DETAILED ACTION
Non-Final Rejection
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
2. Applicant’s election of Group I claims 1-4 in the reply filed on 10/24/2025 is acknowledged.
Applicant elected species (i) SEQ ID NO: 1, and (ii) Zika virus.
Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Status of Claims
3. Claims 1-4,6-10,12,14-19,21 and 25-27 are pending.
4. Claims 6-10,12,14-19,21 and 25-27 are withdrawn from consideration due to restriction/election.
5. Claims 1-4 are under examination.
Priority
6. This application is a National Stage application of PCT/US2021/038386, filed June 22, 2021, which claims priority to U.S. Provisional Application 63/042,173, filed June 22, 2020.
Information Disclosure Statement
7. The information disclosure statement (IDS) submitted on 03/27/2025 is in compliance with the provisions of 37 CFR 1.97 and is considered.
The IDS submitted on 12/21/2022 is objected for not being in compliance because the cited publications (1) 2010003273, (2) 2010040643, and (4) 2017252425 appears to be missing a digital number and are not searchable and therefore, is not in compliance as listed and is partially considered. Applicant is required to correct and resubmit the IDS dated 12/21/2022.
Claim Interpretation
8. The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art.
The instant claims 1 and 4 are interpreted to be directed to an engineered signal peptide comprising the amino acid sequence X1GAX2TSVGIVGLLLTTAMA (elected subgenus, SEQ ID NO: 1), wherein X1 is M or absent and X2 is A, I, L, M, F, H, V, P, G, Y, W, R, or K. The engineered signal peptide is interpreted to be directed to be in-ORF frame fused to the elected species Zika virus protein(s) (e.g. envelope, capsid) to increase the production of the protein(s) for applications as immunogens, VLPs or diagnostic proteins. The instant claims 2-3 are directed to substitute amino acid position X2 with amino acid W or K (claim 2) or amino acid W (claim 3).
Claim Rejections - 35 USC § 103
9. 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 (i.e., changing from AIA to pre-AIA ) 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 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
10. Claims 1-4 are rejected under 35 U.S.C. 103 as being unpatentable over Akahata et al 2017 (US20170252425A1, 09/07/2017), and further in view of Clements 2018 (WO2018022790A1, 02/01/2018), Petersen et al 2011 (Nat Methods 8, 785–786 (2011), Petsch et al 2017 (WO2017140905A1 published 08/24/2017), Zhang et al 2005 (J Gene Med, 2005 Mar;7(3):354-65), and Klatt et al 2012 (Microb Cell Fact. 2012 Jul 25; 11:97).
Claims 1-4: Akahata et al 2017 (US20170252425A1, 09/07/2017, see entire prior art) is in the art and is directed to a Zika virus like particle (Zika VLPs) comprising one or more zika virus structural proteins including envelope protein, wherein the envelope protein of the zika virus structural protein contains at least one alteration in the amino acid sequence (See, abstract, claim 1). Akahata et al 2017 (US20170252425A1) teaches SEQ ID NO: 10 (Db) that has 98.8% identity match with instant claims 1-4 signal peptide amino acid sequence and has only one amino acid mismatch at position +4 represented by X2 in the instant SEQ ID NO: 1. Akahata et al 2017 teaches amino acid “M”at position 1 (See US20170252425A1, para [0026]-[0027]). Akahata et al 2017 (US20170252425A1) teaches SEQ ID NOs: 1, 3, 5, 7 that has signal peptide of SEQ ID NO: 10 fused in ORF frame to the Zika virus envelope protein (E) used for transfection to produce secreted Zika virus envelope the protein of VLPs (See US20170252425A1, para [0027]-[0036]-[0038], [0073]-[0074]). Mammalian cells (e.g. CHO cells, human embryonic kidney (HEK) 293F cells) are used for transfection to produce the VLPs or the proteins (See US20170252425A1, para [0061], [0073], [0075]).
Query Match 98.8%; Score 82; DB 1; Length 19;
Best Local Similarity 94.7%;
Matches 18; Conservative 0; Mismatches 1; Indels 0; Gaps 0;
Qy 1 MGAX2TSVGIVGLLLTTAMA 19
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Db 1 MGAD TSVGIVGLLLTTAMA 19
X1= M at position 1, and X2 = A, I, L, M, F, H, V, P, G, Y, W, R, or K (instant claim 1), or X2 is W (instant claim 2) or K, or X2 is W (instant claim 3).
Akahata et al 2017 (US20170252425A1) does not teach the claimed alternative amino acid represented by X2 = A, I, L, M, F, H, V, P, G, Y, W, R, or K (instant claim 1), or X2 is W (instant claim 2) or K, or X2 is W (instant claim 3) at position 4 (X2) as claimed in instant claims 1-4.
Clements 2018 (WO2018022790A1, 02/01/2018) is directed to an expression vector comprising a DNA sequence encoding a Zika virus pre- membrane and envelope protein, wherein transient transfection of insect cell lines or generation of stable insect cell lines and expression of the DNA sequence in insect cell lines results in secretion of a soluble envelope protein in a culture medium (See, abstract, claims 1-7). Most proteins that are secreted from cells contain an N-terminal signal sequence that directs the protein into the cell's secretion pathway. Optimization of internal secretion signal or signal peptide sequence that interact with the endoplasmic membrane to initiate the secretion process has the potential to increase the efficiency of processing and hence and increase in protein expression. One report that describes the optimization of the IL-2 secretion signal clearly demonstrates the benefits of optimization (See, para [0015], [0019], [0044], [0056], [0073]- [0082], [0014] Figure 4). The expressed and purified product is suitable as a vaccine antigen. Clements 2018 teaches design of synthetic secretion signal for enhanced expression of flavivirus or zika virus E protein. A survey of flavivirus prM- E secretion signals was conducted. The putative secretion signals from prM and the E protein N-terminus were analyzed using the SignalP software program as described by Petersen et al (Nat. Methods, (2011) 8(10): 785-6), which predicts the strength of the secretion signal based on an established algorithm and also predicts the cleavage site of the sequence analyzed. (See, Example 2, and para [0073]-[0079]). See also MPEP 2144.05 II. Routine Optimization subsections A and B: and In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955)
Clements 2018 (WO2018022790A1) teaches an example of design and optimization of of synthetic secretion signal sequence for Zika virus using SignalP software program for enhanced expression and secretion in medium of of Zika virus envelope protein E (prM-80E) signal peptide optimized, and codon optimized for expression in the insect S2 cells (See, example 2, pages 17-18, para [0073]- [0079]). See, below (Clements 2018, WO2018022790A1, page 18). The score 0.703 on right side for sequence in para [0077] is an engineered or optimized synthetic signal peptide sequence that reasonably predicts the signal peptidase cleavage and secretion efficiency of the optimized signal peptide that is operatively linked to the Zika virus envelope protein E (prM-80E) in the insect cells. Similarly, the claimed signal peptide sequence (instant claims 1-4) is obvious to optimize for Zika virus E or C proteins in mammalian, human or insect cells for expression and secretion of the Zika virus E or C protein in medium.
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Petersen et al 2011 is in the art and teaches as SignalP software program that uses amino acid sequence as an input and perform analysis of the cleavage-site pattern in a selected species cell type for the signal peptides, and also discriminate signal peptides from transmembrane regions (See, Petersen et al 2011, abstract, entire article).
Petsch et al 2017 (WO2017140905A1 published 08/24/2017, see entire prior art) is directed to Zika virus envelope (E) protein, VLPs and polypeptides. Petsch et al 2017 teaches artificial nucleic acid comprising at least one coding region encoding at least one polypeptide comprising at least one protein selected from the group consisting of Zika virus capsid protein (C), Zika virus premembrane protein (pr ), Zika virus pr protein (pr), Zika virus membrane protein (M), Zika virus envelope protein (E) and a Zika virus non-structural protein, or a fragment or variant of any of these proteins (See, claim 1); the artificial nucleic acid according to claim 1 , wherein the at least one encoded polypeptide comprises Zika virus envelope protein (E), or a fragment or variant thereof (See, claim 2, dependent on claim 1). The artificial nucleic acid according to claim 21, wherein the at least one amino acid sequence derived from a signal sequence comprises an amino acid sequence that is recognized by signal peptide peptidase (SPP), by a viral protease and/or by furin or a furin-like protease (See, claim 22, dependent on claim 1). Petsch et al 2017 (WO2017140905A1) further teaches requirement for a signal peptide sequence (See, page 40 lines 32-35, page 41 lines 1-3). in claim 93 is directed to the polypeptide (according to any one of claims 89 to 92), wherein the amino acid sequence derived from a signal sequence of Zika virus capsid protein (C) comprises an amino acid sequence according to any one of SEQ ID NO: 343 to 345, or a fragment or variant of any of these sequences (See, claim 93). Zika virus vaccine and ZIKV constructs are translated and secreted in form of VLPs, Zika virus E protein, preferably in a mammalian cell, such as a human cells (See, page 245, lines 5-20; page 243 lines 4-11; See abstract, entire prior art).
Zhang et al 2005 is in the art of signal peptide optimization and teaches optimization and engineering or alteration in the IL-2 signal peptide affects secretion of proteins in vitro and in vivo (See, abstract, Table 1, 4, Fig 3, entire article).
Klatt et al 2012 is in the signal peptide optimization art and teaches improved antibody-fragment scFv expression and secretion by secretory signal peptide modification for optimized antibody-fragment scFv expression-secretion in Leishmania tarentolae. SignalP software program was used for in-silico optimization of the sequence prior to secretory expression of scFv (See, Figures 1-4, Table 1). Secretory signal peptides (SPs) are well-known sequence motifs targeting proteins for translocation across the endoplasmic reticulum membrane. After passing through the secretory pathway, most proteins are secreted to the environment. Here, we describe the modification of an expression vector containing the SP from secreted acid phosphatase 1 (SAP1) of Leishmania mexicana for optimized protein expression-secretion in the eukaryotic parasite Leishmania tarentolae with regard to recombinant antibody fragments. For experimental design the online tool SignalP was used, which predicts the presence and location of SPs and their cleavage sites in polypeptides. To evaluate the signal peptide cleavage site as well as changes of expression, SPs were N-terminally linked to single-chain Fragment variables (scFv's). The ability of L. tarentolae to express complex eukaryotic proteins with highly diverse post-translational modifications and its easy bacteria-like handling, makes the parasite a promising expression system for secretory proteins. Zhang et al 2005 demonstrated the importance of SP-sequence optimization for efficient expression-secretion of scFv's. We could successfully demonstrate that minor modifications in the AA-sequence in the c-region of the natural SP from SAP1, based on in-silico predictions following the (-3, -1) rule, resulted in different expression-secretion rates of the protein of interest. The yield of scFv production could be improved close to one order of magnitude. Therefore, SP-sequence optimization is a viable option to increase the overall yield of recombinant protein production (See, abstract, entire article).
The instant claims 1-4 has claimed an engineered signal peptide comprising alternative substitution amino acids at position +4 (X2) for the prior art wild type amino acid sequence Aspartic acid (Asp, D) at position +4 to arrive at the inventions of the instant claims 1-4.
It would have been obvious to one of the ordinary skills in the art before the effective filing date of the claimed invention to modify the prior art teachings of Akahata et al 2017 with additional teachings of Clements 2018 that provide a suggestion and express motivation to engineer and optimize the signal peptide sequence for improved secretion of Zika virus envelope protein as recited supra, Petsch et al 2017 (Zika virus E and C protein secretion signal sequence) and teachings of Petersen et al 2011 on SignalP software analysis of signal peptide sequence for optimal design, and generalized teachings of Zhang et al 2005, and Klatt et al 2012 on signal peptide optimization for improved secretory expression of proteins as recited supra. It would have been obvious to one of the ordinary skills to use limited known and available 19-20 amino acids (genetic code encodes a maximum 20 amino acids) for engineering and optimization of the claimed signal peptides to arrive at the inventions of claims 1-4. One of the ordinary skills would have been motivated to develop the claimed (claims 1-4) engineered signal peptide(s) comprising the claimed amino acid sequence for secretory expression of the Zika virus Envelope (E ) or Capsid proteins (C ) for increased secretory production of the proteins or the VLPs as taught by the applied prior arts as recited supra for commercial success. There would be a reasonable expectation of success given the applied prior art teachings in the art to render the claims 1-4 obvious as recited supra. This is analogous to some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed inventions of claims 1-4. See KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395-97 (2007) (see MPEP § 2143, example of rationales, A-G).
11. Relevant Prior Arts:
Ruhe Mein K, Michael B, Ching-Juh L. Carboxy-terminally truncated dengue virus envelope glycoproteins expressed on the cell surface and secreted extracellularly exhibit increased immunogencity in mice. J Virol 1991; 65:1400–7.
Chen P, Liu J, Jiang Y, Zhao Y, Li Q, Wu L, He X, Chen H. The vaccine efficacy of recombinant duck enteritis virus expressing secreted E with or without PrM proteins of duck tembusu virus. Vaccine. 2014 Sep 15;32(41):5271-7.
Inchauspe G, Vitvitski L, Major ME, Jung G, Spengler U, Maisonnas M, et al. (1997). Plasmid DNA expressing a secreted or a non-secreted form of hepatitis C virus nucleocapsid: comparative studies of antibody and T-helper responses following genetic immunization. DNA Cell Biol 1997; 16:185–95.
Chang 2012. (US8232379B2, 07/31/2012). Nucleic acid vaccines for prevention of flavivirus infection.
Tauber et al 2019. (US20190083601A1, 03/21/2019). Recombinant Zika vaccines.
Chang 2010. (US20100040643A1, 02/18/2010). Flavivirus immunogens and methods of use.
Conclusion
12. No claim is allowed.
13. Any inquiry concerning this communication or earlier communications from the examiner should be directed to SAMADHAN J JADHAO whose telephone number is (703)756-1223. The examiner can normally be reached M-F 8:00-5:00.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Thomas J Visone can be reached at 571-270-0684. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/SAMADHAN JAISING JADHAO/Examiner, Art Unit 1672
/BENNETT M CELSA/Primary Examiner, Art Unit 1600