Ventures v. Syngenta Seeds, Inc.

[984 F.Supp.2d 960]

Geoffrey D. Biegler, Fish, Richardson Law Firm, San Diego, CA, Jeremy T. Fitzpatrick, Kutak, Rock Law Firm, Omaha, NE, John C. Adkisson, William R. Woodford, Fish, Richardson Law Firm, Minneapolis, MN, Limin Zheng, Fish, Richardson Law Firm, Redwood City, CA, Matthew M. Enenbach, Kutak, Rock Law Firm, Omaha, NE, for Plaintiff.

Gerald L. Friedrichsen, Fitzgerald, Schorr Law Firm, Omaha, NE, Hari Santhanam, Marcus E. Sernel, Mishele N. Kieffer, Russell E. Levine, Serena J. Pruitt, Kirkland, Ellis Law Firm, Chicago, IL, for Defendants.

This matter is before the Court on the parties' Joint Claim Construction Statement

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(Filing No. 75). Plaintiff and Counterclaim Defendant NuTech Ventures (“NUTech”) has sued Defendants and Counterclaim Plaintiffs Syngenta Seeds, Inc. (“Syngenta”) and Trenton Agri Products LLC (“Trenton”) (collectively “Defendants”) alleging that the Defendants have infringed U.S. Patent No. 6,506,592B1 (the “'592 Patent”). The parties collectively have requested that the Court construe certain terms in the '592 Patent.

The '592 Patent is titled “Hyperthermophilic Alpha–Glucosidase Gene and Its Use,” and generally relates to plant matter that has been genetically transformed so that it produces an enzyme not naturally produced in the plant. (Filing No. 1–1, summary; Filing No. 85 at 2.) The patent application was filed on August 18, 1999, and claims priority to a provisional application that was filed a year earlier. The '592 Patent issued on January 14, 2003, and includes nine claims directed to a “method of converting plant substrate.” Dr. Paul Blum (“Dr. Blum”), a professor and researcher at the University of Nebraska in Lincoln, Nebraska, developed the technology used in the '592 Patent, and NUTech owns the '592 Patent. NUTech claims that the Defendants' use of a bio-engineered corn called Enogen relies on technology from the ' 592 Patent to convert the starch in corn into smaller sugars during ethanol production.

The '592 Patent relates to reactions that occur during a chemical process called hydrolysis. Carbohydrates can be considered a group of sugar molecules joined by chemical bonds. Carbohydrates, such as starch, store energy. When the chemical bonds in a group of sugar molecules are broken, the starch can be processed for use in different industries, such as the production of ethanol. The chemical bonds between sugar molecules in starch are called “glycosidic bonds.” To convert starch into sugars, the chemical bonds between the sugar molecules are broken by water through hydrolysis.

The natural hydrolysis reaction can be very slow, so ethanol producers add proteins to the process called “enzymes” to act as catalysts to speed up the reactions. Enzymes are proteins that function as catalysts in biochemical reactions by acting on one or more starting plant materials called “substrates.” Environmental conditions, such as temperature and pH, can greatly affect the activity of an enzyme. In general, the activity of an enzyme increases with temperature because molecules move and interact more quickly at higher temperatures. Temperature also affects the integrity and stability of enzymes. Increased temperature can cause the protein structure of an enzyme to weaken, which can hinder its ability to catalyze reactions. Depending on their structure and other characteristics, some enzymes are only active at moderate temperatures, whereas other related enzymes catalyzing the same reactions are capable of activity at relatively high temperatures. The thermophilicity of an enzyme relates to the ability of the enzyme to catalyze reactions at relatively high temperatures.

While active enzymes can convert plant material to products such as ethanol, continued activity at times may not be desirable. For this reason, cells of living organisms have evolved to regulate enzyme activity. For example, cells can regulate when and where an enzyme is produced. Those skilled in the art can take advantage of natural regulatory mechanisms in living cells to design recombinant enzymes to catalyze desired activity. For example,

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those skilled in the art can engineer the cellular location and activity of enzymes to control when certain processes occur.

The claims in the '592 Patent involves a specific type of enzymes called “glycosyl hydrolases” that aid in breaking glycosidic bonds during hydrolysis. NUTech claims that, prior to the invention, companies typically added enzymes at some point during the hydrolysis process to speed up production. This is because industrial hydrolysis involved not only adding water and enzymes to a mixture of plant material, but also heating the mixture to a very high temperature. Thus, the enzymes had to be heat resistant to perform their function at high temperatures. Enzymes that can resist heat and perform their function at high temperatures are called “thermostable” enzymes. Purchasing and storing thermostable enzyme additives is expensive and represents a significant cost in the starch hydrolysis process.

In the '592 Patent, Dr. Blum claims to have identified and cloned a glycosyl hydrolase derived from an organism that grows in locations that experience high temperatures. Dr. Blum also developed a bioengineered plant containing glycosyl hydrolases from these organisms. Because the organisms could survive in high temperatures, the glycosyl hydrolases derived from the organisms were thermostable, and could survive at high temperatures. Further, the enzymes were already located in the bioengineered plants, so companies would not have to purchase, store, and then add the enzyme additives to convert the starch in the plant material. Because of their hyperthermophilic origin, the enzymes would not significantly interfere with the plants' normal metabolism, and were not toxic to the plants even when the enzymes were found inside the same cells as the plant substrate.

Dr. Blum originally filed a provisional patent application in 1998, and a formal patent application in 1999. The United States Patent and Trademark Office (“USPTO”) spent over three years reviewing the application before a patent was issued in 2003. Both parties' arguments reference the prosecution history to aid their respective claim constructions. By reviewing the prosecution history, the Court does not prejudge infringement or validity of the '592 Patent. However, this information is useful for background, and can be considered in interpreting terms.¹

The parties agree that, generally in the 1990s, the method in the industry was to add separately produced enzymes to plant material for use in hydrolysis. The '592 Patent states that “[a] variety of industries, such as food and chemical, employ hydrolases for the production of glucose, sucrose and other sugars,” and that “[h]igh value is placed on thermostability and thermoactivity of enzymes for use in the

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bioprocessing of starch....” (Filing No. 1–1 at 1:25–30.) The '592 Patent also notes that “the current method used in the industry” in the 1990s was “to add separately produced commodity enzymes to plant material.” ( Id. at 3:1–2.)

The USPTO Examiner originally rejected Dr. Blum's pending claims as obvious. The USPTO explained that the original application lacked reference to previously published papers on related subjects, and thus failed to disclose the prior art. Much of the prosecution history concerned a 1992 article entitled “Production of Active Bacillus Licheniformis Alpha–Amylase in Tobacco and Its Application in Starch Liquiefaction” written by Jan Pen and others (the “Pen Article”).² The USPTO noted that the Pen Article concerned a tobacco plant with enzymes that had the characteristic of being less active at lower temperatures and highly active at high temperatures. Accordingly, the USPTO rejected the application as obvious considering the prior art.

Dr. Blum responded to the USPTO by differentiating the enzymes described in the Pen Article from the enzymes in his application. Br. Blum explained that in the Pen Article, the plant substrate was located inside the plant cells, and the enzyme was outside the plant cells. Thus, the enzyme and the plant substrate were separated into different cellular compartments, and were brought together for the processing through homogenization. In contrast, the Dr. Blum argued that his invention used a “hyperthermophilic” glycosyl hydrolase. According to Dr. Blum's application, his invention did not require separation of the plant substrate from the enzymes, because the activity of the enzyme was not detectable at normal plant growth temperatures. The USPTO Examiner initially rejected this argument because the patent itself did not specifically state that the enzyme and the plant material could coexist in the cells. Specifically, the USPTO noted that the claims in the application “did not specifically require nonsequestered localization of the transgenic enzyme in the plant.” (Filing No. 86–5 at ECF 82.)

Dr. Blum responded by amending the '592 Patent's claims to include the phrase “wherein the glycosyl hydrolase is located with the substrate in tissue of the plant.” ( See Filing No. 1–1 at ECF 40.) Dr. Blum distinguished his invention from the prior art mentioned in the Pen Article by explaining that “[s]ince enzyme and substrate are present in different cellular compartments [in the method of the Pen Article], no degradation of the substrate occurs during growth. The enzymatic reaction is initiated ... when by homogenation the enzyme and the substrate are brought together.” (Filing No....