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 .
Application Status
In response to Non-Final Office Action mailed on 06/18/2025, applicants' response, arguments and amendments filed on dated 12/18/2025 is acknowledged; in said response applicants’ have amended claim 16, canceled claims 19, 21-23 and 27 and added new claims 38-40. Thus, amended claims 16-18, 20, 24-26 and 28-40 are pending and are now under consideration. Rejections and/or objections not reiterated from previous office action are hereby withdrawn.
New-Claim Rejections: 35 U.S.C. 112(d)
Necessitated by claim amendments
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.
New claim 38 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. Claim 38 recites “…wherein the signal peptide is a variant of SEQ ID NO: 2 having three alterations compared to SEQ ID NO: 2” and depends from independent claim 16; said claim 16 recites “…wherein the signal peptide has a sequence identity of at least 90% to SEQ ID NO:2”; in dependent claim 38, three alterations in SEQ ID NO: 2 comprising 27 amino acid residues is equivalent to 88.89% sequence identity to SEQ ID NO: 2 and thus broadens the scope of dependent claim 38; new claim 38 which depends from claim 16 and does not further limit claim 16. Dependent claim 38 broadens the scope of independent claim 16.
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.
The U.S. Court of Appeals for the Federal Circuit indicated that although the requirements of pre-AIA 35 U.S.C. 112, 4th paragraph, are related to matters of form, non-compliance with pre-AIA 35 U.S.C. 112, 4th paragraph, renders the claim unpatentable just as non-compliance with other paragraphs of 35 U.S.C. 112 would. See Pfizer, Inc. v. Ranbaxy Labs., Ltd., 457 F.3d 1284, 1291-92, 79 USPQ2d 1583, 1589-90 (Fed. Cir. 2006) (holding a dependent claim in a patent invalid for failure to comply with pre-AIA 35 U.S.C. 112, 4th paragraph). Therefore, if a dependent claim does not comply with the requirements of 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, the dependent claim should be rejected under pre-AIA 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as unpatentable rather than objecting to the claim. See also MPEP § 608.01(n),subsection III, “Infringement Test” for dependent claims.
Maintained-Claim Rejections: 35 USC § 112(a)
The following is a quotation 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.
Written Description
I. Claims 16-18, 20, 24-26 , 28-29 and 32-40 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112, first paragraph, as containing 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(s), at the time the application was filed, had possession of the claimed invention.
Claims 16-18, 20, 24-26, 28-29 and 32-40, as interpreted are directed to encompass any nucleic acid construct encoding a fusion protein comprising: (i) a first polynucleotide encoding a signal peptide having a sequence identity of at least 90% to SEQ ID NO: 2 and (ii) a second polynucleotide encoding any hexosaminidase of undefined and unlimited structures, wherein the polypeptide having hexosaminidase activity belongs to the Terribacillus clade and comprise the motif [VIM][LIV]G[GAV]DE[VI][PSA] (SEQ ID NO: 11) (only partial structure/motif is defined, remainder of the structure is undefined, as in claims 16-18, 20, 24-26, and 32-40); and said hexosaminidase polypeptide(s) having 80%-90% sequence identity to the mature polypeptide of SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8 or SEQ ID NO: 10 (as in claims 28-29; also see 35 U.S.C. 112(d) rejection above for claim interpretation).
In University of California v. Eli Lilly & Co., 43 USPQ2d 1938, the Court of Appeals for the Federal Circuit has held that “A written description of an invention involving a chemical genus, like a description of a chemical species, ‘requires a precise definition, such as by structure, formula, [or] chemical name,’ of the claimed subject matter sufficient to distinguish it from other materials”. As indicated in MPEP § 2163, the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show that Applicant was in possession of the claimed genus. In addition, MPEP § 2163 states that 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.
In the instant case, there is no structure associated with function with regard to the members of the genus of polypeptides and the encoding polynucleotides i.e., any nucleic acid construct encoding a fusion protein comprising: (i) a first polynucleotide encoding a signal peptide having a sequence identity of at least 90% to SEQ ID NO: 2 and (ii) a second polynucleotide encoding any hexosaminidase of undefined and unlimited structures, wherein the polypeptide having hexosaminidase activity belongs to the Terribacillus clade and comprise the motif [VIM][LIV]G[GAV]DE[VI][PSA] (SEQ ID NO: 11) (only partial structure/motif is defined, remainder of the structure is undefined, as in claims 16-18, 20, 24-26, and 32-40); and said hexosaminidase polypeptide(s) having 80%-90% sequence identity to the mature polypeptide of SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8 or SEQ ID NO: 10 (as in claims 28-29; also see 35 U.S.C. 112(d) rejection above for claim interpretation).
No information, beyond the characterization of nucleic acid construct encoding a fusion protein comprising: (i) a first polynucleotide encoding a signal peptide comprising the amino acid sequence of SEQ ID NO: 2 and (ii) a second polynucleotide encoding hexosaminidase polypeptide(s) comprising the amino acid sequence(s) of SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8 or SEQ ID NO: 10 has been provided by the applicants’, which would indicate that they had possession of the claimed genus of polypeptides and the encoding polynucleotides i.e., any nucleic acid construct encoding a fusion protein comprising: (i) a first polynucleotide encoding a signal peptide having a sequence identity of at least 90% to SEQ ID NO: 2 and (ii) a second polynucleotide encoding any hexosaminidase of undefined and unlimited structures, wherein the polypeptide having hexosaminidase activity belongs to the Terribacillus clade and comprise the motif [VIM][LIV]G[GAV]DE[VI][PSA] (SEQ ID NO: 11) (only partial structure/motif is defined, remainder of the structure is undefined, as in claims 16-18, 20, 24-26, and 32-40); and said hexosaminidase polypeptide(s) having 80%-90% sequence identity to the mature polypeptide of SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8 or SEQ ID NO: 10 (as in claims 28-29; also see 35 U.S.C. 112(d) rejection above for claim interpretation).
The claimed genus of polypeptides and the encoding polynucleotides is an extremely large structurally and functionally variable genus. While the argument can be made that the recited genus of polypeptides and the encoding polynucleotides is adequately described by the disclosure of the structures of the amino acid sequences fusion protein comprising: (i) a first polynucleotide encoding a signal peptide comprising the amino acid sequence of SEQ ID NO: 2 and (ii) a second polynucleotide encoding hexosaminidase polypeptide(s) comprising the amino acid sequence(s) of SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8 or SEQ ID NO: 10, since one could use structural homology to isolate those encoding polynucleotides and encoded polypeptides recited in the claims. The art clearly teaches the “Practical Limits of Function Prediction”: (i) Devos et al., (Proteins: Structure, Function and Genetics, 2000, Vol. 41: 98-107), teach that the results obtained by analyzing a significant number of true sequence similarities, derived directly from structural alignments, point to the complexity of function prediction. Different aspects of protein function, including (i) enzymatic function classification, (ii) functional annotations in the form of key words, (iii) classes of cellular function, and (iv) conservation of binding sites can only be reliably transferred between similar sequences to a modest degree. The reason for this difficulty is a combination of the unavoidable database inaccuracies and plasticity of proteins (Abstract, page 98) and the analysis poses interesting questions about the reliability of current function prediction exercises and the intrinsic limitation of protein function prediction (Column 1, paragraph 3, page 99) and conclude that “Despite widespread use of database searching techniques followed by function inference as standard procedures in Bioinformatics, the results presented here illustrate that transfer of function between similar sequences involves more difficulties than commonly believed. Our data show that even true pair-wise sequence relations, identified by their structural similarity, correspond in many cases to different functions (column 2, paragraph 2, page 105).
(ii) Whisstock et al., (Quarterly Reviews of Biophysics 2003, Vol. 36 (3): 307-340) also highlight the difficulties associated with “Prediction of protein function from protein sequence and structure”; “To reason from sequence and structure to function is to step onto much shakier ground”, closely related proteins can change function, either through divergence to a related function or by recruitment for a very different function, in such cases, assignment of function on the basis of homology, in the absence of direct experimental evidence, will give the wrong answer (page 309, paragraph 4), it is difficult to state criteria for successful prediction of function, since function is in principle a fuzzy concept. Given three sequences, it is possible to decide which of the three possible pairs is most closely related. Given three structures, methods are also available to measure and compare similarity of the pairs. However, in many cases, given three protein functions, it would be more difficult to choose the pair with most similar function, although it is possible to define metrics for quantitative comparisons of different protein sequences and structures, this is more difficult for proteins of different functions (page 312, paragraph 5), in families of closely related proteins, mutations usually conserve function but modulate specificity i.e., mutations tend to leave the backbone conformation of the pocket unchanged but to affect the shape and charge of its lining, altering specificity (page 313, paragraph 4), although the hope is that highly similar proteins will share similar functions, substitutions of a single, critically placed amino acid in an active-site residue may be sufficient to alter a protein’s role fundamentally (page 323, paragraph 1).
(iii) This finding is reinforced in the following scientific teachings for specific proteins in the art that suggest, even highly structurally homologous polynucleotides and encoded polypeptides do not necessarily share the same function. For example, Witkowski et al., (Biochemistry 38:11643-11650, 1999), teaches that one conservative amino acid substitution transforms a b-ketoacyl synthase into a malonyl decarboxylase and completely eliminates b-ketoacyl synthase activity. Seffernick et al., (J. Bacteriol. 183(8): 2405-2410, 2001), teaches that two naturally occurring Pseudomonas enzymes having 98% amino acid sequence identity catalyze two different reactions: deamination and dehalogenation, therefore having different function. Broun et al., (Science 282:1315-1317, 1998), teaches that as few as four amino acid substitutions can convert an oleate 12-desaturase into a hydrolase and as few as six amino acid substitutions can transform a hydrolase to a desaturase.
As the claimed genera of polypeptides and encoding polynucleotides include widely variable structure and associated function, since minor changes in structure may result in changes affecting function and no additional information (species/variant/mutant) correlating structure with function has been provided. Furthermore, “Possession may not be shown by merely describing how to obtain possession of members of the claimed genus or how to identify their common structural features” (See University of Rochester, 358 F.3d at 927, 69 USPQ2d at 1895).
Therefore, one skilled in the art cannot reasonably conclude that applicant had possession of the claimed invention at the time the instant application was filed. Applicants’ are referred to the revised guidelines concerning compliance with the written description requirement of 35 U.S.C. 112(a) or 35 U.S.C. 112, first paragraph, published in the Official Gazette and also available at www.uspto.gov.
Applicants’ have traversed the above written-description with the following arguments: (see pages 5-6 of Applicants’ REMARKS dated 12/18/2025).
Applicants’ argue: “…The Applicant further notes that for the sole purpose of advancing prosecution, claim 16 is amended to provide significant structural limitations to the claimed nucleic acid construct that are clearly reflected in the Applicant's specification, including both parts a) "at least 90% to SEQ ID NO: 2" (which corresponds to only three amino acid variations of the signal sequence), and part b) wherein the polypeptide having hexosaminidase "belongs to the Terribacillus clade and comprises the motif [VIM][LIV]G[GAV]DE[VI][PSA] (SEQ ID NO: 11)" (the structure-function aspects are described in detail in Applicant's specification, e.g., page 9, line 26 to page 10, line 2)”.
Reply: Applicants' arguments have been considered but are found to be non-persuasive for the following reasons. Examiner continues to maintain the rejection for reasons stated on record (dated 06/18/2025) and additionally for the following reasons. Contrary to applicants arguments, while methods to produce variants of a known sequence, such as site-specific mutagenesis, random mutagenesis, etc., are well known to the skilled artisan, producing variants capable of having the associated function/activity i.e., any nucleic acid construct encoding a fusion protein comprising: (i) a first polynucleotide encoding a signal peptide having a sequence identity of at least 90% to SEQ ID NO: 2 and (ii) a second polynucleotide encoding any hexosaminidase of undefined and unlimited structures, wherein the polypeptide having hexosaminidase activity belongs to the Terribacillus clade and comprise the motif [VIM][LIV]G[GAV]DE[VI][PSA] (SEQ ID NO: 11) (only partial structure/motif is defined, remainder of the structure is undefined, as in claims 16-18, 20, 24-26, and 32-40); and said hexosaminidase polypeptide(s) having 80%-90% sequence identity to the mature polypeptide of SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8 or SEQ ID NO: 10 (as in claims 28-29; also see 35 U.S.C. 112(d) rejection above for claim interpretation) requires that one of ordinary skill in the art know or be provided with guidance for the selection of which, of the infinite number of variants, have the activity. Without such guidance, one of ordinary skill would be reduced to the necessity of producing and testing all of the virtually infinite possibilities. For the rejected claims, this would clearly constitute undue experimentation and lack of evidence of possession.
Examiner’s position is supported by the following scientific evidence: Guo et al., (2004) teach that the percentage of random single-substitution mutations, which inactivate a protein, using a protein 3-methyladenine DNA glycosylase as a model, is 34% and that this number is consistent with other studies in other proteins (p 9206, paragraph 4). Guo et al., (supra) further show that the percentage of active mutants for multiple mutations appears to be exponentially related to this by the simple formula (0.66)^X X 100% where x is the number of mutations introduced (Table 1). Applying this estimate to the protein recited in the instant application, an amino acid sequence of 80% sequence identity to SEQ ID NO: 4 allows up to 70 random mutations within the 349 amino acid residues of SEQ ID NO: 4 and, thus, only (0.66)^70 X 100% or 2.33 x 10-11 % of random mutants having 80% sequence identity to of SEQ ID NO:4 would be active. While these calculations are only estimates of the actual situation, they are presented to provide a basis for understanding the examiner’s decision on which claim scope would require only routine experimentation and which would reach a level which is undue. The guidance in the instant case and current techniques in the art (i.e., high throughput mutagenesis and screening techniques) would allow for finding a reasonable number of active mutants within hundred thousand inactive mutants. Finding a few mutants within several trillions or more, would not be possible; an extremely low number of active mutants will be present among an enormously large number of inactive mutants and as such screening for these active mutants would be burdensome and undue experimentation when there is no guidance provided in the specification and there is no evidence of possession. While enablement is not precluded by the necessity for routine screening, if a large amount of screening is required, the specification must provide a reasonable amount of guidance with respect to the direction in which the experimentation should proceed (guided mutants). Such guidance has not been provided in the instant specification or in the prior art.
Furthermore, the art teaches the following regarding complexity of the structure/function relationship: The reference of Chica et al., (Curr. Opin. Biotechnol., 2005, Vol. 16: 378-384) teaches that the complexity of the structure/function relationship in enzymes has proven to be the factor limiting the general application of rational enzyme modification and design, where rational enzyme modification and design requires in-depth understanding of structure/function relationships. The reference of Sen et al., (Appl. Biochem. Biotechnol., 2007, Vol.143: 212-223), teaches in vitro recombination techniques such as DNA shuffling, staggered extension process (STEP), random chimera genesis on transient templates (RACHITT), iterative truncation for the creation of hybrid enzymes (ITCHY), recombined extension on truncated templates (RETT), and so on have been developed to mimic and accelerate nature's recombination strategy. However, such rational design and directed evolution techniques only provide guidance for searching and screening for the claimed polypeptide which is not guidance for making and/or using the claimed polypeptide.
Therefore, taking into consideration the extremely broad scope of the claims, the lack of guidance, the amount of information provided, the lack of knowledge about a correlation between structure and the desired function, and the high degree of unpredictability of the prior art in regard to structural changes and their effect on function, one of ordinary skill in the art would have to go through the burden of undue experimentation in order to practice the claimed invention. Thus, Applicant has not provided sufficient guidance to enable one of ordinary skill in the art to make and use the invention in a manner reasonably correlated with the scope of the claims in the claimed method.
MPEP 2163.II.A.2. (a).i) states, “Whether the specification shows that applicant was in possession of the claimed invention is not a single, simple determination, but rather is a factual determination reached by considering a number of factors. Factors to be considered in determining whether there is sufficient evidence of possession include the level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention”;
Examiner would like to reiterate
“The basic quid pro quo contemplated by the Constitution and the Congress for granting a patent monopoly is the benefit derived by the public from an invention with substantial utility”, [u]nless and until a process is refined and developed to this point-where specific benefit exists in currently available form-there is insufficient justification for permitting an applicant to engross what may prove to be a broad field”, and “a patent is not a hunting license”,[i]t is not a reward for the search, but compensation for its successful conclusion.”
Enablement
II. Claims 16-18, 20, 24-26, 28-29 and 32-40 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, scope of enablement, because the specification, while being enabling for the characterization of nucleic acid construct encoding a fusion protein comprising: (i) a first polynucleotide encoding a signal peptide comprising the amino acid sequence of SEQ ID NO: 2 and (ii) a second polynucleotide encoding hexosaminidase polypeptide(s) comprising the amino acid sequence(s) of SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8 or SEQ ID NO: 10; does not reasonably provide enablement for genus of polypeptides and the encoding polynucleotides i.e., any nucleic acid construct encoding a fusion protein comprising: (i) a first polynucleotide encoding a signal peptide having a sequence identity of at least 90% to SEQ ID NO: 2 and (ii) a second polynucleotide encoding any hexosaminidase of undefined and unlimited structures, wherein the polypeptide having hexosaminidase activity belongs to the Terribacillus clade and comprise the motif [VIM][LIV]G[GAV]DE[VI][PSA] (SEQ ID NO: 11) (only partial structure/motif is defined, remainder of the structure is undefined, as in claims 16-18, 20, 24-26, and 32-40); and said hexosaminidase polypeptide(s) having 80%-90% sequence identity to the mature polypeptide of SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8 or SEQ ID NO: 10 (as in claims 28-29; also see 35 U.S.C. 112(d) rejection above for claim interpretation). 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.
The factors to be considered in determining whether undue experimentation is required are summarized In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988). The Court in Wands states: "Enablement is not precluded by the necessity for some experimentation such as routine screening. However, experimentation needed to practice the invention must not be undue experimentation. The key word is 'undue,' not 'experimentation.' " (Wands, 8 USPQ2d 1404). Clearly, enablement of a claimed invention cannot be predicated on the basis of quantity of experimentation required to make or use the invention. "Whether undue experimentation is needed is not a single, simple factual determination, but rather is a conclusion reached by weighing many factual considerations." (Wands, 8 USPQ2d 1404). The factors to be considered in determining whether undue experimentation is required include: (1) the quantity of experimentation necessary, (2) the amount or 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 claims. While all of these factors are considered, a sufficient amount for a prima facie case are discussed below.
The breadth of claims includes overly broad genus, applicants’ disclose no direction or guidance on how to design and make any polypeptide and the encoding polynucleotide of undefined structure having desired activity as noted in the breadth above. Thus, instant specification and prior art failed to describe how to make and use the claimed genus of polypeptides and the encoding polynucleotides sufficiently. Although, it is possible to display and create any protein structure in computer (in silico) and manipulate in any possible way, such as inserting any amino acid(s) into preexisting three-dimensional scaffold; the creation of desired catalytic/biologic activity in a solution is highly unpredictable.
According to MPEP § 2164.02: “All questions of enablement are evaluated against the claimed subject matter. The focus of the examination inquiry is whether everything within the scope of the claim is enabled.”; “The Federal Circuit has repeatedly held that “the specification must teach those skilled in the art how to make and use the full scope of the claimed invention without ‘undue experimentation’.” In re Wright, 999 F.2d 1557, 1561, 27 USPQ2d 1510, 1513 (Fed. Cir. 1993). Nevertheless, not everything necessary to practice the invention need be disclosed. In fact, what is well-known is best omitted. In re Buchner, 929 F.2d 660, 661, 18 USPQ2d 1331, 1332 (Fed. Cir. 1991). All that is necessary is that one skilled in the art be able to practice the claimed invention, given the level of knowledge and skill in the art. Further the scope of enablement must only bear a “reasonable correlation” to the scope of the claims. See, e.g., In re Fisher, 427 F.2d 833, 839, 166 USPQ 18, 24 (CCPA 1970).”; and “As concerns the breadth of a claim relevant to enablement, the only relevant concern should be whether the scope of enablement provided to one skilled in the art by the disclosure is commensurate with the scope of protection sought by the claims. > AK Steel Corp. v. Sollac, 344 F.3d 1234, 1244, 68 USPQ2d 1280, 1287 (Fed. Cir. 2003); < In re Moore, 439 F.2d 1232, 1236, 169 USPQ 236, 239 (CCPA 1971). See also Plant Genetic Sys., N.V. v. DeKalb Genetics Corp., 315 F.3d 1335, 1339, 65 USPQ2d 1452, 1455 (Fed. Cir. 2003) (alleged “pioneer status” of invention irrelevant to enablement determination).”
Instant claims are so broad such that, instant disclosure of instant specification and a general knowledge in the art are not commensurate with the scope of instant claims for one skilled in the art to make and use claimed invention without undue experimentation. As noted above, the breadth of instant claims encompass an overly broad genus of undefined structure including variants, mutants and homologs.
Therefore, taking into consideration the extremely broad scope of the claims, the lack of guidance, the amount of information provided, the lack of knowledge about a correlation between structure and the desired function, and the high degree of unpredictability of the prior art in regard to structural variability and its effect on function, one of ordinary skill in the art would have to go through the burden of undue experimentation in order to practice the claimed invention. 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. The scope of the claim must bear a reasonable correlation with the scope of enablement (In re Fisher, 166 USPQ 19 24 (CCPA 1970)). Without sufficient guidance, determination of genus of polypeptides and the encoding polynucleotides i.e., any nucleic acid construct encoding a fusion protein comprising: (i) a first polynucleotide encoding a signal peptide having a sequence identity of at least 90% to SEQ ID NO: 2 and (ii) a second polynucleotide encoding any hexosaminidase of undefined and unlimited structures, wherein the polypeptide having hexosaminidase activity belongs to the Terribacillus clade and comprise the motif [VIM][LIV]G[GAV]DE[VI][PSA] (SEQ ID NO: 11) (only partial structure/motif is defined, remainder of the structure is undefined, as in claims 16-18, 20, 24-26, and 32-40); and said hexosaminidase polypeptide(s) having 80%-90% sequence identity to the mature polypeptide of SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8 or SEQ ID NO: 10 (as in claims 28-29; also see 35 U.S.C. 112(d) rejection above for claim interpretation), having the desired biological characteristics in a genus of host cells 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).
Applicants’ have traversed the above enablement rejection with the following arguments: (see pages 5-6 of Applicants’ REMARKS dated 12/18/2025).
Applicants’ argue: “…The Applicant further notes that for the sole purpose of advancing prosecution, claim 16 is amended to provide significant structural limitations to the claimed nucleic acid construct that are clearly reflected in the Applicant's specification, including both parts a) "at least 90% to SEQ ID NO: 2" (which corresponds to only three amino acid variations of the signal sequence), and part b) wherein the polypeptide having hexosaminidase "belongs to the Terribacillus clade and comprises the motif [VIM][LIV]G[GAV]DE[VI][PSA] (SEQ ID NO: 11)" (the structure-function aspects are described in detail in Applicant's specification, e.g., page 9, line 26 to page 10, line 2)”.
Reply: Applicants' arguments have been considered but are found to be non-persuasive for the following reasons. Applicants’ arguments filed on 12/18/2025 for the traversal of enablement rejection is on similar lines to the arguments presented for traversing the written-description, said arguments have been fully considered but they are not persuasive. Examiner continues to maintain the rejection for reasons stated on record, supporting evidence and arguments presented above in maintaining the written-description rejection also applies to enablement rejection.
For the above cited reasons, examiner is maintaining the written-description and enablement rejection for claims 16-18, 20, 24-26, 28-29 and 32-40.
New-Claim Rejections: 35 USC § 103
Necessitated by claim amendments
The following is a quotation of 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims under 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of 35 U.S.C. 103(c) and potential 35 U.S.C. 102(e), (f) or (g) prior art under 35 U.S.C. 103(a).
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103(a) are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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 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.
Claims 16-18, 20, 24-26 and 28-40 are rejected under 35 U.S.C. 103(a) as being unpatentable over Ooehlenschlaeger1 et al., (US 10,626,354) or Ooehlenschlaeger2 et al., (US 10,954,478) and further in view of Borchert et al., (US 9,909,115) and see Chapters 1-3, 16 and Vectors-Appendix 5 in Current Protocols in Molecular Biology, Ed., Ausubel et al., Published by John Wiley and Sons, New York, NY, USA, 1990; reference not enclosed), Conneely et al., (US 6,228,614 B1), Guller-Gane et al., (PLOS ONE, 2016, DOI:10.1371/journal.pone.0155340, pages 1-15), Quax et al., (US 5,364,782) and Hau et al., (US 9,206,434 B2).
Ooehlenschlaeger1 et al., (US 10,626,354) disclose nucleic acid constructs encoding polypeptides having 100% sequence identity to SEQ ID NO: 4; having 93.7% sequence identity to SEQ ID NO: 6; having 94.5% sequence identity to SEQ ID NO: 8; and having 93.6% sequence identity to SEQ ID NO: 10 of the instant application and having hexosaminidase activity (see provided sequence alignments); and said polypeptides belonging to Terribacillus clade (col. 1 lines 55-67; reproduced below):
US 10,626,354; Col. 1
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Ooehlenschlaeger1 disclose said reference polypeptide is obtained from Terribacillus clade, having 100% sequence identity to SEQ ID NO: 4 and comprises the motif [VIM][LIV]G[GAV]DE[VI][PSA] (SEQ ID NO: 11); see amino acid residues 181-188 “VLGGDEVP” of reference polypeptide. Ooehlenschlaeger1 et al., also disclose said reference nucleic acid constructs comprising control sequences comprising cryIIIA promoter and as fusion proteins comprising various signal peptides (see Abstract; col. 5, lines 52-67; col. 39, lines 60-67 to col. 40, lines 1-22); said reference host cell comprising expression constructs and encoding polynucleotides includes Bacillus licheniformis (col. 46, lines 54-67; and entire document).
Similarly, Ooehlenschlaeger2 et al., (US 10,954,478) also disclose nucleic acid constructs encoding polypeptides having 95.5% sequence identity to SEQ ID NO: 4 and many variants; having 89.5% sequence identity to SEQ ID NO: 6 instant application and having hexosaminidase activity (see provided sequence alignments). Ooehlenschlaeger2 et al., also disclose said reference nucleic acid constructs comprising control sequences comprising cryIIIA promoter and as fusion proteins comprising various signal peptides (see Abstract; col. 5, lines 1-20; col. 7, lines 40-45; col. 6, lines 15-30; col. 9, lines 50-67 to col. 10, lines 1-20; col. 51, lines 5-36; col. 53, lines 3-25); said reference host cell comprising expression constructs and encoding polynucleotides includes Bacillus licheniformis (col. 58, lines 40-46; and entire document).
Ooehlenschlaeger1 et al., or Ooehlenschlaeger2 et al., are silent regarding nucleic acid construct comprising (i) a first polynucleotide encoding a signal peptide having a sequence identity of at least 80% to SEQ ID NO: 2, wherein the signal peptide has an additional Ala at the C-terminus compared to SEQ ID NO: 2 (as in claim 16); wherein the signal peptide is a variant of SEQ ID NO: 2 having three alterations compared to SEQ ID NO: 2; wherein the signal peptide is a variant of SEQ ID NO: 2 having two alterations compared to SEQ ID NO: 2 (as in claims 38-39).
Regarding claims 16 and 40, Borchert et al., (US 9,909,115) teach the use of promoters, expression constructs comprising cryIIIA promoter and fusion proteins driving the expression of enzymes/genes of interest (see Abstract; Fig. 3; col. 23, lines 60-67 to col. 25, lines 1-45; and entire document) and encoded fusion proteins comprising a signal peptide having 100% sequence identity to SEQ ID NO: 2 wherein the signal peptide has an additional Ala at the C-terminus compared to SEQ ID NO: 2 (as in claim 16; see Col. 35, reproduced below); and wherein the signal peptide is a variant of SEQ ID NO: 2 having one alteration compared to SEQ ID NO: 2 (as in claim 40) of the instant invention (see col. 35, Us 9,909,115 B2, reproduced below; and see provided sequence alignment);
US 9,909,115 B2; Col. 35
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Guller-Gane et al., (PLOS ONE, 2016, DOI:10.1371/journal.pone.0155340, pages 1-15), also provide teaching, suggestion and motivation for the addition of alanine residues to the C-terminus of signal peptides and additional alanine at the C-terminus improves expression and secretion of secreted recombinant proteins (see Abstract; Fig. 1, page 6; Fig. 2, page 7; Figs. 3-4, pages 9-10; and entire document).
Furthermore, the many advantages of recombinant production of useful proteins, construction of fusion proteins, selection of vectors including vectors comprising constitutive and inducible promoters, transformation of host cells with any desired characteristics and cellular context are well known within the art (for example, see Chapters 1-3, 16 and Vectors-Appendix 5 in Current Protocols in Molecular Biology, Ed., Ausubel et al., Published by John Wiley and Sons, New York, NY, USA, 1990; reference not enclosed), as are recombinant methods of obtaining the necessary genes. These advantages include a) the ability to produce much larger quantities of the protein cloned into suitable expression vectors, b) being able to produce the protein in more easily handled organisms or organisms of interest with suitable characteristics depending on the experimental need (host cells), c) construction of fusion proteins with suitable tags/heterologous polypeptides for easy detection and purification of expressed proteins or endowing said polypeptide with additional biological and biochemical properties, d) appropriate targeting of expressed polypeptides to the sub-cellular compartment of interest in the host cell of interest by expressing said polypeptide as a fusion protein comprising heterologous signals such as leader sequences, e) for reducing the number of steps necessary for the purification of a protein, f) producing the protein in a purer form by using an organism that does not include naturally occurring contaminants of the protein, and g) and advantages of using different cellular context for the expression and production of polypeptide or fusion protein of interest.
Regarding claims 38-39, wherein the signal peptide is a variant of SEQ ID NO: 2 having three alterations compared to SEQ ID NO: 2; and wherein the signal peptide is a variant of SEQ ID NO: 2 having two alterations compared to SEQ ID NO: 2, the following references provide the structural and functional information (see provided sequence alignments):
Quax et al., (US 5,364,782) disclose signal peptide is a variant of SEQ ID NO: 2 having two alterations compared to SEQ ID NO: 2; and
Hau et al., (US 9,206,434 B2) disclose signal peptide is a variant of SEQ ID NO: 2 having three alterations compared to SEQ ID NO: 2.
As such, disclosure of expression constructs comprising cryIIIA promoter and fusion proteins driving the expression of enzymes/genes of interest and encoded fusion proteins comprising a signal peptide having 100% sequence identity to SEQ ID NO: 2, wherein the signal peptide has an additional Ala at the C-terminus compared to SEQ ID NO: 2 or having two alterations and three alterations compared to SEQ ID NO: 2 of the instant application, such as that of Borchert et al., Guller-Gane et al., Quax et al., and Hau et al., clearly suggests to a skilled artisan to modify the teachings of Ooehlenschlaeger1 et al., or Ooehlenschlaeger2 et al., and express the isolated hexosaminidase in suitable host cells and comprising the reference signal peptides, as suggested by Borchert et al., Guller-Gane et al., Quax et al., and Hau et al., and to construct an expression vector by employing the methods disclosed in Chapters 1-3, 16 and Vectors-Appendix 5 in Current Protocols in Molecular Biology, Ed., Ausubel et al., Published by John Wiley and Sons, New York, NY, USA, 1990. One of ordinary skill in the art would have a reasonable expectation of success, since polypeptides having hexosaminidase activity, said polypeptide encoded by a polynucleotides and wherein the encoded polypeptide having 100% sequence identity to SEQ ID NO: 4; having 93.7% sequence identity to SEQ ID NO: 6; having 94.5% sequence identity to SEQ ID NO: 8; and having 93.6% sequence identity to SEQ ID NO: 10, method of making said polypeptide wherein said encoding nucleic acid is in an expression vector under the control of cryIIIA promoter and transforming a plurality of host cells and method of making and using said polypeptide are well known in the art.
Therefore, claims 16-18, 20, 24-26 and 28-40 are rejected under 35 U.S.C. 103(a) as being unpatentable over Ooehlenschlaeger1 et al., (US 10,626,354) or Ooehlenschlaeger2 et al., (US 10,954,478) and further in view of Borchert et al., (US 9,909,115) and see Chapters 1-3, 16 and Vectors-Appendix 5 in Current Protocols in Molecular Biology, Ed., Ausubel et al., Published by John Wiley and Sons, New York, NY, USA, 1990; reference not enclosed), Conneely et al., (US 6,228,614 B1), Guller-Gane et al., (PLOS ONE, 2016, DOI:10.1371/journal.pone.0155340, pages 1-15), Quax et al., (US 5,364,782) and Hau et al., (US 9,206,434 B2).
Applicants’ have traversed the above 35 USC § 103 rejection with the following arguments in the light of claim amendments: (see pages 6-7of Applicants’ REMARKS dated 12/18/2025).
Applicants’ argue (A): “…The Applicant notes that for the sole purpose of advancing prosecution, amended claim 16 recites:
A nucleic acid construct comprising:
a) a first polynucleotide encoding a signal peptide from a bacterial alpha- amylase, wherein the signal peptide has a sequence identity of at least 90% to SEQ ID
NO: 2; and
b) a second polynucleotide encoding a polypeptide having hexosaminidase
activity, wherein the polypeptide having hexosaminidase activity belongs to the Terribacillus clade and comprises the motif [VIM][LIV]G[GAV]DE[VI][PSA] (SEQ ID NO:
11);
wherein the signal peptide has an additional Ala at the C-terminus compared to
SEQ ID NO: 2; and
wherein the first polynucleotide and the second polynucleotide are operably
linked in translational fusion.
Reply (A): Applicants' arguments have been considered but are found to be non-persuasive for the following reasons. Examiner continues to maintain the rejection for reasons stated on record (dated 06/18/2025) and additionally for the following reasons.
Contrary to applicants’ arguments, Ooehlenschlaeger1 disclose said reference polypeptide is obtained from Terribacillus clade, having 100% sequence identity to SEQ ID NO: 4 and comprises the motif [VIM][LIV]G[GAV]DE[VI][PSA] (SEQ ID NO: 11); see amino acid residues 181-188 “VLGGDEVP” of the reference polypeptide; and
Contrary to applicants’ arguments, Borchert et al., (US 9,909,115) teach the use of promoters, expression constructs comprising cryIIIA promoter and fusion proteins driving the expression of enzymes/genes of interest (see Abstract; Fig. 3; col. 23, lines 60-67 to col. 25, lines 1-45; and entire document) and encoded fusion proteins comprising a signal peptide having 100% sequence identity to SEQ ID NO: 2 wherein the signal peptide has an additional Ala at the C-terminus compared to SEQ ID NO: 2 (as in claim 16).
Applicants’ further argue (B): “…The amended claims capture what is demonstrated by the Applicant, and more specifically throughout the examples of the pending application, that the claimed signal peptide sequence has provided high expression yield for hexosaminidases. As shown in the examples, compared to other signal peptides, such result is totally unexpected and in fact was surprising. This was affirmed in the International Preliminary Report on Patentability (IPRP) Section 2.8, which recites "this cannot be predicted from the prior art', which includes consideration of D1 (i.e. W02017/186943, the international equivalent of Ooehlenschlaeger) among other cited publications.
Accordingly, the combination of Ooehlenschlaeger, Borchert, and Mo/Bio fails to teach or suggest each and every limitation as arranged in the amended claims, nor does the combination of cited references provide a predictable outcome to the skilled artisan that leads to the Applicant's invention.”
Reply (B): Applicants' arguments have been considered but are found to be non-persuasive for the following reasons. Examiner continues to maintain the rejection for reasons stated on record (dated 06/18/2025) and additionally for the following reasons. Applicants’ have mischaracterized the International Preliminary Report on Patentability (IPRP) Section 2.8; a careful scrutiny of the report very clearly argues and suggests the following:
“Hence the B.lichenisformis amyL signal peptide appears to provide the technical effect of increased expression yield for the Disp43 and Disp45 hexosaminidases from Terribacillus saccharophilus when expressed in B.subtilis. There is an argument that this cannot be predicted from the prior art. The application teaches that the amyL signal peptide is disclosed in SEQ ID NO.2 (page 10 lines 1-8), and may have an additional Ala at the C-terminus; SEQ ID NO.2 is 27aa. However, the prior art teaches that the B.lichenisformis amyL signal sequence is 29aa (D5, Figure 2). The sequence difference between the two occurs at the C-terminus, where the B.lichenifsormis signal peptide sequence of D5 has in total four alanine residues, and the sequence of SEQ ID NO.2 has only two. According to the sequence listing, the fusion proteins used in the application comprise the full B.lichenisformis amyL signal sequence of 29aa (see SEQ ID NOs 6 and 10). This means that the effect on yield demonstrated in the application is only demonstrated when the signal sequence represented by SEQ ID NO.2 is extended to 29aa by an additional two C-terminal alanine residues. positions -3, -1 and +1 of the B.stearothermophilus alpha amylase caused reduced production of the enzyme in B.brevis (page 1384, left column). Accordingly, it would appear likely that omission of the two C-terminal alanines of the B.lichenisformis amyL signal sequence signal peptide has a detrimental effect on expression yield. Furthermore, given the sensitivity of expression yield to signal peptide sequence, there is no evidence provided that the increase in expression yield is also obtained using a signal peptide whose sequence comprises 80% identity to SEQ ID NO.2. In the absence of a technical effect across the scope of the claims, no inventive step can be attributed to the selection of the signal sequence as set out in SEQ ID NO.2 or a sequence comprising at least 80% identity thereto, for expressing the Disp43 and Disp45 hexosaminidases, never mind any undefined polypeptide sequence having hexosaminidase activity.
International Report PCT/ISA 237 also asserts claims 1-15 lack Novelty (N) and Inventive step (IS).
Summary of Pending Issues
The following is a summary of issues pending in the instant application.
New claim 38 is rejected under 35 U.S.C. 112(d).
Claims 16-18, 20, 24-26 , 28-29 and 32-40 are rejected under 35 U.S.C. 112(a) for written-description and enablement.
Claims 16-18, 20, 24-26 and 28-40 are rejected under 35 U.S.C. 103(a) as being unpatentable over Ooehlenschlaeger1 et al., (US 10,626,354) or Ooehlenschlaeger2 et al., (US 10,954,478) and further in view of Borchert et al., (US 9,909,115) and see Chapters 1-3, 16 and Vectors-Appendix 5 in Current Protocols in Molecular Biology, Ed., Ausubel et al., Published by John Wiley and Sons, New York, NY, USA, 1990; reference not enclosed), Conneely et al., (US 6,228,614 B1), Guller-Gane et al., (PLOS ONE, 2016, DOI:10.1371/journal.pone.0155340, pages 1-15), Quax et al., (US 5,364,782) and Hau et al., (US 9,206,434 B2).
Conclusion
None of the claims are allowable. Claims 16-18, 20, 24-26 and 28-40 are rejected for the reasons identified in the Rejections and Summary sections of this Office Action. Applicants’ must respond to the rejections in each of the sections in this Office Action to be fully responsive for prosecution.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Regarding filing an After Final amendment, Applicants are directed to MPEP 714.13, which states:
II. ENTRY NOT A MATTER OF RIGHT
It should be kept in mind that applicant cannot, as a matter of right, amend any finally rejected claims, add new claims after a final rejection (see 37 CFR 1.116) or reinstate previously canceled claims. Except where an amendment merely cancels claims, adopts examiner suggestions, removes issues for appeal, or in some other way requires ONLY A CURSORY REVIEW by the examiner (e.g., typographical errors), compliance with the requirement of a showing under 37 CFR 1.116(b)(3) is expected in all amendments after final rejection. An affidavit or other evidence filed after a final rejection, but before or on the same date of filing an appeal, may be entered upon a showing of good and sufficient reasons why the affidavit or other evidence is necessary and was not earlier presented in compliance with 37 CFR 1.116(e). See 37 CFR 41.33 and MPEP § 1206 for information on affidavit or other evidence filed after appeal. (Examiner's emphasis) If more than a cursory review is required, Applicants are referred to CFR §1.114.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to GANAPATHIRAMA RAGHU whose telephone number is (571)272-4533. The examiner can normally be reached on M-F 8:30am-5pm EST.
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/GANAPATHIRAMA RAGHU/ Primary Examiner, Art Unit 1652