DETAILED CORRESPONDENCE
Status of the Application
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s amendment to the claims, filed September 18, 2026, is acknowledged. This listing of the claims replaces all prior versions and listings of the claims.
Claims 1, 2, 4, 5, 8, 9, 11-14, 16-19, 21-23, 25-27, 29, 30, and 33-37 are pending in the application.
Applicant’s amendment to the abstract of the disclosure, filed September 18, 2026, is acknowledged.
Applicant’s amendment to the drawings, filed September 18, 2026, is acknowledged.
Applicant’s remarks filed September 18, 2026 in response to the non-final rejection filed June 22, 2026 are acknowledged and have been fully considered.
Claim 3 has been canceled by applicant’s amendment to the claims filed September 18, 2026 and rejections previously applied to claim 3 are withdrawn.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Restriction/Election
In response to a requirement for restriction/election filed April 8, 2026, applicant elected without traverse Group I, corresponding to pending claims 1, 2, 4, 5, 8, 9, 11-14, and 16, and elected with traverse the species of SEQ ID NO: 28 in the reply filed on June 2, 2026. The requirement was deemed proper and made final in the non-final rejection filed June 22, 2026.
Claims 17-19, 21-23, 25-27, 29, 30, and 33-37 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected inventions, there being no allowable generic or linking claim.
Claims 1, 2, 4, 5, 8, 9, 11-14, and 16 are being examined on the merits with claim 1 being examined only to the extent the claim reads on the elected subject matter. In the interest of clarity, it is noted that at least one of the following claim rejections is directed to a non-elected species. However, the non-elected species has yet to be searched and examined on the merits because the prior art directed to the non-elected species was identified during a search of the elected species of SEQ ID NO: 28.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on June 13, 2024 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS has been considered by the examiner.
Specification/Informalities
The objection to the abstract of the disclosure is withdrawn in view of applicant’s amendment to delete reference to [Figure 1].
Drawing Figures
The objection to the drawing figures is withdrawn in view of applicant’s amendment to the drawings.
Claim Objections
The objection to claim 9 is withdrawn in view of applicant’s amendment to clam 9 to replace “a” with “the.”
Claim Rejections - 35 USC § 112(b)
The rejection of claims 2 and 14 under 35 U.S.C. 112(b) is withdrawn in view of applicant’s amendment to claim 2 to delete the phrase “more preferably about 20 amino acids” and applicant’s amendments to claim 14 to delete the phrase “wherein the biological molecule is not constitutively expressed to detectable levels in an expression system in which the fusion protein is expressed” and the term “usually.”
Claim Interpretation
The following comments regarding claim interpretation are provided for clarity of the record.
As amended, claim 1 is drawn to an isolated vesicle nucleating polypeptide (VNp) that promotes formation of vesicles in a recombinant expression system, the VNp consisting essentially of an amphipathic alpha helix polypeptide derived obtained from the amino terminus of synuclein isoforms and variants thereof, wherein the polypeptide has between 9 and 38 amino acids and wherein the amino terminus is selected from beta synuclein, gamma synuclein or any one of SEQ ID NOs: 2 to 28.
According to MPEP 2111.03.III, the transitional phrase "consisting essentially of" limits the scope of a claim to the specified materials or steps and those that do not materially affect the basic and novel characteristic(s) of the claimed invention and for the purposes of searching for and applying prior art under 35 U.S.C. 102 and 103, absent a clear indication in the specification or claims of what the basic and novel characteristics actually are, "consisting essentially of" will be construed as equivalent to "comprising." In this case, there is no indication in the instant specification or claims as to what the basic and novel characteristics actually are and in accordance with MPEP 2111.03.III, "consisting essentially of" in claim 1 is being construed as equivalent to "comprising.”
Given a broadest reasonable interpretation, the type of “vesicles” and the type of “recombinant expression system” in claim 1 are unlimited.
Given a broadest reasonable interpretation, the recitation of “has” in the phrase “wherein the polypeptide has between 9 and 38 amino acids” in claim 1 is interpreted as equivalent to “comprising.”
Given a broadest reasonable interpretation, the recitation of “the amino terminus is selected from beta synuclein, gamma synuclein or any one of SEQ ID NOs: 2 to 28” in claim 1 is interpreted as referencing “the amino terminus of synuclein isoforms” and the recitation of “and variants thereof” is interpreted as encompassing variants of “the amino terminus of synuclein isoforms.”
As amended, claim 2 is drawn to the isolated vesicle nucleating polypeptide of claim 1, wherein the polypeptide has 20 amino acids.
Given a broadest reasonable interpretation, the recitation of “has” in the phrase “wherein the polypeptide has 20 amino acids” in claim 2 is interpreted as equivalent to “comprising.”
Claim Rejections - 35 USC § 101
Claims 1, 2, 4, 8, 9, 11-14, and 16 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more. Applicant’s attention is directed to the "Guidance for Determining Subject Matter Eligibility Of Claims Reciting Or Involving Laws of Nature, Natural Phenomena, & Natural Products”, released on December 16, 2014.
This rejection has been modified from its previous version in order to address applicant’s amendments to the claims.
Claim Interpretation: As amended, claims 1, 2, 4, and 8 are drawn to an isolated vesicle nucleating polypeptide (VNp) that promotes formation of vesicles in a recombinant expression system, the VNp consisting essentially of an amphipathic alpha helix polypeptide derived obtained from the amino terminus of synuclein isoforms and variants thereof, wherein the polypeptide has between 9 and 38 amino acids and wherein the amino terminus is selected from beta synuclein, gamma synuclein or any one of SEQ ID NOs: 2 to 28 (claim 1),
wherein the polypeptide has 20 amino acids (claim 2),
wherein the polypeptide is acetylated at its amino terminus (claim 4), and
wherein the polypeptide further comprises a protease cleavage site (claim 8).
As amended, claims 9, 11-14, and 16 are drawn to a fusion protein comprising the vesicle nucleating polypeptide as claimed in claim 1 fused to the amino terminus of a biological molecule, optionally wherein the vesicle nucleating polypeptide is fused to the amino terminus of the biological molecule via a protease cleavage site (claim 9),
wherein the protease cleavage site is for a viral protease or a viral 3C-like protease (claim 11),
wherein the protease cleavage site is scarless (claim 12),
wherein the protease cleavage site is specific for one or more membrane-bound or cytosolic proteases (claim 13),
wherein the biological molecule is a membrane binding protein, an insoluble protein, or a protein toxic to a host cell in which the fusion protein is expressed (claim 14), and
wherein the biological molecule has a size in the range of from less than 1 kDa to 100 kDa (claim 16).
The reference of Vinnakota et al. (ACS Chem. Neurosci. 9:2948-2958, 2018; cited on Form PTO-892 filed June 22, 2026) discloses that alpha-synuclein is a 140 amino acid protein (p. 2948, column 1) and discloses alternatively spliced alpha-synuclein isoforms that generate, e.g., a 41 amino acid N-terminal truncated peptide, 41-syn (p. 2948, Abstract; p. 2951, Figure 2B). The sequences of full-length alpha-synuclein and 41-syn disclosed by Vinnakota et al. each comprises instant SEQ ID NO: 2 as the first 38 amino acids.
The reference of Fusco et al. (Nature Communications 7:12563, 2016, 11 pages; cited on the attached Form PTO-892; hereafter “Fusco”) discloses that alpha-synuclein promotes the assembly of synaptic vesicles (p. 2, column 1, bottom; p. 5, column 1, middle to column 2, middle).
The instant specification discloses that the sequence having the first 38 residues of VNp2 (human alpha-synuclein) interacted with the cell membrane and, from 4 hours, VNp expression induced localised curvature of the bacterial membrane that extended outwards until formation of a distinct vesicle, which was released into the growth media upon membrane scission (p. 28, lines 27-31).
The reference of Davidson et al. (J. Biol. Chem. 27:9443-9449, 1998; cited on Form PTO-892 filed June 22, 2026) discloses the presence of helices within the N-terminal sequence of alpha-synuclein (p. 9447, Figure 6), which conform to the class A2 amphipathic alpha-helix consensus sequence (p. 9447, column 1, top), and is consistent with the capacity to fold into an amphipathic alpha-helix (p. 9443, column 2, middle). As such, 41-syn disclosed by Vinnakota et al. is considered to comprise “an amphipathic alpha helix polypeptide.”
The reference of de Oliveira et al. (PLOS Biology 15: e2000374, 2017, 27 pages; cited on Form PTO-892 filed June 22, 2026) discloses alpha-synuclein is acetylated on lysines 6 and 10 (p. 1, Abstract; p. 2, top).
The reference of Bluhm et al. (Int. J. Mol. Sci. 22:5450, May 2021, 14 pages; cited on Form PTO-892 filed June 22, 2026) discloses that alpha-synuclein comprises protease cleavage sites including cleavage sites within the first 41 amino acids (p. 2, Figure 1).
Regarding claims 1, 2, 4, and 8, in view of the cited teachings above and given a broadest reasonable interpretation, the isolated vesicle nucleating polypeptide of claims 1, 2, 4, and 8 encompasses a naturally-occurring full-length alpha-synuclein polypeptide and a naturally-occurring N-terminal fragment of alpha-synuclein polypeptide, e.g., 41-syn.
Regarding claim 9, when instant SEQ ID NO: 2 is considered to be the sequence of the “vesicle nucleating polypeptide as claimed in claim 1” and amino acids 39-140 of a naturally-occurring full-length alpha-synuclein polypeptide and amino acids 39-41 of 41-syn disclosed by Vinnakota et al. (supra) are considered to be the “biological molecule,” the fusion protein of claim 9 encompasses a naturally-occurring full-length alpha-synuclein polypeptide and a naturally-occurring N-terminal fragment of alpha-synuclein polypeptide.
Regarding claims 11-13, given that the limitation “the vesicle nucleating polypeptide is fused to the amino terminus of the biological molecule via a protease cleavage site” in claim 9 is optional, the fusion protein of claims 11-13 does not require the structural limitations recited in claims 11-13. As such, the fusion protein of claims 11-13 encompasses a naturally-occurring full-length alpha-synuclein polypeptide and a naturally-occurring N-terminal fragment of alpha-synuclein polypeptide.
Regarding claim 14, any peptide or protein expressed to a sufficient level in a host cell would be toxic to the host cell and thus, given a broadest reasonable interpretation, the limitation “wherein the biological molecule is…toxic to a host cell in which the fusion protein is expressed” encompasses any peptide or protein, e.g., amino acids 39-140 of alpha-synuclein or amino acids 39-41 of 41-syn disclosed by Vinnakota et al. (supra).
Regarding claim 16, when instant SEQ ID NO: 2 is considered to be the sequence of the “vesicle nucleating polypeptide as claimed in claim 1” and amino acids 39-41 of 41-syn disclosed by Vinnakota et al. (supra), which are less than 1 kDa, are considered to be the “biological molecule,” the fusion protein of claim 16 encompasses a naturally-occurring N-terminal fragment of alpha-synuclein.
Patent Eligibility Analysis Step 1: The claims are drawn to a composition of matter, which is one of the statutory categories of invention.
Patent Eligibility Analysis Step 2A Prong 1: The claims recite naturally-occurring polypeptides, which are considered to be laws of nature or natural phenomena (natural products). The claimed polypeptides are not considered to have markedly different characteristics from what occurs in nature, and are considered to be “product of nature” exceptions. Accordingly, the polypeptide of claims 1, 2, 4, and 8 and the fusion protein of claims 9, 11-14, and 16 are directed to judicial exceptions.
Patent Eligibility Analysis Step 2A Prong 2: There are no additional elements recited in the claims beyond the judicial exceptions.
Patent Eligibility Analysis Step 2B: The claims only recite the products of nature, without more and do not include any additional elements that could add significantly more to the judicial exceptions.
As such, the claims do not qualify as eligible subject matter. For these reasons the claim is rejected under section 101 as being directed to non-statutory subject matter.
RESPONSE TO REMARKS: Applicant argues the claimed VNp and fusion protein do not occur in nature and have markedly different characteristics from a natural polypeptide.
Applicant’s arguments are not found persuasive. When given a broadest reasonable interpretation as described in detail above, the claims encompass naturally-occurring polypeptides.
Addressing claims 4 and 8, applicant argues the recitation of “acetylated at its amino terminus” requires acetylation of the alpha-amino group of the amino terminal residue and claim 8 requires a deliberately engineered protease cleavage site.
Applicant’s arguments are not found persuasive. Claim 4 does not recite acetylation of the alpha-amino group of the amino terminal residue and claim 8 does not recite a deliberately engineered protease cleavage site. Rather, given a broadest reasonable interpretation, the recitation of “acetylated at its amino terminus” is interpreted to mean acetylated at the amino terminal region, e.g., acetylation at lysines 6 and 8 of full-length alpha-synuclein polypeptide or 41-syn, and the recitation of “comprises a protease cleavage site” encompasses an existing protease cleavage site in the sequence of full-length alpha-synuclein and 41-syn.
Addressing the fusion protein claims, applicant argues that “fusion protein” must be interpreted in light of the specification as a fusion of the VNp and a heterologous biological molecule and thus, the claimed fusion protein does not encompass a naturally-occurring polypeptide.
Applicant’s arguments are not found persuasive. There is no special definition of “fusion protein” in the specification that requires the biological molecule to be heterologous to the VNp. Rather, given a broadest reasonable interpretation, amino acids 39-140 of full-length alpha-synuclein or amino acids 39-41 of 41-syn are encompassed by the “biological molecule” in claim 9.
Claim Rejections - 35 USC § 112(a)
Claims 1, 2, 4, 5, 8, 9, 11-14, and 16 are rejected under 35 U.S.C. 112(a) 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 at the time the application was filed, had possession of the claimed invention.
This rejection has been modified from its previous version in order to address applicant’s amendments to the claims.
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”.
For claims drawn to a genus, MPEP § 2163 states 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 the applicant was in possession of the claimed genus. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
MPEP § 2163 further states that “[s]atisfactory disclosure of a ‘representative number’ depends on whether one of skill in the art would recognize that the applicant was in possession of the necessary common attributes or features possessed by the members of the genus in view of the species disclosed. For inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus…Instead, the disclosure must adequately reflect the structural diversity of the claimed genus, either through the disclosure of sufficient species that are ‘representative of the full variety or scope of the genus,’ or by the establishment of ‘a reasonable structure-function correlation.’ Such correlations may be established ‘by the inventor as described in the specification,’ or they may be ‘known in the art at the time of the filing date.’"
The factors considered in the Written Description requirement are (1) level of skill and knowledge in the art, (2) partial structure, (3) physical and/or chemical properties, (4) functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and (5) the method of making the claimed invention. Disclosure of any combination of such identifying characteristics that distinguish the claimed invention from other materials and would lead one of skill in the art to the conclusion that the applicant was in possession of the claimed species is sufficient." MPEP § 2163.
Claim 1 (claims 2, 4, 5, 8, 9, 11-14, and 16 dependent therefrom) is drawn to a genus of isolated vesicle nucleating polypeptides that promote formation of vesicles in a recombinant expression system, the VNp consisting essentially of an amphipathic alpha helix polypeptide derived obtained from the amino terminus of synuclein isoforms and variants thereof, wherein the polypeptide has between 9 and 38 amino acids and wherein the amino terminus is selected from beta synuclein, gamma synuclein or any one of SEQ ID NOs: 2 to 28.
As previously stated, given a broadest reasonable interpretation, the recitation of “the amino terminus is selected from beta synuclein, gamma synuclein or any one of SEQ ID NOs: 2 to 28” in claim 1 is interpreted as referencing “the amino terminus of synuclein isoforms” and the recitation of “and variants thereof” is interpreted as encompassing variants of “the amino terminus of synuclein isoforms.”
Given a broadest reasonable interpretation, the amino acid sequences of the genus of isolated vesicle nucleating polypeptides is unlimited and in view of the substantial structural variation among the members of the genus of recited isolated vesicle nucleating polypeptides, the genus is considered to encompass species with widely variant amino acid sequences.
The specification discloses the actual reduction to practice of the following representative species of the genus of isolated vesicle nucleating polypeptides – an isolated vesicle nucleating polypeptide consisting of the amino acid sequence of any one of SEQ ID NO: 2 to 28 and at a critical cytosolic concentration of at least 18.8 ± 0.14 µM to induce formation of vesicles in a recombinant bacterial expression system. Other than these disclosed representative species, the specification fails to disclose other isolated vesicle nucleating polypeptides as encompassed by the claims that promote formation of vesicles in a recombinant expression system.
Regarding the level of skill and knowledge in the art of amino acid modification, MPEP 2144.08.II.A.4.(c) states, "[i]n the area of biotechnology, an exemplified species may differ from a claimed species by a conservative substitution ("the replacement in a protein of one amino acid by another, chemically similar, amino acid... [which] is generally expected to lead to either no change or only a small change in the properties of the protein." Dictionary of Biochemistry and Molecular Biology 97 (John Wiley & Sons, 2d ed. 1989)). The effect of a conservative substitution on protein function depends on the nature of the substitution and its location in the chain. Although at some locations a conservative substitution may be benign, in some proteins only one amino acid is allowed at a given position. For example, the gain or loss of even one methyl group can destabilize the structure if close packing is required in the interior of domains. James Darnell et al., Molecular Cell Biology 51 (2d ed. 1990)."
The reference of Singh et al. (Curr. Protein Pept. Sci. 18:1-11, 2017; cited on Form PTO-892 filed June 22, 2026) reviews various protein engineering methods and discloses that despite the availability of an ever-growing database of protein structures and highly sophisticated computational algorithms, protein engineering is still limited by the incomplete understanding of protein functions, folding, flexibility, and conformational changes (see p. 7, column 1, top).
The unpredictability associated with amino acid substitution is exemplified by the reference of Zhang et al. (Structure 26:1474-1485, 2018; cited on Form PTO-892 filed June 22, 2026), which discloses that even a substitution of a surface residue that was predicted to be benign caused significant structural changes and unexpected effects on the function of a polypeptide (p. 1475, column 1).
Regarding the level of skill and knowledge in the art of VNp-induced vesicle formation, the instant specification discloses VNp-induced vesicle formation requires a critical cytosolic concentration of 18.8 ± 0.14 μM of the VNp-fusion protein to promote vesiculation of a bacterial membrane (p. 38, lines 20-25).
Given that the claimed genus of isolated vesicle nucleating polypeptides encompasses species having unlimited, widely variant sequences while the specification discloses only a relative few representative species of isolated vesicle nucleating polypeptides and their corresponding critical concentrations to achieve promotion of vesicle formation in a recombinant expression system, and given the high level of unpredictability in the art of amino acid modification at the time of the invention, the specification is considered to be insufficient to describe the recited genus of isolated vesicle nucleating polypeptides. In this case, the specification at best describes a research plan for making, testing, and identifying those species that are encompassed by the recited genus of isolated vesicle nucleating polypeptides, however, a plan for making the claimed invention is not sufficient to show possession at the time of filing. One of skill in the art would reasonably conclude that the disclosure fails to provide a representative number of species to describe the genus, and thus, that the applicant was not in possession of the recited genus.
For these reasons, it is the examiner’s position that the specification fails to adequately describe the claimed invention.
RESPONSE TO REMARKS: Applicant argues the genus of claimed isolated vesicle nucleating polypeptides is finite and every member of the genus is described by its structure; all members of the genus are reduced to practice by the disclosure of the specification; and because the claims do not encompass amino acid modifications, the references of Singh and Zhang are not relevant to the written description analysis.
Applicant’s arguments are not found persuasive. When given a broadest reasonable interpretation as described in detail above, the amino acid sequences of the genus of isolated vesicle nucleating polypeptides is unlimited and the specification fails to disclose a representative number of species sufficient to describe the genus.
Claims 1, 2, 4, 5, 8, 9, 11-14, and 16 are rejected under 35 U.S.C. 112(a) because the specification, while being enabling for an isolated vesicle nucleating polypeptide comprising or consisting of the amino acid sequence of any one of SEQ ID NO: 2 to 28, does not reasonably provide enablement for all isolated vesicle nucleating polypeptides that promote formation of vesicles in a recombinant expression system as broadly encompassed by the claims. 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/or use the invention commensurate in scope with these claims.
“The test of enablement is not whether any experimentation is necessary, but whether, if experimentation is necessary, it is undue.” In re Angstadt, 537 F.2d 498, 504, 190 USPQ 214, 219 (CCPA 1976). Factors to be considered in determining whether undue experimentation is required are summarized in In re Wands (858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988)) as follows: (A) The breadth of the claims; (B) The nature of the invention; (C) The state of the prior art; (D) The level of one of ordinary skill; (E) The level of predictability in the art; (F) The amount of direction provided by the inventor; (G) The existence of working examples; and (H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. See MPEP § 2164.01(a). The Factors considered to be most relevant to the instant rejection are addressed in detail below.
The nature of the invention: According to the instant specification, “the present invention encompasses a polypeptide sequence and method that provides a simple mechanism for targeted release of specific membrane packaged biological molecules such as proteins into cell media which can be continuously isolated from active cultures. This results in a significant increase in yields of functional soluble molecules, such as proteins, from cultures and facilitates efficient downstream processing for a wide range of biotechnology applications…the invention resides in variants of a short amphipathic alpha helix polypeptide that is based on the amino terminus of synuclein isoforms and designed variants thereof” (p. 2, lines 22-33).
The breadth of the claims: Claim 1 (claims 2, 4, 5, 8, 9, 11-14, and 16 dependent therefrom) is drawn to a genus of isolated vesicle nucleating polypeptides that promote formation of vesicles in a recombinant expression system, the VNp consisting essentially of an amphipathic alpha helix polypeptide derived obtained from the amino terminus of synuclein isoforms and variants thereof, wherein the polypeptide has between 9 and 38 amino acids and wherein the amino terminus is selected from beta synuclein, gamma synuclein or any one of SEQ ID NOs: 2 to 28.
As previously stated, given a broadest reasonable interpretation, the recitation of “the amino terminus is selected from beta synuclein, gamma synuclein or any one of SEQ ID NOs: 2 to 28” in claim 1 is interpreted as referencing “the amino terminus of synuclein isoforms” and the recitation of “and variants thereof” is interpreted as encompassing variants of “the amino terminus of synuclein isoforms.”
The state of the prior art; The level of one of ordinary skill; and The level of predictability in the art: According to MPEP 2164.03, “…what is known in the art provides evidence as to the question of predictability.” “[I]f one skilled in the art cannot readily anticipate the effect of a change within the subject matter to which that claimed invention pertains, then there is lack of predictability in the art.” See MPEP § 2164.03.
Regarding the level of skill and knowledge in the art of amino acid modification, MPEP 2144.08.II.A.4.(c) states, "[i]n the area of biotechnology, an exemplified species may differ from a claimed species by a conservative substitution ("the replacement in a protein of one amino acid by another, chemically similar, amino acid... [which] is generally expected to lead to either no change or only a small change in the properties of the protein." Dictionary of Biochemistry and Molecular Biology 97 (John Wiley & Sons, 2d ed. 1989)). The effect of a conservative substitution on protein function depends on the nature of the substitution and its location in the chain. Although at some locations a conservative substitution may be benign, in some proteins only one amino acid is allowed at a given position. For example, the gain or loss of even one methyl group can destabilize the structure if close packing is required in the interior of domains. James Darnell et al., Molecular Cell Biology 51 (2d ed. 1990)."
The reference of Singh et al. (Curr. Protein Pept. Sci. 18:1-11, 2017; cited on Form PTO-892 filed June 22, 2026) reviews various protein engineering methods and discloses that despite the availability of an ever-growing database of protein structures and highly sophisticated computational algorithms, protein engineering is still limited by the incomplete understanding of protein functions, folding, flexibility, and conformational changes (see p. 7, column 1, top).
The unpredictability associated with amino acid substitution is exemplified by the reference of Zhang et al. (Structure 26:1474-1485, 2018; cited on Form PTO-892 filed June 22, 2026), which discloses that even a substitution of a surface residue that was predicted to be benign caused significant structural changes and unexpected effects on the function of a polypeptide (p. 1475, column 1).
Based on the evidence of record, one of skill in the art would recognize a high level of unpredictability in the art of amino acid modification before the effective filing date.
The amount of direction provided by the inventor and The existence of working examples: The specification discloses the following working examples of the recited isolated vesicle nucleating polypeptide – an isolated vesicle nucleating polypeptide consisting of the amino acid sequence of any one of SEQ ID NO: 2 to 28 at a critical cytosolic concentration of at least 18.8 ± 0.14 µM to induce formation of vesicles in a recombinant bacterial expression system. Other than these working examples, the specification fails to disclose other working examples of isolated vesicle nucleating polypeptides that promote formation of vesicles in a recombinant expression system as encompassed by the claims.
The quantity of experimentation needed to make or use the invention based on the content of the disclosure: In the Federal Circuit decision of Idenix Pharmaceuticals LLC v. Gilead Sciences Inc., 941 F.3d 1149, 1156 (Fed. Cir. 2019), the court stated that “the key enablement question is whether a person of ordinary skill in the art would know, without undue experimentation, which [species] would be effective….because of the many thousands of [species] which need to be screened for…efficacy, the quantity of experimentation needed is large and weighs in favor of non-enablement.” While methods for modifying the amino acid sequence of a polypeptide were known before the effective filing date, it was not routine in the art to screen by a trial and error process for a vast number of polypeptides as broadly encompassed by the claims.
In view of the broad scope of the claimed genus, the lack of guidance and working examples provided in the specification, and the high level of unpredictability as evidenced by the prior art, undue experimentation would be necessary for a skilled artisan to make and use the entire scope of the claimed invention. 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 claims must bear a reasonable correlation with the scope of enablement (In re Fisher, 166 USPQ 19 24 (CCPA 1970)). Without sufficient guidance, determination of having the desired biological characteristics is unpredictable and the experimentation left to those skilled in the art is unnecessarily, and improperly, extensive and undue. See In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988).
RESPONSE TO REMARKS: Applicant argues the specification enables the full scope of the isolated vesicle nucleating polypeptide of claims 1, 2, 4, 5, 8, 9, 11-14, and 16.
Applicant’s arguments are not found persuasive. In view of the detailed analysis of the Factors of In re Wands as set forth above, particularly a broad, yet reasonable interpretation of the claims as encompassing a broad scope of isolated vesicle nucleating polypeptides, the specification fails to enable the full scope of the claimed invention.
Claim Rejections - 35 USC § 102
The rejection of Claims 1, 2, 4, 5, 8, 9, 11-14, and 16 under 35 U.S.C. 102(a)(1) as being anticipated by Jiang et al. (FASEB J. 22:3165-174, 2008; cited on Form PTO-892 filed April 8, 2026; hereafter “Jiang”) as evidenced by Davidson et al. (J. Biol. Chem. 27:9443-9449, 1998; cited on Form PTO-892 filed June 22, 2026; hereafter “Davidson”), Vinnakota et al. (ACS Chem. Neurosci. 9:2948-2958, 2018; cited on Form PTO-892 filed June 22, 2026; hereafter “Vinnakota”), de Oliveira et al. (PLOS Biology 15: e2000374, 2017, 27 pages; cited on Form PTO-892 filed June 22, 2026; hereafter “de Oliveira”), and Bluhm et al. (Int. J. Mol. Sci. 22:5450, May 2021, 14 pages; cited on Form PTO-892 filed June 22, 2026; hereafter “Bluhm”) is withdrawn in view of applicant’s amendment to claim 1 to recite “promotes formation of vesicles in a recombinant expression system.”
Claims 1, 2, 4, 8, 9, 11-14, and 16 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Vinnakota as evidenced by Davidson, de Oliveira, and Bluhm.
See MPEP 2131.01.III regarding a multiple reference 35 U.S.C. 102 rejection citing extra reference or evidence to show that a characteristic not disclosed in the reference is inherent.
Claims 1, 2, 4 and 8 are drawn to an isolated vesicle nucleating polypeptide (VNp) that promotes formation of vesicles in a recombinant expression system, the VNp consisting essentially of an amphipathic alpha helix polypeptide derived obtained from the amino terminus of synuclein isoforms and variants thereof, wherein the polypeptide has between 9 and 38 amino acids and wherein the amino terminus is selected from beta synuclein, gamma synuclein or any one of SEQ ID NOs: 2 to 28 (claim 1),
wherein the polypeptide has 20 amino acids (claim 2),
wherein the polypeptide is acetylated at its amino terminus (claim 4), and
wherein the polypeptide further comprises a protease cleavage site (claim 8).
As amended, claims 9, 11-14, and 16 are drawn to a fusion protein comprising the vesicle nucleating polypeptide as claimed in claim 1 fused to the amino terminus of a biological molecule, optionally wherein the vesicle nucleating polypeptide is fused to the amino terminus of the biological molecule via a protease cleavage site (claim 9),
wherein the protease cleavage site is for a viral protease or a viral 3C-like protease (claim 11),
wherein the protease cleavage site is scarless (claim 12),
wherein the protease cleavage site is specific for one or more membrane-bound or cytosolic proteases (claim 13),
wherein the biological molecule is a membrane binding protein, an insoluble protein, or a protein toxic to a host cell in which the fusion protein is expressed (claim 14), and
wherein the biological molecule has a size in the range of from less than 1 kDa to 100 kDa (claim 16).
Regarding claims 1 and 2, Vinnakota discloses an alternatively spliced alpha-synuclein isoform that generates a 41 amino acid N-terminal truncated peptide, 41-syn (p. 2948, Abstract; p. 2951, Figure 2B). 41-syn disclosed by Vinnakota comprises instant SEQ ID NO: 2 as the first 38 amino acids (p. 2951, Figure 2B).
Vinnakota does not disclose 41-syn is a “vesicle nucleating” polypeptide that promotes formation of vesicles in a recombinant expression system as recited in claim 1. However, according to MPEP 2112.01, when the structure recited in the reference is substantially identical to that of the claims, claimed properties or functions are presumed to be inherent. Since the structure of 41-syn disclosed by Vinnakota is substantially identical to that of the claims, the claimed property of “vesicle nucleating polypeptide that promotes formation of vesicles in a recombinant expression system” is presumed to be inherent.
Vinnakota does not disclose 41-syn consists essentially of (interpreted as comprising) an amphipathic alpha helix polypeptide as recited in claim 1. However, evidentiary reference Davidson is cited in accordance with MPEP 2131.01.III to show that the N-termini of 41-syn comprises a helix (p. 9447, Figure 6), which conform to the class A2 amphipathic alpha-helix consensus sequence (p. 9447, column 1, top), and is consistent with the capacity to fold into an amphipathic alpha-helix (p. 9443, column 2, middle). Also, according to MPEP 2112.01, when the structure recited in the reference is substantially identical to that of the claims, claimed properties or functions are presumed to be inherent. Since the structure of 41-syn disclosed by Vinnakota is substantially identical to that of the claims, the claimed property of “an amphipathic alpha helix polypeptide” is presumed to be inherent. As such, 41-syn disclosed by Vinnakota is considered to comprise “an amphipathic alpha helix polypeptide.”
Regarding claim 4, Vinnakota does not disclose 41-syn is acetylated at its amino terminus as recited in claim 4. However, evidentiary reference de Oliveira is cited in accordance with MPEP 2131.01.III to show that alpha-synuclein is acetylated on lysines 6 and 10 (p. 1, Abstract; p. 2, top).
Regarding claim 8, Vinnakota does not disclose 41-syn comprises a protease cleavage site as recited in claim 8. However, evidentiary reference Bluhm is cited in accordance with MPEP 2131.01.III to show that alpha-synuclein comprises protease cleavage sites including cleavage sites within the first 41 amino acids (p. 2, Figure 1).
Regarding claim 9, when instant SEQ ID NO: 2 is considered to be the sequence of the “vesicle nucleating polypeptide as claimed in claim 1” and amino acids 39-41 of 41-syn disclosed by Vinnakota are considered to be the “biological molecule,” the fusion protein of claim 9 encompasses full-length alpha-synuclein polypeptide and 41-syn as disclosed by Vinnakota.
Regarding claims 11-13, given that the limitation “the vesicle nucleating polypeptide is fused to the amino terminus of the biological molecule via a protease cleavage site” in claim 9 is optional, the fusion protein of claims 11-13 does not require the structural limitations recited in claims 11-13. As such, the fusion protein of claims 11-13 encompasses 41-syn as disclosed by Vinnakota.
Regarding claim 14, any peptide or protein expressed to a sufficient level in a host cell would be toxic to the host cell and thus, given a broadest reasonable interpretation, the limitation “wherein the biological molecule is…toxic to a host cell in which the fusion protein is expressed” encompasses any peptide or protein, e.g., amino acids 39-41 of 41-syn disclosed by Vinnakota.
Regarding claim 16, the structure of the “biological molecule” is undefined and unlimited. When instant SEQ ID NO: 2 is considered to be the sequence of the “vesicle nucleating polypeptide as claimed in claim 1” and amino acids 39-41 of 41-syn disclosed by Vinnakota, which are less than 1 kDa, are considered to be the “biological molecule,” the fusion protein of claim 16 encompasses 41-syn as disclosed by Vinnakota.
Therefore, Vinnakota anticipates claims 1-4, 8, 9, 11-14, and 16 as written.
RESPONSE TO REMARKS: Applicant argues Vinnakota does not teach or suggest a polypeptide of between 9 and 38 amino acids as required by the amended claim 1.
Applicant’s arguments are not found persuasive. When given a broadest reasonable interpretation as described in detail above, claim 1 encompasses 41-syn disclosed by Vinnakota.
Applicant argues the presumption that "an amphipathic alpha helix polypeptide" and "vesicle nucleating polypeptide" are inherent features of 41-syn does not apply to the amended claim 1, which requires between 9 and 38 amino acids, and there is no explicit teaching by Vinnakota that 41-syn promotes formation of vesicles in a recombinant expression system.
Applicant’s arguments are not found persuasive. As previously stated, when given a broadest reasonable interpretation, claim 1 encompasses 41-syn disclosed by Vinnakota. Inherent disclosures of a reference may be relied upon in a rejection under 35 U.S.C. 102 or 103 (MPEP 2112) and since the structure of 41-syn is substantially identical to that of the claims, the features of “vesicle nucleating,” “promotes formation of vesicles in a recombinant expression system,” and "an amphipathic alpha helix polypeptide" are presumed to be inherent to 41-syn.
Applicant argues claim 4 is not anticipated because the recitation of “acetylated at its amino terminus” requires acetylation of the alpha-amino group of the amino terminal residue.
Applicant’s arguments are not found persuasive. Claim 4 does not recite acetylation of the alpha-amino group of the amino terminal residue. Rather, given a broadest reasonable interpretation, the recitation of “acetylated at its amino terminus” is interpreted to mean acetylated at the amino terminal region, e.g., acetylation at lysine 6 of 41-syn.
Applicant argues that “fusion protein” must be interpreted in light of the specification as a fusion of the VNp and a heterologous biological molecule and thus, the fusion protein of claims 9, 11-14, and 16 is not anticipated by Vinnakota.
Applicant’s arguments are not found persuasive. There is no special definition of “fusion protein” in the specification and/or a claim limitation that requires the biological molecule to be heterologous to the VNp. Rather, given a broadest reasonable interpretation, amino acids 39-41 of 41-syn are encompassed by the “biological molecule” in claim 9 and claims 9, 11-14, and 16 are anticipated by Vinnakota.
Claims 1, 2, 4, 5, 8, 9, 11-14, and 16 are newly rejected under 35 U.S.C. 102(a)(1) as being anticipated by Jiang as evidenced by Fusco et al. (Nature Communications 7:12563, 2016, 11 pages; cited on the attached Form PTO-892; hereafter “Fusco”), Davidson, Vinnakota, de Oliveira, and Bluhm.
See MPEP 2131.01.III regarding a multiple reference 35 U.S.C. 102 rejection citing extra reference or evidence to show that a characteristic not disclosed in the reference is inherent.
Regarding claims 1, 5, and 9, Jiang discloses fusion proteins comprising wild-type human alpha-synuclein and a leucine zipper, referred to as SZAHA (p. 3166, Figure 1) and SZA (p. 3167, column 2, bottom).
Jiang does not disclose SZAHA and SZA are vesicle nucleating polypeptides that promote formation of vesicles in a recombinant expression system as recited in claim 1. However, as noted above, the recited “vesicles” and “recombinant expression system” in claim 1 are unlimited and evidentiary reference Fusco is cited to show that alpha-synuclein promotes the assembly of synaptic vesicles (p. 2, column 1, bottom; p. 5, column 1, middle to column 2, middle).
Jiang does not disclose SZAHA and SZA comprise an amphipathic alpha helix polypeptide as recited in claim 1. However, evidentiary reference Davidson is cited in accordance with MPEP 2131.01.III to that the N-terminus of alpha-synuclein comprises helices (p. 9447, Figure 6), which conform to the class A2 amphipathic alpha-helix consensus sequence (p. 9447, column 1, top), and is consistent with the capacity to fold into an amphipathic alpha-helix (p. 9443, column 2, middle).
Jiang does not disclose SZAHA and SZA comprise the amino terminus of beta synuclein, gamma synuclein or any one of SEQ ID NOs: 2 to 28, however, evidentiary reference Vinnakota is cited to show that wild-type alpha-synuclein comprises instant SEQ ID NO: 2 as the first 38 amino acids (p. 2951, Figure 2B).
Regarding claim 2, the recitation of “has” in the phrase “the polypeptide has between 9 and 140 amino acids” is interpreted as “comprising,” which is inclusive of additional amino acids beyond 140 amino acids (MPEP 2111.03.I).
Regarding claim 4, Jiang does not disclose SZAHA and SZA are acetylated at their respective amino terminus as recited in claim 4. However, evidentiary reference de Oliveira is cited in accordance with MPEP 2131.01.III to show that alpha-synuclein is acetylated on lysines 6 and 10 (p. 1, Abstract; p. 2, top).
Regarding claim 8, Jiang does not disclose SZAHA and SZA comprise a protease cleavage site as recited in claim 8. However, evidentiary reference Bluhm is cited in accordance with MPEP 2131.01.III to show that alpha-synuclein comprises protease cleavage sites (p. 2, Figure 1).
Regarding claims 11-13, given that the limitation “the vesicle nucleating polypeptide is fused to the amino terminus of the biological molecule via a protease cleavage site” in claim 9 is optional, the fusion protein of claims 11-13 does not require the structural limitations recited in claims 11-13. As such, the fusion protein of claims 11-13 encompasses SZAHA and SZA as disclosed by Jiang.
Regarding claim 14, any protein expressed to a sufficient level in a host cell would be toxic to the host cell and thus, given a broadest reasonable interpretation, the limitation “wherein the biological molecule is…toxic to a host cell in which the fusion protein is expressed” encompasses any protein, e.g., amino acids following alpha-synuclein amino acids 1-28 of SZAHA and SZA as disclosed by Jiang.
Regarding claim 16, the structure of the “biological molecule” is undefined and unlimited. Given a broadest reasonable interpretation, instant SEQ ID NO: 2 can be interpreted as the sequence of the “vesicle nucleating polypeptide as claimed in claim 1” and any remaining amino acid sequence of SZAHA and SZA disclosed by Jiang, e.g., amino acids 39-41 of SZAHA and SZA, which are less than 1 kDa, can be interpreted as the “biological molecule,” and the fusion protein of claim 16 encompasses SZAHA and SZA as disclosed by Jiang.
Therefore, Jiang anticipates claims 1, 2, 4, 5, 8, 9, 11-14, and 16 as written.
RESPONSE TO REMARKS: Applicant argues the alpha-synuclein of SZAHA and SZA is full-length and not between 9 and 38 amino acids as required by claim 1; Jiang does not teach or suggest a polypeptide that promotes formation of vesicles in a recombinant expression system as required by claim 1; and the presumption of inherent features is unavailable.
Applicant’s arguments are not found persuasive. When given a broadest reasonable interpretation as described in detail above, claim 1 encompasses the structures of SZAHA and SZA disclosed by Jiang. Inherent disclosures of a reference may be relied upon in a rejection under 35 U.S.C. 102 or 103 (MPEP 2112) and since the structures of SZAHA and SZA are substantially identical to that of the claims and given the teachings of evidentiary references Fusco, Davidson, Vinnakota, de Oliveira, and Bluhm, the features of “vesicle nucleating,” “promotes formation of vesicles in a recombinant expression system,” and "an amphipathic alpha helix polypeptide" are presumed to be inherent to SZAHA and SZA.
Applicant argues claims 2, 5, and 8 are not anticipated because the limitations of claim 1 require the isolated vesicle nucleating polypeptide of claims 2, 5, and 8 to be between 9 and 38 amino acids.
Applicant’s arguments are not found persuasive. When given a broadest reasonable interpretation as described in detail above, claim 1 encompasses the structures of SZAHA and SZA disclosed by Jiang.
Applicant argues claims 9, 11-14, and 16 are not anticipated because “fusion protein” must be interpreted in light of the specification as a fusion of the VNp and a heterologous biological molecule.
Applicant’s arguments are not found persuasive. There is no special definition of “fusion protein” in the specification and/or a claim limitation that requires the biological molecule to be heterologous to the VNp. Rather, given a broadest reasonable interpretation, amino acids following alpha-synuclein amino acids 1-28 of SZAHA and SZA are encompassed by the “biological molecule” in claim 9 and claims 9, 11-14, and 16 are anticipated by Jiang.
Conclusion
Status of the claims:
Claims 1, 2, 4, 5, 8, 9, 11-14, 16-19, 21-23, 25-27, 29, 30, and 33-37 are pending.
Claims 17-19, 21-23, 25-27, 29, 30, and 33-37 are withdrawn from consideration.
Claims 1, 2, 4, 5, 8, 9, 11-14, and 16 are rejected.
No claim is in condition for allowance.
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 nonprovisional extension fee (37 CFR 1.17(a)) 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.
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/David Steadman/Primary Examiner, Art Unit 1656
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