DETAILED ACTION
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 .
Claims 39-52 are still at issue and are present for examination.
Election/Restrictions
Applicant's election without traverse of the invention of Group 1, claims 1-13, 15, 17, 37, 38 (new claims 39-50), to a polypeptide, in the paper of 10/13/2025, is acknowledged. Applicant's election without traverse of the species of SEQ ID NO:11, in the paper of 10/13/2025, is acknowledged.
Claims 51 and 52 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609 A(1) states, "the list may not be incorporated into the specification but must be submitted in a separate paper."
Applicants filing of information disclosure statements on 6/30/2023 are acknowledged and have been considered.
Claim Objections
Claim 39 and 40 are objected to because of the following informalities:
Claim 39 recites “or a sequence having at least 70% identity to SEQ ID NO: 1”. It is suggested that be amended to “or an amino acid sequence having at least 70% identity to SEQ ID NO: 1”.
Claim 40 recites “wherein the sequence is having at least 75% identity to SEQ ID NO: 1”. It is suggested that be amended to “wherein the sequence has at least 75% identity to SEQ ID NO: 1”.
Appropriate correction and/or comment is required.
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.
Claims 39, 40, 42-45, 50 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Claims 39, 40, 42-45, 50 are directed any polypeptide comprising or consisting of the amino acid sequence the amino acid sequence of SEQ ID NO: 1, or a sequence having at least 70% identity to SEQ ID NO: 1, wherein: a) X1 is arginine (R), lysine (K), or histidine (H), and the side chain of the residue at position X2 is negatively charged (D and E), or b) X1 is cysteine (C), and X2 is cysteine (C); and wherein the polypeptide is capable of degrading a polyester, that is not patent-eligible pursuant to the Supreme Court decision in Association for Molecular Pathology v. Myriad Genetics, Inc., 106 USPQ2d 1972 (June 13, 2013). Liu et al. (Biochemical and Biophyscal Research Communications Vol 508, No. 1, pp 289-294) which discloses the polyethylene terephthalate hydrolase from Ideonella sakaiensis and has greater than 95% sequence identity to instant SEQ ID NO:1, evidence that a polypeptide comprising or consisting of the amino acid sequence of SEQ ID NO: 1, or a sequence having at least 70% identity to SEQ ID NO: 1, wherein: a) X1 is arginine (R), lysine (K), or histidine (H), and the side chain of the residue at position X2 is negatively charged (D and E as per google), or b) X1 is cysteine (C), and X2 is cysteine (C); and wherein the polypeptide is capable of degrading a polyester is a naturally occurring method and is thus not patent eligible.
Claim Rejections - 35 USC § 112
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.
Claims 40 and 41 are 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.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 40 recites the broad recitation “having at least 75% identity to SEQ ID NO: 1,” and the claim also recites “such as at least 80 % identity to SEQ ID NO: 1” which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Claim 41 is indefinite in that it is drawn to the polypeptide according to claim 39, wherein the polypeptide comprises or consists of an amino acid sequence of the elected species of SEQ ID NO: 11. The claim is indefinite because SEQ ID NO:11 comprises a Glycine (G) at position 93 and a lysine (K) at position 158 which is inconsistent with position 93 and 158 of SEQ ID NO:1 in claim 39 from which claim 41 depends.
Appropriate correction and/or comment is required.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 41 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. As stated above, claim 41 is drawn toa number of specific polypeptide sequences (i.e. SEQ ID NO:11) which do not appear to comprise the limitations of claim 39 from which claim 41 depends. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 112
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.
Claim(s) 39-50 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim(s) 39-50 are directed to all possible polypeptide comprising or consisting of the amino acid sequence SEQ ID NO: 1, or a sequence having a mere 70% identity to SEQ ID NO: 1, wherein: a) X1 is arginine (R), lysine (K), or histidine (H), and the side chain of the residue at position X2 is negatively charged (D and E as per google), or b) X1 is cysteine (C), and X2 is cysteine (C); and wherein the polypeptide is capable of degrading a polyester. The specification, however, only provides the representative species of that polyethylene terephthalate hydrolase comprising the amino acid sequence of SEQ ID NO:1 wherein the polypeptide has the following substitutions, S93R, S93K, or S93H and position 158 has a negatively charged amino acid, encompassed by these claims. There is no disclosure of any particular structure to function/activity relationship in the disclosed species. The molecular mechanism of poly(ethylene terephthalate) (PET) degradation is not known (Joo et al., Nature Communications Vol 9, p1-12 382, 2018). The specification also fails to describe additional representative species of these enzymes by any identifying structural characteristics or properties, for which no predictability of structure is apparent.
Regarding the level of skill and knowledge in the art of amino acid mutation, the reference of Singh et al. (Curr. Protein Pept. Sci. 18:1-11, 2017; cited on the attached Form PTO-892) reviews various protein engineering methods and discloses that despite the availability of an ever-growing database of protein structures and highly sophisticated computational algorithms, protein engineering is still limited by the incomplete understanding of protein functions, folding, flexibility, and conformational changes (see p. 7, column 1, top). Also, the unpredictability associated with amino acid mutations is exemplified by the reference of Zhang et al. (Structure 26:1474-1485, 2018; cited on the attached Form PTO-892), which discloses that even a mutation of a surface residue that was predicted to be benign caused significant structural changes and unexpected effects on the function of a polypeptide (p. 1475, column 1).
Given this lack of additional representative species as encompassed by the claims, Applicants have failed to sufficiently describe the claimed invention, in such full, clear, concise, and exact terms that a skilled artisan would recognize Applicants were in possession of the claimed invention.
Applicant is referred to the revised guidelines concerning compliance with the written description requirement of U.S.C. 112, first paragraph, published in the Official Gazette and also available at www.uspto.gov.
Claim(s) 39-50 are rejected under 35 U.S.C. 112, first paragraph, because the specification, while being enabling for that polyethylene terephthalate hydrolase comprising the amino acid sequence of SEQ ID NO:1, wherein the polypeptide has the following substitutions, S93R, S93K, or S93H and position 158 has a negatively charged amino acid, does not reasonably provide enablement for all polypeptides comprising or consisting of the amino acid sequence SEQ ID NO: 1, or a sequence having a mere 70% identity to SEQ ID NO: 1, wherein: a) X1 of SEQ ID NO:1 is arginine (R), lysine (K), or histidine (H), and the side chain of the residue at position X2 of SEQ ID NO:1 is negatively charged (D and E), or b) X1 of SEQ ID NO:1 is cysteine (C), and X2 of SEQ ID NO:1 is cysteine (C), and wherein the polypeptide is capable of degrading a polyester. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
Factors to be considered in determining whether undue experimentation is required, are summarized in In re Wands (858 F.2d 731, 8 USPQ 2nd 1400 (Fed. Cir. 1988)) as follows: (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claim(s).
Claim(s) 39-50 are so broad as to encompass all possible polypeptides comprising or consisting of the amino acid sequence SEQ ID NO: 1, or a sequence having a mere 70% identity to SEQ ID NO: 1, wherein: a) X1 of SEQ ID NO:1 is arginine (R), lysine (K), or histidine (H), and the side chain of the residue at position X2 of SEQ ID NO:1 is negatively charged (D and E), or b) X1 of SEQ ID NO:1 is cysteine (C), and X2 of SEQ ID NO:1 is cysteine (C), and wherein the polypeptide is capable of degrading a polyester. The scope of the claims is not commensurate with the enablement provided by the disclosure with regard to the extremely large number of polypeptides and variants broadly encompassed by the claims. The claims rejected under this section of U.S.C. 112, first paragraph, place minimal structural limits on the variant polyethylene terephthalate hydrolases encompassed by the claims. Since the amino acid sequence of a protein determines its structural and functional properties, predictability of which changes can be tolerated in a protein's amino acid sequence and obtain the desired activity requires a knowledge of and guidance with regard to which amino acids in the protein's sequence, if any, are tolerant of modification and which are conserved (i.e. expectedly intolerant to modification), and detailed knowledge of the ways in which the proteins' structure relates to its function. However, in this case the disclosure is limited to that polyethylene terephthalate hydrolase comprising the amino acid sequence of SEQ ID NO:1, wherein the polypeptide has the following substitutions, S93R, S93K, or S93H and position 158 has a negatively charged amino acid,
While recombinant and mutagenesis techniques are known, it is not routine in the art to screen for multiple substitutions or multiple modifications, as encompassed by the instant claims, and the positions within a protein's sequence where amino acid modifications can be made with a reasonable expectation of success in obtaining the desired activity/utility are limited in any protein and the result of such modifications is unpredictable. In addition, one skilled in the art would expect any tolerance to modification for a given protein to diminish with each further and additional modification, e.g. multiple substitutions.
The specification does not support the broad scope of the claims which encompass any possible polypeptide comprising or consisting of the amino acid sequence SEQ ID NO: 1, or a sequence having a mere 70% identity to SEQ ID NO: 1, wherein: a) X1 of SEQ ID NO:1 is arginine (R), lysine (K), or histidine (H), and the side chain of the residue at position X2 of SEQ ID NO:1 is negatively charged (D and E), or b) X1 of SEQ ID NO:1 is cysteine (C), and X2 of SEQ ID NO:1 is cysteine (C), and wherein the polypeptide is capable of degrading a polyester, because the specification does not establish: (A) regions of the polypeptide which may be modified effecting the polyethylene terephthalate hydrolase activity; (B) the general tolerance of polyethylene terephthalate hydrolases to modification and extent of such tolerance; (C) a rational and predictable scheme for modifying any amino acid residue of an enzyme of the polyethylene terephthalate hydrolase group with an expectation of obtaining the desired biological function; and (D) the specification provides insufficient guidance as to which of the essentially infinite possible choices is likely to be successful. Because of this lack of guidance, the extended experimentation that would be required to determine which substitutions would be acceptable to retain the required polyethylene terephthalate hydrolase activities and the fact that the relationship between the sequence of a peptide and its tertiary structure (i.e. its activity) are not well understood and are not predictable (e.g., see Joo et al., Nature Communications Vol 9 (1), p 382, 2019, Ngo et al. in The Protein Folding Problem and Tertiary Structure Prediction, 1994, Merz et al. (ed.), Birkhauser, Boston, MA, pp. 433 and 492-495; Franceus et al., J. Ind. Microbiol. Biotechnol. Vol 44, pp 687-695, 2017), it would require undue experimentation for one skilled in the art to arrive at the majority of those polypeptides of the claimed genus.
Thus, applicants have not provided sufficient guidance to enable one of ordinary skill in the art to make and use the claimed invention in a manner reasonably correlated with the scope of the claims broadly including any polypeptide comprising or consisting of the amino acid sequence SEQ ID NO: 1, or a sequence having a mere 70% identity to SEQ ID NO: 1, wherein: a) X1 is arginine (R), lysine (K), or histidine (H), and the side chain of the residue at position X2 is negatively charged (D and E as per google), or b) X1 is cysteine (C), and X2 is cysteine (C); and wherein the polypeptide is capable of degrading a polyester. The scope of the claims must bear a reasonable correlation with the scope of enablement (In re Fisher, 166 USPQ 19 24 (CCPA 1970)). Without sufficient guidance, determination of those polypeptides having the desired biological characteristics is unpredictable and the experimentation left to those skilled in the art is unnecessarily, and improperly, extensive and undue. See In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988).
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 39, 40, 42- 45, 48-50 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Liu et al. (Biochemical and Biophyscal Research Communications Vol 508, No. 1, pp 289-294).
Liu et al. (Biochemical and Biophyscal Research Communications Vol 508, No. 1, pp 289-294) teach the structural and functional characterization of polyethylene terephthalate (PET) hydrolase from Ideonella sakaiensis as a means of degrading PET. Lit et al. teach the naturally occurring polyethylene terephthalate hydrolase from Ideonella sakaiensis which has greater than 95% sequence identity to instant SEQ ID NO:1, as well as mutants of the enzyme (i.e. S93M, W159F and N241F). The Ideonella sakaiensis polyethylene terephthalate hydrolase mutants taught by Liu et al. have greater than 70% amino acid sequence identity to instant SEQ ID NO:1 from which has greater than 95% sequence identity to instant SEQ ID NO:1 and are capable of degrading a polyester.
It is noted that the PET hydrolases taught by Liu et al. do not comprise an arginine (R), lysine (K), histidine (H), or cysteine (C), at position X1, however applicants claimed polypeptide is not required to have the referred to mutants at positions X1. Given the broadest reasonable interpretation of applicants claims, the claimed polypeptide must merely comprise a sequence having at least 70% identity to SEQ ID NO: 1 and are capable of degrading a polyester.
Thus, claim(s) 39, 40, 42- 45, 48-50 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Liu et al. (Biochemical and Biophyscal Research Communications Vol 508, No. 1, pp 289-294).
Remarks
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to RICHARD G HUTSON whose telephone number is (571)272-0930. The examiner can normally be reached 6-3 EST Mon-Fri.
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rgh
10/30/2025
/RICHARD G HUTSON/Primary Examiner, Art Unit 1652