Exhibit 10.10

THIS WARRANT HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS
AMENDED OR ANY STATE SECURITIES LAWS. NO SALE OR DISPOSITION MAY BE EFFECTED
WITHOUT (i) EFFECTIVE REGISTRATION STATEMENTS RELATED THERETO, (ii) AN OPINION
OF COUNSEL OR OTHER EVIDENCE, REASONABLY SATISFACTORY TO THE COMPANY, THAT SUCH
REGISTRATIONS ARE NOT REQUIRED, (iii) RECEIPT OF NO-ACTION LETTERS FROM THE
APPROPRIATE GOVERNMENTAL AUTHORITIES, OR (iv) OTHERWISE COMPLYING WITH THE
PROVISIONS OF SECTION 7 OF THIS WARRANT.

INOTEK PHARMACEUTICALS CORPORATION

WARRANT TO PURCHASE SHARES

OF SERIES PREFERRED STOCK

(Loan A)

THIS CERTIFIES THAT, for value received, HORIZON TECHNOLOGY FINANCE CORPORATION
and its assignees are entitled to subscribe for and purchase that number of the
fully paid and nonassessable shares of Series Preferred Stock (as adjusted
pursuant to Section 4 hereof, the “Shares”) of INOTEK PHARMACEUTICALS
CORPORATION, a Delaware corporation (the “Company”), as is determined pursuant
to the next paragraph hereof at the price per share as is determined pursuant to
the next paragraph hereof (such price and such other price as shall result, from
time to time, from the adjustments specified in Section 4 hereof is herein
referred to as the “Warrant Price”), subject to the provisions and upon the
terms and conditions hereinafter set forth. As used herein, (a) the term “Series
Preferred” shall mean, at the holder’s election, either (i) the Company’s
presently authorized Series AA Convertible Preferred Stock, par value $0.001 per
share (the “Series AA Preferred Stock”) and any stock into or for which such
Series AA Preferred Stock may hereafter be converted or exchanged, and after the
automatic conversion of the Series AA Preferred Stock to Common Stock shall mean
the Company’s Common Stock, or (ii) the Next Round Stock (as defined below), and
any stock into or for which such Next Round Stock may hereafter be converted or
exchanged, and after the automatic conversion of the Next Round Stock to Common
Stock shall mean the Company’s Common Stock and (b) the term “Date of Grant”
shall mean June 28, 2013.

The Warrant Price shall be (i) if the holder elects to exercise this Warrant for
Series AA Preferred Stock, $1.529 or (ii) if the holder elects to exercise this
Warrant for Next Round Stock, the lowest effective price per share (on a common
stock equivalent basis and taking into account any securities issued together
with the preferred stock) at which shares of the Company’s convertible preferred
stock are sold in a Qualified Financing (the “Next Round Stock”). A “Qualified
Financing” shall mean the sale of the convertible preferred stock of the Company
to purchasers which include instititutional investors in an aggregate cash
amount not less than $10,000,000. The number of shares for which this Warrant is
exercisable shall rounded down to the nearest whole number determined by
dividing One Hundred Seventy-Five Thousand Dollars ($175,000) by the Warrant
Price determined pursuant to this paragraph.

--------------------------------------------------------------------------------

1. Term. The purchase right represented by this Warrant is exercisable, in whole
or in part, at any time and from time to time from the Date of Grant through the
earlier of (a) ten (10) years after the Date of Grant and (b) immediately prior
to the closing of an Acquisition Transaction (as defined below) in which the
consideration is cash, Marketable Securities or a combination thereof. As used
herein, “Marketable Securities” means securities meeting all of the following
requirements: (1) the issuer thereof is then subject to the reporting
requirements of Section 13 or Section 15(d) of the Exchange Act, and is then
current in its filing of all required reports and other information under the
Act and the Exchange Act, (2) the class and series of shares or other security
of the issuer that would be received by the holder of this Warrant in connection
with a merger were such holder to exercise or convert this Warrant on or prior
to the closing thereof is then traded on a national securities exchange or
over-the-counter market, (3) the issuer thereof has a market cap of at least
Seven Hundred Fifty Million Dollars ($750,000,000) and (4) such holder would not
be restricted by contract or by applicable federal and state securities laws
from publicly re-selling, within six (6) months and one day following the
closing of such Acquisition, all of the issuer’s shares and/or other securities
that would be received by such holder in such merger were such holder to
exercise or convert this Warrant in full on or prior to the closing of such
merger.

2. Method of Exercise; Payment; Issuance of New Warrant. Subject to Section 1
hereof, the purchase right represented by this Warrant may be exercised by the
holder hereof, in whole or in part and from time to time, at the election of the
holder hereof, by (a) the surrender of this Warrant (with the notice of exercise
substantially in the form attached hereto as Exhibit A-1 duly completed and
executed) at the principal office of the Company and by the payment to the
Company, by certified or bank check, or by wire transfer to an account
designated by the Company (a “Wire Transfer”) of an amount equal to the then
applicable Warrant Price multiplied by the number of Shares then being
purchased; (b) if in connection with a registered public offering of the
Company’s securities, the surrender of this Warrant (with the notice of exercise
form attached hereto as Exhibit A-2 duly completed and executed) at the
principal office of the Company together with notice of arrangements reasonably
satisfactory to the Company for payment to the Company either by certified or
bank check or by Wire Transfer from the proceeds of the sale of shares to be
sold by the holder in such public offering of an amount equal to the then
applicable Warrant Price per share multiplied by the number of Shares then being
purchased; or (c) exercise of the “net issuance” right provided for in
Section 10.2 hereof. The person or persons in whose name(s) any certificate(s)
representing shares of Series Preferred shall be issuable upon exercise of this
Warrant shall be deemed to have become the holder(s) of record of, and shall be
treated for all purposes as the record holder(s) of, the shares represented
thereby (and such shares shall be deemed to have been issued) immediately prior
to the close of business on the date or dates upon which this Warrant is
exercised. In the event of any exercise of the rights represented by this
Warrant, certificates for the shares of stock so purchased shall be delivered to
the holder hereof as soon as possible and in any event within thirty (30) days
after such exercise and, unless this Warrant has been fully exercised or
expired, a new Warrant representing the portion of the Shares, if any, with
respect to which this Warrant shall not then have been exercised shall also be
issued to the holder hereof as soon as possible and in any event within such
thirty-day period; provided, however, at such time as the Company is subject to
the reporting requirements of the Securities Exchange Act of 1934, as amended,
if requested by the holder of this Warrant, the Company shall cause its transfer
agent to deliver the certificate

 

-2-

--------------------------------------------------------------------------------

representing Shares issued upon exercise of this Warrant to a broker or other
person (as directed by the holder exercising this Warrant) within the time
period required to settle any trade made by the holder after exercise of this
Warrant. Each holder, as a condition to the issuance of shares of Series
Preferred upon exercise of this Warrant, shall become party to (i) that certain
Third Amended and Restated Investor Rights Agreement, dated as of June 9, 2010,
by and between the Company and the persons and entities identified therein, as
amended from time to time (the “Investor Rights Agreement”), as an “Investor”
for all purposes thereunder by executing and delivering the Adoption Agreement
attached to the Investor Rights Agreement as Schedule I and (ii) that certain
Third Amended and Restated Stockholders Agreement, dated as of June 9, 2010, by
and between the Company and the persons and entities identified therein, as
amended from time to time (the “Stockholders Agreement”), as an “Investor” and
“Stockholder” for all purposes thereunder by executing and delivering the
Adoption Agreement attached to the Stockholders Agreement as Schedule III.

3. Stock Fully Paid; Reservation of Shares. All Shares that may be issued upon
the exercise of the rights represented by this Warrant will, upon issuance
pursuant to the terms and conditions herein, be fully paid and nonassessable,
and free from all preemptive rights and taxes, liens and charges with respect to
the issue thereof. During the period within which the rights represented by this
Warrant may be exercised, the Company will at all times have authorized, and
reserved for the purpose of the issue upon exercise of the purchase rights
evidenced by this Warrant, a sufficient number of shares of its Series Preferred
to provide for the exercise of the rights represented by this Warrant and a
sufficient number of shares of its Common Stock to provide for the conversion of
the Series Preferred into Common Stock.

4. Adjustment of Warrant Price and Number of Shares. The number and kind of
securities purchasable upon the exercise of this Warrant and the Warrant Price
shall be subject to adjustment from time to time upon the occurrence of certain
events, as follows:

(a) Reclassification or Merger. Except for an Acquisition Transaction that
causes an expiration of the term of this Warrant as set forth in Section 1
above, in case of any reclassification or change of securities of the class
issuable upon exercise of this Warrant (other than a change in par value, or
from par value to no par value, or from no par value to par value, or as a
result of a subdivision or combination), or in case of any merger of the Company
with or into another corporation (other than a merger with another corporation
in which the Company is the acquiring and the surviving corporation and which
does not result in any reclassification or change of outstanding securities
issuable upon exercise of this Warrant), or in case of any sale of all or
substantially all of the assets of the Company, the Company, or such successor
or purchasing corporation, as the case may be, shall duly execute and deliver to
the holder of this Warrant a new Warrant (in form and substance satisfactory to
the holder of this Warrant), so that the holder of this Warrant shall have the
right to receive upon exercise of this Warrant, at a total purchase price not to
exceed that payable upon the exercise of the unexercised portion of this
Warrant, and in lieu of the shares of Series Preferred theretofore issuable upon
exercise of this Warrant, (i) the kind and amount of shares of stock, other
securities, money and property receivable upon such reclassification, change,
merger or sale by a holder of the number of shares of Series Preferred then
purchasable under this Warrant, or (ii) in the case of such a merger or sale in
which the consideration paid consists all or in part of assets

 

-3-

--------------------------------------------------------------------------------

other than securities of the successor or purchasing corporation, at the option
of the holder of this Warrant, the securities of the successor or purchasing
corporation having a value at the time of the transaction equivalent to the
value of the Series Preferred purchasable upon exorcise of this Warrant at the
time of the transaction. Any new Warrant shall provide for adjustments that
shall be as nearly equivalent as may be practicable to the adjustments provided
for in this Section 4. The provisions of this Section 4(a) shall similarly apply
to successive reclassifications, changes, mergers and sales.

(b) Subdivision or Combination of Shares. If the Company at any time while this
Warrant remains outstanding and unexpired shall subdivide or combine its
outstanding shares of Series Preferred, the Warrant Price shall be
proportionately decreased and the number of Shares issuable hereunder shall be
proportionately increased in the case of a subdivision and the Warrant Price
shall be proportionately increased and the number of Shares issuable hereunder
shall be proportionately decreased in the case of a combination.

(c) Stock Dividends and Other Distributions. If the Company at any time while
this Warrant is outstanding and unexpired shall (i) pay a dividend with respect
to Series Preferred payable in Series Preferred, then the Warrant Price shall be
adjusted, from and after the date of determination of shareholders entitled to
receive such dividend or distribution, to that price determined by multiplying
the Warrant Price in effect immediately prior to such date of determination by a
fraction (A) the numerator of which shall be the total number of shares of
Series Preferred outstanding immediately prior to such dividend or distribution,
and (B) the denominator of which shall be the total number of shares of Series
Preferred outstanding immediately after such dividend or distribution; or
(ii) make any other distribution with respect to Series Preferred (except any
distribution specifically provided for in Sections 4(a) and 4(b)), then, in each
such case, provision shall be made by the Company such that the holder of this
Warrant shall receive upon exercise of this Warrant a proportionate share of any
such dividend or distribution as though it were the holder of the Series
Preferred (or Common Stock issuable upon conversion thereof) as of the record
date fixed for the determination of the shareholders of the Company entitled to
receive such dividend or distribution.

(d) Adjustment of Number of Shares. Upon each adjustment in the Warrant Price,
the number of Shares of Series Preferred purchasable hereunder shall be
adjusted, to the nearest whole share, to the product obtained by multiplying the
number of Shares purchasable immediately prior to such adjustment in the Warrant
Price by a fraction, the numerator of which shall be the Warrant Price
immediately prior to such adjustment and the denominator of which shall be the
Warrant Price immediately thereafter.

(e) Antidilution Rights. The other antidilution rights applicable to the Shares
of Series Preferred purchasable hereunder are set forth in the Company’s Fifth
Amended and Restated Certificate of Incorporation, as amended from time to time
(the “Charter”). Such antidilution rights shall not be restated, amended,
modified or waived without the prior written consent of the holder hereof unless
such amendment, restatement, modification or waiver affects the rights
associated with the Shares of Series Preferred Stock in the same manner as such
amendment, restatement, modification or waiver affects the rights associated
with all other outstanding shares of Series Preferred Stock. The Company shall
promptly provide the holder hereof with any restatement, amendment, modification
or waiver of the Charter promptly after the same has been made.

 

-4-

--------------------------------------------------------------------------------

5. Notice of Adjustments. Whenever the Warrant Price or the number of Shares
purchasable hereunder shall be adjusted pursuant to Section 4 hereof, the
Company shall make a certificate signed by its 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, and the
Warrant Price and the number of Shares purchasable hereunder after giving effect
to such adjustment, and shall cause copies of such certificate to be mailed
(without regard to Section 13 hereof, by first class mail, postage prepaid) to
the holder of this Warrant. In addition, whenever the conversion price or
conversion ratio of the Series Preferred shall be adjusted, the Company shall
make a certificate signed by its 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, and the
conversion price or ratio of the Series Preferred after giving effect to such
adjustment, and shall cause copies of such certificate to be mailed (without
regard to Section 13 hereof, by first class mail, postage prepaid) to the holder
of this Warrant.

6. Fractional Shares. No fractional shares of Series Preferred will be issued in
connection with any exercise hereunder, but in lieu of such fractional shares
the Company shall make a cash payment therefor based on the fair market value of
the Series Preferred on the date of exercise as reasonably determined in good
faith by the Company’s Board of Directors.

7. Compliance with Act; Disposition of Warrant or Shares of Series Preferred.

(a) Compliance with Act. The holder of this Warrant, by acceptance hereof,
agrees that this Warrant, and the shares of Series Preferred to be issued upon
exercise hereof and any Common Stock issued upon conversion thereof are being
acquired for investment and that such holder will not offer, sell or otherwise
dispose of this Warrant, or any shares of Series Preferred to be issued upon
exercise hereof or any Common Stock issued upon conversion thereof except under
circumstances which will not result in a violation of the Act or any applicable
state securities laws. Upon exercise of this Warrant, unless the Shares being
acquired are registered under the Act and any applicable state securities laws
or an exemption from such registration is available, the holder hereof shall
confirm in writing that the shares of Series Preferred so purchased (and any
shares of Common Stock issued upon conversion thereof) are being acquired for
investment and not with a view toward distribution or resale in violation of the
Act and shall confirm such other matters related thereto as may be reasonably
requested by the Company. This Warrant and all shares of Series Preferred issued
upon exercise of this Warrant and all shares of Common Stock issued upon
conversion thereof (unless registered under the Act and any applicable state
securities laws) shall be stamped or imprinted with a legend in substantially
the following form:

“THE SECURITIES EVIDENCED HEREBY HAVE NOT BEEN REGISTERED UNDER THE SECURITIES
ACT OF 1933, AS AMENDED, OR ANY STATE SECURITIES LAWS. NO SALE OR DISPOSITION
MAY BE EFFECTED WITHOUT (i) EFFECTIVE REGISTRATION STATEMENTS RELATED THERETO,
(ii) AN OPINION OF COUNSEL OR OTHER EVIDENCE, REASONABLY SATISFACTORY TO THE
COMPANY, THAT SUCH

 

-5-

--------------------------------------------------------------------------------

REGISTRATIONS ARE NOT REQUIRED, (iii) RECEIPT OF NO-ACTION LETTERS FROM THE
APPROPRIATE GOVERNMENTAL AUTHORITIES, OR (iv) OTHERWISE COMPLYING WITH THE
PROVISIONS OF SECTION 7 OF THE WARRANT UNDER WHICH THESE SECURITIES WERE ISSUED,
DIRECTLY OR INDIRECTLY.”

Said legend shall be removed by the Company, upon the request of a holder, at
such time as the restrictions on the transfer of the applicable security shall
have terminated. In addition, in connection with the issuance of this Warrant,
the holder specifically represents to the Company by acceptance of this Warrant
as follows:

(1) The holder is aware of the Company’s business affairs and financial
condition, and has acquired information about the Company sufficient to reach an
informed and knowledgeable decision to acquire this Warrant. The holder is
acquiring this Warrant for its own account for investment purposes only and not
with a view to, or for the resale in connection with, any “distribution” thereof
in violation of the Act.

(2) The holder understands that this Warrant has not been registered under the
Act in reliance upon a specific exemption therefrom, which exemption depends
upon, among other things, the bona fide nature of the holder’s investment intent
as expressed herein.

(3) The holder further understands that this Warrant must be held indefinitely
unless subsequently registered under the Act and qualified under any applicable
state securities laws, or unless exemptions from registration and qualification
are otherwise available. The holder is aware of the provisions of Rule 144,
promulgated under the Act.

(4) The holder is an “accredited investor” as such term is defined in Rule 501
of Regulation D promulgated under the Act.

(b) Disposition of Warrant or Shares. With respect to any offer, sale or other
disposition of this Warrant or any shares of Series Preferred acquired pursuant
to the exercise of this Warrant prior to registration of such Warrant or shares,
the holder hereof agrees to give written notice to the Company prior thereto,
describing briefly the manner thereof, together with a written opinion of such
holder’s counsel, or other evidence, if reasonably satisfactory to the Company,
to the effect that such offer, sale or other disposition may be effected without
registration or qualification (under the Act as then in effect or any federal or
state securities law then in effect) of this Warrant or such shares of Series
Preferred or Common Stock and indicating whether or not under the Act
certificates for this Warrant or such shares of Series Preferred to be sold or
otherwise disposed of require any restrictive legend as to applicable
restrictions on transferability in order to ensure compliance with such law.
Upon receiving such written notice and reasonably satisfactory opinion or other
evidence, the Company, as promptly as practicable but no later than fifteen
(15) days after receipt of the written notice, shall notify such holder that
such holder may sell or otherwise dispose of this Warrant or such shares of
Series Preferred or Common Stock, all in accordance with the terms of the notice
delivered to the Company. If a determination has been made pursuant to this
Section 7(b) that the opinion of counsel for the holder or other evidence is not
reasonably satisfactory to the Company, the Company shall so notify the holder
promptly with details thereof after such

 

-6-

--------------------------------------------------------------------------------

determination has been made. Notwithstanding the foregoing, this Warrant or such
shares of Series Preferred or Common Stock may, as to such federal laws, be
offered, sold or otherwise disposed of in accordance with Rule 144 or 144A under
the Act, provided that the Company shall have been furnished with such
information as the Company may reasonably request to provide a reasonable
assurance that the provisions of Rule 144 or 144A have been satisfied. Each
certificate representing this Warrant or the shares of Series Preferred thus
transferred (except a transfer pursuant to Rule 144 or 144A) shall bear a legend
as to the applicable restrictions on transferability in order to ensure
compliance with such laws, unless in the aforesaid opinion of counsel for the
holder, such legend is not required in order to ensure compliance with such
laws. The Company may issue stop transfer instructions to its transfer agent in
connection with such restrictions.

(c) Applicability of Restrictions. Neither any restrictions of any legend
described in this Warrant nor the requirements of Section 7(b) above shall apply
to any transfer of, or grant of a security interest in, this Warrant (or the
Series Preferred or Common Stock obtainable upon exercise thereof) or any part
hereof (i) to a partner of the holder if the holder is a partnership or to a
member of the holder if the holder is a limited liability company, (ii) to a
partnership of which the holder is a partner or to a limited liability company
of which the holder is a member, (iii) to any affiliate of the holder if the
holder is a corporation, (iv) notwithstanding the foregoing, to any corporation,
company, limited liability company, limited partnership, partnership, or other
person managed or sponsored by Horizon Technology Finance Corporation (“HRZN”)
or in which HRZN has an interest, (v) or to a lender to the holder or any of the
foregoing; provided, however, in any such transfer, if applicable, the
transferee shall on the Company’s request agree in writing to be bound by the
terms of this Warrant as if an original holder hereof.

(d) Market Stand-Off Agreement. The holder of this Warrant (“Holder”) shall not
sell, dispose of, transfer, make any short sale of, grant any option for the
purchase of, or enter into any hedging or similar transaction with the same
economic effect as a sale, any Common Stock of the Company held by such Holder,
for a period of time specified by the managing underwriter(s) (such period not
to exceed one hundred eighty (180) days, except in order to comply with
Financial Industry Regulatory Authority (FINRA) Rule 2711 or a successor rule
thereto) following the effective date of a registration statement of the Company
filed under the Act. Holder agrees to execute and deliver such other agreements
as may be reasonably requested by the Company and/or the managing underwriter(s)
which are consistent with the foregoing or which are necessary to give further
effect thereto, provided that all officers and directors of the Company and all
holders of at least one percent (1%) of the Company’s voting securities enter
into similar agreements. In order to enforce the foregoing covenant, the Company
may impose stop-transfer instructions with respect to such Common Stock (or
other securities) until the end of such period. The underwriters of the
Company’s stock are intended third party beneficiaries of this Section 7(d) and
shall have the right, power and authority to enforce the provisions hereof as
though they were a party hereto.

8. Rights as Shareholders; Information. No holder of this Warrant, as such,
shall be entitled to vote or receive dividends or be deemed the holder of Series
Preferred or any other securities of the Company which may at any time be
issuable upon the exercise hereof for any purpose, nor shall anything contained
herein be construed to confer upon the holder of this Warrant, as such, any of
the rights of a shareholder of the Company or any right to vote for the election
of

 

-7-

--------------------------------------------------------------------------------

directors or upon any matter submitted to shareholders at any meeting thereof,
or to receive notice of meetings, or to receive dividends or subscription rights
or otherwise until this Warrant shall have been exercised and the Shares
purchasable upon the exercise hereof shall have become deliverable, as provided
herein. Notwithstanding the foregoing, the Company will transmit to the holder
of this Warrant such information, documents and reports as are generally
distributed to the holders of any class or series of the securities of the
Company concurrently with the distribution thereof to the shareholders.

9. Registration Rights. The Company grants registration rights to the holder of
this Warrant for any Common Stock of the Company obtained upon conversion of the
Series Preferred, comparable to the registration rights granted to the investors
in the Investor Rights Agreement, with the following exceptions and
clarifications:

(1) The holder will not have the right to demand registration, but can otherwise
participate in any registration demanded by others.

(2) The holder will be subject to the same provisions regarding indemnification
as contained in the Registration Rights Agreement.

(3) The registration rights are freely assignable by the holder of this Warrant
in connection with a permitted transfer of this Warrant or the Shares.

10. Additional Rights.

10.1 Acquisition Transactions. The Company shall provide the holder of this
Warrant with at least ten (10) days’ written notice prior to closing thereof of
the terms and conditions of any of the following transactions (to the extent the
Company has notice thereof), each of which shall constitute an “Acquisition
Transaction”: (i) the sale, lease, exchange, conveyance or other disposition of
all or substantially all of the Company’s property or business, or (ii) its
merger into or consolidation with any other corporation (other than a
wholly-owned subsidiary of the Company), or any transaction (including a merger
or other reorganization) or series of related transactions, in which more than
50% of the voting power of the Company is disposed of (other than the sale of
the Company’s capital stock in a transaction or series of transactions primarily
for capital raising purposes).

10.2 Right to Convert Warrant into Stock: Net Issuance.

(a) Right to Convert. In addition to and without limiting the rights of the
holder under the terms of this Warrant, the holder shall have the right to
convert this Warrant or any portion thereof (the “Conversion Right”) into shares
of Series Preferred as provided in this Section 10.2 at any time or from time to
time during the term of this Warrant. Upon exercise of the Conversion Right with
respect to a particular number of shares subject to this Warrant (the “Converted
Warrant Shares”), the Company shall deliver to the holder (without payment by
the holder of any exercise price or any cash or other consideration) that number
of shares of fully paid and nonassessable Series Preferred as is determined
according to the following formula:

X = B - A

 

-8-

--------------------------------------------------------------------------------

             Y

 

Where: X =

the number of shares of Series Preferred that shall be issued to holder
             Y = the fair market value of one share of Series Preferred
             A = the aggregate Warrant Price of the specified number of
Converted Warrant Shares immediately prior to the exercise of the Conversion
Right (i.e., the number of Converted Warrant Shares multiplied by the Warrant
Price)              B = the aggregate fair market value of the specified number
of Converted Warrant Shares (i.e., the number of Converted Warrant Shares
multiplied by the fair market value of one Converted Warrant Share)

No fractional shares shall be issuable upon exercise of the Conversion Right,
and, if the number of shares to be issued determined in accordance with the
foregoing formula is other than a whole number, the Company shall pay to the
holder an amount in cash equal to the fair market value of the resulting
fractional share on the Conversion Date (as hereinafter defined). For purposes
of Section 10 of this Warrant, shares issued pursuant to the Conversion Right
shall be treated as if they were issued upon the exercise of this Warrant.

(b) Method of Exercise. The Conversion Right may be exercised by the holder by
the surrender of this Warrant at the principal office of the Company together
with a written statement (which may be in the form of Exhibit A-1 or Exhibit A-2
hereto) specifying that the holder thereby intends to exercise the Conversion
Right and indicating the number of shares subject to this Warrant which are
being surrendered (referred to in Section 10.2(a) hereof as the Converted
Warrant Shares) in exercise of the Conversion Right. Such conversion shall be
effective upon receipt by the Company of this Warrant together with the
aforesaid written statement, or on such later date as is specified therein (the
“Conversion Date”), and, at the election of the holder hereof, may be made
contingent upon the closing of the sale of the Company’s Common Stock to the
public in a public offering pursuant to a Registration Statement under the Act
(a “Public Offering”). Certificates for the shares issuable upon exercise of the
Conversion Right and, if applicable, a new warrant evidencing the balance of the
shares remaining subject to this Warrant, shall be issued as of the Conversion
Date and shall be delivered to the holder within thirty (30) days following the
Conversion Date.

(c) Determination of Fair Market Value. For purposes of this Section 10.2, “fair
market value” of a share of Series Preferred (or Common Stock if the Series
Preferred has been automatically converted into Common Stock) as of a particular
date (the “Determination Date”) shall mean:

(i) If the Conversion Right is exercised in connection with and contingent upon
a Public Offering, and if the Company’s Registration Statement relating to such
Public Offering (“Registration Statement”) has been declared effective by the
Securities and Exchange Commission, then the initial “Price to Public” specified
in the final prospectus with respect to such offering.

 

-9-

--------------------------------------------------------------------------------

(ii) If the Conversion Right is not exercised in connection with and contingent
upon a Public Offering, then as follows:

(A) If traded on a securities exchange, the fair market value of the Common
Stock shall be deemed to be the average of the closing prices of the Common
Stock on such exchange over the five trading days immediately prior to the
Determination Date, and the fair market value of the Series Preferred shall be
deemed to be such fair market value of the Common Stock multiplied by the number
of shares of Common Stock into which each share of Series Preferred is then
convertible;

(B) If traded on the Nasdaq Stock Market or other over-the-counter system, the
fair market value of the Common Stock shall be deemed to be the average of the
closing prices of the Common Stock over the five trading days immediately prior
to the Determination Date, and the fair market value of the Series Preferred
shall be deemed to be such fair market value of the Common Stock multiplied by
the number of shares of Common Stock into which each share of Series Preferred
is then convertible; and

(C) If there is no public market for the Common Stock, then fair market value
shall be determined by the Board of Directors of the Company in good faith.

In making a determination under clauses (A) or (B) above, if on the
Determination Date, five trading days had not passed since the IPO, then the
fair market value of the Common Stock shall be the average closing prices or
closing bid prices, as applicable, for the shorter period beginning on and
including the date of the IPO and ending on the trading day prior to the
Determination Date (or if such period includes only one trading day, the closing
price or closing bid price, as applicable, for such trading day). If closing
prices or closing bid prices are no longer reported by a securities exchange or
other trading system, the closing price or closing bid price shall be that which
is reported by such securities exchange or other trading system at 4:00 p.m. New
York City time on the applicable trading day.

10.3 Exercise Prior to Expiration. To the extent this Warrant is not previously
exercised as to all of the Shares subject hereto, and if the fair market value
of one share of the Series Preferred is greater than the Warrant Price then in
effect, this Warrant shall be deemed automatically exercised pursuant to
Section 10.2 above (even if not surrendered) immediately before its expiration.
For purposes of such automatic exercise, the fair market value of one share of
the Series Preferred upon such expiration shall be determined pursuant to
Section 10.2(c). To the extent this Warrant or any portion thereof is deemed
automatically exercised pursuant to this Section 10.3, the Company agrees to
promptly notify the holder hereof of the number of Shares, if any, the holder
hereof is to receive by reason of such automatic exercise.

 

-10-

--------------------------------------------------------------------------------

11. Representations and Warranties. The Company represents and warrants to the
holder of this Warrant as follows:

(a) This Warrant has been duly authorized and executed by the Company and is a
valid and binding obligation of the Company enforceable in accordance with its
terms, subject to laws of general application relating to bankruptcy, insolvency
and the relief of debtors and the rules of law or principles at equity governing
specific performance, injunctive relief and other equitable remedies.

(b) The Shares have been duly authorized and reserved for issuance by the
Company and, when issued in accordance with the terms hereof, will be validly
issued, fully paid and nonassessable and free from preemptive rights.

(c) The rights, preferences, privileges and restrictions granted to or imposed
upon the Series Preferred and the holders thereof are as set forth in the
Charter, and on the Date of Grant, each share of the Series Preferred
represented by this Warrant is convertible into one share of Common Stock.

(d) The shares of Common Stock issuable upon conversion of the Shares have been
duly authorized and reserved for issuance by the Company and, when issued in
accordance with the terms of the Charter will be validly issued, fully paid and
nonassessable.

(e) The execution and delivery of this Warrant are not, and the issuance of the
Shares upon exercise of this Warrant in accordance with the terms hereof will
not be, inconsistent with the Company’s Charter or by-laws, do not and will not
contravene any law, governmental rule or regulation, judgment or order
applicable to the Company, and do not and will not conflict with or contravene
any provision of, or constitute a default under, any indenture, mortgage,
contract or other instrument of which the Company is a party or by which it is
bound or require the consent or approval of, the giving of notice to, the
registration or filing with or the taking of any action in respect of or by, any
Federal, state or local government authority or agency or other person, except
for the filing of notices pursuant to federal and state securities laws, which
filings will be effected by the time required thereby.

(f) There are no actions, suits, audits, investigations or proceedings pending
or, to the knowledge of the Company, threatened against the Company in any court
or before any governmental commission, board or authority which, if adversely
determined, could have a material adverse effect on the ability of the Company
to perform its obligations under this Warrant.

(g) The number of shares of Common Stock of the Company outstanding on the date
hereof, on a fully diluted basis (assuming the conversion of all outstanding
convertible securities and the exercise of all outstanding options and
warrants), does not exceed 35,000,000 shares.

12. Modification and Waiver. This Warrant and any provision hereof may be
changed, waived, discharged or terminated only by an instrument in writing
signed by the party against which enforcement of the same is sought.

13. Notices. Any notice, request, communication or other document required or
permitted to be given or delivered to the holder hereof or the Company shall be
delivered, or shall be sent by certified or registered mail, postage prepaid, to
each such holder at its address as shown on the books of the Company or to the
Company at the address indicated therefor on the signature page of this Warrant.

 

-11-

--------------------------------------------------------------------------------

14. Binding Effect on Successors. This Warrant shall be binding upon any
corporation succeeding the Company by merger, consolidation or acquisition of
all or substantially all of the Company’s assets, and all of the covenants and
agreements of the Company shall inure to the benefit of the successors and
assigns of the holder hereof.

15. Lost Warrants or Stock Certificates. The Company covenants to the holder
hereof that, upon receipt of evidence reasonably satisfactory to the Company of
the loss, theft, destruction or mutilation of this Warrant or any stock
certificate and, in the case of any such loss, theft or destruction, upon
receipt of an indemnity reasonably satisfactory to the Company, or in the case
of any such mutilation upon surrender and cancellation of such Warrant or stock
certificate, the Company will make and deliver a new Warrant or stock
certificate, of like tenor, in lieu of the lost, stolen, destroyed or mutilated
Warrant or stock certificate.

16. Descriptive Headings. The descriptive headings of the various Sections of
this Warrant are inserted for convenience only and do not constitute a part of
this Warrant. The language in this Warrant shall be construed as to its fair
meaning without regard to which party drafted this Warrant.

17. Governing Law. This Warrant shall be construed and enforced in accordance
with, and the rights of the parties shall be governed by, the laws of the State
of Delaware.

18. Survival of Representations, Warranties and Agreements. All representations
and warranties of the Company and the holder hereof contained herein shall
survive the Date of Grant, the exercise or conversion of this Warrant (or any
part hereof) or the termination or expiration of rights hereunder. All
agreements of the Company and the holder hereof contained herein shall survive
indefinitely until, by their respective terms, they are no longer operative.

19. Remedies. In case any one or more of the covenants and agreements contained
in this Warrant shall have been breached, the holders hereof (in the case of a
breach by the Company), or the Company (in the case of a breach by a holder),
may proceed to protect and enforce their or its rights either by suit in equity
and/or by action at law, including, but not limited to, an action for damages as
a result of any such breach and/or an action for specific performance of any
such covenant or agreement contained in this Warrant.

20. No Impairment of Rights. The Company will not, by amendment of its Charter
or through any other means, 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 holder of
this Warrant against impairment.

 

-12-

--------------------------------------------------------------------------------

21. Severability. The invalidity or unenforceability of any provision of this
Warrant in any jurisdiction shall not affect the validity or enforceability of
such provision in any other jurisdiction, or affect any other provision of this
Warrant, which shall remain in full force and effect.

22. Recovery of Litigation Costs. If any legal action or other proceeding is
brought for the enforcement of this Warrant, or because of an alleged dispute,
breach, default, or misrepresentation in connection with any of the provisions
of this Warrant, the successful or prevailing party or parties shall be entitled
to recover reasonable attorneys’ fees and other costs incurred in that action or
proceeding, in addition to any other relief to which it or they may be entitled.

23. Entire Agreement Modification. This Warrant constitutes the entire agreement
between the parties pertaining to the subject matter contained in it and
supersedes all prior and contemporaneous agreements, representations, and
undertakings of the parties, whether oral or written, with respect to such
subject matter.

[Remainder of page intentionally blank. Signature page follows.]

 

-13-

--------------------------------------------------------------------------------

The Company has caused this Warrant to be duly executed and delivered as of the
Date of Grant specified above.

 

INOTEK PHARMACEUTICALS CORPORATION By:

/s/ James G. Ham, III

Name: James G. Ham, III Title: CFO Address:

131 Hartwell Avenue, 1st Floor

Lexington, MA 02421

[SIGNATURE PAGE TO WARRANT (Loan A)]

--------------------------------------------------------------------------------

EXHIBIT A-1

NOTICE OF EXERCISE

 

To: INOTEK PHARMACEUTICALS CORPORATION (the “Company”)

1. The undersigned hereby:

 

  ¨ elects to purchase                 shares of [Series Preferred Stock]
[Common Stock] of the Company pursuant to the terms of the attached Warrant, and
tenders herewith payment of the purchase price of such shares in full, or

 

  ¨ elects to exercise its net issuance rights pursuant to Section 10.2 of the
attached Warrant with respect to                 Shares of [Series Preferred
Stock] [Common Stock].

2. Please issue a certificate or certificates representing            shares in
the name of the undersigned or in such other name or names as are specified
below:

 

 

(Name)

 

 

 

 

(Address)

3. The undersigned represents that the aforesaid shares are being acquired for
the account of the undersigned for investment and not with a view to, or for
resale in connection with, the distribution thereof and that the undersigned has
no present intention of distributing or reselling such shares, all except as in
compliance with applicable securities laws.

 

 

 

(Signature)

 

                             

        (Date)

--------------------------------------------------------------------------------

EXHIBIT A-2

NOTICE OF EXERCISE

 

To: INOTEK PHARMACEUTICALS CORPORATION (the “Company”)

1. Contingent upon and effective immediately prior to the closing (the
“Closing”) of the Company’s public offering contemplated by the Registration
Statement on Form S    , filed                , 200    , the undersigned hereby:

¨ elects to purchase                     shares of [Series Preferred Stock]
[Common Stock] of the Company (or such lesser number of shares as may be sold on
behalf of the undersigned at the Closing) pursuant to the terms of the attached
Warrant, or

¨ elects to exercise its net issuance rights pursuant to Section 10.2 of the
attached Warrant with respect to                    Shares of [Series Preferred
Stock] [Common Stock].

2. Please deliver to the custodian for the selling shareholders a stock
certificate representing such                shares.

3. The undersigned has instructed the custodian for the selling shareholders to
deliver to the Company $                 or, if less, the net proceeds due the
undersigned from the sale of shares in the aforesaid public offering. If such
net proceeds are less than the purchase price for such shares, the undersigned
agrees to deliver the difference to the Company prior to the Closing.

 

 

 

(Signature)

 

                             

        (Date)