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 .
Election/Restrictions
Applicant's election with traverse of Group 1, claims 1-13 and the species of SEQ ID NO: 13 which corresponds to claims 1, 3-6, and 9-13 in the reply filed on December 25, 2025 is acknowledged. The traversal is on the ground(s) that the common technical feature shared by all groups is a polynucleotide encoding an antibody-related molecule and a polynucleotide encoding a modified signal peptide having a specific 6-mer of amino acid residues at the C-terminus which has the same function of extracellularly secreting the antibody related molecule in all groups (Pg. 8 of Remarks). Applicant asserts that the claims of Groups 2 and 3 drawn to the Bacillus host cell and method of producing an antibody related molecule comprising culture of the Bacillus host cell depend on the limitations of claim 1 (Pg. 10). Applicant further traverses that the species of C-terminal amino acid residues in the modified signal peptide do share a common core structure (see table on Pg. 10).
In view of the prior art and Applicant’s traversal related to Groups 2 and 3, Group 2, claim 14 and Group 3, claim 15 have been rejoined. Additionally, all species have been rejoined, which encompass claims 1-13.
Group 4, Claim 16 remains withdrawn as claim 16 recites limitations which are not shared by Groups 1-3. Specifically, claim 16 does not require the same functional language of extracellular secretion of an antibody-related molecule.
The requirement is still deemed proper and is therefore made FINAL.
Claims 16 is withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected inventions, there being no allowable generic or linking claim Applicant timely traversed the restriction (election) requirement in the reply filed on December 24, 2025.
Claim 1 has been amended to recite that the protein of interest is an antibody-related molecule and that X2 is G and claims 15 and 16 have been similarly been amended to recite that the protein of interest is an antibody-related molecule. Dependent claims 9, 10, and 15 have been amended to reflect updated claim dependency.
Claims 8 and 17 have been cancelled. Claims 2, 4, 7, 14, and 15 have been rejoined. Claim 16 is withdrawn.
Claims 1-15 are examined on the merits.
Priority
The instant application is a 35 U.S.C 371 national stage filing of the International Application No. PCT/JP2021/039410 filed on October 26, 2021. The instant application claims foreign priority under 35 U.S.C 119(a)-(d) to Japanese Patent Application JP2020-180382, filed on October 28, 2020. Receipt is acknowledged of a certified copy of the foreign patent application in the original language as required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on April 25, 2023; November 13, 2023; and January 24, 2025 are in compliance with the provisions of 37 CFR 1.97 and are being considered by the examiner.
Applicant is reminded that 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 § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Claim Objections
Claim 1 is objected to because of the following informalities: As claimed, claim 1 recites that positions 1 to 6 are counted from the C-terminus, which suggests that position 1 would be closest to the C-terminus, and also that X6 is located at the C-terminus. This could be clarified by reciting language similar to Para. [0031] of the specification stating that X6 is the residue located at the C-terminus and X1 is the residue located at position 6 as counted from the C-terminus. Appropriate correction is required.
Claim 9 is objected to because of the following informalities: Claim 9 recites abbreviations for Fab, ScFv, and VHH which are not defined by their full terminology prior to use of the abbreviation. Appropriate correction is required.
Claim Rejections - 35 USC § 112(a) - Written Description
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 1-7, 9-15 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.
Independent claim 1 encompasses a nucleic acid construct for the expression and extracellular secretion of an antibody-related molecule comprising a genus of polynucleotides encoding an antibody-related molecule a genus of polynucleotides encoding a modified signal peptide comprising the amino acid residues of X1X2X3X4X5X6 at the final 6 positions of the C terminus where X1 is G, P, or A; X2 is G; X3 is P, S, or A and X1X2X3 are not GGP; X4 is A; X5 is S, H, or F; and X6 is A, while the specification only discloses a fixed number of species of 6-mers of amino acids at the C-terminus of the modified signal peptide.
In regard to the scope of antibody-related molecule, Applicant’s specification describes the genus of antibody-related molecules to include an immunoglobulin or a single domain or combination of two or more domains selected from the domains constituting an immunoglobulin and provides examples of domains of immunoglobulin heavy chain, i.e. VH, CH1, CH1, and CH3, and domains of immunoglobulin light chain, i.e., VL and CL. Applicant further provides exemplary embodiments of IgG, Fab, F(ab’)2, ScFv, a diabody, and a VHH (Para. [0007]).
In regard to the scope of modified signal peptides, Applicant’s specification describes the genus of modified signal peptides as being produced by modification of the C-terminal region of parent signal peptides (Para. [0029]), comprising the amino acid residues of X1X2X3X4X5X6 at the final 6 positions of the C terminus where X1 is G, P, or A; X2 is G; X3 is P, S, or A and X1X2X3 are not GGP; X4 is A; X5 is S, H, or F; and X6 is A (Para. [0031]), and comprising a region from the N-terminus to position 7 as counted from the C-terminus which consists of the amino acid sequence of a signal peptide of Bacillus bacteria other than the C-terminal region or an amino acid sequence having at least 90% sequence identity to a signal peptide of Bacillus bacteria (Para. [0032]). Additionally, Applicant’s specification also describes modifications to the N-terminal region which may consist of amino acid sequences having deletions, substitutions, additions, or insertions of one or several amino acid residues (Para. [0032]) where “one or several” can be defined as 1-15 nucleotides (Para. [0012]).
In regard to the scope of the host cell, Applicant’s specification describes a genus of Bacillus bacteria and provides examples of Bacillus subtilis, Bacillus cereus, Bacillus thuringiensis, Bacillus megaterium, Bacillus liqueniformis, and mutant strains thereof (Para. [0024]).
Dependent claims 2 encompasses a genus of polynucleotides encoding a modified signal peptide comprising the amino acid residues of X1X2X3X4X5X6 at the final 6 positions of the C terminus where X1 is G, P, or A; X2 is G; X3 is P or S; X4 is A; X5 is S or H; and X6 is A.
Dependent claims 3-4 encompass a genus of polynucleotides encoding a modified signal peptide comprising the amino acid residues having SEQ ID NOs: 13-30.
Dependent claims 5-6 encompass a genus of N-terminal regions comprising an amino acid sequences of any of instant SEQ ID NOs: 7-12 or an amino acid sequence having at least 90% identity thereto.
Dependent claim 7 encompasses a genus of modified signal peptides consisting of an amino acid sequence of SEQ ID NOs: 31-35, (i.e. an N-terminal region of SEQ ID NO: 10 and C-terminus of SEQ ID NOs: 25-28 or N-terminal region of SEQ ID NO: 11 and C-terminus of SEQ ID NO: 15).
Dependent claims 9-10 encompasses a genus of antibody-related molecules consisting of a Fab, an ScFv, and a VHH.
Dependent claims 11-12 encompasses a genus of promoters operably linked to the antibody-related molecules.
Dependent claim 13 encompasses a genus of expression vectors comprising the nucleic acid construct of claim 1.
Dependent claim 14 encompasses a genus of Bacillus bacteria comprising the nucleic acid construct of claim 1.
Dependent claim 15 encompasses a genus of methods of producing an antibody-related molecule comprising culturing the Bacillus of claim 14 and collecting the extracellularly secreted antibody-related molecule.
Under the written description guidelines (see MPEP 2163) the Examiner is directed to determine whether one skilled in the art would recognize that the Applicant was in possession of the claimed invention as a whole at the time of filing. The following considerations are critical to this determination.
To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. See, e.g., Moba, B.V. v. Diamond Automation, Inc., 325 F.3d 1306, 1319, 66 USPQ2d 1429, 1438 (Fed. Cir. 2003); Vas-Cath, Inc. v. Mahurkar, 935 F.2d at 1563, 19 USPQ2d at 1116. An original claim may lack written description support when (1) the claim defines the invention in functional language specifying a desired result but the disclosure fails to sufficiently identify how the function is performed or the result is achieved or (2) a broad genus claim is presented but the disclosure only describes a narrow species with no evidence that the genus is contemplated. See Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1349-50 (Fed. Cir. 2010) (en banc). The written description requirement is not necessarily met when the claim language appears in ipsis verbis in the specification. "Even if a claim is supported by the specification, the language of the specification, to the extent possible, must describe the claimed invention so that one skilled in the art can recognize what is claimed. The appearance of mere indistinct words in a specification or a claim, even an original claim, does not necessarily satisfy that requirement." Enzo Biochem, Inc. v. Gen-Probe, Inc., 323 F.3d 956, 968, 63 USPQ2d 1609, 1616 (Fed. Cir. 2002).
Accordingly, to satisfy the written description requirement, the specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1562-63, 19 USPQ2d 1111 (Fed. Cir. 1991). See also MPEP 2163.
ACTUAL REDUCTION TO PRACTICE
In regard to independent claims 1 and dependent claims 2-4 encompassing a nucleic acid construct for the expression and extracellular secretion of an antibody-related molecule comprising a genus of polynucleotides encoding an antibody-related molecule a genus of polynucleotides encoding a modified signal peptide comprising the amino acid residues of X1X2X3X4X5X6 at the final 6 positions of the C terminus, Applicant discloses a limited number of modified signal peptides comprising specific amino acid residues (SEQ ID NO: 13-30, 82-84; see Tables 3 and 4).
In regard to dependent claims 5-6 encompassing a genus of N-terminal regions comprising an amino acid sequences of any of instant SEQ ID NOs: 7-12 or an amino acid sequence having at least 90% identity thereto, Applicant discloses a limited number of N-terminal regions of S237 (SEQ ID NO: 11) and yncM (SEQ ID NO: 10) (See Table 3). It is noted that while Applicant has disclosed signal peptide combinations of N-terminal region of SEQ ID NO: 11 with C-terminus regions of SEQ ID NOs: 13-30 and 82-84, Applicant has only disclosed signal peptide combinations of N-terminal region of SEQ ID NO: 10 with C-terminus regions of SEQ ID NO: 13-18 and 23.
In regard to dependent claims 9-10 encompassing a genus of antibody-related molecules consisting of a Fab, an ScFv, and a VHH, Applicant discloses a limited number of antibody-related molecules which are VHHs, specifically 1ZVY and 5IMM (see Table 3).
In regard to dependent claims 11- 13 encompassing a genus of vectors and promoters comprising the nucleic acid construct of claim 1, as stated above Applicant discloses a limited number of nucleic acid constructs of claim 1.
In regard to dependent claims 14-15 encompassing a genus of host cells which are Bacillus bacteria comprising the nucleic acid construct of claim 1 and a method of producing an antibody-related molecule comprising culturing the Bacillus of claim 14, as stated above, Applicant discloses a limited number of nucleic acid constructs of claim 1 and also a limited number of Bacillus host cells, specifically a Bacillus subtilis Dpr9 ΔsigF strain.
However, as stated above, Applicant was only in possession of a limited number of nucleic acid constructs comprising C-terminal SEQ ID NOs for expression and extracellular secretion of a limited number of VHHs in a single strain of Bacillus.
DISCLOSURE OF STRUCTURE
Applicant has provided sequence listings of SEQ ID NOs of the C-terminus of the modified signal peptides (SEQ ID NO: 13-30), sequence listings of SEQ ID NOs of the N-terminus of the modified signal peptides (SEQ ID NO: 7-12), two embodiments of an antibody-related molecule which is a VHH (1ZVY and 5IMM), and a single embodiment of host cell, Bacillus subtilis Dpr9 ΔsigF. With the help of signal peptide screening library and high throughput system, a skilled artisan could determine which specific amino acid sequences were likely to function as a signal peptide for expression and extracellular secretion of an antibody-related molecule in a particular host cell, since host cell specific signal peptides used for extracellular secretion of proteins are known. However, neither the specification nor the art indicate a relationship between the structure of the instantly claimed genus of modified signal peptides and the ability to function in a nucleic acid construct for the expression and extracellular secretion of any antibody-related molecule in any host Bacillus.
SUFFICIENT RELEVENT IDENTIFYING CHARACTERISTICS
As stated above, the embodiments of specific C-terminal amino acid SEQ ID NOs (SEQ ID NOs: 13-30) which are able to be linked to specific N-terminal amino acid SEQ ID NOs (S237/SEQ ID : 11 or yncM/SEQ ID NO:10) in order to generate modified signal peptides which can be used for expression and extracellular secretion of specific VHHs (1ZVY or 5IMM) in a Bacillus subtilis Dpr9 ΔsigF strain are provided (see Tables 3-5).
Accordingly, if a skilled artisan sought to generate the claimed genus of nucleic acid constructs for expression and extracellular secretion of antibody-related molecules, they would need to know which specific 6-mer amino acid sequence of the C-terminus could be linked to which specific amino acid sequence of the N-terminus and be able to predictably produce a construct which can be used for the expression and extracellular secretion of any antibody related molecule in any Bacillus host cell.
The breadth of the claims encompass a genus of C-terminal and N-terminal amino acid sequences which can be linked and used as a signal peptide for expression and extracellular secretion of any antibody-related molecule in any Bacillus. However, the specification provides no guidance nor description as to any rationale in choosing the amino acid sequences that were identified, therefore the skilled artisan would not know what approach to take to select C-terminus amino acid sequences or combinations of N-terminal and C-terminus amino acid sequences which could be used as a signal peptide with any predictable outcome on expression and extracellular secretion of any antibody-related molecule in any Bacillus. Therefore, it is incumbent on the applicant to provide this nexus between structure and function in order to be given credit for possession of a larger genus of polynucleotides comprising amino acid sequences used as a modified signal peptide for expression and extracellular secretion of an antibody-related molecule in Bacillus beyond those comprising the individual disclosed species. Otherwise, the Written Description guidelines suggest that the Applicant is entitled to only the species specifically recited as having this activity. Moreover, even when several species are disclosed, these are not necessarily representative of the entire genus. AbbVie Deutschland GMBH v. Janssen Biotech, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014) (“The ’128 and ’485 patents, however, only describe species of structurally similar antibodies that were derived from Joe-9. Although the number of the described species appears high quantitatively, the described species are all of the similar type and do not qualitatively represent other types of antibodies encompassed by the 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 to provide a "representative number” of species.
An applicant may show that an invention is complete by disclosure of sufficiently detailed, relevant identifying characteristics which provide evidence that applicant was in possession of the claimed invention, i.e., complete or partial structure, other physical and/or chemical properties, functional characteristics when coupled with a known or disclosed correlation between function and structure, or some combination of such characteristics. Enzo Biochem, 323 F.3d at 964, 63 USPQ2d at 1613.
STATE OF THE ART AND QUANTITY OF EXPERIMENTATION
The nucleic acid construct comprising signal peptides which can be used for expression and extracellular secretion of an antibody-related molecule of the claimed invention is not well established. Although the use and screening of signal peptides for expression and extracellular secretion of a protein is routine and conventional, one of ordinary skill in the art would neither expect nor predict the claimed functioning of the modified signal peptide according to the genus of nucleic acid constructs comprising a modified signal peptide for the expression and secretion of an antibody-related molecule as broadly as is instantly claimed.
Brockmeier et al. (found in IDS dated 04/25/2025) teaches that the most effective signal peptide for use in secretion of one protein is not necessarily the most effective or even a sufficient signal peptide for secretion of a different target protein in B. subtilis that signal peptides must be optimized based on the individual protein of interest which is to be secreted (Abstract; Fig 5; Pg. 399, left col. 2nd para.). Additionally, Brockmeier et al. teaches that known programs which purport to predict optimal signal peptides for heterologous protein secretion are unreliable (Table 1, Pg. 399, left col., 3rd para.). Further, Brockmeier et al. teaches that the N-terminal region of the protein also plays a role in the secretion efficiency and that optimal interaction between signal peptide and target protein for secretion is critical (Pg. 399, left col., 1st para.). Brockmeier et al. ultimately concludes that secretion efficiency for a protein in B. subtilis is determined by “a complex pattern of events.” (Pg. 399, right col. 3rd para.).
Freudl (2018, Signal peptides for recombinant protein secretion in bacterial expression systems. Microbial Cell Factories, 17(1), 52) teaches that effectiveness of signal peptides related to target protein secretion also differs between host cells, indicating that the optimal signal peptide for extracellular secretion of a target protein also must be chosen/optimized based on the host (Pg. 6, right col, 1st full para.). Freudl teaches that modifications to signal peptides in the N-terminal region which result in alterations of the net charge of the N-terminal region can either increase or decrease secretion efficiency based on the signal peptide being modified and target protein being secreted (Pg. 6, right col., last para. and Pg. 7, left col. 1st para.). Ultimately, Freudl concludes that an optimally fitted signal peptide must be identified for every individual target protein to allow for optimal extracellular secretion in the chosen host organism (Pg. 8, left col., 1st para) and that it is “almost impossible” to predict in advance which signal peptide will perform best in the context of a given target protein and bacterial expression host (Abstract; Pg. 8, left col., 1st para.)
In fact, Applicant’s specification appears to indicate that a structural modification of a single amino acid in the C-terminal region results in a modified signal peptide which eliminates the functional ability of the signal peptide in extracellular secretion (See SEQ ID NOs: 82-83 in Table 4). Additionally, it is noted that Applicant has reduced to practice signal peptides having C-terminus amino acid residues of SEQ ID NOs 13-30 combined with the N-terminal region of S237 signal peptide for the VHH 1ZVY. However, for the VHH 5IMM, Applicant has only reduced to practice signal peptides having C-terminus amino acid residues of SEQ ID NOs 13-18 and 23 combined with the N-terminal region of yncM signal peptide. Further, Applicant’s specification indicates that a wildtype S237 signal peptide was unable to produce the VHH 1ZVY in a B. subtilis DprΔsigF strain, requiring the use of a different B. subtilis strain (DprΔsigFΔrecA) for the control signal peptide in production of VHH 1ZVY (See Example 2 and Table 3).
Applicant has claimed a genus of nucleic acid constructs comprising a genus of modified signal peptides comprising a genus of 6-mers of C-terminus amino acid sequences used with a genus of N-terminal regions which can be used for expression and extracellular secretion of a genus of antibody-related molecules in a genus of host Bacillus. However, the specification only identifies specific modified signal peptides comprising combinations of C- and N- termini which can be used for extracellular expression of a few specific antibody-related molecules in a single Bacillus host strain. Regardless of how the specific sequences of modified signal peptides were derived by Applicant, based on the teachings of the prior art, any chosen signal peptide is not guaranteed to function for extracellular secretion of any antibody-related molecule in any host cell. Because Applicant has no manner a priori to predict which modified signal peptides can be used for extracellular expression of which antibody-related molecules, the genus of nucleic acid constructs comprising a genus of modified signal peptides which can be used for expression and extracellular secretion of a genus of antibody-related molecules in a genus of Bacillus host cells as claimed by Applicant cannot be predictably chosen or used by the ordinary artisan.
CONCLUSION
Therefore, the Examiner concludes that there is insufficient written description of the instantly claimed genus of nucleic acid constructs for the expression and extracellular secretion of an antibody-related molecule comprising a genus of polynucleotides encoding an antibody-related molecule a genus of polynucleotides encoding a modified signal peptide comprising the amino acid residues of X1X2X3X4X5X6 at the final 6 positions of the C terminus where X1 is G, P, or A; X2 is G; X3 is P, S, or A and X1X2X3 are not GGP; X4 is A; X5 is S, H, or F; and X6. Specifically, there is limited description of the structure-function relationship between the claimed genus of polynucleotides encoding the modified signal peptide and their ability to function in a nucleic acid construct for expression and extracellular secretion of antibody-related molecules and the Examiner further concludes that a skilled artisan would find that the specification inadequately describes the claimed genus of nucleic acid constructs for expression and extracellular secretion of antibody-related molecules.
Claim Rejections - 35 USC § 112(a) - Enablement
Claims 1-7, 9-15 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a modified signal peptide having a specific amino acid sequence for use in expression and extracellular secretion of a specific VHH in a specific B. subtilis strain, does not reasonably provide enablement for a nucleic acid construct for expression and extracellular secretion of any an antibody-related molecule comprising any modified signal peptide having amino acid residues of X1X2X3X4X5X6 at the final 6 positions of the C terminus where X1 is G, P, or A; X2 is G; X3 is P, S, or A and X1X2X3 are not GGP; X4 is A; X5 is S, H, or F; and X6 is A which can be used in any Bacillus host. 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.
SCOPE OF THE INVENTION
The breadth of the claims encompasses a genus of nucleic acid constructs for expression and secretion of an antibody-related molecule comprising a modified signal peptide having an amino acid sequence of X1X2X3X4X5X6 at the final 6 positions of the C terminus where X1 is G, P, or A; X2 is G; X3 is P, S, or A and X1X2X3 are not GGP; X4 is A; X5 is S, H, or F; and X6 is A which can be used in a Bacillus host cell in order to produce an antibody-related molecule via extracellular secretion of the antibody-related molecule. As discussed supra, the specification fails to describe the genus of modified signal peptides which could be used for expression and extracellular secretion of any antibody-related molecule in any Bacillus and would require undue experimentation to discover these modified signal peptides. The specification only discloses and provides guidance for a limited genus of C-terminus amino acid sequences which can be used with a limited genus of N-terminal regions for expression and extracellular secretion of a limited genus of antibody-related molecules in a limited genus of host cell types.
Independent claim 1 encompasses a nucleic acid construct for the expression and extracellular secretion of an antibody-related molecule comprising a genus of polynucleotides encoding an antibody-related molecule a genus of polynucleotides encoding a modified signal peptide comprising the amino acid residues of X1X2X3X4X5X6 at the final 6 positions of the C terminus where X1 is G, P, or A; X2 is G; X3 is P, S, or A and X1X2X3 are not GGP; X4 is A; X5 is S, H, or F; and X6 is A, while the specification only discloses a fixed number of species of 6-mers of amino acids at the C-terminus of the modified signal peptide.
Dependent claims 2 encompasses a genus of polynucleotides encoding a modified signal peptide comprising the amino acid residues of X1X2X3X4X5X6 at the final 6 positions of the C terminus where X1 is G, P, or A; X2 is G; X3 is P or S; X4 is A; X5 is S or H; and X6 is A.
Dependent claims 3-4 encompass a genus of polynucleotides encoding a modified signal peptide comprising the amino acid residues having SEQ ID NOs: 13-30.
Dependent claims 5 and 6 encompass a genus of N-terminal regions comprising an amino acid sequences of any of instant SEQ ID NOs: 7-12 or an amino acid sequence having at least 90% identity thereto.
Dependent claim 7 encompasses a genus of modified signal peptides consisting of an amino acid sequence of SEQ ID NOs: 31-35, (i.e. an N-terminal region of SEQ ID NO: 10 and C-terminus of SEQ ID NOs: 25-28 or N-terminal region of SEQ ID NO: 11 and C-terminus of SEQ ID NO: 15).
Dependent claims 9 and 10 encompasses a genus of antibody-related molecules consisting of a Fab, an ScFv, and a VHH.
Dependent claims 11-13 encompasses a genus of expression vectors and promoters comprising the nucleic acid construct of claim 1.
Dependent claim 14 encompasses a genus of Bacillus bacteria comprising the nucleic acid construct of claim 1.
Dependent claim 15 encompasses a genus of methods of producing an antibody-related molecule comprising culturing the Bacillus of claim 14 and collecting the extracellularly secreted antibody-related molecule.
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.'” 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 is discussed below.
The office has analyzed the specification in direct accordance to the factors outlined in In re Wands. MPEP 2164.04 states: "[W]hile the analysis and conclusion of a lack of enablement are based on factors discussed in MPEP 2164.01(a) and the evidence as whole, it is not necessary to discuss each factor in written enablement rejection." These factors will be analyzed, in turn, to demonstrate that one of ordinary skill in the art would have had to perform "undue experimentation" to make and/or use the invention and therefore, Applicant's claims are not enabled commensurate with the scope of the invention.
ACTUAL REDUCTION TO PRACTICE
The specification does not provide guidance for or a working example for modified signal peptides with C-termini sequences other than SEQ ID NOs: 13-30 and N-termini other than SEQ ID NOs: 10 and 11. Additionally, no working examples were provided for secretion of an antibody-related molecule that is not a VHH in a host other than B. subtilis DprΔsigF. The absence of working examples directed to other modified signal peptides which can be used for extracellular secretion of any antibody-related molecule in any Bacillus necessitates further experimentation. Therefore, the specification does not provide sufficient guidance on how to make and use the full scope of the modified signal peptide for use in expression and secretion of an antibody-related molecule in a Bacillus as claimed.
In regard to independent claims 1 and dependent claims 2-4 encompassing a nucleic acid construct for the expression and extracellular secretion of an antibody-related molecule comprising a genus of polynucleotides encoding an antibody-related molecule a genus of polynucleotides encoding a modified signal peptide comprising the amino acid residues of X1X2X3X4X5X6 at the final 6 positions of the C terminus, Applicant discloses a limited number of modified signal peptides comprising specific amino acid residues (SEQ ID NO: 13-30, 82-84; see Tables 3 and 4).
In regard to dependent claims 5 and 6 encompassing a genus of N-terminal regions comprising an amino acid sequences of any of instant SEQ ID NOs: 7-12 or an amino acid sequence having at least 90% identity thereto, Applicant discloses a limited number of N-terminal regions of S237 (SEQ ID NO: 11) and yncM (SEQ ID NO: 10) (See Table 3). It is noted that while Applicant has disclosed signal peptide combinations of N-terminal region of SEQ ID NO: 11 with C-terminus regions of SEQ ID NOs: 13-30 and 82-84, Applicant has only disclosed signal peptide combinations of N-terminal region of SEQ ID NO: 10 with C-terminus regions of SEQ ID NO: 13-18 and 23.
In regard to dependent claims 9 and 10 encompassing a genus of antibody-related molecules consisting of a Fab, an ScFv, and a VHH, Applicant discloses a limited number of antibody-related molecules which are VHHs, specifically 1ZVY and 5IMM (see Table 3).
In regard to dependent claims 11-13, encompassing a genus of vectors and promoters comprising the nucleic acid construct of claim 1, as stated above Applicant discloses a limited number of nucleic acid constructs of claim 1.
In regard to dependent claims 14 and 15, encompassing a genus of host cells which are Bacillus bacteria comprising the nucleic acid construct of claim 1 and a method of producing an antibody-related molecule comprising culturing the Bacillus of claim 14, as stated above, Applicant discloses a limited number of nucleic acid constructs of claim 1 and also a limited number of Bacillus host cells, specifically a Bacillus subtilis Dpr9 ΔsigF strain.
STATE OF THE ART & QUANTITY OF EXPERIMENTATION
Brockmeier et al. (found in IDS dated 04/25/2025) teaches that the most effective signal peptide for use in secretion of one protein is not necessarily the most effective or even a sufficient signal peptide for secretion of a different target protein in B. subtilis that signal peptides must be optimized based on the individual protein of interest which is to be secreted (Abstract; Fig 5; Pg. 399, left col. 2nd para.). Additionally, Brockmeier et al. teaches that known programs which purport to predict optimal signal peptides for heterologous protein secretion are unreliable (Table 1, Pg. 399, left col., 3rd para.). Further, Brockmeier et al. teaches that the N-terminal region of the protein also plays a role in the secretion efficiency and that optimal interaction between signal peptide and target protein for secretion is critical (Pg. 399, left col., 1st para.). Brockmeier et al. ultimately concludes that secretion efficiency for a protein in B. subtilis is determined by “a complex pattern of events.” (Pg. 399, right col. 3rd para.). Thus, Brockmeier et al. teaches that determining which signal peptide can be used for extracellular secretion in B. subtilis is unpredictable and that effective signal peptides for extracellular secretion much be chosen/optimized based on the specific target protein (Abstract).
Freudl (2018, Signal peptides for recombinant protein secretion in bacterial expression systems. Microbial Cell Factories, 17(1), 52) teaches that effectiveness of signal peptides related to target protein secretion also differs between host cells, indicating that the optimal signal peptide for extracellular secretion of a target protein also must be chosen/optimized based on the host (Pg. 6, right col, 1st full para.). Freudl teaches that modifications to signal peptides in the N-terminal region which result in alterations of the net charge of the N-terminal region can either increase or decrease secretion efficiency based on the signal peptide being modified and target protein being secreted (Pg. 6, right col., last para. and Pg. 7, left col. 1st para.). Ultimately, Freudl concludes that an optimally fitted signal peptide must be identified for every individual target protein to allow for optimal extracellular secretion in the chosen host organism (Pg. 8, left col., 1st para) and that it is “almost impossible” to predict in advance which signal peptide will perform best in the context of a given target protein and bacterial expression host (Abstract; Pg. 8, left col., 1st para.) Thus, Freudl teaches that is it similarly unpredictable to choose a signal peptide which can be used to express any target protein in any host cell.
In fact, Applicant’s specification appears to indicate that a structural modification of a single amino acid in the C-terminal region results in a modified signal peptide which eliminates the functional ability of the signal peptide in extracellular secretion (See SEQ ID NOs: 82-83 in Table 4). Additionally, it is noted that Applicant has reduced to practice signal peptides having C-terminus amino acid residues of SEQ ID NOs 13-30 combined with the N-terminal region of S237 signal peptide for the VHH 1ZVY. However, for the VHH 5IMM, Applicant has only reduced to practice signal peptides having C-terminus amino acid residues of SEQ ID NOs 13-18 and 23 combined with the N-terminal region of yncM signal peptide. Further, Applicant’s specification indicates that a wildtype S237 signal peptide was unable to produce the VHH 1ZVY in a B. subtilis DprΔsigF strain, requiring the use of a different B. subtilis strain (DprΔsigFΔrecA) for the control signal peptide in production of VHH 1ZVY (See Example 2 and Table 3). Thus, Applicant appears to provide evidence that determining which modified C-terminus of a signal peptide can be used with which N-terminal region for expression of which antibody-related molecule in which host cell is unpredictable.
In light of the above factors, Applicant provides enablement for a limited genus of modified signal peptides having a limited genus of C-termini amino acid sequences (SEQ ID NOs: 13-30) which can be used with a limited genus of N-terminal regions (SEQ ID NOs: 10 and 11). Further Applicant provides enablement for use of the modified signal peptides with a limited genus of antibody-related molecules which are VHHs and in a limited genus of host cells which are B. subtilis.
CONCLUSION
In conclusion, since the art teaches that success of choosing a signal peptide which can be used for extracellular secretion of any antibody-related molecule in any host cell is highly unpredictable and must be individually chosen/optimized for specific target proteins and specific host cells and the specification does not provide ample guidance as to which modified signal peptide could be used with respect to achieving the unexpected results, one would be burdened with undue experimentation as to which modified signal peptide could be used with which antibody-related molecule in which host cell in order to produce an antibody-related molecule of interest via extracellular secretion. In conclusion, given the breadth of the claims and the limited scope of the specification, an undue quantity of experimentation is required to make and use the invention beyond the scope of the limited genus of C-terminal amino acid sequences which can be used with the limited genus of N-terminal regions which can be used to express and secrete the limited genus of VHHs in the limited genus of B. subtilis host strain for which Applicant is enabled.
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.
Claims 1-7 and 9-13 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 1 recites the limitation "the polynucleotide" in line 4. Since there are two previous recitations of “a polynucleotide” in claim 1 which appear to be in reference to different polynucleotides, it is unclear which polynucleotide is being referred to, thus rendering the claim indefinite. Appropriate correction is required. It is recommended that Applicant amend claim 1 to incorporate language clearly defining first and second polynucleotides or defining “the polynucleotide encoding the antibody-related molecule” and “the polynucleotide encoding the modified signal peptide” (as recited in claim 11).
Claims 2-7 and 9-13 are similarly rejected as incorporating the limitations of a rejected claim while failing to correct the deficiencies.
Conclusion
No claims are allowed.
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/ERIN V PAULUS/Examiner, Art Unit 1631
/ARTHUR S LEONARD/Examiner, Art Unit 1631