Document:

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Exhibit 4.1

WARRANT

THE SECURITIES EVIDENCED BY THIS WARRANT HAVE NOT BEEN REGISTERED UNDER THE U.S. SECURITIES ACT OF
1933, AS AMENDED (THE “SECURITIES ACT”), OR ANY OTHER APPLICABLE SECURITIES LAWS AND HAVE BEEN
ISSUED IN RELIANCE UPON AN EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF THE SECURITIES ACT AND
SUCH OTHER SECURITIES LAWS. NEITHER THIS SECURITY NOR ANY INTEREST OR PARTICIPATION HEREIN MAY BE
REOFFERED, SOLD, ASSIGNED, TRANSFERRED, PLEDGED, ENCUMBERED, HYPOTHECATED OR OTHERWISE DISPOSED OF,
EXCEPT PURSUANT TO AN EFFECTIVE REGISTRATION STATEMENT UNDER THE SECURITIES ACT OR PURSUANT TO A
TRANSACTION WHICH IS EXEMPT FROM, OR NOT SUBJECT TO, SUCH REGISTRATION, IN EACH CASE IN ACCORDANCE
WITH ALL APPLICABLE SECURITIES LAWS, AND IN THE CASE OF A TRANSACTION EXEMPT FROM, OR NOT SUBJECT
TO, SUCH REGISTRATION, UNLESS THE COMPANY HAS RECEIVED AN OPINION OF COUNSEL REASONABLY
SATISFACTORY TO IT THAT SUCH TRANSACTION DOES NOT REQUIRE REGISTRATION UNDER THE SECURITIES ACT AND
SUCH OTHER APPLICABLE LAWS.

FEBRUARY 3, 2006

     Warrant to Purchase up to 365,000 shares of Common Stock of Santarus, Inc. (the
“Company”).

     In consideration for Kingsbridge Capital Limited (the “Investor”) agreeing to enter into that
certain Common Stock Purchase Agreement, dated as of the date hereof, between the Investor and the
Company (the “Agreement”), the Company hereby agrees that the Investor or any other Warrant Holder
(as defined below) is entitled, on the terms and conditions set forth below, to purchase from the
Company at any time during the Exercise Period (as defined below) up to 365,000 fully paid and
nonassessable shares of common stock, par value $.0001 per share, of the Company (the “Common
Stock”) at the Exercise Price (hereinafter defined), as the same may be adjusted from time to time
pursuant to Section 6 hereof. The resale of the shares of Common Stock or other securities
issuable upon exercise or exchange of this Warrant is subject to the provisions of the Registration
Rights Agreement. Capitalized terms used herein and not otherwise defined shall have the meanings
given them in the Agreement.

     Section 1. Definitions.

     “Affiliate” shall mean any Person that, directly or indirectly through one or more
intermediaries, controls or is controlled by, or is under direct or indirect common control with
any other Person. For the purposes of this definition, “control,” when used with respect to any
Person, means the power to direct the management and policies of such Person, directly or
indirectly, whether through the ownership of voting securities, by contract or otherwise, and the
term “controls” and “controlled” have meanings correlative to the foregoing.

     “Closing Price” as of any particular day shall mean the closing price per share of the
Company’s Common Stock as reported by Bloomberg L.P. on such day.

     “Exercise Period” shall mean that period beginning six months after the date of this
Warrant and continuing until (i) the expiration of the five-year period thereafter, or (ii) a
Funding Default, subject in each case to earlier termination in accordance with Section 6 hereof.

     “Exercise Price” as of the date hereof shall mean eight dollars and twenty-eight and
thirty-six hundredths cents ($8.2836), representing 130% of the average Closing Price of the Common
Stock during the five (5) Trading Days immediately preceding the date of this Warrant.

 

 

     “Funding Default” shall mean a failure by Investor to accept a Draw Down Notice made
by the Company and to acquire and pay for the Shares in accordance therewith within three (3)
Trading Days following the delivery of such Shares to the Investor, provided such Draw Down Notice
was made in accordance with the terms and conditions of the Agreement (including the satisfaction
or waiver of the conditions to the obligation of the Investor to accept a Draw Down set forth in
Article VII of the Agreement), provided further, that such failure was reasonably within the
control of the Investor.

     “Per Share Warrant Value” shall mean the difference resulting from subtracting the
Exercise Price from the Closing Price on the Trading Day immediately preceding the Exercise Date.

     “Person” shall mean an individual, a corporation, a partnership, a limited liability
company, an association, a trust or other entity or organization, including a government or
political subdivision or an agency or instrumentality thereof.

     “Principal Market” shall mean the Nasdaq National Market, the Nasdaq SmallCap Market,
the American Stock Exchange or the New York Stock Exchange, whichever is at the time the principal
trading exchange or market for the Common Stock.

     “SEC” shall mean the United States Securities and Exchange Commission.

     “Trading Day” shall mean any day other than a Saturday or a Sunday on which the
Principal Market is open for trading in equity securities.

     “Warrant Holder” shall mean the Investor or any permitted assignee or permitted
transferee of all or any portion of this Warrant.

     “Warrant Shares” shall mean those shares of Common Stock received upon exercise of
this Warrant.

     Section 2. Exercise.

     (a) Method of Exercise. This Warrant may be exercised in whole or in part (but not as
to a fractional share of Common Stock), at any time and from time to time during the Exercise
Period, by the Warrant Holder by (i) surrender of this Warrant, with the form of exercise attached
hereto as Exhibit A completed and duly executed by the Warrant Holder (the “Exercise Notice”), to
the Company at the address set forth in Section 10.04 of the Agreement, accompanied by payment of
the Exercise Price multiplied by the number of shares of Common Stock for which this Warrant is
being exercised (the “Aggregate Exercise Price”) or (ii) telecopying an executed and
completed Exercise Notice to the Company and delivering to the Company within five (5) business
days thereafter the original Exercise Notice, this Warrant and the Aggregate Exercise Price. Each
date on which an Exercise Notice is received by the Company in accordance with clause (i) and each
date on which the Exercise Notice is telecopied to the Company in accordance with clause (ii) above
shall be deemed an “Exercise Date.”

     (b) Payment of Aggregate Exercise Price. Subject to paragraph (c) below, payment of
the Aggregate Exercise Price shall be made by wire transfer of immediately available funds to an
account designated by the Company. If the amount of the payment received by the Company is less
than the Aggregate Exercise Price, the Warrant Holder will be notified of the deficiency and shall
make payment in that amount within three (3) Trading Days. In the event the payment exceeds the
Aggregate Exercise Price, the Company will refund the excess to the Warrant Holder within five (5)
Trading Days of receipt.

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     (c) Cashless Exercise. In the event that the Warrant Shares to be received by the
Warrant Holder upon exercise of the Warrant may not be resold pursuant to an effective registration
statement or an exemption to the registration requirements of the Securities Act of 1933, as
amended, and applicable state laws, the Warrant Holder may, as an alternative to payment of the
Aggregate Exercise Price upon exercise in accordance with paragraph (b) above, elect to effect a
cashless exercise by so indicating on the Exercise Notice and including a calculation of the number
of shares of Common Stock to be issued upon such exercise in accordance with the terms hereof (a
“Cashless Exercise”). If a registration statement on Form S-1 under the Securities Act of
1933, as amended, or such other form as deemed appropriate by counsel to the Company for the
registration for the resale by the Warrant Holder of (x) the shares of Common Stock of the Company
that may be purchased under the Agreement, (y) the Warrant Shares, or (z) any securities issued or
issuable with respect to any of the foregoing by way of exchange, stock dividend or stock split or
in connection with a combination of shares, recapitalization, merger, consolidation or other
reorganization or otherwise, has been declared effective by the SEC and remains effective, the
Company may permit or require the Warrant Holder to effect a Cashless Exercise. In the event of a
Cashless Exercise, the Warrant Holder shall receive that number of shares of Common Stock
determined by (i) multiplying the number of Warrant Shares for which this Warrant is being
exercised by the Per Share Warrant Value and (ii) dividing the product by the Closing Price on the
Trading Day immediately preceding the Exercise Date, rounded to the nearest whole share. The
Company shall cancel the total number of Warrant Shares equal to the excess of the number of the
Warrant Shares for which this Warrant is being exercised over the number of Warrant Shares to be
received by the Warrant Holder pursuant to such Cashless Exercise.

     (d) Replacement Warrant. In the event that the Warrant is not exercised in full, the
number of Warrant Shares shall be reduced by the number of such Warrant Shares for which this
Warrant is exercised, and the Company, at its expense, shall forthwith issue and deliver to or upon
the order of the Warrant Holder a new Warrant of like tenor in the name of the Warrant Holder,
reflecting such adjusted number of Warrant Shares.

     Section 3. Ten Percent Limitation. The Warrant Holder may not exercise this Warrant
such that the number of Warrant Shares to be received pursuant to such exercise aggregated with all
other shares of Common Stock then owned by the Warrant Holder beneficially or deemed beneficially
owned by the Warrant Holder would result in the Warrant Holder owning more than 9.9% of all of such
Common Stock as would be outstanding on such Exercise Date, as determined in accordance with
Section 13(d) of the Exchange Act of 1934 and the rules and regulations promulgated thereunder.

     Section 4. Delivery of Warrant Shares.

     (a) Subject to the terms and conditions of this Warrant, as soon as practicable after the
exercise of this Warrant in full or in part, and in any event within ten (10) Trading Days
thereafter, the Company at its expense will cause to be issued in the name of and delivered to the
Warrant Holder, or as the Warrant Holder may lawfully direct, a certificate or certificates for,
or, to the extent the Warrant Shares are not restricted securities, make deposit with the
Depositary Trust Company via book-entry of, the number of validly issued, fully paid and
non-assessable Warrant Shares to which the Warrant Holder shall be entitled on such exercise,
together with any other stock or other securities or property (including cash, where applicable) to
which the Warrant Holder is entitled upon such exercise in accordance with the provisions hereof.

     (b) This Warrant may not be exercised as to fractional shares of Common Stock. In the event
that the exercise of this Warrant, in full or in part, would result in the issuance of any
fractional share of
Common Stock, then in such event the Warrant Holder shall receive the number of shares rounded
to the nearest whole share.

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     Section 5. Representations, Warranties and Covenants of the Company.

     (a) The Warrant Shares, when issued in accordance with the terms hereof, will be duly
authorized and, when paid for or issued in accordance with the terms hereof, shall be validly
issued, fully paid and non-assessable.

     (b) The Company shall take all commercially reasonable action and proceedings as may be
required and permitted by applicable law, rule and regulation for the legal and valid issuance of
this Warrant and the Warrant Shares to the Warrant Holder.

     (c) The Company has authorized and reserved for issuance to the Warrant Holder the requisite
number of shares of Common Stock to be issued pursuant to this Warrant. The Company shall at all
times reserve and keep available, solely for issuance and delivery as Warrant Shares hereunder,
such shares of Common Stock as shall from time to time be issuable as Warrant Shares.

     (d) From the date hereof through the last date on which this Warrant is exercisable, the
Company shall take all steps commercially reasonable to ensure that the Common Stock remains listed
or quoted on the Principal Market.

     Section 6. Adjustment of the Exercise Price. The Exercise Price and, accordingly, the
number of Warrant Shares issuable upon exercise of the Warrant, shall be subject to adjustment from
time to time upon the happening of certain events as follows:

     (a) Reclassification, Consolidation, Merger, Mandatory Share Exchange, Sale or Transfer.

          (i) Upon occurrence of any of the events specified in subsection (a)(ii) below (the
“Adjustment Events”) while this Warrant is unexpired and not exercised in full, the Warrant
Holder may in its sole discretion require the Company, or any successor or purchasing corporation,
as the case may be, without payment of any additional consideration therefor, to execute and
deliver to the Warrant Holder a new Warrant providing that the Warrant Holder shall have the right
to exercise such new Warrant (upon terms not less favorable to the Warrant Holder than those then
applicable to this Warrant) and to receive upon such exercise, in lieu of each share of Common
Stock theretofore issuable upon exercise of this Warrant, the kind and amount of shares of stock,
other securities, money or property receivable upon such Adjustment Event by the holder of one
share of Common Stock issuable upon exercise of this Warrant had this Warrant been exercised
immediately prior to such Adjustment Event. Such new Warrant shall provide for adjustments that
shall be as nearly equivalent as may be practicable to the adjustments provided for in this Section
6.

          (ii) The Adjustment Events shall be (1) any reclassification or change of Common Stock (other
than a change in par value, as a result of a subdivision or combination of Common Stock or in
connection with an Excluded Merger or Sale), (2) any consolidation, merger or mandatory share
exchange of the Company with or into another corporation (other than a merger or mandatory share
exchange with another corporation in which the Company is a continuing corporation and which does
not result in any reclassification or change other than a change in par value or as a result of a
subdivision or combination of Common Stock), other than (each of the following referred to as an
“Excluded Merger or Sale”) a transaction involving (A) sale of all or substantially all of
the assets of the Company, (B) any merger, consolidation or similar transaction where the
consideration payable to the shareholders of the Company by the acquiring Person consists
substantially of cash or publicly traded securities, or a
combination thereof, or where the acquiring Person does not agree to assume the obligations of
the Company under outstanding warrants (including this Warrant). In the event of an Excluded
Merger or Sale, if the surviving, successor or purchasing Person does not agree to assume the
obligations under this

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Warrant, then the Company shall deliver a notice to the Warrant Holder at
least 10 days before the consummation of such Excluded Merger or Sale, the Warrant Holder may
exercise this Warrant at any time before the consummation of such Excluded Merger or Sale (and such
exercise may be made contingent upon the consummation of such Excluded Merger or Sale), and any
portion of this Warrant that has not been exercised before consummation of such Excluded Merger or
Sale shall terminate and expire, and shall no longer be outstanding.

     (b) Subdivision or Combination of Shares. If the Company, at any time while this
Warrant is unexpired and not exercised in full, shall subdivide its Common Stock, the Exercise
Price shall be proportionately reduced as of the effective date of such subdivision, or, if the
Company shall take a record of holders of its Common Stock for the purpose of so subdividing, as of
such record date, whichever is earlier. If the Company, at any time while this Warrant is
unexpired and not exercised in full, shall combine its Common Stock, the Exercise Price shall be
proportionately increased as of the effective date of such combination, or, if the Company shall
take a record of holders of its Common Stock for the purpose of so combining, as of such record
date, whichever is earlier.

     (c) Stock Dividends. If the Company, at any time while this Warrant is unexpired and
not exercised in full, shall pay a dividend or other distribution in shares of Common Stock to all
holders of Common Stock, then the Exercise Price shall be adjusted, as of the date the Company
shall take a record of the holders of its Common Stock for the purpose of receiving such dividend
or other distribution (or if no such record is taken, as at the date of such payment or other
distribution), to that price determined by multiplying the Exercise Price in effect immediately
prior to such payment or other distribution by a fraction: (i) the numerator of which shall be the
total number of shares of Common Stock outstanding immediately prior to such dividend or
distribution, and (ii) the denominator of which shall be the total number of shares of Common Stock
outstanding immediately after such dividend or distribution. The provisions of this subsection (c)
shall not apply under any of the circumstances for which an adjustment is provided in subsections
(a) or (b).

     (d) Liquidating Dividends, Etc. If the Company, at any time while this Warrant is
unexpired and not exercised in full, makes a distribution of its assets or evidences of
indebtedness to the holders of its Common Stock as a dividend in liquidation or by way of return of
capital or other than as a dividend payable out of earnings or surplus legally available for
dividends under applicable law or any distribution to such holders made in respect of the sale of
all or substantially all of the Company’s assets (other than under the circumstances provided for
in the foregoing subsections (a) through (c)), then the Warrant Holder shall be entitled to receive
upon exercise of this Warrant in addition to the Warrant Shares receivable in connection therewith,
and without payment of any consideration other than the Exercise Price, the kind and amount of such
distribution per share of Common Stock multiplied by the number of Warrant Shares that, on the
record date for such distribution, are issuable upon such exercise of the Warrant (with no further
adjustment being made following any event which causes a subsequent adjustment in the number of
Warrant Shares issuable), and an appropriate provision therefor shall be made a part of any such
distribution. The value of a distribution that is paid in other than cash shall be determined in
good faith by the Board of Directors of the Company. Notwithstanding the foregoing, in the event
of a proposed dividend in liquidation or distribution to the shareholders made in respect of the
sale of all or substantially all of the Company’s assets, the Company shall deliver a notice to the
Warrant Holder at least 10 days before the consummation of such event, the Warrant Holder may
exercise this Warrant at any time before the consummation of such event (and such exercise may be
made contingent
upon the consummation of such event), and any portion of this Warrant that has not been
exercised before consummation of such event shall terminate and expire, and shall no longer be
outstanding.

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     Section 7. Notice of Adjustments. Whenever the Exercise Price or number of Warrant
Shares shall be adjusted pursuant to Section 6 hereof, the Company shall promptly prepare a
certificate signed by its Chief Executive Officer or Chief Financial Officer setting forth in
reasonable detail the event requiring the adjustment, the amount of the adjustment, the method by
which such adjustment was calculated (including a description of the basis on which the Company’s
Board of Directors made any determination hereunder), and the Exercise Price and number of Warrant
Shares purchasable at that Exercise Price after giving effect to such adjustment, and shall
promptly cause copies of such certificate to be sent by overnight courier to the Warrant Holder.

     Section 8. No Impairment. The Company will not, by amendment of its Amended and
Restated Certificate of Incorporation or Amended and Restated By-Laws or through any
reorganization, transfer of assets, consolidation, merger, dissolution or issue or sale of
securities, avoid or seek to avoid the observance or performance of any of the terms of this
Warrant, but will at all times in good faith assist in the carrying out of all such terms and in
the taking of all such action as may be necessary or appropriate in order to protect the rights of
the Warrant Holder against impairment. Without limiting the generality of the foregoing, the
Company (a) will not increase the par value of any Warrant Shares above the amount payable therefor
on such exercise, and (b) will take all such action as may be reasonably necessary or appropriate
in order that the Company may validly and legally issue fully paid and nonassessable Warrant Shares
on the exercise of this Warrant.

     Section 9. Rights As Stockholder. Except as set forth in Section 6 above, prior to
exercise of this Warrant, the Warrant Holder shall not be entitled to any rights as a stockholder
of the Company with respect to the Warrant Shares, including (without limitation) the right to vote
such shares, receive dividends or other distributions thereon or be notified of stockholder
meetings.

     Section 10. Replacement of Warrant. Upon receipt of evidence reasonably satisfactory
to the Company of the loss, theft, destruction or mutilation of the Warrant and, in the case of any
such loss, theft or destruction of the Warrant, upon delivery of an indemnity agreement or security
reasonably satisfactory in form and amount to the Company or, in the case of any such mutilation,
on surrender and cancellation of such Warrant, the Company at its expense will execute and deliver,
in lieu thereof, a new Warrant of like tenor.

     Section 11. Choice of Law. This Warrant shall be construed under the laws of the
State of New York.

     Section 12. Entire Agreement; Amendments. Except for any written instrument
concurrent or subsequent to the date hereof executed by the Company and the Investor, this Warrant
and the Agreement contain the entire understanding of the parties with respect to the matters
covered hereby and thereby. No provision of this Warrant may be waived or amended other than by a
written instrument signed by the party against whom enforcement of any such amendment or waiver is
sought.

     Section 13. Restricted Securities.

     (a) Registration or Exemption Required. This Warrant has been issued in a transaction
exempt from the registration requirements of the Securities Act of 1933, as amended, (the
“Securities Act”) in reliance upon the provisions of Section 4(2) thereof and Regulation D thereof,
and/or upon such other exemption from the registration requirements of the Securities Act as may be
available with respect to this
Warrant. This Warrant and the Warrant Shares issuable upon exercise of this Warrant may not
be resold except pursuant to an effective registration statement or an exemption to the
registration requirements of the Securities Act and applicable state laws. The Company shall have
no obligation to register the Warrant or the Warrant Shares except as explicitly set forth in that
certain Registration Rights Agreement entered into between Investor and Company on even date
hereof.

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     (b) Legend. Any replacement Warrants issued pursuant to Section 2 and Section 10
hereof and, unless a registration statement has been declared effective by the SEC in accordance
with the Securities Act of 1933, as amended, with respect thereto, any Warrant Shares issued upon
exercise hereof, shall bear the following legend:

“THE SECURITIES EVIDENCED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER
THE U.S. SECURITIES ACT OF 1933, AS AMENDED (THE “SECURITIES ACT”), OR ANY
OTHER APPLICABLE SECURITIES LAWS AND HAVE BEEN ISSUED IN RELIANCE UPON AN
EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF THE SECURITIES ACT AND SUCH
OTHER SECURITIES LAWS. NEITHER THIS SECURITY NOR ANY INTEREST OR
PARTICIPATION HEREIN MAY BE REOFFERED, SOLD, ASSIGNED, TRANSFERRED, PLEDGED,
ENCUMBERED, HYPOTHECATED OR OTHERWISE DISPOSED OF, EXCEPT PURSUANT TO AN
EFFECTIVE REGISTRATION STATEMENT UNDER THE SECURITIES ACT OR PURSUANT TO A
TRANSACTION WHICH IS EXEMPT FROM, OR NOT SUBJECT TO, SUCH REGISTRATION, IN
EACH CASE IN ACCORDANCE WITH ALL APPLICABLE SECURITIES LAWS, AND IN THE CASE
OF A TRANSACTION EXEMPT FROM, OR NOT SUBJECT TO, SUCH REGISTRATION, UNLESS
THE COMPANY HAS RECEIVED AN OPINION OF COUNSEL REASONABLY SATISFACTORY TO IT
THAT SUCH TRANSACTION DOES NOT REQUIRE REGISTRATION UNDER THE SECURITIES ACT
AND SUCH OTHER APPLICABLE LAWS.”

     (c) No Other Legend or Stock Transfer Restrictions. No legend other than the one
specified in Section 13(b) has been or shall be placed on the share certificates representing the
Warrant Shares and no instructions or “stop transfer orders” (so called “stock transfer
restrictions”) or other restrictions have been or shall be given to the Company’s transfer agent
with respect thereto other than as expressly set forth in this Section 13.

     (d) Assignment. Assuming the conditions of Section 13(a) above regarding registration
or exemption have been satisfied, the Warrant Holder may sell, transfer, assign, pledge or
otherwise dispose of this Warrant (each of the foregoing, a “Transfer”), in whole or in part, but
only to an Affiliate of the Warrant Holder. The Warrant Holder shall deliver a written notice to
Company, substantially in the form of the Assignment attached hereto as Exhibit B, indicating the
person or persons to whom the Warrant shall be Transferred and the respective number of warrants to
be Transferred to each assignee. The Company shall effect the Transfer within ten (10) days, and
shall deliver to the Transferee(s) designated by the Warrant Holder a Warrant or Warrants of like
tenor and terms for the appropriate number of shares. In connection with and as a condition of any
such proposed Transfer, the Company may require (i) the Warrant Holder to provide an opinion of
counsel to the Warrant Holder in form and substance reasonably satisfactory to the Company to the
effect that the proposed Transfer complies with all applicable federal and state securities laws
and (ii) any such Transferee to provide customary representations and warranties attendant to the
acquisition of unregistered securities, including without
limitation the Transferee’s investment intent and status as an “accredited investor” within
the meaning of Regulation D.

     (e) Investor’s Compliance. Nothing in this Section 13 shall affect in any way the
Investor’s obligations under any agreement to comply with all applicable securities laws upon
resale of the Common Stock.

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     Section 14. Notices. All notices, demands, requests, consents, approvals, and other
communications required or permitted hereunder shall be given in accordance with Section 10.04 of
the Purchase Agreement.

     Section 15. Miscellaneous. 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. The headings in this
Warrant are for purposes of reference only, and shall not limit or otherwise affect any of the
terms hereof. The invalidity or unenforceability of any provision hereof shall in no way affect
the validity or enforceability of any other provision.

     Section 16. Company Call Right.

     (a) If a Funding Default occurs, the Company shall have the right to demand the surrender of
this Warrant or any remaining portion thereof, Shares and/or cash from the Investor as follows (the
“Call Right”):

          (i) If the Investor has not previously exercised this Warrant in full, then the Company shall
have a right to demand the surrender of this Warrant, or remaining portion thereof, from the
Investor without compensation, and the Investor shall promptly surrender this Warrant, or remaining
portion thereof. Following such demand for surrender, this Warrant shall automatically be deemed to
have been canceled and shall have no further force or effect.

          (ii) If, prior to receiving a Call Right Notice, the Investor has previously exercised this
Warrant with respect to some or all of the Warrant Shares, and the Investor has not previously sold
such Warrant Shares, then the Company shall have a right to purchase from the Investor that number
of shares of Common Stock equal to the number of shares of Common Stock issued in connection with
the exercise(s) of the Warrant, at a repurchase price per share equal to the price per share paid
by the Investor in connection with such exercise(s). For greater certainty, (a) if Warrant Shares
were exercised for cash, the purchase price per share under the Call Right shall be equal to the
Exercise Price, (b) if Warrant Shares were exercised on a cashless exercise basis, the purchase
price per share for such Warrant Shares under the Call Right shall be zero, and (c) if such Warrant
Shares were exercised on both a cash and cashless exercise basis, the purchase price per share
under the Call Right shall be equal to the total amount of cash paid in connection with such cash
exercise(s) divided by the total number of shares of Common Stock issued in connection with all
exercises of the Warrant (whether on a cash or cashless basis).

          (iii) If, prior to receiving a Call Right Notice, the Investor has previously exercised this
Warrant with respect to some or all of the Warrant Shares, and the Investor subsequently sold such
Warrant Shares, then the Investor shall remit to the Company the excess, if any, of (x) the
proceeds received by Investor through the sale of such Warrant Shares, over (y) the aggregate
Exercise Price for such Warrant Shares. In the event that the Investor obtained such Warrant Shares
through a Cashless Exercise, then the Investor shall instead remit to the Company all proceeds
received by the Investor
through the sale of such Warrant Shares. For the avoidance of doubt, in the event that the
Investor has sold some or all of the Warrant Shares prior to receiving a Call Right Notice, then
the right set forth in this paragraph (iii) shall constitute the sole Call Right of the Company
with respect to such Warrant Shares which have been sold.

     (b) Company may exercise the Call Right by delivering a notice (the “Call Right
Notice”) to Investor within thirty (30) days after the occurrence of a Funding Default. On the
tenth (10th) business day following delivery of the Call Right Notice to Investor,
Company shall tender the purchase price, if any,

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and Investor shall tender shares of Common Stock,
if any, to be sold to Company pursuant to the Call Right Notice, immediately following which
Company and Investor shall consummate such purchase and sale. The Call Right shall survive both the
assignment of the Warrant by the Investor and the disposition of the Warrant Shares by the Investor
following exercise of the Warrant.

     Section 17. Absence of Presumption. This Agreement shall be construed without regard
to any presumption or rule requiring construction or interpretation against the party drafting or
causing any instrument to be drafted.

[Remainder of this page intentionally left blank]

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     IN WITNESS WHEREOF, this Warrant was duly executed by the undersigned, thereunto duly
authorized, as of the date first set forth above.

	 	 	 	 	 
	 	SANTARUS, INC.

 	 
	 	By:  	/s/ Gerald T. Proehl
 	 
	 	 	Gerald T. Proehl 	 
	 	 	President and Chief Executive Officer 	 
	 

Investor acknowledges and agrees to the terms and conditions of this Warrant.

	 	 	 	 	 
	 

	 	 	 	 
	By:

	 	/s/ Maria O’Donoghue	 	 
	 	 	 	 	 
	 

	 	Maria O’Donoghue	 	 
	 

	 	Director	 	 

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EXHIBIT A TO THE WARRANT

EXERCISE FORM

SANTARUS, INC.

     The
undersigned hereby irrevocably exercises the right to purchase ______ shares
of Common Stock of Santarus, Inc., a Delaware corporation, evidenced by the attached Warrant, and
(CIRCLE EITHER (i) or (ii)) (i) tenders herewith payment of the Aggregate Exercise Price with
respect to such shares in full, in the amount of $___, in cash, by certified or official bank
check or by wire transfer for the account of the Company or (ii) elects, pursuant to Section 2(c)
of the Warrant, to convert such Warrant into shares of Common Stock of Santarus, Inc. on a cashless
exercise basis, all in accordance with the conditions and provisions of said Warrant.

     The undersigned requests that stock certificates for such Warrant Shares be issued, and a
Warrant representing any unexercised portion hereof be issued, pursuant to this Warrant, in the
name of the registered Warrant Holder and delivered to the undersigned at the address set forth
below.

	 	 	 	 	 
	 

	 	 	 	 
	Dated:
	 	 	 	 
	 	 	 	 	 
	 
	 	 	 	 
	 	 	 
	Signature of Registered Holder	 	 
	 
	 	 	 	 
	 	 	 
	Name of Registered Holder (Print)	 	 
	 
	 	 	 	 
	 	 	 
	Address	 	 

 

 

EXHIBIT B TO THE WARRANT

ASSIGNMENT

     (To be executed by the registered Warrant Holder desiring to transfer the Warrant)

     FOR VALUED RECEIVED, the undersigned Warrant Holder of the attached Warrant hereby sells,
assigns and transfers unto the persons below named the right to
purchase ______ shares of
Common Stock of Santarus, Inc. (the “Company”) evidenced by the attached Warrant and does hereby
irrevocably constitute and appoint ______ attorney to transfer the said Warrant on
the books of the Company, with full power of substitution in the premises.

	 	 	 	 	 
	 

	 	 	 	 
	Dated:
	 	 	 	 
	 
	 	 	 	 
	 	 	 
	Signature	 	 
	 
	 	 	 	 
	Fill in for new Registration of Warrant:	 	 
	 
	 	 	 	 
	 	 	 
	Name	 	 
	 
	 	 	 	 
	 	 	 
	Address	 	 
	 
	 	 	 	 
	 	 	 
	Please print name and address of assignee
(including zip code number)exv4w2

 

Exhibit 4.2

REGISTRATION RIGHTS AGREEMENT

     This REGISTRATION RIGHTS AGREEMENT (this “Agreement”), dated as of February 3, 2006,
is by and between SANTARUS, INC. (the “Company”) and KINGSBRIDGE CAPITAL LIMITED (the
“Investor”).

     WHEREAS, the Company and the Investor have entered into that certain Common Stock Purchase
Agreement, dated as of the date hereof (the “Purchase Agreement”), pursuant to which the
Company may issue, from time to time, to the Investor up to $75 million worth of shares of Common
Stock as provided for therein;

     WHEREAS, pursuant to the terms of, and in partial consideration for the Investor entering
into, the Purchase Agreement, the Company has issued to the Investor a warrant, exercisable from
time to time within five (5) years following the six-month anniversary of the date of issuance (the
“Warrant”) for the purchase of an aggregate of up to 365,000 shares of Common Stock at a
price specified in such Warrant;

     WHEREAS, pursuant to the terms of, and in partial consideration for, the Investor’s agreement
to enter into the Purchase Agreement, the Company has agreed to provide the Investor with certain
registration rights with respect to the Registrable Securities (as defined in the Purchase
Agreement) as set forth herein;

     NOW, THEREFORE, in consideration of the premises, the representations, warranties, covenants
and agreements contained herein, in the Warrant, and in the Purchase Agreement, and for other good
and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, intending
to be legally bound hereby, the parties hereto agree as follows (capitalized terms used herein and
not defined herein shall have the respective meanings ascribed to them in the Purchase Agreement):

ARTICLE I

REGISTRATION RIGHTS

     Section 1.1. Registration Statement.

     (a) Filing of the Registration Statement. Upon the terms and subject to the
conditions set forth in this Agreement, the Company shall file with the Commission within sixty
(60) calendar days after the Closing Date a registration statement on Form S-3 under the Securities
Act or such other form as deemed appropriate by counsel to the Company for the registration for the
resale by the Investor of the Registrable Securities (the “Registration Statement”).

     (b) Effectiveness of the Registration Statement. The Company shall use commercially
reasonable efforts (i) to have the Registration Statement declared effective by the Commission as
soon as reasonably practicable, but in any event no later than one hundred eighty (180) calendar
days after the Closing Date and (ii) to ensure that the Registration Statement remains in effect
throughout the term of this Agreement as set forth in Section 4.2, subject to the terms and
conditions of this Agreement.

     (c) Regulatory Disapproval. The contemplated effective date for the Registration
Statement as described in Section 1.1(b) shall be extended without default or liquidated damages
hereunder or under the Purchase Agreement in the event that the Company’s failure to obtain the
effectiveness of the Registration Statement on a timely basis results solely from the Commission’s
disapproval of the structure of the transactions contemplated by the Purchase Agreement. In such
event, the parties agree to cooperate with one another in good faith to arrive at a resolution
acceptable to the Commission.

 

 

     (d) Failure to Maintain Effectiveness of Registration Statement. In the event the
Company fails to maintain the effectiveness of the Registration Statement (or the Prospectus)
throughout the period set forth in Section 4.2, other than temporary suspensions as set forth in
Section 1.1(e) and the Investor holds any Registrable Securities at any time during the period of
such ineffectiveness (an “Ineffective Period”), the Company shall pay to the Investor in
immediately available funds into an account designated by the Investor an amount equal to the
product of (x) the total number of Registrable Securities issued to the Investor under the Purchase
Agreement and owned by the Investor at any time during such Ineffective Period and (y) the result,
if greater than zero, obtained by subtracting the VWAP on the Trading Day immediately following the
last day of such Ineffective Period from the VWAP on the Trading Day immediately preceding the day
on which any such Ineffective Period began; provided, however, (i) that the
foregoing payments shall not apply in respect of Registrable Securities that are otherwise freely
tradable by the Investor and (ii) that the Company shall be under no obligation to supplement the
Prospectus to reflect the issuance of any Shares pursuant to a Draw Down at any time prior to the
day following the Settlement Date with respect to such Shares and that the failure to supplement
the Prospectus prior to such time period shall not be deemed a failure to maintain the
effectiveness of the Registration Statement (or Prospectus) for purposes of this Agreement
(including this Section 1.1(d)).

     (e) Deferral or Suspension During a Blackout Period. Notwithstanding the provisions
of Section 1.1(d), if in the good faith judgment of the Company, following consultation with legal
counsel, it would be detrimental to the Company or its stockholders for the Registration Statement
to be filed or for resales of Registrable Securities to be made pursuant to the Registration
Statement due to (i) the existence of a material development or potential material development
involving the Company that the Company would be obligated to disclose in the Registration
Statement, which disclosure would be premature or otherwise inadvisable at such time or would have
a Material Adverse Effect on the Company or its stockholders, or (ii) a filing of a
Company-initiated registration of any class of its equity securities, which, in the good faith
judgment of the Company, would adversely effect or require premature disclosure of the filing of
such Company-initiated registration (notice thereof, a “Blackout Notice”), the Company
shall have the right to (A) immediately defer such filing for a period of not more than sixty (60)
days beyond the date by which such Registration Statement was otherwise required hereunder to be
filed or (B) suspend use of such Registration Statement for a period of not more than thirty (30)
days (any such deferral or suspension period, a “Blackout Period”). The Investor
acknowledges that it would be seriously detrimental to the Company and its stockholders for such
Registration Statement to be filed (or remain in effect) during a Blackout Period and therefore
essential to defer such filing (or suspend the use thereof) during such Blackout Period and agrees
to cease any disposition of the Registrable Securities during such Blackout Period. The Company
may not utilize any of its rights under this Section 1.1(e) to defer the filing of a Registration
Statement (or suspend its effectiveness) more than six (6) times in any twelve (12) month period.
In the event that, within fifteen (15) Trading Days following any Settlement Date, the Company
gives a Blackout Notice to the Investor and the VWAP on the Trading Day immediately preceding such
Blackout Period (“Old VWAP”) is greater than the VWAP on the first Trading Day following
such Blackout Period that the Investor may sell its Registrable Securities pursuant to an effective
Registration Statement (“New VWAP”), then the Company shall pay to the Investor, by wire
transfer of immediately available funds to an account designated by the Investor, the “Blackout
Amount.” For the purposes of this Agreement, Blackout Amount means a percentage equal to: (1)
seventy-five percent (75%) if such Blackout Notice is delivered prior to the fifth (5th)
Trading Day following such Settlement Date; (2) fifty percent (50%) if such Blackout Notice is
delivered on or after the fifth (5th) Trading Day following such Settlement Date, but
prior to the tenth (10th) Trading Day following such Settlement Date; (3) twenty-five
percent (25%) if such Blackout Notice is delivered on or after the tenth (10th) Trading
Day following such Settlement Date, but prior to the fifteenth (15th) Trading Day
following such Settlement Date; and (4) zero percent (0%) thereafter of: the product of (i) the
number of Registrable Securities purchased by the Investor pursuant to the most recent Draw Down
and actually held by the Investor immediately prior to the Blackout Period and (ii) the result, if
greater than zero,

2

 

obtained by subtracting the New VWAP from the Old VWAP. For any Blackout Period in respect of
which a Blackout Amount becomes due and payable, rather than paying the Blackout Amount, the
Company may at is sole discretion, issue to the Investor shares of Common Stock with an aggregate
market value determined as of the first Trading Day following such Blackout Period equal to the
Blackout Amount (“Blackout Shares”).

     (f) Liquidated Damages. The Company and the Investor hereto acknowledge and agree
that the amounts payable under Sections 1.1(d) and 1.1(e) and the Blackout Shares, if any,
deliverable under Section 1.1(e) above shall constitute liquidated damages and not penalties. The
parties further acknowledge that (i) the amount of loss or damages likely to be incurred by the
Investor is incapable or is difficult to precisely estimate, (ii) the amounts specified in such
subsections bear a reasonable proportion and are not plainly or grossly disproportionate to the
probable loss likely to be incurred in connection with any failure by the Company to obtain or
maintain the effectiveness of the Registration Statement, (iii) one of the reasons for the Company
and the Investor reaching an agreement as to such amounts was the uncertainty and cost of
litigation regarding the question of actual damages, and (iv) the Company and the Investor are
sophisticated business parties and have been represented by sophisticated and able legal and
financial counsel and negotiated this Agreement at arm’s length.

     (g) Additional Registration Statements. In the event and to the extent that the
Registration Statement fails to register a sufficient amount of Common Stock necessary for the
Company to issue and sell to the Investor and the Investor to purchase from the Company all of the
Registrable Securities to be issued, sold and purchased under the Purchase Agreement and the
Warrant, the Company shall, upon a timetable mutually agreeable to both the Company and the
Investor, prepare and file with the Commission an additional registration statement or statements
in order to effectuate the purpose of this Agreement, the Purchase Agreement, and the Warrant.

ARTICLE II

REGISTRATION PROCEDURES

     Section 2.1. Filings; Information. The Company shall effect the registration with
respect to the sale of the Registrable Securities by the Investor in accordance with the intended
methods of disposition thereof. Without limiting the foregoing, the Company in each such case will
do the following as expeditiously as possible, but in no event later than the deadline, if any,
prescribed therefor in this Agreement:

     (a) Subject to Section 1.1(e), the Company shall (i) prepare and file with the Commission the
Registration Statement; (ii) use commercially reasonable efforts to cause such filed Registration
Statement to become and to remain effective (pursuant to Rule 415 under the Securities Act or
otherwise); (iii) prepare and file with the Commission such amendments and supplements to the
Registration Statement and the Prospectus used in connection therewith as may be necessary to keep
such Registration Statement effective for the time period prescribed by Section 4.2 and in order to
effectuate the purpose of this Agreement, the Purchase Agreement, and the Warrant; and (iv) comply
with the provisions of the Securities Act with respect to the disposition of all securities covered
by such Registration Statement during such period in accordance with the intended methods of
disposition by the Investor set forth in such Registration Statement; provided,
however, that the Company shall be under no obligation to supplement the Prospectus to
reflect the issuance of any Shares pursuant to a Draw Down at any time prior to the Trading Day
following the Settlement Date with respect to such Shares; and; provided further,
that the Investor shall be responsible for the delivery of the Prospectus to the Persons
to whom the Investor sells the Shares and the Warrant Shares, and the Investor agrees to dispose of
Registrable Securities in compliance with the plan of distribution described in the Registration
Statement and otherwise in compliance with applicable federal and state securities laws.

3

 

     (b) Three (3) Trading Days prior to filing the Registration Statement or Prospectus, or any
amendment or supplement thereto (excluding amendments deemed to result from the filing of documents
incorporated by reference therein, and excluding supplements to the Registration Statement for
which consent of or notice to the Investor is not required pursuant to Section 6.12 of the Purchase
Agreement), the Company shall deliver to the Investor and to counsel representing the Investor, in
accordance with the notice provisions of Section 4.8, copies of the Registration Statement,
Prospectus and/or any amendments or supplements thereto as proposed to be filed, together with
exhibits thereto, which documents will be subject to review by the Investor and such counsel, and
thereafter deliver to the Investor and such counsel, in accordance with the notice provisions of
Section 4.8, such number of copies of the Registration Statement, each amendment and supplement
thereto (in each case including all exhibits thereto), the Prospectus (including each preliminary
prospectus) and such other documents or information as the Investor or counsel may reasonably
request in order to facilitate the disposition of the Registrable Securities, provided, however,
that to the extent reasonably practicable, such delivery may be accomplished via electronic means.

     (c) After the filing of the Registration Statement, the Company shall promptly notify the
Investor of any stop order issued or threatened by the Commission in connection therewith and take
all commercially reasonable actions required to prevent the entry of such stop order or to remove
it if entered.

     (d) The Company shall use commercially reasonable efforts to (i) register or qualify the
Registrable Securities under such other securities or blue sky laws of each jurisdiction in the
United States as the Investor may reasonably (in light of its intended plan of distribution)
request, and (ii) cause the Registrable Securities to be registered with or approved by such other
governmental agencies or authorities in the United States as may be necessary by virtue of the
business and operations of the Company and do any and all other customary acts and things that may
be reasonably necessary or advisable to enable the Investor to consummate the disposition of the
Registrable Securities; provided, however, that the Company will not be required to
qualify generally to do business in any jurisdiction where it would not otherwise be required to
qualify but for this Section 2.1(e), subject itself to taxation in any such jurisdiction, consent
or subject itself to general service of process in any such jurisdiction, change any existing
business practices, benefit plans or outstanding securities or amend or otherwise modify the
Charter or Bylaws.

     (e) The Company shall make available to the Investor (and will deliver to Investor’s counsel),
(A) subject to restrictions imposed by the United States federal government or any agency or
instrumentality thereof, copies of all public correspondence between the Commission and the Company
concerning the Registration Statement and will also make available for inspection by the Investor
and any attorney, accountant or other professional retained by the Investor (collectively, the
“Inspectors”), (B) upon reasonable advance notice during normal business hours all
financial and other records, pertinent corporate documents and properties of the Company
(collectively, the “Records”) as shall be reasonably necessary to enable them to exercise
their due diligence responsibility, and cause the Company’s officers and employees to supply all
information reasonably requested by any Inspectors in connection with the Registration Statement;
provided, however, that any such Inspectors must agree in writing for the benefit
of the Company not to use or disclose any such Records except as provided in this Section 2.1(f).
Records that the Company determines, in good faith, to be confidential and that it notifies the
Inspectors are confidential shall not be disclosed by the Inspectors unless the disclosure or
release of such Records is requested or required pursuant to oral questions, interrogatories,
requests for information or documents or a subpoena or other order from a court of competent
jurisdiction or other judicial or governmental process; provided, however, that
prior to any disclosure or release pursuant to the immediately preceding clause, the Inspectors
shall provide the Company with prompt notice of any such request or requirement so that the Company
may seek an appropriate protective order or waive such Inspectors’ obligation not to

4

 

disclose such Records; and, provided, further, that if failing the entry of a
protective order or the waiver by the Company permitting the disclosure or release of such Records,
the Inspectors, upon advice of counsel, are compelled to disclose such Records, the Inspectors may
disclose that portion of the Records that counsel has advised the Inspectors that the Inspectors
are compelled to disclose; provided, however, that upon any such required
disclosure, such Inspector shall use his or her best efforts to obtain reasonable assurances that
confidential treatment will be afforded such information. The Investor agrees that information
obtained by it solely as a result of such inspections (not including any information obtained from
a third party who, insofar as is known to the Investor after reasonable inquiry, is not prohibited
from providing such information by a contractual, legal or fiduciary obligation to the Company)
shall be deemed confidential and shall not be used for any purposes other than as indicated above
or by it as the basis for any market transactions in the securities of the Company or its
affiliates unless and until such information is made generally available to the public. The
Investor further agrees that it will, upon learning that disclosure of such Records is sought in a
court of competent jurisdiction, give notice to the Company and allow the Company, at its expense,
to undertake appropriate action to prevent disclosure of the Records deemed confidential.

     (f) The Company shall otherwise comply with all applicable rules and regulations of the
Commission, including, without limitation, compliance with applicable reporting requirements under
the Exchange Act.

     (g) The Company shall appoint a transfer agent and registrar for all of the Registrable
Securities covered by such Registration Statement not later than the effective date of such
Registration Statement.

     (h) The Investor shall cooperate with the Company, as reasonably requested by the Company, in
connection with the preparation and filing of any Registration Statement hereunder. The Company
may require the Investor to promptly furnish in writing to the Company such information as may be
required in connection with such registration including, without limitation, all such information
as may be requested by the Commission or the NASD or any state securities commission and all such
information regarding the Investor, the Registrable Securities held by the Investor and the
intended method of disposition of the Registrable Securities. The Investor agrees to provide such
information requested in connection with such registration within five (5) business days after
receiving such written request and the Company shall not be responsible for any delays in obtaining
or maintaining the effectiveness of the Registration Statement caused by the Investor’s failure to
timely provide such information.

     (i) Upon receipt of a Blackout Notice from the Company, the Investor shall immediately
discontinue disposition of Registrable Securities pursuant to the Registration Statement covering
such Registrable Securities until (i) the Company advises the Investor that the Blackout Period has
terminated and (ii) the Investor receives copies of a supplemented or amended prospectus, if
necessary. If so directed by the Company, the Investor will deliver to the Company (at the expense
of the Company) or destroy (and deliver to the Company a certificate of destruction) all copies in
the Investor’s possession (other than a limited number of file copies) of the prospectus covering
such Registrable Securities that is current at the time of receipt of such notice.

     Section 2.2. Registration Expenses. The Company shall pay all registration expenses
incurred in connection with the Registration Statement (the “Registration Expenses”),
including, without limitation: (i) all registration, filing, securities exchange listing and fees
required by the National Association of Securities Dealers, (ii) all registration, filing,
qualification and other fees and expenses of compliance with securities or blue sky laws (including
reasonable fees and disbursements of counsel in connection with blue sky qualifications of the
Registrable Securities), (iii) all word processing, duplicating, printing, messenger and delivery
expenses, (iv) the Company’s internal expenses (including, without limitation, all salaries and
expenses of its officers and employees performing legal or accounting

5

 

duties), (v) the fees and expenses incurred by the Company in connection with the listing of
the Registrable Securities, (vi) reasonable fees and disbursements of counsel for the Company and
customary fees and expenses for independent certified public accountants retained by the Company
(including the expenses of any special audits or comfort letters or costs associated with the
delivery by independent certified public accountants of such special audit(s) or comfort letter(s),
(vii) the fees and expenses of any special experts retained by the Company in connection with such
registration and amendments and supplements to the Registration Statement and Prospectus and (viii)
premiums and other costs of the Company for policies of insurance against liabilities arising out
of any public offering of the Registrable Securities being registered. Any fees and disbursements
of underwriters, broker-dealers or investment bankers, including without limitation underwriting
fees, discounts, transfer taxes or commissions, and any other fees or expenses (including legal
fees and expenses) if any, attributable to the sale of Registrable Securities, shall be payable by
each holder of Registrable Securities pro rata on the basis of the number of Registrable Securities
of each such holder that are included in a registration under this Agreement.

ARTICLE III

INDEMNIFICATION

     Section 3.1. Indemnification. The Company agrees to indemnify and hold harmless the
Investor, its partners, affiliates, officers, directors, employees and duly authorized agents, and
each Person or entity, if any, who controls the Investor within the meaning of Section 15 of the
Securities Act or Section 20 of the Exchange Act, together with the partners, affiliates, officers,
directors, employees and duly authorized agents of such controlling Person or entity (collectively,
the “Controlling Persons”), from and against any loss, claim, damage, liability, costs and
expenses (including, without limitation, reasonable attorneys’ fees and disbursements and costs and
expenses of investigating and defending any such claim) (collectively, “Damages”), joint or
several, and any action or proceeding in respect thereof to which the Investor, its partners,
affiliates, officers, directors, employees and duly authorized agents, and any Controlling Person,
may become subject under the Securities Act or otherwise, as incurred, insofar as such Damages (or
actions or proceedings in respect thereof) arise out of, or are based upon, any untrue statement or
alleged untrue statement of a material fact contained in any Registration Statement, or in any
preliminary prospectus, final prospectus, summary prospectus, amendment or supplement relating to
the Registrable Securities or arises out of, or are based upon, any omission or alleged omission to
state therein a material fact required to be stated therein or necessary to make the statements
therein under the circumstances not misleading, and shall reimburse the Investor, its partners,
affiliates, officers, directors, employees and duly authorized agents, and each such Controlling
Person, for any legal and other expenses reasonably incurred by the Investor, its partners,
affiliates, officers, directors, employees and duly authorized agents, or any such Controlling
Person, as incurred, in investigating or defending or preparing to defend against any such Damages
or actions or proceedings; provided, however, that the Company shall not be liable
to the extent that any such Damages arise out of the Investor’s (or any other indemnified Person’s)
failure to send or give a copy of the final prospectus or supplement (as then amended or
supplemented) to the persons asserting an untrue statement or alleged untrue statement or omission
or alleged omission at or prior to the written confirmation of the sale of Registrable Securities
to such person if such statement or omission was corrected in such final prospectus or supplement;
provided, further, that the Company shall not be liable to the extent that any such
Damages arise out of or are based upon an untrue statement or alleged untrue statement or omission
or alleged omission made in such Registration Statement, or any such preliminary prospectus, final
prospectus, summary prospectus, amendment or supplement in reliance upon and in conformity with
written information furnished to the Company by or on behalf of the Investor or any other person
who participates as an underwriter in the offering or sale of such securities, in either case,
specifically stating that it is for use in the preparation thereof. In connection with any
Registration Statement with respect to which the Investor is participating, such Investor will
indemnify and hold harmless, to the same extent and in the same manner as set forth in the
preceding paragraph, the Company, each of its partners, affiliates, officers, directors, employees
and

6

 

duly authorized agents of such controlling Person (each a “Company Indemnified
Person”) against any Damages to which any Company Indemnified Person may become subject under
the Securities Act, the Exchange Act or otherwise, insofar as such Damages arise out of or are
based upon (a) any untrue statement or alleged untrue statement of a material fact contained in any
Registration Statement, or in any preliminary prospectus, final prospectus, summary prospectus,
amendment or supplement relating to the Registrable Securities or arise out of, or are based upon,
any omission or alleged omission to state therein a material fact required to be stated therein or
necessary to make the statements therein under the circumstances not misleading to the extent that
such violation occurs in reliance upon and in conformity with written information furnished to the
Company by the Investor or on behalf of the Investor expressly for use in connection with such
Registration Statement or (b) any failure by the Investor to comply with prospectus delivery
requirements of the Securities Act, the Exchange Act or any other law or legal requirement
applicable to sales under the Registration Statement.

     Section 3.2. Conduct of Indemnification Proceedings. All claims for indemnification
under Section 3.1 shall be asserted and resolved in accordance with the provisions of Section 9.02
of the Purchase Agreement.

     Section 3.3. Additional Indemnification. Indemnification similar to that specified in
the preceding paragraphs of this Article 3 (with appropriate modifications) shall be given by the
Company and the Investor with respect to any required registration or other qualification of
securities under any federal or state law or regulation of any governmental authority other than
the Securities Act. The provisions of this Article III shall be in addition to any other rights to
indemnification, contribution or other remedies which an Indemnified Party or a Company Indemnified
Person may have pursuant to law, equity, contract or otherwise.

     To the extent that any indemnification provided for herein is prohibited or limited by law,
the indemnifying party will make the maximum contribution with respect to any amounts for which it
would otherwise be liable under this Article III to the fullest extent permitted by law. However,
(a) no contribution will be made under circumstances where maker of such contribution would not
have been required to indemnify the indemnified party under the fault standards set forth in this
Article III, (b) no seller of Registrable Securities guilty of fraudulent misrepresentation (within
the meaning of Section 11(f) of the Securities Act) will be entitled to contribution from any
Person who is not guilty of such fraudulent misrepresentation, and (c) contribution (together with
any indemnification obligations under this Agreement) by any seller of Registrable Securities will
be limited in amount to the proceeds received by such seller from the sale of such Registrable
Securities.

ARTICLE IV

MISCELLANEOUS

     Section 4.1. No Outstanding Registration Rights. Except as otherwise disclosed in
accordance with the Purchase Agreement or in the Commission Documents, the Company represents and
warrants to the Investor that there is not in effect on the date hereof any agreement by the
Company pursuant to which any holders of securities of the Company have a right to cause the
Company to register or qualify such securities under the Securities Act or any securities or blue
sky laws of any jurisdiction.

     Section 4.2. Term. The registration rights provided to the holders of Registrable
Securities hereunder, and the Company’s obligation to keep the Registration Statement effective,
shall terminate at the earlier of (i) such time that is two years following the termination of the
Purchase Agreement, (ii) such time as all Registrable Securities have been issued and have ceased
to be Registrable Securities, or (iii) upon the consummation of an “Excluded Merger or Sale” as
defined in the Warrant.
Notwithstanding the foregoing, paragraph (d) of Section 1.1, Article III, Section 4.7, Section
4.8, Section 4.9, Section 4.10 and Section 4.13 shall survive the termination of this Agreement.

7

 

     Section 4.3. Rule 144. The Company will, at its expense, promptly take such action as
holders of Registrable Securities may reasonably request to enable such holders of Registrable
Securities to sell Registrable Securities without registration under the Securities Act within the
limitation of the exemptions provided by (a) Rule 144 under the Securities Act (“Rule
144”), as such Rule may be amended from time to time, or (b) any similar rule or regulation
hereafter adopted by the Commission. If at any time the Company is not required to file such
reports, it will, at its expense, forthwith upon the written request of any holder of Registrable
Securities, make available adequate current public information with respect to the Company within
the meaning of paragraph (c)(2) of Rule 144 or such other information as necessary to permit sales
pursuant to Rule 144. Upon the request of the Investor, the Company will deliver to the Investor a
written statement, signed by the Company’s principal financial officer, as to whether it has
complied with such requirements.

     Section 4.4. Certificate. The Company will, at its expense, forthwith upon the
request of any holder of Registrable Securities, deliver to such holder a certificate, signed by
the Company’s principal financial officer, stating (a) the Company’s name, address and telephone
number (including area code), (b) the Company’s Internal Revenue Service identification number, (c)
the Company’s Commission file number, (d) the number of shares of each class of Stock outstanding
as shown by the most recent report or statement published by the Company, and (e) whether the
Company has filed the reports required to be filed under the Exchange Act for a period of at least
ninety (90) days prior to the date of such certificate and in addition has filed the most recent
annual report required to be filed thereunder.

     Section 4.5. Amendment And Modification. Any provision of this Agreement may be
waived, provided that such waiver is set forth in a writing executed by both parties to this
Agreement. The provisions of this Agreement, including the provisions of this sentence, may be
amended, modified or supplemented, and waivers or consents to departures from the provisions hereof
may be given, only with the written consent of the Investor and the Company. No course of dealing
between or among any Person having any interest in this Agreement will be deemed effective to
modify, amend or discharge any part of this Agreement or any rights or obligations of any person
under or by reason of this Agreement.

     Section 4.6. Successors and Assigns; Entire Agreement. This Agreement and all of the
provisions hereof shall be binding upon and inure to the benefit of the parties hereto and their
respective successors and permitted assigns. The Company may assign this Agreement at any time in
connection with a sale or acquisition of the Company, whether by merger, consolidation, sale of all
or substantially all of the Company’s assets, or similar transaction, without the consent of the
Investor, provided that the successor or acquiring Person or entity agrees in writing to assume all
of the Company’s rights and obligations under this Agreement. The Investor may assign its rights
and obligations under this Agreement only with the prior written consent of the Company, and any
purported assignment by the Investor absent the Company’s consent shall be null and void. This
Agreement, together with the Purchase Agreement and the Warrant sets forth the entire agreement and
understanding between the parties as to the subject matter hereof and merges and supersedes all
prior discussions, agreements and understandings of any and every nature among them.

     Section 4.7. Severability. In the event that any provision of this Agreement becomes
or is declared by a court of competent jurisdiction to be illegal, unenforceable or void, this
Agreement shall continue in full force and effect without said provision; provided that such
severability shall be ineffective if it materially changes the economic benefit of this Agreement
to any party hereto.

8

 

     Section 4.8. Notices. All notices, demands, requests, consents, approvals, and other
communications required or permitted hereunder shall be given in accordance with Section 10.04 of
the Purchase Agreement.

     Section 4.9. Governing Law; Dispute Resolution. This Agreement shall be construed
under the laws of the State of New York.

     Section 4.10. Headings. The headings in this Agreement are for convenience of
reference only and shall not constitute a part of this Agreement, nor shall they affect their
meaning, construction or effect.

     Section 4.11. Counterparts. This Agreement may be executed in multiple counterparts,
each of which shall be deemed to be an original instrument and all of which together shall
constitute one and the same instrument.

     Section 4.12. Further Assurances. Each party shall cooperate and take such action as
may be reasonably requested by another party in order to carry out the provisions and purposes of
this Agreement and the transactions contemplated hereby.

     Section 4.13. Absence of Presumption. This Agreement shall be construed without
regard to any presumption or rule requiring construction or interpretation against the party
drafting or causing any instrument to be drafted.

[Remainder of this page intentionally left blank]

9

 

     IN WITNESS WHEREOF, the parties hereto have caused this Agreement to be executed by the
undersigned, thereunto duly authorized, as of the date first set forth above.

	 	 	 	 	 
	 	 	KINGSBRIDGE CAPITAL LIMITED
	 
	 	 	 	 
	 

	 	By:
	 	/s/ Maria O’Donoghue
	 

	 	 	 	 
	 

	 	 	 	Maria O’Donoghue

Director
	 
	 	 	 	 
	 	 	SANTARUS, INC.
	 
	 	 	 	 
	 

	 	By:
	 	/s/ Gerald T. Proehl
	 

	 	 	 	 
	 

	 	 	 	Gerald T. Proehl

President and Chief Executive Officer

10

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