Exhibit 10.10 *** Text Omitted and Filed Separately CONFIDENTIAL TREATMENT REQUESTED Under 17 C.F.R. §§ 200.80(b)(4) and 230.406 LICENSE AGREEMENT

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Exhibit 10.10

*** Text Omitted and Filed Separately
CONFIDENTIAL TREATMENT REQUESTED
Under 17 C.F.R. §§ 200.80(b)(4) and 230.406

LICENSE AGREEMENT

by and between

THE SCRIPPS RESEARCH INSTITUTE,
a California nonprofit
public benefit corporation

and

OPTIMER PHARMACEUTICALS, Inc.
a Delaware corporation

TABLE OF CONTENTS

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LICENSE AGREEMENT

        This License Agreement is entered into and made effective as of this 1 ^st  day of June 2004, (the "Effective Date") by and between THE SCRIPPS RESEARCH INSTITUTE, a California nonprofit public benefit corporation ("Scripps") located at 10550 North Torrey Pines Road, La Jolla, California 92037, and OPTIMER PHARMACEUTICALS, INC., a Delaware corporation ("Licensee") located at 10130 Sorrento Valley Road, Suite D, San Diego, California 92121 with respect to the facts set forth below.

RECITALS

        A.    Scripps is engaged in fundamental scientific biomedical and biochemical research including research relating to treatments for Feline Immunodefficiency Virus ("FIV") and Human Immunodefficiency Virus ("HIV").

        B.    Licensee is engaged in research and development of treatments for FIV and HIV for human and veterinarian therapeutics.

        C.    Scripps has disclosed to Licensee certain technology described in certain technology disclosures, patents and patent applications listed on Exhibit A attached hereto and incorporated herein by reference.

        D.    Scripps has the exclusive right to grant a license to the technology listed on Exhibit A, subject to certain rights of the U.S. Government to use such technology for its own purposes, resulting from the receipt by Scripps of certain funding from the U.S. Government.

        E.    Scripps desires to grant to Licensee, and Licensee wishes to acquire, an exclusive worldwide right and license to the technology listed on Exhibit A and to certain patent rights and know-how of Scripps with respect thereto, subject to the terms and conditions set forth herein, with a view to developing and marketing diagnostic and therapeutic products within the Field (as defined below).

AGREEMENT

        NOW, THEREFORE, in consideration of the mutual covenants and conditions set forth herein, Scripps and Licensee hereby agree as follows:

        1.     Definitions .    Capitalized terms shall have the meaning set forth below.

        1.1     Affiliate .    The term "Affiliate" shall mean any entity which directly or indirectly controls, is controlled by or is under common control with Licensee. The term "control" as used herein means the possession of the power to direct or cause the direction of the management and the policies of an entity, whether through the ownership of a majority of the outstanding voting securities or by contract or otherwise.

        1.2     Agricultural Products .    The term "Agricultural Product", individually, or "Agricultural Products", collectively, shall mean any one or more product, device, method, procedure, software, computer program, material, or element utilized by the agricultural and farming industry for the purpose of improving, restricting or otherwise modifying growth or productivity of plants; or preventing or treating disease or insect or fungal infestation in plants; or controlling or modifying certain traits of plants or producing improved or modified seeds and plants; or techniques and methods for evaluating efficacy or determining the safety of an Agricultural Product such as utilization in determining toxicity to living things or otherwise involved in the general field of agriculture.

        1.3     Confidential Information .    The term "Confidential Information" shall mean any and all proprietary or confidential information of Scripps or Licensee which may be exchanged between the

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parties at any time and from time to time during the term of this Agreement. Information shall not be considered confidential to the extent that it:

• •         a.     Is publicly disclosed through no fault of any party hereto, either before or after it becomes known to the receiving party; or

            b.     Was known to the receiving party prior to the date of this Agreement, which knowledge was acquired independently and not from another party hereto (or such party's employees); or

            c.     Is subsequently disclosed to the receiving party in good faith by a third party who has a right to make such disclosure; or

            d.     Has been published by a third party as a matter of right.

        1.4     Field .    The term "Field" shall mean all human and veterinarian applications and shall exclude Agricultural Products.

        1.5     Licensed Product .    The term "Licensed Product" shall mean any product which cannot be developed, manufactured, offered for sale, imported, used or sold without (i) infringing one or more claims under Scripps Patent Rights; or (ii) utilizing any part of Scripps Technology not otherwise included within Scripps Patent Rights.

        1.6     Major Market Country .    The term "Major Market Country" shall mean any of the following countries and their respective territories and possessions: Canada, France, Germany, Italy, Japan, Thailand, the United Kingdom and the United States.

        1.7     Net Sales .    The term "Net Sales" shall mean the gross amount invoiced by Licensee, or its Affiliates and sublicensees, or any of them, on all sales of Licensed Products, less (i) discounts actually allowed, (ii) credits for claims, allowances, retroactive price reductions or returned goods, (iii) prepaid freight and (iv) sales taxes or other governmental charges actually paid in connection with sales of Licensed Products. For purposes of determining Net Sales, a sale shall be deemed to have occurred when an invoice therefor shall be generated or the Licensed Product is shipped for delivery. Sales of Licensed Products by Licensee, or an Affiliate or sublicensee of Licensee to any Affiliate or sublicensee which is a reseller thereof shall be excluded, and only the subsequent sale of such Licensed Products by Affiliates or sublicensees of Licensee to unrelated parties shall be deemed Net Sales hereunder.

        1.8     Scripps Patent Rights .    The term "Scripps Patent Rights" shall mean rights arising out of or resulting from (i) any and all U.S. and foreign patent applications and patents covering Scripps Technology, (ii) the patents proceeding from such applications, (iii) all claims of continuations-in-part directed solely to subject matter specifically described in Scripps Technology, and (iv) divisional, continuations, reissues, reexaminations, and extensions of any patent or application set forth in (i)-(iii) above, so long as said patents have not been held invalid and/or unenforceable by a court of competent jurisdiction from which there is no appeal or, if appealable, from which no appeal has been taken.

        1.9     Scripps Technology .    The term "Scripps Technology" shall mean so much of the technology as is proprietary to Scripps and disclosed in the patents, patent applications and disclosures listed on Exhibit A which is attached hereto and incorporated herein by reference, together with materials, information and know-how that are specifically related to the subject matter of the patents, patent applications, and disclosures listed on Exhibit A and are proprietary to Scripps, whether or not the same is eligible for protection under the patent laws of the United States or elsewhere, and whether or not the same would be enforceable as a trade secret or the copying of which would be enjoined or restrained by a court as constituting unfair competition.

        1.10     Valid Claim .    The term "Valid Claim" shall mean a claim of any issued and unexpired patent within the Scripps Patent Rights which has not been held unenforceable, unpatentable or invalid by a decision of a court or governmental body of competent jurisdiction in a ruling that is unappealable

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or unappealed within the time allowed for appeal, which has not been rendered unenforceable through disclaimer or otherwise, and which has not been lost through an interference proceeding; provided that if a claim of a pending patent application has not issued as a claim of an issued patent within the Scripps Patent Rights within ten (10) years after the filing date from which such claim takes priority, such pending claim shall not be a Valid Claim for the purposes of this Agreement.

        2.     License Terms and Conditions .    

        2.1     Grant of License .    Scripps hereby grants to Licensee an exclusive, worldwide license, including the right to sublicense, to Scripps Technology and under Scripps Patent Rights, to make, to have made, to import, to use, to offer for sell, and to sell Licensed Products in the Field, subject to the terms of this Agreement.

        2.2     Initial License Fee .    In partial consideration for the exclusive license granted pursuant to Section 2.1 hereof, Licensee shall pay to Scripps a nonrefundable license fee upon execution of this Agreement in the amount of fifty thousand (50,000) shares of Optimer Pharmaceutical Inc.'s common stock. The license fee described in this Section is consideration for the grant and continuation of the license hereunder, and Scripps shall have no obligation to return any portion of such license fee, notwithstanding any failure by Licensee to develop any Licensed Product or market any Licensed Product commercially, and notwithstanding the volume of sales of any such Licensed Product.

        2.3     Three Year Anniversary Fee .    Upon the third anniversary of the Effective Date of this License Agreement, Licensee shall pay to Scripps a nonrefundable anniversary fee of [***] [***] ($[***]) dollars.

        2.4     Royalties .    

        2.4.1     Percentage Royalty for Human Licensed Products .    As additional consideration for the exclusive license granted pursuant to Section 2.1 hereof, Licensee shall pay to Scripps a continuing royalty for human Licensed Products on a country-by-country basis in the amount of (i) [***] percent ([***]%) of Net Sales by Licensee of Licensed Products which cannot be made, imported, used or sold in such country without utilizing one or more Valid Claims with offsets allowed for royalties paid to third parties for required licenses for the commercialization of a Licensed Product, however, the percentage royalty paid to Scripps may not be reduced below [***] percent ([***]%), (ii) of [***] percent ([***]%) of Net Sales of Licensed Products, in all countries where the manufacture, use or sale of such Licensed Product is not covered by a Valid Claim in such country but is covered by Scripps Technology with offsets allowed for royalties paid to third parties for required licenses for the commercialization of a Licensed Product, however, the percentage royalty paid to Scripps may not be reduced below [***] [***] percent ([***]%).

        2.4.2     Percentage Royalty for Veterinarian Licensed Products .    As additional consideration for the exclusive license granted pursuant to Section 2.1 hereof, Licensee shall pay to Scripps a continuing royalty for veterinarian Licensed Products on a country-by-country basis in the amount of (i) [***] percent ([***]%) of Net Sales by Licensee of Licensed Products which cannot be made, imported, used or sold in such country without utilizing one or more Valid Claims with offsets allowed for royalties paid to third parties for required licenses for the commercialization of a Licensed Product, however, the percentage royalty paid to Scripps may not be reduced below [***] percent ([***]%); (ii) of [***] percent ([***]%) of Net Sales of Licensed Products, in all countries where the manufacture, use or sale of such Licensed Product is not covered by a Valid Claim in such country but is covered by Scripps Technology with offsets allowed for royalties paid to third parties for required licenses for the commercialization of a Licensed Product, however, the percentage royalty paid to Scripps may not be reduced below [***] [***] percent ([***]%).

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        2.4.3     Percentage Royalty on sales by Sublicensees for Human and Veterinarian Licensed Products .    

For the royalty on Net Sales by sublicensees the following formula will be used to determine the percentage royalty that Licensee shall pay to Scripps:

        R=[***][***] (T-P),

where, R= the percentage of royalty to be paid to Scripps;

where, T= the percentage royalty paid to Licensee on Net Sales of Licensed Product covered by Scripps Patent Rights by a sublicensee; and

where, P= the percentage royalty paid to third parties by Licensee

Provided that R shall not be less than [***]% for patented human products covered by an issued claim; and [***]% for human unpatented products; and [***]% for patented veterinarian products covered by an issued claim; and [***]% for unpatented veterinarian products.

        2.5     Milestone Payments .    In consideration for the license granted to Licensee, Licensee shall pay to Scripps within thirty (30) days upon the first occurrence, in a Major Market Country, of each milestone specified below for the first Licensed Product to meet such milestone. Payment of the milestones shall be in cash or common stock or a combination thereof at Licensee's option. If registered common stock comprises part of the payment, the registered common stock shall be priced at the arithmetic average of the closing trading prices for the twenty (20) trading days just prior to the date of the milestone.

        2.6     Quarterly Payments .    

        2.6.1     Sales by Licensee .    With regard to Net Sales made by Licensee or its Affiliates, royalties shall be payable by Licensee quarterly, within sixty (60) days after the end of each calendar quarter, based upon the Net Sales of Licensed Products during such preceding calendar quarter, commencing with the calendar quarter in which the first commercial sale of any Licensed Product is made.

        2.6.2     Sales by Sublicensees .    With regard to Net Sales made by sublicensees of Licensee or its Affiliates, royalties shall be payable by Licensee quarterly, within ninety (90) days after the end of each calendar quarter, based upon the Net Sales of Licensed Products by such sublicensee during such preceding calendar quarter, commencing with the calendar quarter in which the first commercial sale of any Licensed Product is made by such sublicensee.

        2.7     Term of License .    Unless terminated sooner in accordance with the provisions of this Agreement, the term of this license shall expire when the last of the royalty obligations set forth in Section 2.10 below have expired. Notwithstanding the foregoing, if applicable government regulations require a shorter term and/or a shorter term of exclusivity than provided for herein, then the term of this License Agreement shall be so shortened or this License Agreement shall be amended to provide for a non-exclusive license, and, in such event, the parties shall negotiate in good faith to reduce appropriately the royalties payable as set forth under the section heading "Royalties" hereof.

        2.8     Sublicense .    Licensee shall have the sole and exclusive right to grant sublicenses to any party with respect to the rights conferred upon Licensee under this Agreement, provided, however, that (i) any such sublicense shall be subject in all respects to the restrictions, exceptions, royalty obligations, reports, termination provisions, and other provisions contained in this Agreement (but not including the payment of a license fee pursuant to Section 2.2 hereof) and (ii) each such sublicensee, and the form and substance of each such sublicense, shall be subject to the prior written approval of Scripps, which

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approval shall not be unreasonably withheld, provided, however, that any sublicense granted to an Affiliate of Licensee shall not be subject to Scripps's prior written approval. No approval shall be required as to any sublicense which utilizes the form of sublicense attached hereto as Exhibit B. Licensee shall pay Scripps, or cause its Affiliate or sublicensee to pay Scripps, the same royalties on all Net Sales made by Licensee, its Affiliate or sublicensee. Each Affiliate and sublicensee shall report its Net Sales to Scripps through Licensee, which Net Sales shall be aggregated with any Net Sales of Licensee for purposes of determining the Net Sales upon which royalties are to be paid to Scripps.

        Except as set forth below, any sublicense revenues, other than royalties, due Licensee pursuant to the grant of a sublicense to a party not an Affiliate but excluding any payments for research, development, or equity ("Sublicense Revenue"), so long as said equity payment reflects the current fair market value of the stock, as determined by such sublicensees' board of directors, which determination will be acceptable as long as it is reasonable and reflects industry standards in comparable arrangements, shall be reported to Scripps by Licensee. For the first three years of this Agreement, the calculation of Scripps' percentage of Sublicense Revenue shall be based on a pro-rata contribution of Scripps Technology if it is sublicensed in combination with non-Scripps technology. For the fourth year and after Scripps shall receive [***]% of the Sublicense Revenue with no reductions if sublicensed in combination with non-Scripps technology. Licensee shall pay Scripps a portion of Sublicense Revenue according to the following schedule:

        2.9     Duration of Royalty Obligations .    The royalty obligations of Licensee as to each Licensed Product shall terminate: (i) on a country-by-country basis concurrently with the expiration of the last to expire of Scripps Patent Rights utilized by or in such Licensed Product in each such country; or (ii) with respect to Licensed Products utilizing only Scripps Technology but not Scripps Patent Rights, fifteen (15) years after the date of first commercial sale of such Licensed Product in such country.

        2.10     Reports .    Licensee shall furnish to Scripps at the same time as each royalty payment is made by Licensee, a detailed written report of Net Sales of the Licensed Products and the royalty due and payable thereon, including a description of any offsets or credits deducted therefrom, on a product-by-product and country-by-country basis, for the calendar quarter upon which the royalty payment is based.

        2.11     Records .    Licensee shall keep, and cause its Affiliates and sublicensees to keep, full, complete and proper records and accounts of all sales of Licensed Products in sufficient detail to enable the royalties payable on Net Sales of each Licensed Product to be determined. Scripps shall have the right to appoint an independent certified public accounting firm approved by Licensee, which approval shall not be unreasonably withheld, to audit the records of Licensee, its Affiliates and sublicensees as necessary to verify the royalties payable pursuant to this Agreement provided such auditor executes a confidentiality agreement standard for the industry. Licensee, its Affiliates and sublicensees shall pay to Scripps an amount equal to any additional royalties to which Scripps is entitled as disclosed by the audit, plus interest thereon at the rate of one and one-half percent (1.5%) per month. Such audit shall be at Scripps's expense; provided, however, that if the audit discloses that Scripps was underpaid royalties wi