Issue 43 | December 12, 2002
World's Major Patent Offices Publish Results: Patentability Issues of 3D Protein Structures
 On Monday December 2, 2002, the United States Patent and Trademark Office (USPTO) announced the joint publication, in association with the European Patent Office (EPO) and Japan Patent Office (JPO), of a report that provides clear guidance for patent application filings relating to three-dimensional protein structure in each of the three offices.

These applications are part of the burgeoning field of bioinformatics fueled by the great mass of genetic information produced by the Human Genome Project. The need to efficiently analyze, understand and apply the lessons learned from genomics is expected to provoke an increased number of patents, both on the deduced protein structures and the methods developed to analyze protein structural information.

"The guidance provided by this study will help Americans who file for patent protection on their proteomics-based inventions both here and abroad comply with the patentability requirements of each office," noted James E. Rogan, Under Secretary of Commerce for Intellectual Property and Director of the United States Patent and Trademark Office.

The report provides valuable insights on each office’s standards regarding patent eligible subject matter, utility, enablement, novelty and inventive-step/nonobviousness. The case studies in the report highlight how the individual offices may reach the same ultimate determinations, or in some cases, how their conclusions diverge. Most notably, the opinions differed among the three offices on questions of whether certain subject matter is patent eligible, and whether claimed subject matter was nonobvious..

There were four general case study categories: (i) claims to the underlying protein structural data; (ii) claims for the proteins, polypeptides and protein domains defined by the data; (iii) in silico screening methods, and; (iv) compounds.

Not surprisingly, all three offices agreed that the claims of group (i), directed to mere data or data representations, were non-patentable subject matter. Such claims included 3-D structural information, data arrays, and data compilations of atomic coordinates of proteins or pharmacophores, computer readable media containing such data, and computer models of proteins based on such data.

All three offices again reached consistent conclusions that claims of groups (ii) and (iv) were patentable, and that certain ones of them satisfied each office’s utility, enablement and novelty/nonobviousness requirements.

Unanimity was lost, however, when they considered group (iii) claims, directed to in silico screening methods. One of the points of disagreement was the question of patentable subject matter. Of the two exemplary claims in this group, the first did not explicitly recite any hardware resources, which led the JPO to conclude that the claim was not patentable subject matter. The second claim recited the use of a data structure containing the data analyzed by the method, which was apparently sufficient for the JPO to infer the use of a computer, and hence to render the claim patentable. The EPO and the USPTO, on the other hand, found both claims to be directed to patentable subject matter.

Different conclusions were again reached with respect to novelty/nonobviousness of group (iii) claims. The EPO found the second claim of the group to be novel and non-obvious. However, the JPO and USPTO found the claim to be obvious, based on two facts. First, the actual steps of the method were known in the prior art, and the only distinction over the prior art was the specific molecular structure(s) defined by atomic position data. Second, the nature of the atom positional data did not otherwise change the steps of the method, rendering it “non-functional” data (non-functional data cannot be relied upon as a sole source of novelty).

Just as they did recently in the area of genomics, patent systems must be able to adapt to new technologies. Now, through the publication of this report, the three Patent Offices are proactively providing guidance to practitioners on how to apply their patent law principles to inventions in the emerging field of 3-D protein structural analysis. Understanding how these patent offices will analyze this type of invention is crucial to formulating winning strategies, not only in prosecution, but in defending or attacking them during litigation. This would appear to be a particular challenge in the area of bioinformatics, where software algorithms and biochemistry meet.

The report is accessible through the USPTO's Trilateral Web Site at http://www.uspto.gov/web/tws/sr-3.htm.

To discuss this topic further, please contact the authors, Robert Irvine III and Kevin E. Noonan, at McDonnell Boehnen Hulbert & Berghoff, Chicago IL. . The information contained in this email is provided for informational purposes only and does not represent legal advice. Neither the APLF nor the author intends to create an attorney client relationship by providing this information to you through this message.