T 1067/02 (Changed epitopes/NOVOZYMES) 30-11-2004

Summary of Facts and Submissions

I. European patent No. 0 561 907, with the title "Proteins with changed epitopes and methods for the production thereof" and based on the European application No. 92. 900 779.7 (published as WO 92/10755), was granted with 11 claims.

II. Notices of opposition were filed by three opponents requesting the revocation of the patent under Articles 100(a),(b) and (c) EPC. The opponent 01 withdrew its opposition when the case was still pending before the opposition division. The patent was revoked by the opposition division on the grounds that the main request, first, second, third and fourth auxiliary requests then on file did not fulfil the requirements of Article 83 EPC.

III. An appeal was lodged by the patentee (appellant), who maintained all the requests put forward before the opposition division.

IV. The opponents 02 and 03 (respondents I and II, respectively) filed jointly written comments on the grounds of appeal.

V. The parties were summoned to oral proceedings and, in a communication under Article 11(1) of the Rules of Procedure of the Boards of Appeal, they were informed of the board's preliminary, non-binding opinion.

VI. In reply to the board's communication, the appellant filed on 29 October 2004 further observations and a clean copy of the first, second, third and fourth auxiliary requests corresponding to the ones originally put forward before the opposition division.

VII. Oral proceedings took place on 30 November 2004. During the oral proceedings, the appellant filed a new first and second auxiliary requests, whereas the previous first, second and third auxiliary requests were maintained as the third, fourth and fifth auxiliary requests, respectively. The previous fourth auxiliary request was amended and filed as a sixth auxiliary request. A seventh auxiliary request, comprising only subject-matter based on product claims, was also filed during the oral proceedings.

VIII. Claim 1 of the main request (claims as granted) read as follows:

"1. A method of producing a protein variant evoking a lowered immunogenic response in animals including man in comparison to the response evoked by its parent protein, whereby said complete protein is epitope mapped using immunological and proteochemical methods, epitopes are determined, and at least one of said epitopes is changed through mutation of a DNA molecule coding for the expression of said complete parent protein or synthesis of a DNA molecule coding for the expression of said variant protein, said mutated or constructed DNA molecule subsequently being inserted into a vector for transformation or transfection into a suitable host, wherein said vector is functional or whereby said mutated or constructed DNA molecule is integrated functionally into the genome of said host, said protein variant is expressed in the host, and recovered." (emphasis added by the board).

IX. Claim 1 of the first auxiliary request read as follows:

"1. A method of producing a variant of a protein of interest, the variant evoking a lowered immunogenic response in animals including man in comparison to the response evoked by its parent protein, whereby said protein of interest is epitope mapped using immunological and proteochemical methods, epitopes are determined, and at least one of said epitopes is changed through mutation of a DNA molecule coding for the expression of said parent protein of interest or synthesis of a DNA molecule coding for the expression of said variant protein, said mutated or constructed DNA molecule subsequently being inserted into a vector for transformation or transfection into a suitable host, wherein said vector is functional or whereby said mutated or constructed DNA molecule is integrated functionally into the genome of said host, said protein variant is expressed in the host, and recovered."

X. Claim 1 of the second auxiliary request read as follows:

"1. A method of producing a variant of a protein of interest which is an industrial enzyme or medicinal product, the variant evoking a lowered immunogenic ... (as claim 1 of the first auxiliary request)."

XI. Claims 1 of the third and fourth auxiliary requests read as claim 1 of the main request with the sentences :

"...in which the parent protein and variants thereof are used for the production of antibodies,..." (3rd AR)

"...in which the epitope mapping uses polyclonal antibodies and is divided into two phases: (i) measuring the reactivity of the antibody preparations toward all proteins of interest; and (ii) measuring the reactivity left over to react with one antigen after reaction with another,..." (4th AR)

added after the reference to the immunological and proteochemical methods.

XII. Claim 1 of the fifth auxiliary request read as claim 1 of the main request with the sentence:

"...by combining this information with a 3-dimensional (3D) view,..."

added after the reference to epitopes are determined.

XIII. Claim 1 of the sixth auxiliary request read as follows:

"1. A method of producing a subtilisin 309 protease variant evoking a lowered immunogenic response in animals including man in comparison to the response evoked by subtilisin 309, whereby said subtilisin 309 is epitope mapped using immunological and proteochemical methods in which subtilisin 309 and variants thereof are used for the production of antibodies, epitopes are determined, and at least one of said epitopes is changed through mutation of a DNA molecule coding for the expression of said subtilisin 309 or synthesis of a DNA molecule coding for the expression of said variant protein, said mutated or constructed DNA molecule subsequently being inserted into a vector for transformation or transfection into a suitable host, wherein said vector is functional or whereby said mutated or constructed DNA molecule is integrated functionally into the genome of said host, said protein variant is expressed in the host, and recovered."

XIV. Claims 1 and 2 of the seventh auxiliary request (claims 8 and 9 as granted) read as follows:

"1. A subtilisin protease variant, wherein the immunological potential has been changed in comparison to the parent protease, in that, in said protease changes have been performed among the amino acid residues at any one or more of positions 151, 174, 176, 193, and 196, by deletion, substitution, or insertion (single or multiple) adjacent to the indicated positions, whereby said subtilisin protease has an immunological potential lower than that of said parent protease, and in that it possesses at least one mutation affecting an amino acid residue occupying a position chosen from the group of positions 151, 174, 176, 193, and 196."

"2. The protease as claimed in claim 1, further characterised in that it contains at least one or more sets of mutations affecting amino acid residues occupying a position chosen from the group of sets of positions:

36+209, 89+120, 136+170, 36+89, 89+235, 136+195, 181+222, 209+222, 235+251."

XV. The following documents are cited in the present decision:

D1: B.J. Walsh and M.E.H. Howden, J. Immunol. Meth., 1989, Vol. 121, pages 275 to 280;

D13: H.M. Geysen et al., Science, 1987, Vol. 235, pages 1184 to 1190;

D14: H.M. Geysen et al., J. Mol. Recognition, 1988, Vol. 1, pages 32 to 41.

XVI. The appellant's arguments in writing and during the oral proceedings, insofar as they are relevant to the present decision, may be summarised as follows:

Main request and third, fourth and fifth auxiliary requests

Article 123(2) EPC

The term "protein" was consistently used in the application as filed in the sense of "complete protein" and clearly distinct from peptides or polypeptides derived from said "protein". The immunological and proteochemical methods referred to in the application as filed always used "the complete protein" and thus, mapped the epitopes of "the protein" in the sense of "the complete protein". In particular, animals were immunised with "the complete protein" - not a peptide or a polypeptide - and sera from those immunised animals were incubated with "the complete protein" in ELISA assays too. The coating of the solid phase and the colorimetric assay used in these ELISA assays as well as the chemical synthesis of protein variants were all proteochemical methods that used "the complete protein". None of the experimental work shown in the application as filed was performed using peptides or polypeptides. This was in contrast to the methods referred to in the prior art which used only peptides. There was a clear distinction between the peptide-based epitope mapping techniques of the prior art and the complete protein-based mapping techniques of the application as filed. It was only "the complete protein" that allowed the detection of conformational epitopes, which were the ones laying at the very heart of the invention.

In agreement with the established case law, the application had to be construed by a mind willing to understand. In the context of the claim itself and of the application as a whole, the interpretation of the term "complete" as requiring to map all the epitopes of the protein was unreasonable. The term "complete" was an adjective qualifying the noun "protein" and not an adverb that required the protein to be completely mapped. The term "complete" only clarified, in an explicit manner, the implicit meaning of the term "protein" as consistently used in the application as filed and it did not imply any change in the teaching of the disclosure as filed.

First and second auxiliary requests

Articles 123(3) and 84 EPC

The term "complete" was introduced during the examination proceedings as a mere clarification only and it did not add any technical feature. The deletion of this term therefore did not amount to a violation of Article 123(3) EPC.

Claim 1 as granted embraced two possible embodiments. In a first embodiment, the protein was "completely" epitope mapped by immunological and proteochemical methods (all the epitopes of the protein were mapped). There were no conditions or limitations associated with those methods, which could be performed using peptides, polypeptides and/or "the complete protein" as well. In a second embodiment, "the complete protein" was mapped by immunological and proteochemical methods in the sense that the epitopes of the protein - not necessarily all epitopes - were mapped by methods that used - only and exclusively - the "complete protein" as opposed to peptides and polypeptides thereof. The first embodiment, however, arose only from an alleged lack of clarity and it went far beyond a reasonable interpretation of the patent when read as a whole. The deletion of the term "complete" removed only this lack of clarity and it did not extend the protection to peptide-based epitope mapping methods since in the patent in suit the term "protein" was consistently used in the sense of "the complete protein". The limitation to protein-based epitope methods was still implicitly present in claim 1 of the first and second auxiliary requests. Thus, claim 1 of these requests complied with Articles 123(3) and 84 EPC.

Sixth auxiliary request

Article 123(3) EPC

This request was restricted to subject-matter that related only to the specific protein "subtilisin 309". The term "complete" in relationship to a particular protein specifically named in the claim was redundant, since the protein itself was always understood as being "complete" (the whole protein), as opposed to fragments (peptides or polypeptides) thereof.

Seventh auxiliary request

Article 83 EPC

There was no evidence on file showing that the immunological potential of a protein (or a variant thereof) could not be experimentally tested. It made no difference whether cell-mediated immunity or the production of antibodies were considered, since methods were available in the prior art for measuring both types of immunological response. On a reasonable interpretation of claim 1, it was apparent that the immunological potential had to be compared in the same species for both the parental and the variant protein - so as to compare like with like.

With regard to the cited case law, decisions T 694/92 (OJ EPO 1997, 408) and T 409/91 (OJ EPO 1994, 653) related both to broad claims functionally defined only, whereas in the patent in suit the desired effect was achieved by structurally well-defined subtilisin protease variants that could be easily constructed without encountering any particular technical problem. They were available to the skilled person without undue burden or inventive talent. The patent in suit further disclosed the presence of heteroclitic effects and of possible effects when combining several mutations. Whether or not these variants solved the technical problem underlying the patent in suit was a question concerning the properties of these variants and merely related to Article 56 EPC. However, the requirements of Article 56 EPC were not assessed in the first instance, and certainly not for the specific variants of this request.

XVII. The respondents' arguments in writing and during the oral proceedings, insofar as they are relevant to the present decision, may be summarised as follows:

Main request and third, fourth and fifth auxiliary requests

Article 123(2) EPC

The term "complete" introduced ambiguity into claim 1 since it could be interpreted as requiring the use of "the complete protein" in epitope mapping or else that the protein had to be "completely" mapped - in the sense that all epitopes had to be characterized. None of these interpretations was directly derivable from the application as filed.

In the application as filed, the term "complete" was only found with reference to the deficiencies of the prior art, i.e. in relation to the problem addressed by the application, but not in relation to their solution. These deficiencies could be overcome with immunological and proteochemical methods that did not necessarily require the use of "the complete protein" as long as the epitopes folded in the same way as in "the complete protein" (use of globular domains, fusion in a display scaffold, etc). The immunological and proteochemical methods known to the skilled person were the ones that used protein fragments and these methods were not excluded in the application as filed. Claim 1 used the term "complete" in a different context and with a technical meaning different from the one of the application as filed and thus, it contained added subject-matter which contravened Article 123(3) EPC.

First and second auxiliary requests

Articles 123(3) and 84 EPC

The term "complete" was a technical feature introduced into claim 1 during the examination proceedings in order to distinguish the claimed subject-matter from the prior art. Thus, the deletion of this term from the claim removed an essential technical feature and extended the scope of protection.

The immunological and proteochemical methods referred to in claim 1 of these auxiliary requests could be performed using protein fragments (peptides) too. If these methods were to be understood according to the appellant's interpretation of granted claim 1, i.e. as methods using - only and exclusively - the complete protein but not fragments thereof, then claim 1 of these requests was ambiguous and unclear.

Sixth auxiliary request

Article 123(3) EPC

The meaning of "subtilisin 309 protease" was not the same as that of "complete subtilisin 309 protease". The former was more generic and embraced variants of the "complete subtilisin 309 protease", such as short forms and small deletions thereof. Claim 1 of this auxiliary request did not exclude the use of fragments of the "subtilisin 309 protease" in the immunological and proteochemical methods referred to in the claim. Thus, the deletion of the term "complete" extended the scope of protection in comparison to the granted claims.

Seventh auxiliary request

Article 83 EPC

The claimed subtilisin protease variants were required to have an immunological potential lower than that of the parent protein. However, the immunological response of a protein (or protein variant) depended on several mechanisms and factors, in particular the response of the B-lymphocyte cells (production of antibodies) and/or T-lymphocyte cells (stimulation of B-cells and cell-mediated immunity) and the immunological variability among different species and individuals of the same species. The patent in suit, however, failed to disclose any method for measuring this immunological potential. The skilled person was left in the dark as to the kind of assay to be used for determining this immunological potential. In the absence of this information, to test and to decide whether a certain subtilisin variant fulfilled the conditions required in the claim, placed an undue burden on the skilled person.

Claim 1 of this auxiliary request referred to changes among the amino acid residues at any one or more of several positions. These positions were cited in the description together with other positions, all of them chosen on the basis of a combination of experimental results and a 3-dimensional (3D) view. However, none of these positions was actually used in an immunological assay. The patent in suit did not provide any experimental evidence supporting that changes in these residues resulted in the expected lower immunological potential. This was even worse for claim 2, which required not only changes at any one of the positions indicated in claim 1 but also the presence of sets of mutations at other positions. In that case, the experimental results disclosed in the patent in suit showed that for some of these sets of mutations the expected effect was not attained. In fact, a greater immunological potential was actually shown for some of them. Thus, the combination of claim 1 (positions with an ambiguous result) and claim 2 (positions that did not attain the desired effect) placed an undue burden on the skilled person. Reference was made to the established case law, in particular to decisions T 694/92 and T 409/91 (supra), which, for sufficiency of disclosure, stated that, after reading the description, the skilled person had to be in a position to perform the invention without undue burden over the whole area claimed. That was not the case for the patent in suit.

XVIII. The appellant (patentee) requested that the decision under appeal be set aside and that the case be remitted to the first instance for consideration of the remaining grounds of opposition on the basis of the claims as granted or, in the alternative, on the basis of the first to second auxiliary requests filed during the oral proceedings, or on the basis of first to third auxiliary requests filed on 29 October 2004, taken as third to fifth auxiliary requests, or on the basis of the sixth to seventh auxiliary requests filed during the oral proceedings.

XIX. The respondents (opponents) requested that the appeal be dismissed.