<PAGE>   1
                                                                  EXHIBIT 10.10

                               [FORM OF WARRANT]


THE SECURITIES REPRESENTED BY THIS CERTIFICATE (THE "SECURITIES") HAVE BEEN
ISSUED AND SOLD IN RELIANCE UPON EXEMPTIONS FROM REGISTRATION UNDER THE
SECURITIES ACT OF 1933 (THE "1933 ACT"), SECTION 10-5-9(13) OF THE OFFICIAL
CODE OF GEORGIA ANNOTATED (THE "GEORGIA CODE"), AND APPROPRIATE EXEMPTIONS FROM
REGISTRATION UNDER THE SECURITIES LAWS OF OTHER APPLICABLE JURISDICTIONS. THE
SECURITIES MAY NOT BE OFFERED FOR SALE, SOLD OR TRANSFERRED OTHER THAN PURSUANT
TO AN EFFECTIVE REGISTRATION OR AN EXEMPTION SATISFACTORY TO THE ISSUER OF
COMPLIANCE WITH THE 1933 ACT, THE GEORGIA CODE AND THE APPLICABLE SECURITIES
LAWS OF ANY OTHER JURISDICTION. THE ISSUER SHALL BE ENTITLED TO REQUIRE AN
OPINION OF COUNSEL REASONABLY SATISFACTORY TO IT WITH RESPECT TO COMPLIANCE
WITH THE 1933 ACT.

No:                                                          Right to Purchase
                                                          Series C Convertible
                                                            Preferred Stock of
                                                            AtheroGenics, Inc.


                                    FORM OF

                               ATHEROGENICS, INC.

             SERIES C CONVERTIBLE PREFERRED STOCK PURCHASE WARRANT


         AtheroGenics, Inc., a Georgia corporation (the "Company"), hereby
certifies that, for value received, ______________________ (the "Holder"), or
its successors or registered assigns, is entitled, subject to the terms set
forth below, to purchase from the Company, commencing on the Exercise Date (as
hereinafter defined) and thereafter, at any time or from time to time before
5:00 p.m., Atlanta, Georgia time, on the Expiration Date (as hereinafter
defined), that number of fully paid and nonassessable Preferred Shares (as
hereinafter defined) as is equal to the Warrant Number (as hereinafter
defined), at a purchase price per share as is equal to the Purchase Price (as
hereinafter defined). The number of such Preferred Shares and the Purchase
Price are subject to adjustment as provided in this Warrant.

         This Warrant is issued as a replacement to the Company's obligation to
issue a "New Warrant" to the Holder pursuant to that certain Loan Agreement,
dated as of August 24, 1998, as amended as of December 17, 1998, as of April
13, 1999 and as otherwise amended, supplemented or modified and in effect from
time to time (the "Loan Agreement") by and among the Company and the lenders
named therein, a copy of which is on file at the principal office of the
Company. This Warrant is one of several warrants (the "Purchase Warrants")
representing the right to purchase Preferred Shares issuable pursuant to and
contemplated by the Loan Agreement.



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         As used herein the following terms, unless the context otherwise
requires, have the respective meanings set forth below:

         (a)      The term "Company" shall include AtheroGenics, Inc., a
Georgia corporation, and any corporation that shall succeed to or assume the
obligations of AtheroGenics, Inc. hereunder.

         (b)      The term "Preferred Shares" means the Company's Series C
Convertible Preferred Stock.

         (c)      The term "Purchase Price" shall mean $3.00 per Preferred
Share, subject to adjustment pursuant to Section 5 hereof.

         (d)      The term "Outstanding Principal Amount" shall mean the
maximum aggregate principal amount then outstanding of one or more Notes (the
"Notes") from the Company to the Holder and the other holders of the Notes and
issued pursuant to the Loan Agreement.

         (e)      The term "Warrant Number" shall mean, subject to adjustment
pursuant to Section 5 hereof, that number of the Company's Preferred Shares
equal to __________.

         1.                Term. This Warrant is exercisable, in whole or in
part, at any time and from time to time commencing on the date hereof (such
date referred to as the "Exercise Date") and prior to the Expiration Date (as
hereinafter defined). This Warrant shall expire and be of no further force and
effect upon the earlier to occur of (x) the time when it has been exercised
with respect to all Preferred Shares which the Holder is or may become entitled
to purchase hereunder or (y) 5:00 p.m. Atlanta, Georgia time on December 31,
2008 (the "Expiration Date").

         2.                Exercise of Warrant. The purchase rights represented
by this Warrant may be exercised by the Holder as provided in Section 1 in
whole or in part by the surrender of this Warrant to the Company at its
principal office in Alpharetta, Georgia, along with a written notice stating
that the Holder intends to purchase all or a specified number of Preferred
Shares pursuant to this Warrant and specifying the name or names in which the
Holder wishes the certificate or certificates for the Preferred Shares to be
issued, and together with payment of the Purchase Price for the shares then
purchased. Such payment shall be made, at the option of the Holder, by
certified or official bank check payable to the order of the Company in same
day funds or by wire transfer of same day funds to an account designated by the
Company for such purpose. At the option of the Holder, the Holder may, as
payment of the Purchase Price for the Preferred Shares then purchased, elect to
receive a number of Preferred Shares equal to the number of Preferred Shares
then purchased, less a number of Preferred Shares then having a fair market
value equal to the Purchase Price of the Preferred Shares then purchased. If
the number of Preferred Shares then purchased is less than the total number of
Preferred Shares then issuable upon exercise of this Warrant, the Company shall
cancel this Warrant upon surrender and shall execute and deliver a new Warrant
of like tenor and date for the balance of the shares issuable upon the exercise
of this Warrant (provided, that if only a fractional share remains unexercised,
the Company shall make a cash payment therefor in lieu of issuing a new
Warrant). As promptly as practicable after such surrender of this Warrant, the
Company shall issue and deliver to the Holder, at the address appearing in the
books of the Company or otherwise designated by Holder,



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a certificate or certificates for the applicable number of Preferred Shares.
Certificates representing Preferred Shares purchased pursuant to this Warrant
shall bear restrictive legends substantially similar to those at the head of
this Warrant and as required by the Loan Agreement, or such other restrictive
legends as the Company and the Company's counsel deem necessary or advisable
under applicable law.

         3.                Reservation of Shares; Validity of Issuance. The
Company covenants and agrees that it shall reserve for issuance as of the
Exercise Date of this Warrant and keep available out of its authorized but
unissued Preferred Shares, free from preemptive rights, such number of
Preferred Shares for which this Warrant shall from time to time be exercisable.
The Company represents and warrants that all shares issued upon the exercise of
this Warrant will, upon issuance, be fully paid and nonassessable and be free
from all taxes, liens and charges in respect of their issuance.

         4.                Merger, Consolidation or Sale of Assets. In the
event of any capital reorganization or any consolidation or merger of the
Company with or into another person (each, a "Reorganization"), the Holder
shall have the right to purchase and receive, upon the basis and upon the terms
and conditions specified in this Warrant and in lieu of the Preferred Shares of
the Company then purchasable and receivable upon the exercise of the rights
represented by this Warrant, the kind and number of shares of stock, securities
or other property (including cash) of the Company, or other corporation
resulting from such consolidation or surviving such merger, to which the holder
of the number of outstanding Preferred Shares equal to the number of shares of
such stock then purchasable and receivable upon the exercise of the rights
represented by this Warrant immediately prior to such Reorganization would have
been entitled to receive with respect to such Reorganization, and in any such
case appropriate provision shall be made in the application of the provisions
herein set forth with respect to the rights and interests thereafter of the
Holder to the end that the provisions herein set forth shall thereafter be
applicable, as nearly as reasonably may be, in relation to any shares, other
securities or property thereafter deliverable upon the exercise of this
Warrant. The Company shall not effect any Reorganization unless prior to or
simultaneously with the consummation of such Reorganization the successor
corporation (if other than the Company) resulting from such Reorganization
shall assume by written instrument executed and delivered to the Holder at the
address of the Holder appearing in the books of the Company, the obligation to
deliver to the Holder such shares, securities or property as, in accordance
with the provisions of this Section 4, the Holder may be entitled to purchase.
The provisions of this Section 4 shall similarly apply to successive
Reorganizations.

         5.                Adjustments. If outstanding Preferred Shares shall
be subdivided into a greater number of shares, or a dividend in Preferred
Shares or other securities of the Corporation convertible or exchangeable into
Preferred Shares (in which latter event the number of Preferred Shares issuable
upon the conversion or exchange of such securities shall be deemed to have been
distributed), shall be paid in respect to the Preferred Shares, the number of
Preferred Shares which may be acquired by the Holder upon the exercise of this
Warrant shall, simultaneously with the effectiveness of such subdivision or
immediately after the record date of such dividend, be proportionately
increased, and conversely, if the outstanding Preferred Shares shall be
combined into a smaller number of shares, the number of Preferred Shares which
may be



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acquired by the Holder upon the exercise of this Warrant shall, simultaneously
with the effectiveness of such combination, be proportionately reduced.

         6.                Notice of Certain Events. In case at any time:

                           (i)      the Company shall declare or pay any
dividend or make any distribution to the holders of its Preferred Shares;

                           (ii)     the Company shall offer for subscription
pro rata to the holders of its Preferred Shares any additional shares of stock
of any class or other rights;

                           (iii)    there shall be any capital reorganization
or reclassification of the capital stock of the Company or consolidation or
merger of the Company with, or sale of all or substantially all of its assets
to, another corporation or entity; or

                           (iv)     there shall be a voluntary or involuntary
dissolution, liquidation or winding up of the Company;

then, in any one or more of the above cases, the Company shall give written
notice, by first class mail, postage prepaid, addressed to the Holder at the
address of the Holder as shown on the books of the Company, of the date on
which (i) the books of the Company shall close or a record shall be taken for
such dividend, distribution or subscription rights or (ii) such reorganization,
reclassification, consolidation, merger, sale, dissolution, liquidation or
winding up shall take place, as the case may be. Such notice shall also specify
the date as of which the holders of Preferred Shares of record shall
participate in said dividend, distribution or subscription rights, or shall be
entitled to exchange their Preferred Shares for securities or other property
deliverable upon such reorganization, reclassification, consolidation, merger,
sale, dissolution, liquidation or winding up, as the case may be. Such written
notice shall be given not less than 30 days prior to the record date or the
date on which the transfer books of the Company are closed in respect to such
record date in the case of an action specified in clause (i) and at least 30
days prior to the action in question in the case of an action specified in
clause (ii). Any notices given pursuant to this Section 6 shall be effective
and deemed received upon the date of actual receipt or upon the fifth calendar
day subsequent to deposit in the United States mail (or other comparable mail
system), whichever is earlier.

         7.                No Impairment. The Company will not, by amendment of
its Articles of Incorporation or through any reorganization, transfer of
assets, consolidation, merger, dissolution, issue or sale of securities or any
other voluntary action, avoid or seek to avoid the observance or performance of
any of the terms to be observed or performed by the Company under this Warrant,
but will at all times in good faith assist in the carrying out of all the
provisions of Sections 3 through 6 and in the taking of all such action as may
be necessary or appropriate in order to protect the rights of the Holder.

         8.                No Voting Rights. This Warrant shall not entitle the
Holder to any voting rights or other rights as a shareholder of the Company,
and no dividend or interest shall be payable or accrue in respect of this
Warrant or the interest represented by or the shares



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<PAGE>   5

purchasable under this Warrant until and unless, and except to the extent that,
this Warrant shall be exercised.

         9.                Stock Certificates. The issue of stock certificates
upon the exercise of this Warrant shall be made without charge to the Holder
for any tax (other than taxes attributable to any difference between the fair
market value and the exercise price of this Warrant on the date of the exercise
of this Warrant or transfer taxes resulting from issuance of stock certificates
to a person other than the Holder) in respect of the issue of such stock. The
Holder shall for all purposes be deemed to have become the holder of record of
the shares issued upon exercise of this Warrant on the date on which the
Warrant was surrendered and payment of the Warrant Price was made, irrespective
of the date of delivery of the certificate for such shares, except that, if the
date of such surrender and payment is a date when the stock transfer books of
the Company are closed the Holder shall be deemed to have become the holder of
such shares at the close of business on the next succeeding date on which the
stock transfer books are open.

         10.               Lost, Stolen, Mutilated or Destroyed Warrant. Upon
receipt of evidence reasonably satisfactory to the Company of the loss, theft,
mutilation or destruction of this Warrant, and in case of loss, theft or
destruction, upon the agreement of the Holder to indemnify the Company, or in
the case of mutilation, upon surrender and cancellation of this Warrant, the
Company shall issue a new Warrant of like denomination and tenor as the Warrant
so lost, stolen, mutilated or destroyed. Any such new Warrant shall constitute
an original contractual obligation of the Company, whether or not the allegedly
lost, stolen, mutilated or destroyed Warrant shall be at any time enforceable
by anyone.

         11.               Applicable Law. This Warrant shall be governed by
and construed in accordance with the internal laws of the State of Georgia,
without regard to the principles of conflicts of law.

         IN WITNESS WHEREOF, the Company has duly executed this Warrant as of
the 13th day of April, 1999.


                             ATHEROGENICS, INC.



                             By: /s/
                                 ----------------------------------------------
                             Name:  Russell M. Medford, M.D., Ph.D.
                             Title:  President and Chief Executive Officer



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<PAGE>   6
                     Series C Convertible Preferred Warrant

Names of investors, amount of shares and warrant number for each Series C
Convertible Preferred Warrant issued by AtheroGenics, Inc.

<TABLE>
<CAPTION>
================================================================================
              Name                          Shares                      No.
================================================================================
<S>                                         <C>                         <C>
Alliance Technology Ventures, L.P.          46,374                      22
--------------------------------------------------------------------------------
ATV/GP, L.P.                                12,859                      23
--------------------------------------------------------------------------------
ATV/MJF, L.P.                                3,514                      24
--------------------------------------------------------------------------------
Domain Partners III, L.P.                   32,219                      25
--------------------------------------------------------------------------------
Biotechnology Investments Limited           23,937                      26
--------------------------------------------------------------------------------
DP III Associates, L.P.                      1,115                      27
--------------------------------------------------------------------------------
Sprout Capital VII, L.P.                    31,234                      28
--------------------------------------------------------------------------------
The Sprout CEO Fund, L.P.                      363                      29
--------------------------------------------------------------------------------
DLJ Capital Corp.                              718                      30
--------------------------------------------------------------------------------
DLJ First ESC L.P.                           3,591                      31
--------------------------------------------------------------------------------
New York Life Insurance Company             20,333                      32
--------------------------------------------------------------------------------
Boston University Nominee Partnership       16,667                      33
--------------------------------------------------------------------------------
Intelligent Systems Corporation              5,000                      34
--------------------------------------------------------------------------------
Arthur M. Pappas                             1,000                      35
--------------------------------------------------------------------------------
Roy M. Barbee                                  359                      36
--------------------------------------------------------------------------------
Vaughn D. Bryson                               359                      37
--------------------------------------------------------------------------------
Joseph C. Cook, Jr.                            359                      38
--------------------------------------------------------------------------------
Sanderling Venture Partners III, L.P.        2,920                      39
--------------------------------------------------------------------------------
Sanderling III Limited                       1,513                      40
--------------------------------------------------------------------------------
Sanderling III Biomedical, L.P.                504                      41
--------------------------------------------------------------------------------
Sanderling Ventures Management                   64                      42
--------------------------------------------------------------------------------
</TABLE>