Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
DETAILED ACTION
Claim Status
Claims 1-12, 16-18, 20-28, 34, 39, 43, 46, 48-52, 58-60, 63, 65-66, and 75-77 are currently pending in this application.
Election/Restrictions
Applicant’s election with traverse of Group I, claims 1-13, 15-18, 20-28, 34, and 38 in the reply filed on June 24, 2024 is acknowledged. Also, Applicant’s election of (e) wherein the peptide insertion comprises a sequence selected from SEQ ID NOs: 84-104, and Applicant’s election of (a) any species of nuclear localization signal (NLS) sequence, (b) species of peptide insertion in an AAV VP1 capsid protein, and (c) species of heterologous nucleic acid encoding Factor VIII. Claims 2-5, 8, 20-23, 25-28, 39, 43, 46, 48-52, 58-60, 63, 65-66, and 75-77 are withdrawn for being directed to non-elected subject matter, and claims 1, 6-7, 9-12, 16-18, 24, and 34 have been considered on the merits.
Benefit of Priority Claim
Acknowledgement is made of applicant’s claim for the benefit of the prior-filed applications US 62/663,963 under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c). Entitlement to priority to April 27, 2018 based on US 62/663,963 does not apply to the subject matter of a peptide insertion in one or more of AAV VP1, VP2 or VP3 capsid proteins of AAV2 having an amino acid sequence of SEQ ID NO: 122, therefore the earliest effective filing date of claims 1, 6-7, 9-12, 16-18, and 34 is April 26, 2019 based on PCT/US2019/029487.
Claim Objection
Claim 7 is objected to because of the following informalities:
Claim 7 recites the phrase “wherein said nuclear localization sequence comprises an additional AAV nuclear localization sequence from an AAV having an AAV serotype, which is the same or different than the parental AAV capsid protein.” Because claim 1 requires an “insertion” of a nuclear localization signal (NLS) sequence, by definition the AAV nuclear localization sequence of claim 7 is understood to be “additional” so including this word is both unnecessary and confusing. In addition, the phrase “from an AAV having an AAV serotype, which is the same or different than the parental AAV capsid protein” is unclear because an AAV serotype is assigned to an AAV virus and not to any particular protein. Further the ending of this phrase would be more grammatically correct if the comma before “which” is removed. Thus, the phrase may be clearer if rewritten as “wherein said nuclear localization sequence comprises an AAV nuclear localization sequence from an AAV having an AAV serotype which is the same or different than an AAV comprising the parental AAV capsid protein.” Appropriate correction is requested.
Previous Rejections
Status of the rejections:
a) The previous claim rejections under 35 USC 112(a) are withdrawn in view of the claim amendments except where specifically maintained below.
b) The previous claim rejections under 35 USC 112(b) are withdrawn in view of the claim amendments except as modified in below in the rejection of claims 11-12.
c) The previous clam rejections under 35 USC 102 and 103 are withdrawn in view of the claim amendments.
Claim Interpretation
In the claims, the technical term “peptide” referring to an inserted plurality of residues within a protein is used contrary to the meaning as commonly understood by those skilled in the relevant art to which this invention belongs; however, in view of the instant application as a whole, the meaning of this term is clear and unambiguous under a broadest reasonable interpretation. As oppose to wherein a “peptide” is limited to being relatively short in length (e.g., < 50 residues), the term “peptide” is instead more broadly interpreted to encompass polypeptides having any length, e.g., a single-chain of 100 or more amino acid residues linked together by peptide bonds (see e.g., instant [0088]).
In the claims, the technical term “insertion” referring to a specific protein modification is used contrary to the meaning as commonly understood by one of ordinary skill in the art to which this invention belongs; however, in view of the instant application as a whole, the meaning of this term is clear and unambiguous. As oppose to being limited to wherein the insertion only adds residues internal to the parental protein as the term is typically used, the term “insertion” is instead more broadly interpreted to encompass wherein the one or more parental residues is modified, such as via substitution and/or deletion. For example, if a parental protein sequence has the sequence LPXY and the modified protein has RPXL, then the “insertion” could be interpreted as beginning at position L and ending at position Y of the parental sequence (i.e., a 4 residue insertion) wherein the total length of the protein remains unchanged and the L and Y have been modified by deletion/substitution. In addition, the term insertion is interpreted to encompass wherein the insertion begins or ends at a terminal end of the capsid protein, instead of being limited to internal positions only.
In claim 1, the phrases “wherein said capsid protein is modified from a parental AAV capsid protein” and “insertion is in one or more of AAV VP1, VP2 or VP3 capsid proteins” is considered and determined to limit the claimed AAV capsid protein to a structure at least retaining partial activity or function of an AAV VP1, VP2, and/or VP3 protein or protein sequence thereof (see e.g. instant [0077]), such as self-assembling with other VP1, VP2, and/or VP3 monomers to form capsid icosahedra structures (either in the presence or absence of AAP) or further forming at least partially functional capsids for packaging an AAV genome, infecting a host cell, and/or delivering/transducing a packaged genome to a host cell (see e.g., Vandenberghe et al., Gene Ther 16: 311-9 (2009) at pg. 309, left col., 1st para.).
Claim Rejections - 35 USC § 112(a), Written Description
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim 1, 6-7, 9-12, 16-18, 24, and 34 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claimed invention as a whole is not adequately described if the claims require essential or critical elements that are not adequately described in the specification and that is not conventional in the art as of applicants effective filing date. Possession may be shown by actual reduction to practice, clear depiction of the invention in a detailed drawing, or by describing the invention with sufficient relevant identifying characteristics such that a person skilled in the art would recognize that the inventor had possession of the claimed invention. Pfaff v. Wells Electronics, Inc., 48 USPQ2d 1641,1646 (1998).
In making a determination of whether the application complies with the written description requirement under 35 U.S.C. 112(a) or 35 U.S.C. 112, first paragraph, it is necessary to understand what Applicant is claiming and what Applicant has possession of.
In the instant case, the claims are directed to a protein comprising an insertion of a nuclear localization signal (NLS), wherein the protein is an AAV capsid protein, such as wherein the capsid protein is modified from a parental AAV capsid protein consisting of SEQ ID NO: 1, 59, or 22.
Claim 1 recites the limitation “wherein said peptide insertion is in one or more of AAV VP1, VP2 or VP3 capsid proteins of Spk200, Spk100, or AAV2” but the terms “Spk200” and “Spk100” each lacks a definition in the claims and the prior art. Thus, this limitation fails to define the VP2 and VP3 capsid proteins of Spk200, Spk100, or AAV2 as recited in the claim and thus claim 1 encompasses wherein the parental VP2 or VP3 capsid protein has any “VP2” or “VP3” protein sequence. Furthermore, claims 6-7, 9, 11-12, 16, and 34 all encompass the VP2 and/or VP3 capsid proteins of Spk200 or Spk100 lacking any structural and/or functional limitation, either implicitly or expressly recited.
Moreover dependent claim 34 recites the insertion “comprises any of SEQ ID NOs: 84-104 having one or more amino acid substitutions,” which encompass virtually any polypeptide sequence, including insertions with so many substitutions there is no apparent connection to any parental sequence (e.g., SEQ ID NOs: 84-104). That broad sequence variance results in a situation in which the sequence identity is less than 15% to any one of parental SEQ ID NOs: 84-104 so long as at least one sequence mediating/facilitating nuclear import (i.e., an NLS) is present therein.
Thus, claim 1 encompasses a “peptide insertion” comprising any NLS at any position in any AAV VP2 or VP3 capsid protein. In addition, the instant application explains the peptide insertion may comprise 50-100 or more amino acid residues ([0088]). Thus, the length of the insertion is unlimited.
In analyzing whether the written description requirement is met for genus claims, it is first determined whether a representative number of species have been described. In the instant case, the specification fails to provide any clear description of a representative number of species for the broad genus of possible insertion sequences, which includes any NLS sequence, and the broad genus of possible insertion positions as detailed below.
Any Insertion Position in an AAV capsid protein while retaining capsid protein function
Claims 1, 6-7, 9, 16, 24, and 34 are broadly directed to a genus of modified AAV capsid proteins comprising an insertion of a “peptide” at any position within an AAV VP1, VP2, and/or VP3 capsid protein.
The prior art teaches that insertions of peptides having 6 and/or 8-10 amino acids (HIS, AU, FLAG, HA, or Ser) into AAV2 capsid proteins at various positions inhibited virion production or produced defective virions (e.g., at position 10, 24, 39, 76, 84, 150, 178, 203, 328, 454, 522, 526, 547, 553, 562, 638, 664, or 682) (Wu et al., J Virol 2000 Sep;74: pg. 8635-47, at Fig. 1, Table 1). For example, these insertions resulted in “noninfectious” virions having an infectivity 5-logs lower compared to wild-type due to being unable to make capsids or failing to make stable capsids (class 4b) or being defective in a host cell binding, internalization, and/or uncoating step(s) (class 4a or 4d) (Wu at Table 2; Fig. 3). In another example, while some prior art teaches position 587 the capsid proteins of AAV2 are permissive for insertions, other prior art shows unpredictability at just this single site with NLS insertions causing a six-fold reduction in capsid assembly, ten-fold drop in packaging efficiency, loss of host cell binding, and a drastic reductions in infectivity (Douar et al. Virology 309: 2003; IDS ref. at Abstract; Table 1; Fig. 2-3C; pg. 206, left col., last para., to right col., 2nd para.).
Thus not any position in an AAV2 capsid protein can tolerate a peptide insertion and it is not predictable which positions will or will not tolerate a given peptide sequence as an insert. As the prior art does not teach any predictable pattern for permissive insertion sites, these aspects must be described to a reasonable extent so that one of the ordinary skills in the art would recognize that Applicant was in possession of these insertion sites at the effective filing date of the claimed invention. Furthermore, as the prior art teaches away specifically from positions 39, 150, 454, and 587, more convincing evidence may be required to sufficiently describe to one of skill in the art that Applicant was in possession of these specific insertion sites in view of the prior art.
Although the instant specification describes insertions in SEQ ID NO: 1, 59, and/or 122 at various positions, the instant application only shows empirical data for insertions at positions 35, 37, 139, 140, and 163 in SEQ ID NO: 1 (Tables 1B, 1E); 33, 35, 140, and 163 in SEQ ID NO: 59 (Table 3); and position 35 in SEQ ID NO: 122 (Example 3). Thus, the descriptions of insertion positions of anywhere between basic region 1 (BR1) and basic region 2 (BR2), anywhere between basic region 2 (BR2) and basic region 3 (BR3), anywhere in loop 3 (i.e., subloop I in loop IV) of a VP1 capsid protein, anywhere in the position ranges 30-40, 135-141, 147-166, 380-390, 445-460, and 585-595 of a VP1 capsid protein are merely prophetic aside for specifically 33, 35, 37, 139, 140, and 163. As [0222] does not clearly describe what is actual versus prophetic, it was not considered to describe any working example other than those expressly listed in Tables 1B and 1E. As shown in instant Figs. 1, 3-5, and Table 5, these working embodiments provide 30% to over 100% of control. The working embodiment insert positions (33, 35, 37, 139, 140, and 163) all lie outside of BR1, BR2, BR3, and BR4 while the prophetic positions overlap with BR3 at position 166 (see Fig. 9).
The instant specification lacks a written description for sufficient number of representative species for any insertion position in a VP1, VP2, or VP3 AAV capsid protein, including wherein the parental protein is SEQ ID NO: 1, 59, and/or 122. Further, the specification lacks a written description for sufficient number of representative species for any insertion position in the ranges 30-40, 135-141, 147-166, 380-390, 445-460, and 585-595 of a VP1 AAV capsid protein, including wherein the parental protein is SEQ ID NO: 1, 59, and/or 122. Due to the unpredictability shown in the prior art, and wide range of insertion sites, more empirical evidence of untested insertion sites is needed to show that Applicant was in possession of all the sites in these insertion ranges.
While claims 10-12 and 17 provide further limitations to the genus of insertion positions (and in the case of claims 10 and 17 also limiting the parental capsid protein sequence to a generic VP1 capsid protein), an insertion position anywhere within a range of positions 1-52, between BR1 and BR2, BR2 and BR3, or loop3 of a VP1; are not described by a sufficient number of representative species for the same reasons detailed above. The skilled artisan cannot envision the variety of possible peptide insertions being permitted in the broadly claimed ranges and regions to provide at least partial capsid function when the disclosure is silent of evidence beyond positions 33, 35, 37, 139, 140, and 163 in VP1, and even some of these had greatly reduced function, e.g., 30-47% yields (Table 5).
Insertions of Any Size and Comprising Virtually Any Sequence
Claims 1, 6-7, 9-12, 16-18, and 34 are broadly directed to a genus of modified AAV capsid proteins comprising an insertion of a “peptide” comprising NLS defined functionally and unlimited additional structure in the form of any peptide/polypeptide sequence (e.g., 50-100 or more residues). It must be emphasized that the scope the claims encompasses insertions with no limitation in sequence nor length/size so long as the insertion comprises at least one NLS (typically having at least four and rarely more than 30 amino acid residues) and so long as the AAV capsid protein possesses at least one known AAV VP1, VP2, or VP3 capsid protein functionality.
The instant application describes putative examples of species of such proteins related to a parental protein having the sequence of SEQ ID NOs: 1, 59, or 122 wherein the insertions have various lengths (Tables 2 and 4), such as shown in some of the proteins having a sequence of SEQ ID NOs: 2-58, 60-83, and 105-121 (Tables 1 and 3; [0223]; [0009]-[0010]). However none of these insertions (e.g., SEQ ID NO: 84-104) exceeds a length of 51 residues. Furthermore, not all of these proteins have been verified to retain a partial (e.g., minimal) AAV capsid protein activity of the parental protein (e.g., a VP1 capsid protein function).
Regardless, the instant specification describes prophetic embodiments comprising three or more tandem repeats of such insertion sequences ([0030]) with an increased length due to as many as 5 additional intervening residues ([0032]). Thus, the application describes species of such proteins comprising insertions of lengths of over 163 amino acid residues with no upper limit, e.g., 6, 7, or 8 tandem repeats etc.
It is too unpredictable for a functional protein (AAV VP1, VP2, or VP3 capsid protein) to tolerate insertions of unlimited size and at any position. As mentioned already above, the prior art teaches that insertions of peptides as small as 6 and/or 8-10 amino acids into AAV2 capsid proteins at various positions can destroy protein function (Wu at Table 2; Fig. 3) and that a AAV2 capsid protein insert site that tolerated a non-NLS insertion could not tolerate a NLS insertion to maintain basic capsid protein functions (Douar at Abstract; Table 1; Fig. 2-3C; pg. 206, left col., last para., to right col., 2nd para.). Further, it is unpredictable specifically for an AAV VP1 protein to tolerate even an insertion with 5 or more tandem NLS repeats even (e.g., > 150 amino acids) when the insertion site was already shown to tolerate a smaller peptide insertion, e.g., of 7-22 amino acids.
Thus, the genus of insertions comprising any sequence with no upper limit is not sufficiently described by a representative number of species. Protein function is too unpredictable in general and in particular the functioning of AAV capsid protein in particular is too easily perturbed as taught by the art. Therefore in the instant case, empirical evidence is needed to show possession for inserts larger than about 50 amino acid residues.
Any NLS as defined functionally
Claims 1, 6-7, 9-12, 16-18, and 34 are broadly directed to a genus of modified AAV capsid proteins comprising an insertion of a “peptide” comprising a merely functionally defined NLS. It must be emphasized that the scope of the claimed NLS peptide feature encompasses a broad genus of amino acid sequences defined functionally as promoting (increasing or enhancing) nuclear localization (transduction) of an AAV capsid protein or virion (see [0084]).
The prior art teaches NLS can differ in structure but typically share the properties of basic residues (K and R) and/or hydrophilic residues, and are divided into classical (monopartite NLS or classical bipartite NLS), non-classical (ncNLS), and other types but all of which function via an importin receptor (Lu et al., Cell Commun Signal. 2021;19: 60, at Table 1, pg. 2, left col.; Fig. 1). Lu et al. teaches that some proteins (β-catenin or MeCP2) translocate to the nucleus without any recognizable featured called an NLS and via an unclear mechanism (pg. 6 to pg. 7, left col., 2nd para.).
The instant specification defines the inserted NLS peptide as typically a short peptide sequence that can mediate or facilitate nuclear import (passage into the cellular nucleus) of molecules. Increased or enhanced nuclear transduction refers to increased tropism for the nucleus, which includes, for example, increased localization into the cell nucleus, increased endocytosis by the cell nucleus, increased penetration of the cell nucleus, increased entry into the cell nucleus, increased importation into the nucleus, increased targeting of the cell nucleus, or increased binding to the cell nucleus, such as by binding to an NLS receptor (e.g., an importins or karyopherin), binding to a protein which functions as a carrier to transport a recombinant AAV into the nucleus, binding to a biomolecule on the nuclear membrane that is subsequently internalized into the nucleus and/or by promoting fusing to the nuclear membrane ([0084-[0086]). The specification provides species of NLS in disclosure of SEQ ID NOs: 84-104 and working embodiments comprising the aforementioned; however, there is not any structural commonality are nexus between nuclear import function and a structure(s).
While such NLS features defined functionally as promoting (increasing or enhancing) nuclear localization (transduction) of an AAV capsid protein or virion (see [0084]) can be predicted in some instances from evidence of the signal motif in another protein or confirmed via biological assay using a working embodiment, not every structure that is capable of providing NLS activity is broadly defined in the specification is currently understood in the prior art. Thus, the skilled artisan cannot envision all the structures providing the claimed function without sufficient written description guidance. Merely generically describing a peptide functionally as promoting nuclear transduction from the cytoplasm alone is not sufficient to show possession. See Centocor Ortho Biotech, Inc. v. Abbott Labs., 636 F.3d 1341, 1351-52, 97 USPQ2d 1870, 1877 (Fed. Cir. 2011).
There is insufficient written description in the specification to reasonably convey to one skilled in the relevant art at the time the application was filed that the inventors had possession of the claimed genus of any NLS defined merely functionally and by such a variety of functional mechanisms. From the combination of the prior art and instant written description, the skilled artisan cannot envision all the amino acid sequences that function as an NLS with the exception of actual NLS sequences disclosed in the application or in the prior art by the earliest effective filing date.
As explained by the Federal Circuit, “(1) examples are not necessary to support the adequacy of a written description; (2) the written description standard may be met … even where actual reduction to practice of an invention is absent; and (3) there is no per se rule that an adequate written description of an invention that involves a biological macromolecule must contain a recitation of known structure. However, the claimed invention itself must be adequately described in the written disclosure and/or the drawings, such as using identifying structural characteristics (e.g., structural motifs or consensus sequences) or combinations of characteristics (e.g., a motif and overall hydrophobicity, polarity or charged side chains or a structural motif conferring an importin receptor binding activity) (see MPEP 2163).
While claim 7 limits the NLS to any AAV NLS, this is similarly broad due to the broad definition of the NLS insert in the specification using such a variety of functional mechanisms, e.g., of binding targets, and the lack of knowledge of AAV virion entry into the nucleus, especially for less well studied variants. Thus the narrower genus of claim 7 also lacks disclosure of a representative number of species over the scope of the genus such that one of skill in the art can envision all the structures therein.
Conclusion
Vas-Cath Inc. v. Mahurkar, 19USPQ2d 1111, clearly states “applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the ‘written description’ inquiry, whatever is now claimed” (pg 1117). The specification does not “clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed” (pg 1116). As discussed above, the skilled artisan cannot envision the structure(s) of the insertions regarding both sequence and length which allow for preservation of at least partial AAV capsid protein function based on the information provided in the instant application, and therefore conception is not achieved until reduction to practice has occurred, regardless of the complexity or simplicity of the method of isolation. Adequate written description requires more than a mere statement that it is part of the invention and reference to potential and generic ways of modifying an AAV capsid protein via insertion of undefined amino acid sequences at virtually any location. The compound itself is required. See Fiers v. Revel, 25 USPQ2d 1601 at 1606 (CAFC 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016.
There is a lack of evidence in the instant specification as filed that the inventors were in possession of any insertion site for any peptide comprising any NLS defined merely functionally wherein the capsid protein retains at least a partial capsid protein function. The written description requirement may be satisfied through actual reduction to practice 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 structure and function, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed invention. In the instant case, examples of identifying characteristics may include a protein sequence, conserved structure-function, capsid monomer binding affinity/specificity, AAV packaging, or AAV replication/infection/transduction assay using the claimed protein to show retention of a partial (minimal) AAV capsid function. The instant application fails to provide sufficient descriptive information across the breadth of the claims.
35 USC § 112(a) – Scope of Enablement (New)
Claims 1, 6-7, 9-12, 16-18, 24, and 34 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because while the claims are enabled for wherein the insertion is less than 50 amino acids and comprises one or more of SEQ ID NOs: 84-104 inserted at one of the group of positions 33, 35, 37, 139, 140, and 163 in SEQ ID NO: 1, 59, or 122; the specification does not enable any person skilled in the art to which it pertains or with which it is most nearly connected to insert any polypeptide into any VP1, VP2 or VP3 AAV capsid at any position whereby the modified protein retains at least partial AAV capsid functionality.
All of the Wands factors have been considered with regard to the instant claims, with the most relevant factors discussed below.
Claim 1 is broadly directed to product (an AAV capsid protein) comprising an insertion at any position (i.e., 1 to the end) of a peptide/polypeptide (of any size and sequence) comprising any functional sequence that facilitates/increases/enhances nuclear import/transduction wherein the protein retains at least partially an AAV capsid function of one or more of an AAV VP1, VP2 or VP3 (see instant [0077]).
The prior art teaches the unpredictability of insertion of a classical NLS into a permissive site in AAV2 capsid protein (Douar at Abstract; Table 1; Fig. 2-3C; pg. 206, left col., last para., to right col., 2nd para.). The prior art also teaches that insertions at various positions peptides having 6 and/or 8-10 amino acids (HIS, AU, FLAG, HA, or Ser) into AAV2 capsid proteins unpredictability affect capsid function with all insertions tested causing at a minimum a partial defect (class 2a) to completely noninfectious (class (Wu at Fig. 1, Table 1). Thus not any position in an AAV2 capsid protein can tolerate a peptide insertion and it is not predictable which positions will or will not tolerate a given peptide sequence as an insert. As the prior art does not teach any predictable pattern for permissive insertion sites, there must be sufficient guidance to enable one of ordinary skill in the art to make/use the claimed invention. Furthermore, as the prior art teaches away specifically from positions 39, 150, 454, and 587, more guidance is required to sufficiently enable one of skill in the art to make/use these specific embodiments.
Although the instant specification describes insertions in SEQ ID NO: 1, 59, and/or 122 at various positions, the instant application only shows empirical data for insertions at positions 35, 37, 139, 140, and 163 in SEQ ID NO: 1 (Tables 1B, 1E); 33, 35, 140, and 163 in SEQ ID NO: 59 (Table 3); and position 35 in SEQ ID NO: 122 (Example 3). Thus, the scope of insertion positions of anywhere between basic region 1 (BR1) and basic region 2 (BR2), anywhere between basic region 2 (BR2) and basic region 3 (BR3), anywhere in loop 3 (i.e., subloop I in loop IV) of a VP1 capsid protein, anywhere in the position ranges 30-40, 135-141, 147-166, 380-390, 445-460, and 585-595 of a VP1 capsid protein are merely prophetic aside for specifically positions 33, 35, 37, 139, 140, and 163. As shown in instant Figs. 1, 3-5, and Table 5, these working embodiments provide 30% (partial parental activity) to over 100% of control. The working embodiment insert positions (33, 35, 37, 139, 140, and 163) all lie outside of BR1, BR2, BR3, and BR4 while the prophetic positions overlap with BR3 at position 166 (see Fig. 9).
Therefore extensive experimentation would be required to bridge these gaps to determine how to use all the modified capsid proteins encompass by the present invention whereby at least one AAV capsid function is present at least with partial activity. The examples provided while extrapolatable to other highly similar parental AAV capsid proteins and similarly sized NLS inserts, without guidance or working examples in the specification regarding additional specific inserts sites, insert structures, and NLS structures, one of skill in the art would be unable to use the claimed protein across its full scope. Thus, undue and unreasonable experimentation is required to determine additional insertion sites and insert sequences not provided in working examples in the instant application.
While claims 10-12 and 17-18 provide further limitations to the genus of insertion positions (and in the case of claims 10 and 17-18 also limiting the parental capsid protein sequence to a generic VP1 capsid protein), an insertion position anywhere within a range of positions 1-52, between BR1 and BR2, BR2 and BR3, or loop3 of a VP1, or in the ranges of 30-40, 135-141, 147-166, 380-390, 445-460, and 585-595; are not enabled over their full scope for the same reasons detailed above.
In summary, claims 1, 6-7, 9-12, 16-18, 24, and 34 are rejected under 35 U.S.C. 112(a) because the specification does not reasonably provide enablement, to a person skilled in the art to which it pertains or with which it is most nearly connected to, to make/use the claimed invention over the entire scope. Given the lack of working examples, the limited guidance provided in the specification, the lack of guidance in the prior art, and the broad scope of the claims; undue and unreasonable experimentation would have been required for one skilled in the art to make the claimed protein across the breadth recited in the claims while providing at least a partial AAV capsid protein activity and which may never be achievable across the entire scope of the claims.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1, 6-7, 9-12, 16-18, 24 and 34 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant) regards as the invention.
Claim 1 recites an adeno-associated virus (AAV) capsid protein having a peptide insertion “in one or more of AAV VP1, VP2 or VP3 capsid proteins,” which is ambiguous, incoherent, or otherwise unclear as to how a single capsid protein comprises multiple insertions into, e.g., VP1 and VP2 capsid proteins, VP1 and VP3 capsid proteins, VP2 and VP3 capsid proteins, or VP1, VP2, and VP3 capsid proteins. Claims 6-7, 9, 11-12, 16, 24, and 34 are included in this rejection for depending from indefinite claim 1.
Claim 1 recites the limitation “wherein said peptide insertion is in one or more of AAV VP1, VP2 or VP3 capsid proteins of Spk200, Spk100, or AAV2,” but the terms “Spk200” and “Spk100” each lacks a definition in the claims and the prior art. Do the terms “Spk100” and “Spk200” refer to a AAV virus strain comprising multiple capsid proteins (e.g., each of VP1, VP2, or VP3) having defined structures (see instant [150]; [0153])? While the claim further limits the “Spk100” and “Spk200” to having a particular amino acid sequence (SEQ ID NO: 1 and 59 respectively), a single capsid amino acid does not necessarily define an AAV virus or AAV serotype such as to define or limit the structure of the other capsid proteins of that virus or serotype/pseudotype. Similarly, an AAV2 having amino acid sequence 122 does not necessarily limit the structure of the VP2 or VP3 capsid protein of the AAV2. Thus, this limitation fails to define the VP2 and VP3 capsid proteins of Spk200, Spk100, or AAV2 as recited in the claim and a practitioner of skill in the art would not understand the metes and bounds of the claim regarding an AAV VP2 capsid protein of Spk200, an AAV VP3 capsid protein of Spk200, an AAV VP2 capsid protein of Spk100, or an AAV VP3 capsid protein of Spk100. Claims 1, 6-7, 9-12, 16-18, 24, and 34 are included in this rejection for depending from indefinite claim 1. For purposes of examination the AAV VP2 or VP3 capsid protein is interpreted without limitation.
In claim 1, the phrases “wherein said capsid protein is modified from a parental AAV capsid protein” and “insertion is in one or more of AAV VP1, VP2 or VP3 capsid proteins” is interpreted to limit the claimed AAV capsid protein to a structure at least retaining partial activity or function of an AAV VP1, VP2, and/or VP3 protein or protein sequence thereof (see e.g. instant [0077]); however as this is merely functionally defined, a practitioner of skill in the art would not understand the metes and bounds of this limitation, such as, e.g., regarding . Claims 1, 6-7, 9-12, 16-18, 24, and 34 are included in this rejection for depending from indefinite claim 1.
In claim 11, the phrase “a position between basic region 1 (BR1) and basic region 2 (BR2) of said AAV capsid protein” is incoherent, ambiguous, or otherwise unclear when not every AAV capsid protein (e.g., VP2 or VP3 of Spk200, Spk100, or AAV2) has both a BR1 and BR2 based on the nomenclature of the relevant prior art. The practitioner in the art would readily understand that although some AAV capsid proteins have positions between a BR1 and BR2, not all capsid proteins of all AAV serotypes comprise two or more such basic regions (see e.g., instant [0002]; Liu et al. 2017; Virology Journal pp. 1-6; abstract). For example, VP3 only contains a single BR4 and VP2 lacks an equivalent to the BR1 of VP1 (see Figure 1a of Liu et al. 2017, shown below).
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In claim 12, the phrase “a position between basic region 2 (BR2) and basic region 2 (BR3) of said AAV capsid protein” is ambiguous, incoherent, or otherwise unclear for the same reasons set forth above regarding claim 11. For example, the practitioner of skill in the art would readily understand that VP3 (e.g., of Spk200, Spk100, or AAV2) only contains a single BR4 as shown in Figure 1a of Liu et al. 2017.
Response to Arguments
Although Applicant argues that claims 10 and 11 as currently amended provide sufficient structure for the parental capsid protein to render the claims definite, this is not found persuasive for the added structural limits are insufficient for the reasons set forth fully above.
Claim Rejections - 35 USC § 102 (New)
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1, 6, 12, and 16 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Schultz et al. (Mol. Ther., July 2008; pp.1189-1199).
The claims are interpreted as provided in a previous section. For patentability analyses, product-by-process claims are not limited to the manipulations of the recited steps, only by the structure implied by such steps (see MPEP 2133). In the instant case because the claims are directed to a product (protein), any process of making the protein product (e.g., deriving the protein from a parental AAV capsid protein) only further limits the claimed product when there is an implied structure, such as to at least partially retain a functional activity of an AAV VP1, VP2, or VP3 capsid protein as implied by the instant application. Thus, a given AAV capsid protein encompassed by the claims is not required to have any identifiable parental AAV capsid protein (or protein sequence thereof) from which it may have been derived (e.g., SEQ ID NO: 1, 59, or 122). However to be encompassed by the claims, the protein must have at least one partial function of any AAV VP1, VP2, or VP3, which provides no particular structural limitation as discussed above regarding claim scope in the 112(a) section.
Regarding claim 1, Schultz et al. discloses an AAV VP1, VP2 or VP3 derived AAV capsid protein comprising an insertion of an NLS (nuclear-localization sequence) wherein the protein construct provides AAV capsid protein functionality as shown by successful host cell infection and transduction (page 1191; column 2, para 2-3). Thus, Schultz et al. discloses a modified AAV capsid protein comprising an inserted NLS in a VP2 or VP3 capsid protein of Spk100 and/or Spk200.
Regarding claim 6, Schultz et al. discloses the inserted NLS is not an AAV NLS but rather a parvovirus NLS (id.).
Regarding claim 12, Schultz et al. discloses wherein the NLS is inserted to replace the basic region 3 (BC3), which would appear as an insertion between basic region 2 (BR2) and basic region 3 (BR3) (id.).
Regarding claim 16, Schultz et al. discloses the parvovirus NLS is not inserted in a phospholipase A2 (PLA2) domain but rather in a cluster of basic residues termed BC3 (id.).
Thus by teaching all the claim limitations, Schultz et al. anticipates claims 1, 6, 12, and 16.
Claims 1, 6, 9, 12, and 16 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Grieger et al. (2006; Journal of Virology; pp. 5199–5210).
The claims are interpreted as provided in a previous section.
Regarding claim 1, Grieger et al. discloses an AAV VP1, VP2 or VP3 derived AAV capsid protein comprising an insertion of an NLS (nuclear-localization sequence) wherein the modified protein provides AAV capsid protein functionality as shown by successful host cell infection and transduction (page 5204, left col., 3rd para.; Fig. 4; Abstract). Thus, Grieger et al. discloses a modified AAV capsid protein comprising an inserted NLS in a VP1, VP2 or VP3 capsid protein of Spk100 and/or Spk200.
Regarding claim 6, Grieger et al. discloses the inserted NLS is not an AAV NLS but rather a heterologous canine parvovirus (CPV) NLS (PAKRARR) (id.).
Regarding claim 9, Grieger et al. discloses wherein the NLS has a length of 7 amino acid residues, i.e., consists of PAKRARR (id.).
Regarding claim 12, Grieger et al. discloses wherein the heterologous NLS is inserted prior to the BR3, which is between basic region 2 (BR2) and basic region 3 (BR3), to replace the endogenous PARKRLNF (id.).
Regarding claim 16, Grieger et al. discloses the parvovirus NLS is not inserted in a phospholipase A2 (PLA2) domain but rather prior to BR3 (id.).
Thus by teaching all the claim limitations, Grieger et al. anticipates claims 1, 6, 9, 12, and 16.
Response to Arguments
Applicant respectfully submits that claim 1 is amended to comprise the limitations of now canceled claim 13; however claim 1 is also amended to recite “of Spk200, Spk100, or AAV2 having a specifically recited sequence,” which is ambiguous in scope as noted in the 112(b) rejections section above. Thus, Applicant's amendment resulted in the new grounds of rejection presented above.
Claim Rejections - 35 USC § 103 (new)
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1, 6, 9, 12, 16, and 34 are rejected under 35 U.S.C. 103 as being unpatentable over Schultz et al. (Mol. Ther., July 2008; pp.1189-1199) in view of Liu et al. (Liu et al. 2017; Virology Journal 14:80 pp. 1-6).
As set forth fully above, Schultz et al. anticipates claims 1, 6, 12, and 16, and thus, renders obvious the subject matter of claims 1, 6, and 16.
Regarding claim 9, Schultz et al. teaches wherein the insert comprises a canine parvovirus NLS (nuclear-localization sequence); however, Schultz does not expressly teach the NLS has a length of about 5 amino acids to about 60 amino acids.
However Liu et al. teaches a classical NLS in the canine parvovirus VP1 capsid protein having the structure PAKRARRGYKC (BR1) (pg. 2, right col., last para., to pg. 3, left col.). Liu et al. teaches inserting this NLS into a protein is capable of efficiently directing transporting a non-nuclear protein (bovine serum albumin) into the nucleus of cells (id.).
It would have been prima facie obvious to one of ordinary skill in the art at the time of filing in making a modified AAV capsid protein taught by Schultz et al. to use the specific canine parvovirus NLS taught by Liu et al. One of ordinary skill in the art with the goal of inserting a canine parvovirus NLS to promote nuclear localization of a protein would be motivated to use an NLS already validated to be sufficient in directing nuclear localization as taught by Liu et al.
Regarding claims 34, Liu et al. teaches wherein the insert comprises or consists of PAKRARRGYKC, which is encompassed by instant SEQ ID NO: 92 having 10 amino acid substitutions.
Therefore, the claimed invention as a whole is prima facie obvious to one of ordinary skill in the art before the earliest effective time of filing.
Claims 1, 6, 12, 16, and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Schultz et al. (Mol. Ther., July 2008; pp.1189-1199) in view of Russell (US Pat. 6,156,303) and Johnson (Johnson et al., J Virol 2010 Sep;84:8888-902).
As set forth fully above, Schultz et al. anticipates claims 1, 6, 12, and 16, and thus, renders obvious the subject matter of claims 1, 6, and 16.
Regarding claim 18, Schultz et al. teaches wherein the insert is positioned at the basic region 3 (BC3) of an AAV2 VP1, which is immediately after position 165 for the specific AAV2 VP1 capsid protein taught by Russell (SEQ ID NO: 4) as taught by Johnson (Fig 1B; P-A-N-N-R-L (PAXXRL)) and shown in the alignments below.
Johnson AAV2 BR3 1 PAXXRL
Russell SEQ ID NO 4 166 PARKRL
Russell SEQ4 1 MAADGYLPDWLEDTLSEGIRQWWKLKPGPPPPKPAERHKDDSRGLVLPGYKYLGPFNGLD
Sequence2 1 MAADGYLPDWLEDTLSEGIRQWWKLKPGPPPPKPAERHKDDSRGLVLPGYKYLGPFNGLD
************************************************************
Russell SEQ4 61 KGEPVNEADAAALEHDKAYDRQLDSGDNPYLKYNHADAEFQERLKEDTSFGGNLGRAVFQ
Sequence2 61 KGEPVNEADAAALEHDKAYDRQLDSGDNPYLKYNHADAEFQERLKEDTSFGGNLGRAVFQ
************************************************************
Russell SEQ4 121 AKKRVLEPLGLVEEPVKTAPGKKRPVEHSPVEPDSSSGTGKAGQQPARKRLNFGQTGDAD
Sequence2 121 AKKRVLEPLGLVEEPVKTAPGKKRPVEHSPVEPDSSSGTGKAGQQPAXXRLNFGQTGDAD
*********************************************** ***********
Russell SEQ4 181 SVPDPQPLGQPPAAPSGLGTNTMATGSGAPMADNNEGADGVGNSSGNWHCDSTWMGDRVI
Sequence2 181 SVPDPQPLGQPPAAPSGLGTNTMATGSGAPMADNNEGADGVGNSSGNWHCDSTWMGDRVI
************************************************************
Russell SEQ4 241 TTSTRTWALPTYNNHLYKQISSQSGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLI
Sequence2 241 TTSTRTWALPTYNNHLYKQISSQSGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLI
************************************************************
Russell SEQ4 301 NNNWGFRPKRLNFKLFNIQVKEVTQNDGTTTIANNLTSTVQVFTDSEYQLPYVLGSAHQG
Sequence2 301 NNNWGFRPKRLNFKLFNIQVKEVTQNDGTTTIANNLTSTVQVFTDSEYQLPYVLGSAHQG
************************************************************
Russell SEQ4 361 CLPPFPADVFMVPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEDVPF
Sequence2 361 CLPPFPADVFMVPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEDVPF
************************************************************
Russell SEQ4 421 HSSYAHSQSLDRLMNPLIDQYLYYLSRTNTPSGTTTQSRLQFSQAGASDIRDQSRNWLPG
Sequence2 421 HSSYAHSQSLDRLMNPLIDQYLYYLSRTNTPSGTTTQSRLQFSQAGASDIRDQSRNWLPG
************************************************************
Russell SEQ4 481 PCYRQQRVSKTSADNNNSEYSWTGATKYHLNGRDSLVNPGPAMASHKDDEEKFFPQSGVL
Sequence2 481 PCYRQQRVSKTSADNNNSEYSWTGATKYHLNGRDSLVNPGPAMASHKDDEEKFFPQSGVL
************************************************************
Russell SEQ4 541 IFGKQGSEKTNVDIEKVMITDEEEIRTTNPVATEQYGSVSTNLQRGNRQAATADVNTQGV
Sequence2 541 IFGKQGSEKTNVDIEKVMITDEEEIRTTNPVATEQYGSVSTNLQRGNRQAATADVNTQGV
************************************************************
Russell SEQ4 601 LPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPSTT
Sequence2 601 LPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPSTT
************************************************************
Russell SEQ4 661 FSAAKFASFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYNKSVNVDFTVDTNGVY
Sequence2 661 FSAAKFASFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYNKSVNVDFTVDTNGVY
************************************************************
Russell SEQ4 721 SEPRPIGTRYLTRNL
Sequence2 721 SEPRPIGTRYLTRNL
***************
It would have been prima facie obvious to one of ordinary skill in the art at the time of filing in making a modified AAV VP1 capsid protein to use the insertion site taught by Schultz et al. starting immediately after position 165 in the AAV2 VP1 capsid protein as taught by Johnson. One of ordinary skill in the art with the goal of selecting a specific AAV2 VP1 capsid protein would be motivated to use the protein taught by Russell as “the capsid protein VP1 for AAV2” (col. 5, 2nd para.; FIG. 2) as a canonical VP1 sequence known in the art since the 1990s.
Therefore, the claimed invention as a whole is prima facie obvious to one of ordinary skill in the art before the earliest effective time of filing.
Claims 1, 7, 9, and 16 are rejected under 35 U.S.C. 103 as being unpatentable over Grieger2 (Grieger et al., Journal of Virology, vol. 81, no. 15, pg. 5199-210 (2007)) in view of Russell (US Pat. 6,156,303).
The claims are interpreted as provided in a previous section.
Regarding claim 1, Grieger2 teaches an AAV2 VP1, VP and VP3 capsid protein construct comprising an NLS insert (RKRLN) (pg. 7836, right col.; Fig. 2A) from an AAV2 serotype VP2 capsid protein and which is functional in forming AAV2 virions (Fig 5; Fig. 2B and 4). Grieger2 teaches the important of surface exposing a VP1 capsid NLS during virion assembly for achieving more optimal levels of AAV2 infectivity (pg. 7842).
Grieger2 does not expressly teach the VP1 capsid protein is derived from SEQ ID NO: 122.
However Russell teaches an AAV2 VP1 capsid protein (SEQ ID NO: 4) consisting of instant SEQ ID NO: 122 as shown below.
100.0% identity in 735 residues overlap; Score: 3994.0; Gap frequency: 0.0%
SEQ ID 122 1 MAADGYLPDWLEDTLSEGIRQWWKLKPGPPPPKPAERHKDDSRGLVLPGYKYLGPFNGLD
SEQ ID 4 1 MAADGYLPDWLEDTLSEGIRQWWKLKPGPPPPKPAERHKDDSRGLVLPGYKYLGPFNGLD
************************************************************
SEQ ID 122 61 KGEPVNEADAAALEHDKAYDRQLDSGDNPYLKYNHADAEFQERLKEDTSFGGNLGRAVFQ
SEQ ID 4 61 KGEPVNEADAAALEHDKAYDRQLDSGDNPYLKYNHADAEFQERLKEDTSFGGNLGRAVFQ
************************************************************
SEQ ID 122 121 AKKRVLEPLGLVEEPVKTAPGKKRPVEHSPVEPDSSSGTGKAGQQPARKRLNFGQTGDAD
SEQ ID 4 121 AKKRVLEPLGLVEEPVKTAPGKKRPVEHSPVEPDSSSGTGKAGQQPARKRLNFGQTGDAD
************************************************************
SEQ ID 122 181 SVPDPQPLGQPPAAPSGLGTNTMATGSGAPMADNNEGADGVGNSSGNWHCDSTWMGDRVI
SEQ ID 4 181 SVPDPQPLGQPPAAPSGLGTNTMATGSGAPMADNNEGADGVGNSSGNWHCDSTWMGDRVI
************************************************************
SEQ ID 122 241 TTSTRTWALPTYNNHLYKQISSQSGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLI
SEQ ID 4 241 TTSTRTWALPTYNNHLYKQISSQSGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLI
************************************************************
SEQ ID 122 301 NNNWGFRPKRLNFKLFNIQVKEVTQNDGTTTIANNLTSTVQVFTDSEYQLPYVLGSAHQG
SEQ ID 4 301 NNNWGFRPKRLNFKLFNIQVKEVTQNDGTTTIANNLTSTVQVFTDSEYQLPYVLGSAHQG
************************************************************
SEQ ID 122 361 CLPPFPADVFMVPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEDVPF
SEQ ID 4 361 CLPPFPADVFMVPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEDVPF
************************************************************
SEQ ID 122 421 HSSYAHSQSLDRLMNPLIDQYLYYLSRTNTPSGTTTQSRLQFSQAGASDIRDQSRNWLPG
SEQ ID 4 421 HSSYAHSQSLDRLMNPLIDQYLYYLSRTNTPSGTTTQSRLQFSQAGASDIRDQSRNWLPG
************************************************************
SEQ ID 122 481 PCYRQQRVSKTSADNNNSEYSWTGATKYHLNGRDSLVNPGPAMASHKDDEEKFFPQSGVL
SEQ ID 4 481 PCYRQQRVSKTSADNNNSEYSWTGATKYHLNGRDSLVNPGPAMASHKDDEEKFFPQSGVL
************************************************************
SEQ ID 122 541 IFGKQGSEKTNVDIEKVMITDEEEIRTTNPVATEQYGSVSTNLQRGNRQAATADVNTQGV
SEQ ID 4 541 IFGKQGSEKTNVDIEKVMITDEEEIRTTNPVATEQYGSVSTNLQRGNRQAATADVNTQGV
************************************************************
SEQ ID 122 601 LPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPSTT
SEQ ID 4 601 LPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPSTT
************************************************************
SEQ ID 122 661 FSAAKFASFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYNKSVNVDFTVDTNGVY
SEQ ID 4 661 FSAAKFASFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYNKSVNVDFTVDTNGVY
************************************************************
SEQ ID 122 721 SEPRPIGTRYLTRNL
SEQ ID 4 721 SEPRPIGTRYLTRNL
***************
It would have been prima facie obvious to one of ordinary skill in the art at the time of filing in making a AAV2 VP1 capsid protein construct taught by Grieger2 to use the AAV2 VP1 capsid protein sequence taught by Russell. One of ordinary skill in the art with the goal of selecting a specific AAV2 VP1 capsid protein would be motivated to use the protein taught by Russell as “the capsid protein VP1 for AAV2” (col. 5, 2nd para.; FIG. 2) as a canonical VP1 sequence known in the art since the 1990s.
Regarding claim 7, Grieger2 teaches wherein said NLS comprises an AAV nuclear localization sequence from an AAV having the same AAV serotype (AAV2) (pg. 7836, right col.).
Regarding claim 9, Grieger2 teaches wherein the NLS peptide insert has a length of 5 amino acid residues (RKRLN) (id.).
Regarding claim 16, Grieger2 teaches the importance to virion function of maintaining the phospholipase A2 (PLA2) domain activity and does not insert anything into this domain (pg. 7835, left col., 2nd para.; Fig. 4; Fig. 2A).
Therefore, the claimed invention as a whole is prima facie obvious to one of ordinary skill in the art before the earliest effective time of filing.
Claims 1, 7, 9-11, and 16-17 are rejected under 35 U.S.C. 103 as being unpatentable over Grieger2 in view of Russell (US Pat. 6,156,303) as applied above, and further in view of Wu (Wu et al., J Virol 2000 Sep;74: pg. 8635-47).
Regarding claims 10-11, the combination of Grieger2 and Russell does not teach wherein the NLS insertion is at a position within 1-52 or between basic region 1 (BR1) and basic region 2 (BR2) of an AAV VP1, VP2 or VP3 capsid protein.
However Wu teaches AAV2 capsid proteins can tolerate insertions at various positions and still provide functional infectivity, such as a 9 amino acid insertion at position 1, 34, 138, 266, or 447 in surface exposed regions of the capsid (Table 5, L1, L3, VPN1, VP1, and VPN2; Table 1; pg. 8638, left col., 2nd para.; pg. 8640, right col., last para., to pg. 8642, left col., 1st para.; Fig. 6-7).
It would have been prima facie obvious to one of ordinary skill in the art at the time of filing in making a AAV2 VP1 capsid protein construct taught by Grieger2 to select an NLS insertion position taught by Wu. One of ordinary skill in the art with the goal of making a functional virion with the modified AAV2 VP1 capsid protein would be motivated to select a surface exposed position for the NLS as taught by Grieger2 and further a surface exposed region tolerating a peptide insertion as taught by Wu as providing infectivity (e.g., position 1 or 34 Table 5). Furthermore, one of ordinary skill in the art with the goal of making a functional virion with the modified AAV2 VP1 capsid protein would be motivated to select the surface exposed position 34 or 138 taught by Wu as providing greater infectivity than other positions tested. Position 138 taught by Wu is between BR1 (QAKKRVL) and BR2 (PGKKRPV) as taught by Johnson (Fig. 1B) and shown above using Russell (SEQ ID NO: 4).
Regarding claim 17, Wu teaches loop IV spans from around 447-591 and showed a 9 amino acid insertion in this loop at position 447 was tolerated by retaining partial functionality provided reduced infectivity (L3 class 2a, Fig. 1; Table 1; pg. 8638, left col., 2nd para.) pg. 8640, right col., last para., to pg. 8641, ).
Therefore, the claimed invention as a whole is prima facie obvious to one of ordinary skill in the art before the earliest effective time of filing.
Response to Arguments
Applicant traverses the previous obviousness rejections by arguing that none of High, Hoque, Grieger and Hallbrink, alone or in combination, teaches a modified capsid protein comprising a nuclear localization sequence inserted in one or more of AAV VP1, VP2 or VP3 capsid proteins of Spk200, Spk100, or AAV2 having amino acid sequences of SEQ ID NOs: 1, 59, and 122, respectively. However the scope of the amended claim 1 regarding the “VP1, VP2 or VP3” parental capsid proteins is considered unclear as noted in the 112(b) rejection and, thus, interpreted without limitation beyond being respectively an AAV VP1, VP2, or VP3 capsid protein of any kind. Thus applicant's claim amendments necessitated the new grounds of obviousness rejection presented above. As set forth above, even if limited to wherein the claimed protein has high sequence identity to instant SEQ ID NO: 122, the prior art made of record does teach such modified capsid proteins as recited in amended claims 1, 6-7, 9-12, 16-18, and 34. Also, there would be a reasonable expectation of successfully inserting a NLS into such AAV capsid proteins and retaining, at least partially, an activity of such a parental protein such as AAV capsid assembly, e.g., in light of Schultz (transduction and infectivity), Grieger2 (infectivity), and/or Wu (infectivity).
As nowhere do the claims require any “increase in the transduction” efficiency (e.g., of an AAV comprising the claimed protein), this function is considered irrelevant to patentability.
Conclusion
Claims 1, 6-7, 9-12, 16-18, 24, and 34 stand rejected.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ERIC J ROGERS whose telephone number is (571)272-8338. The examiner can normally be reached Monday - Friday 9:00-6:00.
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/ERIC J ROGERS/Examiner, Art Unit 1638
/Tracy Vivlemore/Supervisory Primary Examiner, Art Unit 1638
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