Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
DETAILED ACTION
The amendment filed 01/06/2025 has been entered. Claim 14 has been cancelled. Claims 1-13, 15, and 16 are pending and under examination.
Claim Interpretation
Based on the information found in the instant disclosure (paras. [0027], [0040]), a mannose-specific glycoprotease is interpreted as a protease that digests mannosylated proteins at amino acid residues (serine and threonine) that are decorated with mannose, and is specific towards protein substrates with mannose-modifications.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim 16 is rejected under 35 U.S.C. 101 because the claimed invention is directed to a product of nature without significantly more. The claim recites a composition requiring a polypeptide having at least 90% sequence identity to any one of the amino acids selected from instant SEQ ID NOs: 1-9, 11-13, 15-24, 26. 36-48, 53-55, 57, or 59, which include naturally occurring proteins found in fungi; and, a target protein having a mannose-decorated amino acid sequence, which includes naturally occurring proteins, such as those found on the surface of multiple different cell types. This judicial exception is not integrated into a practical application because both the protein having mannose-specific glycoprotease activity and the target protein having a mannose-decorated amino acid sequence are naturally occurring, as interpreted in the instant disclosure, and the claims do not include any additional elements other than the naturally occurring proteins.
Prong 1 - Statutory category: Here, the claimed invention is either a composition of matter or a manufacture. Under 35 USC 101, the claimed invention must be “any new and useful process, machine, manufacture, or composition of matter.” The invention falls under one of the statutory categories (composition of matter) identified in 35 USC 101.
Prong 2A – Judicial exception: Here, the claimed invention is a composition or a manufactured product but is directed to the judicial exception, specifically a law of nature or a natural phenomenon (product of nature). Even a composition of matter or a manufacture may not be patent eligible if it falls under a judicial exception. The three judicial exception categories are: enumerated abstract idea, law of nature, and natural phenomenon (product of nature). Nature based products include both naturally occurring as well as non-naturally occurring products that have characteristics that are not markedly different from a natural occurring counterpart and fall within the judicial exception.
Here, the composition comprises naturally occurring proteins and is therefore directed to products of nature and fall within the judicial exception category.
Prong 2B: Judicial Exception/Significantly More: The “significantly more” analysis is a determination whether a claim is eligible if the claim recites additional elements that integrate the judicial exception into a practical application. Integration requires an additional element in the claim to apply, rely on, or use the judicial exception in a manner than imposes a meaningful limit on the judicial exception. Claim 16 is drawn to a composition comprising naturally occurring proteins with no additional elements. These limitations do not recite any meaningful additional limitations, modifications or transformations that indicate that the composition comprises anything other than a naturally occurring proteins, and there is no information to suggest that either protein has been genetically modified by the applicant (i.e., it is interpreted that they are naturally occurring). Although the claim recites that the mannose-specific glycoprotease is a recombinant polypeptide, the polypeptide is not limited by its method of production, but instead is only limited by its structure. Recombinant production of the polypeptide does not impart any structural differences that differentiates the polypeptide from its naturally produced counterpart. Therefore, claim 16 does not recite any limitations significantly more than the judicial exception and is rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon or a law of nature without significantly more.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 16 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 16 recites the limitation "the target mannose-modified protein" in the wherein clause. There is insufficient antecedent basis for this limitation in the claim. To obviate the rejection, “the target mannose-modified protein” may be amended to “the target protein having a mannose-decorated amino acid sequence”.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-13, and 15-17 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 1-7 are drawn to a method of modifying a mannose-decorated amino acid sequence present in a target protein comprising contacting the protein with a recombinant polypeptide having mannose-specific glycoprotease activity. Claims 8-10 are drawn to a method for agglomerating organisms displaying mannose-decorated amino acid sequences on their surface comprising contacting the organisms with a recombinant polypeptide having mannose-specific glycoprotease activity. Claims 11-13 are drawn to a method for modifying a fermentation product produced by yeast cells comprising contacting the fermentation product with a recombinant polypeptide having mannose-specific glycoprotease activity. Claim 15 limits the recombinant polypeptide of claim 1 to one having at least 90% sequence similarity to any one of instant SEQ ID NOs:1-9, 11-13, 15-24, 26. 36-48, 53-55, 57, or 59. Claim 16 is drawn to a modified stillage product obtained by the method of claim 13. Claim 17 is drawn to a composition comprising a recombinant polypeptide having mannose-specific glycoprotease activity wherein said recombinant polypeptide has an amino acid sequence with at least 90% sequence similarity to any one of instant SEQ ID NOs: 1-9, 11-13, 15-24, 26. 36-48, 53-55, 57, or 59.
MPEP 2163.05 II states “the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species. A ‘representative number of species’ means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. See AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014) (Claims directed to a functionally defined genus of antibodies were not supported by a disclosure that ‘only describe[d] one type of structurally similar antibodies’ that ‘are not representative of the full variety or scope of the genus.’). The disclosure of only one species encompassed within a genus adequately describes a claim directed to that genus only if the disclosure "indicates that the patentee has invented species sufficient to constitute the gen[us].’”
The instant specification only reduces to practice the mannose-specific glycoprotease activity of one recombinant polypeptide, IFF05497 (SEQ ID NO: 1) (Examples 10 and 11), and only discloses one organism, budding yeast, displaying mannose-decorated amino acid sequences on its surface (Example 7). The specification does not disclose the entire genus of organisms displaying mannose-decorated amino acids or the entire genus of mannose-specific glycoproteases as claimed, and does not demonstrate the enzymatic activity of any one of SEQ ID NOs:2-9, 11-13, 15-24, 26. 36-48, 53-55, 57, or 59. The instant specification does not disclose what structural properties are required for the enzymes to have specific cleavage activity against mannosylated amino acids, or disclose which regions the amino acid sequence of the glycoproteases are the active site residue(s) for conserving the claimed enzyme activity. Therefore, the disclosed species are not representative of the entire genus of claimed organisms or mannose-specific glycoprotease variants.
Leo et al., (US 2020/0172889 A1) teaches a novel polypeptide that acts as an endoprotease and cleaves amino acid bonds N terminal to and in proximity of an O-linked glycan without showing any specificity to a particular amino acid sequence (para. [0005]). Leo does not teach a sequence with 90% sequence similarity to any one of the SEQ ID NO:’s recited in the instant claims, and does not teach that the endoprotease is specific to mannosylated amino acids. Leo does not teach organisms displaying mannose-decorated amino acids sequences on their surface.
In summary, neither the instant specification, nor the prior art, discloses a structure-function relationship between conserved amino acid residues in the claimed enzyme structure and the claimed mannose-specific glycoprotease activity. Neither the specification, nor the prior art, teach all organisms displaying mannose-decorated amino acids on their surface. One of ordinary skill in the art cannot reasonably predict which residues of SEQ ID NOs: 1-9, 11-13, 15-24, 26. 36-48, 53-55, 57, or 59 may be modified to generate a functional glycoprotease with specificity towards mannosylated amino acids. Based on the instant disclosure, those skilled in the art would not conclude that the applicant was in possession of all claimed variants and organisms.
Pertinent Prior Art
The closes prior art reference is US 2020/0172889 A1 by Leo et al. (IDS filed 01/06/2025). Leo teaches a novel polypeptide that acts as an endoprotease and cleaves amino acid bonds N terminal to and in proximity of an O-linked glycan without showing any specificity to a particular amino acid sequence (para. [0005]). Leo teaches variants of the polypeptide that are capable of selective removal, enrichment, or purification of free O-glycans, O-glycopeptides, and/or O-glycoproteins (para. [0006]). Nowhere in the disclosure of Leo is mannose mentioned specifically. Leo does not teach a sequence with 90% sequence similarity to any one of the SEQ ID NO:’s recited in the instant claims.
The Examiner is unaware of any prior art references that teach a glycoprotease that is specific against mannosylated proteins.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to RACHEL EMILY MARTIN whose telephone number is (703)756-1416. The examiner can normally be reached M-Th 8:30-16:00, F 8:30-10:00 EST.
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/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/RACHEL EMILY MARTIN/Examiner, Art Unit 1657
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