonable notice and during normal business hours, for inspection by
any Holders selling any Registrable Securities hereunder, any underwriter participating in any
disposition pursuant to such registration statement and any attorney, accountant or other agent
retained by such Holder or underwriter (collectively, the “Inspectors”), all pertinent
financial and other records, pertinent documents and properties of the Corporation (collectively,
the “Records”), as shall be reasonably necessary to enable them to exercise their due
diligence responsibility, and cause the Corporation’s officers, directors and employees to supply
all information (together with the Records, the “Information”) reasonably requested by any
such Inspector in connection with such registration statement. Any of the Information which the
Corporation determines in good faith to be confidential, and of which determination the Inspectors
are so notified, shall not be disclosed by the Inspectors unless (i) the disclosure of such
Information is necessary to avoid or correct a material misstatement or omission in the
registration statement, (ii) the release of such Information is ordered pursuant to a subpoena or



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other order from a court or governmental agency or authority of competent jurisdiction, (iii)
such Information has been made generally available to the public through no breach of the
nondisclosure obligations of the Inspectors or their affiliates or (iv) such disclosure is required
to be made under applicable law. Each selling Holder of such Registrable Securities agrees that
Information obtained by it as a result of such inspections shall be deemed confidential and shall
not be used by it as the basis for any market transactions in the securities of the Corporation or
its affiliates unless and until such is made generally available to the public. Each selling Holder
of such Registrable Securities further agrees that it will, upon learning that disclosure of such
Information is sought in a court of competent jurisdiction, give notice to the Corporation and
allow the Corporation, at its expense, to undertake appropriate action to prevent disclosure of the
Information deemed confidential;



          4.9 Use its best efforts to obtain from its independent certified public accountants “cold
comfort” letters, addressed to each Holder and to each underwriter, in customary form and at
customary times and covering matters of the type customarily covered by cold comfort letters;



          4.10 Use its best efforts to obtain from its counsel an opinion or opinions, addressed to each
Holder and to each underwriter, in customary form and covering matters of the type customarily
covered by opinions in registered public offerings;



          4.11 Provide a transfer agent and registrar (which may be the same entity and which may be the
Corporation) for such Registrable Securities;



          4.12 Promptly following the effective date of any registration statement, issue to any
underwriter to which the selling Holders may sell Registrable Securities in such offering,
certificates evidencing such Registrable Securities;



          4.13 List such Registrable Securities on any national securities exchange on which any shares
of the Corporation’s common stock are listed or, if the Corporation’s common stock is not listed on
a national securities exchange, use its best efforts to qualify such Registrable Securities for
inclusion on NASDAQ;



          4.14 Otherwise use its best efforts to comply with all applicable rules and regulations of the
SEC and make available to its security-holders, as soon as reasonably practicable, earnings
statements covering a period of 12 months beginning within three months after the effective date of
the subject registration statement, which earnings statement shall satisfy the provisions of
Section 11(a) of the Securities Act; and



          4.15 Otherwise use its best efforts to take all other steps necessary to effect the
registration of such Registrable Securities contemplated hereby.



          Each Holder, upon receipt of any notice from the Corporation of any event of the kind
described in Section 4.7 hereof, shall forthwith discontinue disposition of the Registrable
Securities pursuant to the registration statement covering such Registrable Securities until such



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holder’s receipt of the copies of the supplemented or amended prospectus contemplated by
Section 4.7 hereof, and, if so directed by the Corporation, such holder shall deliver to the
Corporation all copies, other than permanent file copies then in such holder’s possession, of the
prospectus covering such Registrable Securities at the time of receipt of such notice.



     5. Furnish Information. It shall be a condition precedent to the obligations of the
Corporation to take any action pursuant to this Agreement that the Holders shall furnish to the
Corporation such information regarding them, the Registrable Securities held by them, and the
intended method of disposition of such securities as the Corporation shall reasonably request and
as shall be required in connection with the action to be taken by the Corporation.



     6. [Intentionally Omitted]



     7. Registration Expenses. All expenses incurred by the Corporation in connection with
the registration and disposition of Registrable Securities under Section 2, 3 and 11 of this
Agreement, including, without limitation, all registration and filing fees (including all expenses
incident to filing with the NASD), fees and expenses of complying with securities and blue sky
laws, fees and expenses incurred in connection with the listing of the Registrable Securities,
printing expenses, fees and expenses of the Corporation’s counsel and accountants (including the
expenses of any comfort letters or costs associated with the delivery by independent certified
public accountants of a comfort letter or comfort letters requested pursuant to Section 4.9
hereof), fees and expenses of any special experts retained by the Corporation in connection with
such registration and fees and expenses of one Investors’ Counsel shall be paid by the Corporation;
provided, however, that all underwriting fees, discounts and selling commissions
applicable to the Registrable Securities shall be borne by the holders selling such Registrable
Securities, in proportion to the number of Registrable Securities sold by each such Holder.



     8. Underwriting Requirements.



          8.1 In connection with any offering involving an underwriting of shares being issued by the
Corporation, the Corporation shall not be required to include any Registrable Securities in such
underwriting unless the Holders of such Registrable Securities accept the terms of the underwriting
as agreed upon between the Corporation and the underwriters selected by it, and then only in such
quantity as will not, in the reasonable opinion of the underwriters, jeopardize the success of the
offering by the Corporation. If the total amount of securities that all Holders request to be
included in an underwritten offering exceeds the amount of securities that the underwriters
reasonably believe compatible with the success of the offering, no other securities of any
stockholder who is not a Holder shall be included in such offering unless all securities which the
Holders have requested to be included are included, and the Corporation shall only be required to
include in the offering so many of the securities of the selling Holders as the underwriters
reasonably believe will not jeopardize the success of the offering (the securities so included to
be apportioned pro rata among the selling Holders according to the total amount of securities owned
by said selling Holders, or in such other proportions as shall mutually be agreed to by such
selling Holders). In the case of the third request to register



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Registrable Securities pursuant to Section 2 hereof, to the extent that 20% or more of the
Registrable Securities requested to be registered are excluded from an offering in accordance with
this Section 8.1, the Holders of Registrable Securities as a group shall have the right to one
additional registration pursuant to Section 2 hereof with respect to such Registrable Securities.



          8.2 With respect to any underwriting of shares, the Corporation shall have the right to
designate the managing underwriter or underwriters; provided, that with respect to an underwriting
of shares to be registered pursuant to a request Holders made in accordance with Section 2, the
designation of the managing underwriter or underwriters shall be subject to the consent of the
Holders of a majority of the Registrable Securities participating in such underwriting, which
consent shall not be unreasonably withheld or delayed.



     9. Delay of Registration. No Holder shall have any right to take any action to
restrain, enjoin, or otherwise delay any registration as the result of any controversy that might
arise with respect to the interpretation or implementation of this Agreement.



     10. Indemnification. In the event any Registrable Securities are included in a
registration statement under this Agreement:



          10.1 To the extent permitted by law, the Corporation will indemnify and hold harmless each
Holder requesting or joining in a registration, any underwriter (as defined in the Securities Act)
for it, and each person, if any, who controls such Holder or underwriter within the meaning of the
Securities Act, against any losses, claims, damages or liabilities, joint or several, to which they
may become subject under the Securities Act or otherwise, insofar as such losses, claims, damages
or liabilities (or actions in respect thereof) arise out of or are based on any untrue or alleged
untrue statement of any material fact contained in such registration statement, including, without
limitation, any preliminary prospectus or final prospectus contained therein or any amendments or
supplements thereto, or arise out of or are based upon the omission or alleged omission to state
therein a material fact required to be stated therein, or necessary to make the statements therein
not misleading or arise out of any violation by the Corporation of any rule or regulation
promulgated under the Securities Act applicable to the Corporation and relating to action or
inaction required of the Corporation in connection with any such registration; and will reimburse
each such Holder, such underwriter, or controlling person for any legal or other expenses
reasonably incurred by them in connection with investigating or defending any such loss, claim,
damage, liability, or action, provided, however, that the Corporation shall not be
liable in any such case for any such loss, claim, damage, liability or action to the extent that it
arises out of or is based upon an untrue statement or alleged untrue statement or omission or
alleged omission made in connection with such registration statement, preliminary prospectus, final
prospectus, or amendments or supplements thereto, in reliance upon and in conformity with written
information furnished expressly for use in connection with such registration by any such Holder,
underwriter or controlling person.



          10.2 To the extent permitted by law, each Holder requesting or joining in a registration will
indemnify and hold harmless the Corporation, each of its directors, each of its



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officers who has signed the registration statement, each person, if any, who controls the
Corporation within the meaning of the Securities Act, and any underwriter for the Corporation
(within the meaning of the Securities Act) against any losses, claims, damages or liabilities to
which the Corporation or any such director, officer, controlling person or underwriter may become
subject, under the Securities Act or otherwise, insofar as such losses, claims, damages or
liabilities (or actions in respect thereto) arise out of or are based upon any untrue statement or
alleged untrue statement of any material fact contained in such registration statement, including
any preliminary prospectus or final prospectus contained therein or any amendments or supplements
thereto, or arise out of or are based upon the omission or alleged omission to state therein a
material fact required to be stated therein or necessary to make the statements therein not
misleading, in each case to the extent, but only to the extent, that such untrue statement or
alleged untrue statement or omission or alleged omission was made in such registration statement,
preliminary prospectus or final prospectus, or amendments or supplements thereto, in reliance upon
and in conformity with written information furnished by such Holder expressly for use in connection
with such registration; and will reimburse the Corporation or any such director, officer,
controlling person or underwriter for any legal or other expenses reasonably incurred by them in
connection with investigating or defending any such loss, claim, damage, liability or action;
provided, however, that no Holder shall have any liability under this Section 10.2
in excess of the net proceeds actually received by such Holder in the relevant public offering.



          10.3 In case any action or proceeding (including any governmental investigation) shall be
instituted involving any person in respect of which indemnity may be sought pursuant to Section
10.1 or 10.2, such person (an “Indemnified Party”) shall promptly notify the person against
whom such indemnity may be sought (an “Indemnifying Party”) in writing and the Indemnifying
Party shall assume the defense thereof, including the employment of counsel reasonably satisfactory
to such Indemnified Party, and shall assume the payment of all fees and expenses, provided
that the failure of any Indemnified Party to so notify an Indemnifying Party of any such action or
proceeding shall relieve the Indemnifying Party from any liability in respect of such action or
proceeding that it may have to an Indemnified Party hereunder under this Section 10 to the extent
that such failure shall be materially prejudicial to the Indemnifying Party’s ability to defend
such action, but the failure of any Indemnified Party to so notify the Indemnifying party of such
action or proceeding will not relieve the Indemnifying Party of any liability that it may have to
the Indemnified Party otherwise than under this Section 10. In any such action or proceeding, any
Indemnified Party shall have the right to retain its own counsel, but the fees and expenses of such
counsel shall be at the expense of such Indemnified Party unless (i) the Indemnifying Party and the
Indemnified Party shall have mutually agreed to the retention of such counsel, (ii) the named
parties to any such proceeding (including any impleaded parties) include both the Indemnified Party
and the Indemnifying Party and representation of both parties by the same counsel would be
inappropriate due to actual or potential differing interests between them, or (iii) the Indemnified
Party shall have reasonably concluded that there may be one or more legal or equitable defenses
available to such Indemnified Party which are additional to or in conflict with those available to
the Indemnifying Party. It is understood that the Indemnifying Party shall not, in connection with
any proceeding or related proceedings in the same jurisdiction, be liable for the reasonable fees
and expenses of



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more than one separate firm of attorneys (in addition to any local counsel) at any time for
all such Indemnified Parties, and that all such fees and expenses shall be reimbursed as they are
incurred. In the case of any such separate firm for the Indemnified Parties, such firm shall be
designated in writing by the Indemnified Parties. The Indemnifying Party shall not be liable under
this Section 10 for any settlement of any loss, claim, damage, liability, action or proceeding
effected without its prior written consent (not to be unreasonably withheld), but if settled with
such consent (or such consent is unreasonably withheld), or if there be a final judgment for the
plaintiff, the Indemnifying Party shall indemnify and hold harmless such Indemnified Parties from
and against any loss or liability (to the extent stated above) by reason of such settlement or
judgment. Notwithstanding the foregoing sentence, if at any time an Indemnified Party shall have
requested an Indemnifying Party to reimburse the Indemnified Party for fees and expenses of counsel
as contemplated by the third sentence of this paragraph, the Indemnifying Party agrees that it
shall be liable for any settlement of any proceeding effected without its written consent if (i)
such settlement is entered into more than 45 business days after receipt by such Indemnifying Party
of the aforesaid request and (ii) such Indemnifying Party shall not have reimbursed the Indemnified
Party for such fees and expenses in accordance with such request prior to the date of such
settlement. No Indemnifying Party shall, without the prior written consent of the Indemnified
Party, effect any settlement of any pending or threatened action or proceeding in respect of which
any Indemnified Party is or could have been a party and indemnity could have been sought hereunder
by such Indemnified Party, unless such settlement includes an unconditional release of such
Indemnified Party from all liability arising out of such action or proceeding.



          10.4 If the indemnification provided for in this Section 10 is held by a court of competent
jurisdiction to be unavailable to an Indemnified Party or insufficient with respect to any loss,
claim, damage, liability or action referred to herein, other than as a result of the operation of
the provisos to Section 10.1 or 10.2, then the Indemnifying Party, in lieu of indemnifying such
Indemnified Party hereunder, shall contribute to the amounts paid or payable by such Indemnified
Party as a result of such loss, claim, damage, liability or action (i) as between the Corporation
and the selling Holders on the one hand and the underwriters of any registration of Registrable
Securities in connection with this Agreement, if any, on the other, in such proportion as is
appropriate to reflect the relative benefits received by the Corporation and the selling Holders on
the one hand and such underwriters on the other from the offering of the securities, or if such
allocation is not permitted by applicable law, in such proportion as is appropriate to reflect not
only the relative benefits but also the relative fault of the Corporation and the selling Holders
on the one hand and of such underwriters on the other in connection with the statements or
omissions which resulted in such losses, claims, damages or liabilities, as well as any other
relevant equitable considerations, and (ii) as between the Corporation on the one hand and each
selling Holder on the other, in such proportion as is appropriate to reflect the relative fault of
the Corporation and of each selling Holder in connection with such statements or omissions, as well
as any other relevant equitable considerations. The relative benefits received by the Corporation
and the selling Holders on the one hand and any underwriters on the other shall be deemed to be in
the same proportion as the total proceeds from the offering (net of underwriting discounts and
commissions but before deducting expenses) received by the



-11-









 







Corporation and the selling Holders bear to the total underwriting discounts and commissions
received by such underwriters, in each case as set forth in the table on the cover page of the
prospectus. The relative fault of the Corporation and the selling Holders on the one hand and of
any such underwriters on the other shall be determined by reference to, among other things, whether
the untrue or alleged untrue statement of a material fact or the omission or alleged omission to
state a material fact relates to information supplied by the Corporation and the selling Holders or
by such underwriters and the parties’ relative intent, knowledge, access to information and
opportunity to correct or prevent such statement or omission. The relative fault of the
Corporation on the one hand and of each selling Holder on the other shall be determined by
reference to, among other things, whether the untrue or alleged untrue statement of a material fact
or the omission or alleged omission to state a material fact relates to information supplied by
such party, and the parties’ relative intent, knowledge, access to information and opportunity to
correct or prevent such statement or omission.



          10.5 The Corporation and the selling Holders agree that it would not be just and equitable if
contribution pursuant to Section 10.4 and this Section 10.5 were determined by pro rata allocation
(even if any underwriters were treated as one entity for such purpose) or by any other method of
allocation which does not take account of the equitable considerations referred to in the
immediately preceding paragraph. The amount paid or payable by an Indemnified Party as a result of
the losses, claims, damages or liabilities referred to in the immediately preceding paragraph shall
be deemed to include, subject to the limitations set forth above, any legal or other expenses
reasonably incurred by such Indemnified Party in connection with investigating or defending any
such action or claim. Notwithstanding the provisions of Section 10.4 and this Section 10.5, no
underwriter shall be required to contribute any amount in excess of the amount by which the total
price at which the securities underwritten by it and distributed to the public were offered to the
public exceeds the amount of any damages which such underwriter has otherwise been required to pay
by reason of such untrue or alleged untrue statement or omission or alleged omission, and no Holder
shall be required to contribute any amount in excess of the amount by which the total price at
which the Registrable Securities of such Holder were offered to the public exceeds the amount of
any damages which such Holder has otherwise been required to pay by reason of such untrue or
alleged untrue statement or omission or alleged omission. No person guilty of fraudulent
misrepresentation (within the meaning of Section 11(f) of the Securities Act) shall be entitled to
contribution from any person who was not guilty of such fraudulent misrepresentation. A Holder’s
obligations to contribute pursuant to Section 10.4 and this Section 10.5 are several, and not
joint, in the same proportion as the proceeds of the offering received by such Holder bear to the
total proceeds of the offering received by all the Holders.



     11. Registrations on Forms S-3.



          11.1 If (i) the Corporation shall receive a written request (specifying that it is being made
pursuant to this Section 11.1) from the Holder or Holders of more than ten percent (10%) of the
then-outstanding Registrable Securities that the Corporation file a registration statement on Form
S-3 (or any successor form to Form S-3 regardless of its designation) for a public offering of
shares of the Registrable Securities (which may, at such Holder’s request, be



-12-









 







shelf registrations pursuant to Rule 415 (or any successor provision) promulgated under the
Securities Act) the reasonably anticipated aggregate price to the public of which would exceed
$1,000,000, and (ii) the Corporation is a registrant entitled to use Form S-3 to register such
shares, then the Corporation shall use its best efforts to cause such shares to be registered on
Form S-3 (or any successor form to Form S-3).



          11.2 Holders’ rights to registration under this Section 11 are in addition to, and not in lieu
of, their rights to registration under Sections 2 and 3 of this Agreement.



     12. Certain Limitations on Registration by Corporation. The Corporation shall be
entitled to include in any registration statement referred to in Section 2 , for sale in accordance
with the method of disposition specified by the requesting Holders, shares of Common Stock to be
sold by the Corporation for its own account, except as and to the extent that, in the opinion the
managing underwriter (if such method of disposition shall be an underwritten public offering), such
inclusion would materially and adversely affect the marketing of the Registrable Stock to be sold.
Except for registration statements on Form S-4, S-8 or any successor thereto, the Corporation will
not file with the Commission any other registration statement with respect to its Common Stock,
whether for its own account or that of other stockholders, from the date of receipt of a notice
from requesting Holders pursuant to Section 2 until the completion of the period of distribution of
the registration contemplated thereby; provided, however, that in no event shall
the Corporation be prohibited from filing with the Commission a registration statement for any
period greater than one hundred twenty (120) days; provided, further, however, that the Corporation
shall have no obligation to effect a registration pursuant to Section 2 during any of the periods
of time described in the second paragraph of Section 2.



     13. Reports Under Securities Exchange Act of 1934. With a view to making available to
the Holders the benefits of Rule 144 promulgated under the Securities Act and any other rule or
regulation of the SEC that may at any time permit a Holder to sell securities of the Corporation to
the public without registration, the Corporation agrees that while it has a class of equity
securities registered under the Exchange Act, it will use its best efforts to:



          13.1 make and keep public information available, as those terms are understood and defined in
Rule 144, at all times subsequent to ninety (90) days after the effective date of the first
registration statement under the Securities Act covering an underwritten public offering filed by
the Corporation;



          13.2 file with the SEC in a timely manner all reports and other documents required of the
Corporation under the Securities Act and the Exchange Act; and



          13.3 furnish to any Holder forthwith upon request a written statement by the Corporation that
it has complied with the reporting requirements of Rule 144 (at any time after ninety (90) days
after the effective date of said first registration statement filed by the Corporation), and the
Exchange Act (at any time after it has become subject to such reporting requirements), a copy of
the most recent annual or quarterly report of the Corporation, and such other reports and documents
so filed by the Corporation as may be reasonably requested in



-13-









 







availing any such holder to take advantage of any rule or regulation of the SEC permitting the
selling of any such securities without registration.



     14. Limitations in Connection with Future Grants of Registration Rights. Without the
prior written consent of the Holder or Holders of a majority of the then outstanding Registrable
Securities, the Corporation shall not grant rights to cause the Corporation to register any of its
securities to any person or entity senior to the rights of the Holders hereunder.



     15. Transfer of Registration Rights. The registration rights of any Holder (and of
any permitted transferee of any Holder or its permitted transferees) under this Agreement with
respect to any shares of Registrable Securities may be transferred to any transferee who acquires
(otherwise than in a registered public offering) Registrable Securities pursuant to, and is granted
registration rights under this Agreement in accordance with, the Stockholders Agreement entered
into among the parties on the date hereof; provided, however, that the Corporation
is given written notice by the Holder at the time of such transfer stating the name and address of
the transferee and identifying the securities with respect to which the rights under this Agreement
are being assigned and the transferee executes a written instrument, in form and substance
reasonably satisfactory to the Corporation, agreeing to be bound by this Agreement.



     16. Termination of Registration Rights. The registration rights of any Holder shall
terminate at the time that all of the Registrable Securities held by such Holder have been sold
pursuant to Rule 144 or are eligible for sale pursuant to Rule 144(k) promulgated under the
Securities Act.



     17. Mergers, Etc. The Corporation shall not, directly or indirectly, enter into any
merger, consolidation or reorganization in which the Corporation shall not be the surviving
corporation unless the proposed surviving corporation shall, prior to such merger, consolidation or
reorganization, agree in writing to assume the obligations of the Corporation under this Agreement,
and for that purpose references hereunder to “Registrable Securities” shall be deemed to be
references to the securities which the Holders would be entitled to receive in exchange for
Registrable Securities under any such merger, consolidation or reorganization; provided,
however, that the provisions of this Agreement shall not apply in the event of any merger,
consolidation or reorganization in which the Corporation is not the surviving corporation if the
Holders of Registrable Securities are entitled to receive in exchange therefor (i) cash, or (ii)
securities of the acquiring corporation which may be immediately sold to the public without any
limitation as to amount and without registration under the Securities Act.



     18. Stand-Off Agreement. Each Holder, if requested by the Corporation and the
managing underwriter of an offering by the Corporation of Common Stock or other securities of the
Corporation pursuant to a registration statement under the Securities Act, shall agree not to sell
publicly or otherwise transfer or dispose of any Registrable Securities or other securities of the
Corporation held by such Holder for a specified period of time (not to exceed 180 days) following
the effective date of such registration statement. The covenant contained in this



-14-









 







Section 18 is in addition to any market stand-off covenant contained in any other agreement
between the Corporation and any Holder.



     19. Notices. All notices, requests, consents and other communications hereunder to a
party shall be deemed to be sufficiently given if contained in a written instrument delivered in
person, sent via a reputable nationwide overnight courier services guaranteeing next business day
delivery, or duly sent by first class registered or certified mail, postage prepaid, addressed in
each case to such party at the address set forth below, the then-current address of a Holder
specified in the stock records of the Corporation or such other address as may hereafter be
designated in writing by such party to all other parties:



	 	 	 
	(a)

	 	if to the Corporation, to:
	 
	 	 
	

	 	Triad Pharmaceuticals, Inc
	

	 	71 Warwick Road
	

	 	Melrose, MA 02176
	

	 	Attention: President
	 
	 	 
	

	 	with a copy to:
	 
	 	 
	

	 	Peter M. Rosenblum, Esq.
	

	 	Foley Hoag llp
	

	 	Seaport World Trade Center West
	

	 	155 Seaport Blvd.
	

	 	Boston, MA 02210
	 
	 	 
	(b)

	 	if to Kos, to:
	 
	 	 
	

	 	Kos Pharmaceuticals, Inc
	

	 	Cedar Brook Corporate Center
	

	 	No. 1 Cedar Brook Drive
	

	 	Cranbury, NJ 08512
	

	 	Attention: President and Chief Executive Officer






-15-









 






	 	 	 
	

	 	with a copy to:
	 
	 	 
	

	 	Kos Pharmaceuticals, Inc
	

	 	Cedar Brook Corporate Center
	

	 	No. 1 Cedar Brook Drive
	

	 	Cranbury, NJ 08512
	

	 	Attention: Andrew I. Koven,
	

	 	Executive Vice President, General Counsel
	

	 	and Corporate Secretary
	 
	 	 
	

	 	and
	 
	 	 
	

	 	James Lurie, Esquire
	

	 	Holland & Knight, LLP
	

	 	195 Broadway, 24th Floor
	

	 	New York, NY 10007
	 
	 	 
	(c)

	 	if to Oikos, to:
	 
	 	 
	

	 	2004 Oikos Investment Partners, LP
	

	 	c/o Oikos Ventures, LLC
	

	 	Attn: Steven Aronoff
	

	 	499 Park Avenue
	

	 	New York, NY 10022
	 
	 	 
	

	 	with a copy to:
	 
	 	 
	

	 	Steven K. Aronoff, Esq.
	

	 	c/o Steven K. Aronoff PC
	

	 	499 Park Avenue
	

	 	New York, NY 10022
	 
	 	 
	(d)

	 	if to Tufts, to:
	 
	 	 
	

	 	Margaret Newell
	

	 	Vice Provost
	

	 	Tufts University
	

	 	136 Harrison Avenue
	

	 	Boston, MA 02111
	 
	 	 
	

	 	with a copy to:
	 
	 	 
	

	 	Office of University Counsel
	

	 	Tufts University
	

	 	Ballou Hall






-16-









 






	 	 	 
	

	 	Medford, MA 02155
	

	 	Attn: Senior Counsel
	 
	 	 
	(e)

	 	if to Bachovchin, to:
	 
	 	 
	

	 	William Bachovchin
	

	 	71 Warwick Road
	

	 	Melrose, MA 02176
	 
	 	 
	

	 	with a copy to:
	 
	 	 
	

	 	Peter M. Rosenblum, Esq.
	

	 	Foley Hoag llp
	

	 	Seaport World Trade Center West
	

	 	155 Seaport Blvd.
	

	 	Boston, MA 02210
	 
	 	 
	(f)

	 	if to Stone Life Sciences Holdings, Ltd, to:
	 
	 	 
	

	 	Stone Life Sciences Holdings, Ltd.
	

	 	3600 Torrey Pines Boulevard
	

	 	Sarasota, FL 34238
	 
	 	 
	

	 	with a copy to:
	 
	 	 
	

	 	Roten Law Firm Chartered
	

	 	Attn: Rex Roten, Esq.
	

	 	411 Clevand Street
	

	 	Box 242
	

	 	Clearwater, FL 33755
	 
	 	 
	(g)

	 	if to Kiritsy, to:
	 
	 	 
	

	 	Christopher P. Kiritsy
	

	 	2217 Columbus Boulevard
	

	 	Coral Gables, FL 33134
	 
	 	 
	

	 	with a copy to:
	 
	 	 
	

	 	Kim A. Hines, Esq.
	

	 	Steel Hector & Davis LLP
	

	 	1900 Phillips Point West
	

	 	777 South Flagler Drive
	

	 	West Palm Beach, Florida 33401-6198






-17-









 





     20. Miscellaneous.



          20.1 Entire Agreement; Effect on Prior Documents. The Agreement contains the entire
agreement of the parties concerning the subject matter hereof, and supersedes all prior
negotiations, commitments, agreements and understandings, written or oral, between or among them
concerning such subject matter.



          20.2 Amendments; Waivers. This Agreement may be amended, and compliance with any
provision of this Agreement may be omitted or waived, only by the written agreement of the
Corporation and the Holders of at least a majority in voting power of the then-outstanding
Registrable Securities and, if and to the extent that its rights are materially and adversely
affected, Tufts. Notwithstanding the foregoing, this Agreement may not be amended or terminated
and the observance of any term hereunder may not be waived with respect to any Holder without the
written consent of such Holder unless such amendment, termination or waiver applies to all Holders
in the same fashion. A waiver or omission on one occasion shall not constitute a waiver or
omission on any further occasion.



          20.3 Governing Law Consent to Jurisdiction and Venue; Waiver of Jury Trial. This
Agreement shall be governed by, and construed and enforced in accordance with, the substantive laws
of The Commonwealth of Massachusetts without regard to its principles of conflicts of laws. Any
litigation arising from or relating to this Agreement shall be filed and prosecuted in any court of
competent subject matter jurisdiction located in the state of New York. The parties stipulate to
the jurisdiction, convenience and efficiency of proceeding in such courts and hereby waive and
covenant not to assert any objections to proceeding in such courts based on any grounds other than
a lack of subject matter jurisdiction.



          20.4 Severability. Any provision of this Agreement that is prohibited or
unenforceable in any jurisdiction shall, as to such jurisdiction, be ineffective to the extent of
such prohibition or unenforceability without invalidating the remaining provisions hereof, and any
such prohibition or unenforceability in any jurisdiction shall not invalidate or render
unenforceable such provision in any other jurisdiction.



          20.5 Certain Matters of Construction. A reference to a Section shall mean a Section in
this Agreement unless otherwise expressly stated. The titles and headings herein are for reference
purposes only and shall not in any manner limit the construction of this Agreement which shall be
considered as a whole. The words “include,” “includes” and “including”
when used herein shall be deemed in each case to be followed by the words “without limitation.”
Whenever the context may require, any pronouns used herein shall include the corresponding
masculine, feminine or neuter forms, and the singular form of names and pronouns shall include the
plural and vice-versa.



          20.6 Counterparts. This Agreement may be executed in any number of counterparts
(including, in the case of the Purchasers, Purchaser Signature Pages (as defined in



-18-









 







the Series F Purchase Agreement)), each such counterpart shall be deemed to be an original
instrument, and all such counterparts shall together constitute but one agreement.



[Remainder of page intentionally left blank.]




-19-









 





     IN WITNESS WHEREOF, the parties have executed this Registration Rights Agreement as a contract
under seal as of the date first above written.


	 	 	 	 	 
	 	TRIAD PHARMACEUTICALS, INC.

 	 
	 	By:  	/s/William Bachovchin
 	 
	 	 	William Bachovchin 	 
	 	 	President 	 
	 





 









 





     IN WITNESS WHEREOF, the parties have executed this Registration Rights Agreement as a contract
under seal as of the date first above written.



	 	 	 
	 

	 	/s/ William Bachovchin
	

	 	

	

	 	William Bachovchin, in his personal capacity






 









 





     IN WITNESS WHEREOF, the parties have executed this Registration Rights Agreement as a contract
under seal as of the date first above written.



	 	 	 	 	 
	 	 	TUFTS UNIVERSITY
	 
	 	 	 	 
	

	 	By:
	 	/s/Steven S. Manos
	

	 	 	 	

	

	 	Name:
	 	Steven S. Manos
	

	 	 	 	

	

	 	Title:
	 	Executive Vice President
	

	 	 	 	







 









 





     IN WITNESS WHEREOF, the parties have executed this Registration Rights Agreement as a contract
under seal as of the date first above written.



	 	 	 	 	 
	 	 	KOS PHARMACEUTICALS, INC.
	 
	 	 	 	 
	

	 	By:
	 	/s/Adrian Adams
	

	 	 	 	

	

	 	Name:
	 	Adrian Adams
	

	 	 	 	

	

	 	 	 	Title: President & CEO
	

	 	 	 	







 









 





     IN WITNESS WHEREOF, the parties have executed this Registration Rights Agreement as a contract
under seal as of the date first above written.



	 	 	 	 	 
	 	 	STONE LIFE SCIENCES HOLDINGS, LTD.
	 
	 	 	 	 
	

	 	By:
	 	/s/Gerd Petrik
	

	 	 	 	

	

	 	Name:
	 	Gerd Petrik
	

	 	 	 	

	

	 	 	 	Title: President of Stone Management, Inc.
	

	 	 	 	

	

	 	 	 	General Partner
	

	 	 	 	







 









 





     IN WITNESS WHEREOF, the parties have executed this Registration Rights Agreement as a contract
under seal as of the date first above written.



	 	 	 
	 

	 	/s/Christopher Kiritsy
	

	 	

	

	 	Christopher Kiritsy






 









 






     IN WITNESS WHEREOF, the parties have executed this Registration Rights Agreement as a contract
under seal as of the date first above written.



	 	 	 	 	 
	 	 	2004 OIKOS INVESTMENT PARTNERS, LP
	 
	 	 	 	 
	

	 	By:
	 	/s/Steven K. Aronoff
	

	 	 	 	

	

	 	Name:
	 	Steven K. Aronoff
	

	 	 	 	

	

	 	Title:
	 	Manager of 500 East General
	

	 	 	 	

	

	 	 	 	Partners LLC General Partner