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 .
Claims 1-5, 8, 9, 11-14, 16-19, 21-23, 25-27, 29, 30, and 33-37 are pending in the application.
Applicant’s claim listing filed June 2, 2026 is acknowledged. This listing of the claims replaces all prior versions and listings of the claims.
Restriction/Election
Applicant’s election without traverse of Group I, claims 1-5, 8, 9, 11-14, and 16, drawn to the technical feature of an isolated vesicle nucleating polypeptide (VNp) comprising an amphipathic alpha helix polypeptide derived from the amino terminus of synuclein isoforms and variants thereof in the reply filed June 2, 2026 is acknowledged.
Claims 17-19, 21-23, 25-27, 29, 30, and 33-37 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected inventions, there being no allowable generic or linking claim.
Applicant's election with traverse of SEQ ID NO: 28 for species election A in the reply filed on June 2, 2026 is acknowledged. The traversal is on the grounds that Bartels et al. (Biophys. J. 99:2116-2124, 2010; cited on Form PTO-892 filed April 8, 2026) do not teach the disclosed N-terminal fragments of alpha-synuclein comprise an amphipathic alpha helix and are vesicle nucleating peptides, and do not teach the recited species of claim 3 including the elected species of SEQ ID NO: 28. Thus, according to applicant, the shared same or corresponding technical feature among the species recited in claim 3 makes a contribution over the prior art and is a special technical feature.
Applicant’s arguments are not found persuasive. Regarding applicant’s argument that Bartels et al. do not teach the alpha-synuclein N-terminal fragments comprise an amphipathic alpha helix, Bartels et al. show the N-terminal fragments of alpha-synuclein comprise at least one repeat that is similar to those found in apolipoprotein A-I, which form amphipathic helices upon lipid binding and disclose the N-terminus of alpha-synuclein has an “amphipathic nature” (p. 2116, column 2; p. 2117, Figure 1). Moreover, as shown by Davidson et al. (J. Biol. Chem. 27:9443-9449, 1998; cited on the attached Form PTO-892), it was well-known in the prior art before the effective filing date that the N-terminal fragments disclosed by Bartels et al. comprise a helix sequence at residues 1-15 (p. 9447, Figure 6), which conforms 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). Furthermore, 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 structures of the N-terminal fragments disclosed by Bartels et al. are substantially identical to that of the claims, the claimed property of “an amphipathic alpha helix polypeptide” is presumed to be inherent. As such, contrary to applicant’s position, the N-terminal fragments disclosed by Bartels et al. are considered to comprise “an amphipathic alpha helix polypeptide.”
Regarding applicant’s argument that Bartels et al. do not teach the alpha-synuclein N-terminal fragments are vesicle nucleating peptides, 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 N-terminal fragments disclosed by Bartels et al. are substantially identical to that of the claims, the claimed property of “vesicle nucleating polypeptide” is presumed to be inherent.
Regarding applicant’s argument that Bartels et al. do not teach the recited species of claim 3 including the elected species of SEQ ID NO: 28, the closest shared same or corresponding technical feature among the species recited in claim 3 is an isolated vesicle nucleating polypeptide (VNp) comprising an amphipathic alpha helix polypeptide derived from the amino terminus of synuclein isoforms and variants thereof. The species lack unity of invention because the closest shared same or corresponding technical feature among the species is not a special technical feature as it does not make a contribution over the prior art in view of Bartels et al. disclosing N-terminal fragments of amino acids 1-20 and amino acids 1-25 of alpha- synuclein (p. 2117, Figure 1), which, for reasons stated above, are considered to be isolated vesicle nucleating polypeptides comprising an amphipathic alpha helix polypeptide derived from the amino terminus of synuclein isoforms and variants thereof.
For these reasons, the shared same or corresponding technical feature among the species of claim 3 is not a contribution over the prior art. The requirement is still deemed proper and is therefore made FINAL.
Claims 1-5, 8, 9, 11-14, and 16 are being examined on the merits with claim 3 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.
Priority
This application is filed under 35 U.S.C. 371 as a national stage of international application PCT/GB2022/053239, filed December 15, 2022, which claims foreign priority under 35 U.S.C. 119(a-d) to UK application 2118435.3, filed December 17, 2021. A certified copy of the foreign priority document has been filed in this application on June 13, 2024.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on June 9, 2026 is in compliance with the provisions of 37 CFR 1.97 and has been considered by the examiner.
Specification/Informalities
The abstract of the disclosure filed June 13, 2024 is objected to for stating “[Figure 1].”
Drawing Figures
According to 37 CFR 1.84(u):
(u) Numbering of views.
(1) The different views must be numbered in consecutive Arabic numerals, starting with 1, independent of the numbering of the sheets and, if possible, in the order in which they appear on the drawing sheet(s). Partial views intended to form one complete view, on one or several sheets, must be identified by the same number followed by a capital letter. View numbers must be preceded by the abbreviation "FIG." Where only a single view is used in an application to illustrate the claimed invention, it must not be numbered and the abbreviation "FIG." must not appear.
(2) Numbers and letters identifying the views must be simple and clear and must not be used in association with brackets, circles, or inverted commas. The view numbers must be larger than the numbers used for reference characters.
The drawings filed on June 13, 2024 are objected to because view numbers must be preceded by the abbreviation "FIG." Appropriate correction is required.
The drawings filed on June 13, 2024 are also objected to because the partial views of Figures 1, 6, and 9 must be identified by the same number followed by a capital letter, e.g., FIG. 1A, FIG. 1B, FIG. 1C, etc. rather than “Figure 1 cont.” Appropriate correction is required.
A corrected drawing sheet in compliance with 37 CFR 1.121(d) is required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claim 9 is objected to in the recitation of “fusion protein comprising a vesicle nucleating polypeptide” and in the interest of improving claim form, it is suggested that the noted phrase be amended to recite (with markings to show changes made) “fusion protein comprising the[[a]] vesicle nucleating polypeptide.”
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.
Claims 2, 3, and 14 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 2 is indefinite in the recitation of “more preferably about 20 amino acids” because it is unclear whether the limitation following the phrase “preferably” is part of the claimed invention. Description of preferences is properly set forth in the specification rather than the claims. See MPEP § 2173.05(d). In the interest of advancing prosecution, applicant may consider amending the phrase “more preferably about 20 amino acids” to recite “optionally 20 amino acids.”
Claim 2 is also indefinite in the recitation of “about 20 amino acids.” The term “about” is a term of approximation (see MPEP 2173.05(b).III.A) and the examiner has reviewed the specification and can find no examples or teachings that can be used for ascertaining the variance intended by the term “about.” Moreover, there is nothing in the specification or prior art of record to indicate that one of ordinary skill in the art could have ascertained the scope of the term “about” in the context of claim 2. In the interest of advancing prosecution, applicant may consider an amendment to delete the term “about.”
Claim 3 recites the limitation "the sequence.” There is insufficient antecedent basis for this limitation in the claim. In the interest of advancing prosecution, claim 3 is interpreted as meaning the vesicle nucleating polypeptide comprises any one of SEQ ID NO: 2 to 28.
Claim 14 is indefinite in the recitation of “wherein the biological molecule is not constitutively expressed to detectable levels in an expression system in which the fusion protein is expressed” because this limitation is a function of an expression system for expressing the fusion protein and not a structural and/or functional limitation of the fusion protein itself. However, claim 14 is drawn to “The fusion protein of claim 9…” and not an expression system for expressing the fusion protein. Applicant is requested to clarify the meaning of the phrase recitation of “wherein the biological molecule is not constitutively expressed to detectable levels in an expression system in which the fusion protein is expressed.”
Claim 14 is also indefinite in the recitation of “a protein usually toxic to the host cell in which the fusion protein is expressed.” The term “usually” is a subjective term (see MPEP 2173.05(b).IV) and the examiner has reviewed the specification and can find no objective standard that can be used for ascertaining the scope of proteins that are “usually toxic to the host cell in which the fusion protein is expressed.” In the interest of advancing prosecution, applicant may consider an amendment to delete the term “usually.”
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-4, 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.
Claim Interpretation: Claims 1-4 and 8 are drawn to an isolated vesicle nucleating polypeptide comprising an amphipathic alpha helix polypeptide derived from the amino terminus of synuclein isoforms and variants thereof (claim 1),
wherein the polypeptide has between 9 and 140 amino acids, optionally between 16 and 40 amino acids, more preferably about 20 amino acids (claim 2),
wherein the sequence is any one of SEQ ID NOs: 2 to 28 (claim 3),
wherein the polypeptide is acetylated at its amino terminus (claim 4), and
wherein the polypeptide further comprises a protease cleavage site (claim 8).
Claims 9, 11-14, and 16 are drawn to a fusion protein comprising a 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 not constitutively expressed to detectable levels in an expression system in which the fusion protein is expressed, optionally wherein the biological molecule is a membrane binding protein, an insoluble protein, or a protein usually toxic to the 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 the attached Form PTO-892) 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 Davidson et al. (J. Biol. Chem. 27:9443-9449, 1998; cited on the attached Form PTO-892) 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, full-length alpha-synuclein and 41-syn disclosed by Vinnakota et al. are considered to comprise “an amphipathic alpha helix polypeptide.”
The reference of de Oliveira et al. (PLOS Biology 15: e2000374, 2017, 27 pages; cited on the attached Form PTO-892) 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 the attached Form PTO-892) discloses that alpha-synuclein comprises protease cleavage sites (p. 2, Figure 1).
Regarding the limitation “vesicle nucleating polypeptide” in claim 1, 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 full-length alpha-synuclein and 41-syn disclosed by Vinnakota et al. are substantially identical to that of the claims, the claimed property of “vesicle nucleating polypeptide” is presumed to be inherent.
Regarding claims 1-4 and 8, in view of the cited teachings above and given a broadest reasonable interpretation, the isolated vesicle nucleating polypeptide of claims 1-4 and 8 encompasses a naturally-occurring full-length alpha-synuclein polypeptide and a naturally-occurring N-terminal fragment thereof, 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 naturally occurring full-length alpha-synuclein polypeptide or 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 thereof.
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 thereof.
Regarding claim 14, the limitation “wherein the biological molecule is not constitutively expressed to detectable levels in an expression system in which the fusion protein is expressed” while being relevant to an expression system for expressing the recited fusion protein, does not structurally and/or functionally limit the recited fusion protein. Also, the recitation “wherein the biological molecule is a membrane binding protein, an insoluble protein, or a protein usually toxic to the host cell in which the fusion protein is expressed” is an optional limitation. As such, given a broadest reasonable interpretation, the fusion protein of claim 14 encompasses a naturally-occurring full-length alpha-synuclein polypeptide and a naturally-occurring N-terminal fragment thereof.
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 1-4 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.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
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.
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 the (5) 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 comprising an amphipathic alpha helix polypeptide derived from the amino terminus of synuclein isoforms and variants thereof. 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. Other than these disclosed representative species, the specification fails to disclose other isolated vesicle nucleating polypeptides as encompassed by the claims.
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 the attached Form PTO-892) reviews various protein engineering methods and discloses that despite the availability of an ever-growing database of protein structures and highly sophisticated computational algorithms, protein engineering is still limited by the incomplete understanding of protein functions, folding, flexibility, and conformational changes (see p. 7, column 1, top).
The unpredictability associated with amino acid substitution is exemplified by the reference of Zhang et al. (Structure 26:1474-1485, 2018; cited on the attached Form PTO-892), which discloses that even a 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).
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 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.
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 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 an isolated vesicle nucleating polypeptide comprising an amphipathic alpha helix polypeptide derived from the amino terminus of synuclein isoforms and variants thereof. Given a broadest reasonable interpretation, the amino acid sequence of the isolated vesicle nucleating polypeptide is unlimited.
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 the attached Form PTO-892) reviews various protein engineering methods and discloses that despite the availability of an ever-growing database of protein structures and highly sophisticated computational algorithms, protein engineering is still limited by the incomplete understanding of protein functions, folding, flexibility, and conformational changes (see p. 7, column 1, top).
The unpredictability associated with amino acid substitution is exemplified by the reference of Zhang et al. (Structure 26:1474-1485, 2018; cited on the attached Form PTO-892), which discloses that even a 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. Other than these working examples, the specification fails to disclose other working examples of isolated vesicle nucleating polypeptides 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 thermostable proteins 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).
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-4, 8, 9, 11-14, and 16 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Vinnakota et al. (ACS Chem. Neurosci. 9:2948-2958, 2018; cited on the attached Form PTO-892; hereafter “Vinnakota”) as evidenced by Davidson et al. (J. Biol. Chem. 27:9443-9449, 1998; cited on the attached Form PTO-892; hereafter “Davidson”), de Oliveira et al. (PLOS Biology 15: e2000374, 2017, 27 pages; cited on the attached Form PTO-892; hereafter “de Oliveira”), and Bluhm et al. (Int. J. Mol. Sci. 22:5450, May 2021, 14 pages; cited on the attached Form PTO-892; hereafter “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 1-4 and 8 are drawn to an isolated vesicle nucleating polypeptide comprising an amphipathic alpha helix polypeptide derived from the amino terminus of synuclein isoforms and variants thereof (claim 1),
wherein the polypeptide has between 9 and 140 amino acids, optionally between 16 and 40 amino acids, more preferably about 20 amino acids (claim 2),
wherein the sequence is any one of SEQ ID NOs: 2 to 28 (claim 3),
wherein the polypeptide is acetylated at its amino terminus (claim 4), and
wherein the polypeptide further comprises a protease cleavage site (claim 8).
Claims 9, 11-14, and 16 are drawn to a fusion protein comprising a 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 not constitutively expressed to detectable levels in an expression system in which the fusion protein is expressed, optionally wherein the biological molecule is a membrane binding protein, an insoluble protein, or a protein usually toxic to the 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 1-3, Vinnakota discloses that alpha-synuclein is a 140 amino acid protein (p. 2948, column 1) 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). Full-length alpha-synuclein and 41-syn disclosed by Vinnakota each comprises instant SEQ ID NO: 2 as the first 38 amino acids (p. 2951, Figure 2B).
Vinnakota does not disclose full-length alpha-synuclein and 41-syn 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 show that the N-termini of full-length alpha-synuclein and 41-syn comprise 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). 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 structures of full-length alpha-synuclein and 41-syn disclosed by Vinnakota are substantially identical to that of the claims, the claimed property of “an amphipathic alpha helix polypeptide” is presumed to be inherent. As such, full-length alpha-synuclein and 41-syn disclosed by Vinnakota are considered to comprise “an amphipathic alpha helix polypeptide.”
Vinnakota does not disclose full-length alpha-synuclein and 41-syn are “vesicle nucleating” polypeptides 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 full-length alpha-synuclein and 41-syn disclosed by Vinnakota are substantially identical to that of the claims, the claimed property of “vesicle nucleating polypeptide” is presumed to be inherent.
Regarding claim 4, Vinnakota does not disclose full-length alpha-synuclein and 41-syn are acetylated at its 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, Vinnakota does not disclose full-length alpha-synuclein and 41-syn 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 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 naturally occurring full-length alpha-synuclein polypeptide or 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 full-length alpha-synuclein polypeptide and 41-syn as disclosed by Vinnakota.
Regarding claim 14, the limitation “wherein the biological molecule is not constitutively expressed to detectable levels in an expression system in which the fusion protein is expressed” while being relevant to an expression system for expressing the recited fusion protein, does not structurally and/or functionally limit the recited fusion protein. Also, the recitation “wherein the biological molecule is a membrane binding protein, an insoluble protein, or a protein usually toxic to the host cell in which the fusion protein is expressed” is an optional limitation. As such, given a broadest reasonable interpretation, the fusion protein of claim 14 encompasses full-length alpha-synuclein polypeptide and 41-syn as 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 full-length alpha-synuclein polypeptide and 41-syn as disclosed by Vinnakota.
Therefore, Vinnakota anticipates claims 1-4, 8, 9, 11-14, and 16 as written.
Claims 1-5, 8, 9, 11-14, and 16 are rejected 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, 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, 3, 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 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). 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 structures of SZAHA and SZA disclosed by Jiang are substantially identical to that of the claims, the claimed property of “an amphipathic alpha helix polypeptide” is presumed to be inherent. As such, SZAHA and SZA disclosed by Jiang are considered to comprise “an amphipathic alpha helix polypeptide.”
Jiang does not disclose SZAHA and SZA are “vesicle nucleating” polypeptides 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 structures of SZAHA and SZA disclosed by Jiang are substantially identical to that of the claims, the claimed property of “vesicle nucleating polypeptide” is presumed to be inherent to SZAHA and SZA.
Jiang does not disclose SZAHA and SZA comprise any one of SEQ ID NO: 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, the limitation “wherein the biological molecule is not constitutively expressed to detectable levels in an expression system in which the fusion protein is expressed” while being relevant to an expression system for expressing the recited fusion protein, does not structurally and/or functionally limit the recited fusion protein. Also, the recitation “wherein the biological molecule is a membrane binding protein, an insoluble protein, or a protein usually toxic to the host cell in which the fusion protein is expressed” is an optional limitation. As such, given a broadest reasonable interpretation, the fusion protein of claim 14 encompasses 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 1-5, 8, 9, 11-14, and 16 as written.
Conclusion
Status of the claims:
Claims 1-5, 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 1-5, 8, 9, 11-14, and 16 are rejected.
No claim is in condition for allowance.
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/David Steadman/Primary Examiner, Art Unit 1656
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