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Isis Pharmaceuticals, Inc. v. Santaris Pharma A/S Corp.

United States District Court, S.D. California

February 27, 2014

ISIS PHARMACEUTICALS, INC., a Delaware Corporation, Plaintiff,
v.
SANTARIS PHARMA A/S CORP., a Delaware Corporation, and SANTARIS PHARMA A/S, a Danish Corporation, Defendants. AND RELATED COUNTERCLAIMS.

ORDER DENYING DEFENDANTS' MOTION FOR PARTIAL SUMMARY JUDGMENT OF NONINFRINGEMENT (ECF NO. 195)

GONZALO P. CURIEL, District Judge

INTRODUCTION

Plaintiff Isis Pharmaceuticals, Inc. (Isis) alleges defendants Santaris Pharma A/S Corp. and Santaris Pharma A/S (together, Santaris) have infringed three of Isis's patents by offering to sell certain drug discovery and development services to several U.S. pharmaceutical companies. (ECF No. 130, First Am. Compl. (FAC).) Before the Court is Santaris's renewed Motion for Summary Judgment of Noninfringement (Motion) pursuant to 35 U.S.C. § 271(e)(1)'s so-called "safe harbor." (ECF No. 195.) Isis has opposed Santaris's Motion, (ECF No. 223), and Santaris has filed a reply, (ECF No. 244). The Court found Santaris's Motion suitable for disposition without oral argument. See CivLR 7.1.d.1. Having considered the parties' submissions, the record in this matter, and the applicable law, and for the reasons that follow, the Court will DENY Santaris's Motion.

BACKGROUND

To avoid duplicative efforts, this Court sets forth the background information of this case as described in Judge Moskowitz's September 19, 2012 Order Denying Defendants' Motion for Summary Judgment Without Prejudice. (See ECF No. 53 at 1-5.) The Court modifies the background provided by Judge Moskowitz as necessary to reflect the additional facts Isis has since alleged in its FAC. (See ECF No. 130.)

The three patents at issue in this litigation cover various forms of antisense technology. The Court thus provides an overview of antisense technology, the three patents-in-suit, and Plaintiff's specific infringement claims.

I. Overview of Antisense Technology

Proteins, fundamental molecules found in all living cells, are primary actors within a cell. They perform a variety of essential functions such as catalyzing chemical reactions, communicating between cells, and providing structural support. The overproduction or abnormal production of proteins can cause disease. One method for treating a disease caused by the overproduction of a certain "target" protein is to create an "antisense" molecule that interrupts the cellular process of creating that protein.

The cellular process of creating proteins begins with genetic information (genes) stored in DNA and proceeds in two stages: transcription and translation. During transcription, the gene for a particular protein is copied from a strand of DNA to a molecule called messenger RNA (mRNA). During translation, cellular machinery converts the information on the mRNA into proteins.

Antisense molecules-typically a type of a nucleic acid that is similar to DNA and mRNA molecules, but much shorter-are able to interrupt the genesis of the target protein at the translation stage by binding to the mRNA molecules containing the genetic information for that protein. Once bound to an mRNA molecule, the antisense molecule can obstruct the chemical process that translates the mRNA into a protein. The three biotechnology patents at issue in this litigation relate to antisense technology.

II. Patents

A. 199 Patent

U.S. Patent No. 6, 326, 199, "Gapped 2' Modified Oligonucleotides" or "gapmers" (199 Patent), claims, in independent claim 1, a method of enhancing an antisense molecule by creating structural features that (a) enable the antisense molecule to resist degradation before it reaches its target mRNA; (b) enhance "binding affinity" (i.e., the strength of the chemical bond between the antisense molecule and the target mRNA); and (c) activate an enzyme called Rnase H that, once activated, severs the target mRNA, preventing translation into the target protein. (See FAC ¶¶ 20-22; 199 Patent Col. 31, ll. 39-49.) Many of the dependent claims cover methods of modifying the molecule described in Claim 1.

Independent claim 11 claims a method of "modifying a sequence-specific ribo-nucleic acid" (i.e., a target mRNA or other type of RNA) using a molecule having the properties claimed in claim 1. (199 Patent Col. 33, ll. 3-15.) In other words, claim 11 covers the method of using the antisense molecule described in claim 1 to affect the function of its target.

B. 500 Patent

U.S. Patent No. 6, 066, 500, "Antisense Modulation of Beta Catenin Expression" (500 Patent), is directed toward antisense technology that is designed specifically to inhibit the expression of a protein called Beta catenin. Beta catenin has been implicated in the development of several types of cancer, including cancer of the colon and of the skin. Independent claims 1 and 3 cover an antisense molecule of a particular size that hybridizes with the mRNA molecule responsible for generating Beta catenin, and thereby "inhibits the expression of Beta catenin." (Col. 65, ll. 53-54.) Many of the dependent claims cover a more specific type of molecule that meets the qualifications of the molecule described in claims 1 and 3.

Claims 11 and 20 cover a "method of inhibiting the expression of human Beta catenin in human cells or tissues comprising contacting said cells or tissues in vitro with the antisense compound of [claims 1 and 3] so that expression of Beta catenin is inhibited." (Col. 66, ll. 56-59; Col. 68, ll. 3-6.)

C. 739 Patent

U.S. Patent No. 6, 440, 739, "Antisense Modulation of Glioma-Associated Oncogene-2 Expression" (739 Patent), is directed toward antisense technology that is designed specifically to inhibit the expression of a protein called glioma-associated oncogene-2. This protein is associated with a number of human development syndromes and cancer. (FAC ¶ 24.) Independent claims 1 and 3 cover an antisense molecule of a certain size that hybridizes with the mRNA molecule responsible for generating glioma-associated oncogene-2, thereby inhibiting the expression of that protein. (Col. 83, ll. 25-41.)

Claims 14 and 23 cover methods of inhibiting glioma-associated oncogene-2 by contacting cells in vitro with the antisense molecules covered in claims 1 and 3. (Col. 84, ll. 25-29, 49-54.)

III. Isis's infringement claims

Isis alleges that Santaris, in direct competition with Isis, "engages in the business of selling antisense drug discovery services and products to pharmaceutical company customers in the United States." (FAC ¶ 25.) Isis alleges that, as part of these "drug discovery services, " Santaris used the methods covered by the 199 Patent "as a research tool to identify targets and/or to screen... antisense molecules for activity inhibiting a target." ( Id. ¶ 26.) Isis alleges that "Santaris's business has been built around exploiting the platform technology pioneered and patented by Isis, and selling and offering it for sale to pharmaceutical companies." (Id.)

Isis further alleges that "Santaris has offered for sale and sold to Enzon Pharmaceuticals, Inc., antisense compounds that inhibit beta-catenin and glioma-associated oncogene-2 production in violation of the 500 Patent and the 739 Patent, respectively." ( Id. ¶ 28.)

Isis alleges four specific agreements between Santaris and pharmaceutical companies based in the United States form the basis of these infringement contentions:

January 4, 2011 announced agreement with Pfizer, Inc. Isis alleges Pfizer paid Santaris "$14 million for access to Santaris Pharma A/S Locked Nucleic Acid (LNA) Drug Platform to develop RNA-targeted drugs." ( Id. ¶ 41 (quoting FAC Ex. 4, Jan. 4, 2011 Press Release).) Pfizer also allegedly "agreed to pay milestones [up to $600 million] to Santaris upon the identification of up to ten gene targets and the discovery of lead antisense LNA molecule candidates."[1] (FAC ¶ 41.)

This agreement allegedly infringes the 199 patented methods by "[o]ffering for sale and selling the process of using gapmers to reduce target RNA for target validation purposes; and/or [o]ffering for sale and selling the process of screening and identifying gapmer compounds to identify drug candidates for drug development." ( Id. ¶ 43.)

July 27, 2006 announced agreement with Enzon Pharmaceuticals, Inc. Plaintiff alleges Santaris "sold two antisense gapmer molecules and targets to Enzon for $6 million, " (id. ¶ 46), and that, pursuant to the agreement, "Enzon nominated six additional targets for which Santaris agreed to identify LNA gapmer compounds that inhibit the nominated targets using Isis's ...


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