DETAILED ACTION
Election/Restrictions
Applicants failed to elect a Group in the reply filed on 9/11/25. Additionally, 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)). Applicants responded:
“In response to the Examiner's correspondence dated September 11, 2025, pursuant to the Examiner's restriction requirement in the above-referenced patent application, Applicant provisionally elects to prosecute an invention which is presented in amended claims 40-49. These claims are directed to MS2 VLPs which display an immunogenic peptide pursuant to SEQ ID NO:60.”
However, the Restriction Requirement contained three Groups. The methods of claims 45-49 were in Groups II and III. The elected product in Group I.
Applicant failed to address the Restriction Requirement with respect to the prior art cited or to the methods being in separate Groups.
Upon consideration of the new claims, the Examiner is withdrawing the prior Restriction Requirement mailed on 9/11/25 and the methods are being rejoined with the elected product.
Accordingly, in view of the withdrawal of the restriction requirement, applicant(s) are advised that if any claim presented in a divisional application is anticipated by, or includes all the limitations of, a claim that is allowable in the present application, such claim may be subject to provisional statutory and/or nonstatutory double patenting rejections over the claims of the instant application. Once the restriction requirement is withdrawn, the provisions of 35 U.S.C. 121 are no longer applicable. See In re Ziegler, 443 F.2d 1211, 1215, 170 USPQ 129, 131-32 (CCPA 1971). See also MPEP § 804.01.
Claim Objections
Claim 46 is objected to because of the following informalities:
Claim 46 recites a “Ct infection.” The first time an abbreviation appears in the claims, it should be spelled out, followed by the abbreviation.
Appropriate correction is required.
Claim Rejections - 35 USC § 112-Scope of Enablement
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 46 and 48 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for:
methods of inducing an immunogenic response in a patient and methods for treating or reducing the likelihood of C. trachomatis (Cf) infection- comprising administering a composition comprising: (a) a virus-like particle (VLP) comprising a population of MS?2 bacteriophage single chain dimer coat polypeptide units comprising upstream and downstream units and a peptide display site at the AB loop of said polypeptide unit, wherein said display site has been modified by insertion of (b) an immunogenic peptide according to SEQ ID NO: 60 into said VLP at said AB loop; and wherein said immunogenic peptide is displayed on said virus-like particle,
does not reasonably provide enablement for:
methods for prevention of a Ct infection, e.g., wherein the composition in the method is prophylactic (claim 46) or methods for inhibiting Ct infection or morbidity of a patient (claim 48).
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.
Vaccines induce protection against infections by stimulating the development of long-lived effector cells and memory cells (Abbas et al. Cellular and Molecular Immunology 4th edition chapter 15 p. 360-362, 2000). Vaccines by definition trigger an immunoprotective response in the host vaccinated and mere antigenic response i.e. immunogenicity is insufficient. It is well recognized in the vaccine art, that it is unclear whether an antigen(s) derived from a pathogen will elicit protective immunity. Ellis, R.W. (Chapter 29 of "VACCINES" [PIotkin, S.A. et al. (eds) published by W. B. Saunders company (Philadelphia) in 1988, especially page 571, 2nd full paragraph] exemplifies this problem in the recitation that "The key to the problem (of vaccine development) is the identification of that protein component of a virus or microbial pathogen that itself can elicit the production of protective antibodies ....and thus protect the host against attack by the pathogen".
Further, with respect to C. trachomatis vaccines in particular, despite C. trachomatis infection being the most prevalent bacterial sexually transmitted infection and can lead to pelvic inflammatory disease and infertility in women. “There is no licensed vaccine for C. trachomatis prevention, in part due to gaps in our knowledge of C. trachomatis-specific immune responses elicited during human infections. Previous investigations of the antibody response to C. trachomatis have identified immunodominant antigens and antibodies that can neutralize infection in cell culture. However, epitope-specific responses to C. trachomatis are not well characterized, and the impact of these antibodies on infection outcome is unknown.” See the abstract of Collar et al. (Msphere. September 2020. Vol. 5 (5):1-12).
Collar further recites (abstract):
Our finding that women produce antibodies to the VD4-MOMP regardless of infection outcome provides insight into vaccine development, suggesting that vaccines targeting VD4-MOMP may need to elicit higher-titer antibody responses than natural infection imparts or that additional vaccine targets should be pursued in the future.
The prior art, as cited in Collar and the Murdin et al and Toru et al references cited in the prior art rejections below, teach that the peptide of SEQ ID NO: 60 is an immunodominant epitope of MOMP; however, immunogenicity does not predict a protective immune response. There are no working examples in the instant specification to guide the skilled artisan in practicing the claimed method. There are no other examples of delivery of any other therapeutic agent present in the specification. Genentech Inc. v. Novo Nordisk A/S (CAFC) 42 USPQ2d 1001 clearly states: “Patent protection is granted in return for an enabling disclosure of an invention, not for vague intimations of general ideas that may or may not be workable. See Brenner v. Manson, 383 U.S. 519, 536, 148 USPQ 689, 696 (1966) (stating, in context of the utility requirement, that "a patent is not a hunting license. It is not a reward for the search, but compensation for its successful conclusion.") Tossing out the mere germ of an idea does not constitute enabling disclosure. While every aspect of a generic claim certainly need not have been carried out by an inventor, or exemplified in the specification, reasonable detail must be provided in order to enable members of the public to understand and carry out the invention.”
There are no results for immunization experiments or challenge experiments with the composition recited in the instant claims.
Given the inherent unpredictability of preventive vaccines for C. trachomatis combined with, it would take one skilled in the art undue experimentation to make and/or use the invention.
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.
Claim(s) 40-43 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Collar et al (Msphere. September 2020. Vol. 5 (5):1-12).
Collar et al teaches a C. trachomatis peptide consisting of SEQ ID NO: 60. See page 6, Figure 3, B) 1). Collar describes a bacteriophage MS2 virus-like particle (VLP) displaying 6 to 10 amino acids from Chlamydia trachomatis (Ct), wherein the C. trachomatis antigens comprise major outer membrane protein (MOMP VD4) comprising epitopes, e.g., TTLNPTIAG, corresponds to Applicants’ SEQ ID NO: 60 (page 6, Figure 3, B) 1). Collar teaches that the MS2 bacteriophage VLP display platform displays short peptides in a constrained β-Hairpin loop on the surface of the VLPs, likely providing the scaffolding necessary for antibodies to bind to these short peptides. See page 9 and page 10 “Materials and Methods.” The β-Hairpin loop refers to a specific protein structural motif, often located on the VLP's surface (like the AB loop in MS2 VLPs). Collar teaches that this is a promising new direction in C. trachomatis vaccine development. The terms “pharmaceutical composition” (claim 42) and “vaccine” (claim 43) are intended uses only. A recitation of the intended use of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. If the prior art structure is capable of performing the intended use, then it meets the claim. A “physiologically acceptable carrier or excipient” reads on water and therefore would be inherent in the preparation of the modified bacteriophage.
Claim Rejections - 35 USC § 103
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.
Claim(s) 44, 45, 47 and 49 is/are rejected under 35 U.S.C. 103 as being unpatentable over Collar et al (Msphere. September 2020. Vol. 5 (5):1-12), Murdin et al (WO9426900-A2. 11/24/94) and Matsuoka Toru et al (JP09031097; 2/4/1997).
Collar et al teaches a C. trachomatis peptide consisting of SEQ ID NO: 60. See page 6, Figure 3, B) 1). Collar describes a bacteriophage MS2 virus-like particle (VLP) displaying 6 to 10 amino acids from Chlamydia trachomatis (Ct), wherein the C. trachomatis antigens comprise major outer membrane protein (MOMP VD4) comprising epitopes, e.g., TTLNPTIAG, corresponds to Applicants’ SEQ ID NO: 60). Collar teaches that the MS2 bacteriophage VLP display platform displays short peptides in a constrained β-Hairpin loop on the surface of the VLPs, likely providing the scaffolding necessary for antibodies to bind to these short peptides. See page 9 and page 10 “Materials and Methods.” The β-Hairpin loop refers to a specific protein structural motif, often located on the VLP's surface (like the AB loop in MS2 VLPs. Collar teaches that this is a promising new direction in C. trachomatis vaccine development.
However, Collar et al does not particularly exemplify the use of an adjuvant in the compositions or a method to treat or reduce the likelikhood of a Chlamydia trachomatis infection is a subject or methods for enhancing an immune response to a peptide.
Murdin et al (WO9426900-A2. 11/24/94) teaches a peptide which is 100% identical to Applicants’ SEQ ID NO: 60, e.g., 9 out of 10 amino acids of Murdin’s peptide is identical to Applicants’ SEQ ID NO: 60. Murdin’s peptide is a single amino acid longer. Murdin et al teaches this epitope as a promising candidate antigen for the development of an immunogenic composition useful as a vaccine is the chlamydial major outer membrane protein (MOMP) (refs. 6, 34). The MOMP, which is the predominant surface protein, is an integral membrane protein with a mass of about 40kDa. which, with the exception of four variable domains (VDs) designated I, II, III, and IV, is highly conserved amongst serovars. Antibodies capable of neutralizing chlamydial infectivity recognize the MOMP (refs. 21, 31, 33, 34, 42, 43). Epitopes to which MOMP-specific neutralizing monoclonal antibodies bind have been mapped for serovars A, B and C (refs. 3, 8, 32, 42, 43), and may represent appropriate targets for the development of synthetic or subunit vaccines. The binding sites are contiguous sequences of six to eight amino acids located within VDs I or II, and IV, depending on the serovar. Subunit immunogens (e.g. isolated MOMP or synthetic peptides) expressing MOMP epitopes can induce antibodies capable of recognizing intact chlamydia (refs. 9, 33). the present invention, at least one chlamydial epitope is contained within a hybrid BC loop sequence of poliovirus capsid protein VP1 or other hybrid loop sequence of a poliovirus capsid protein, in particular a BC loop sequence extended by the chlamydial epitope, which may be a serovar-specific epitope. Murdin teaches the use of an adjuvant. See claim 57. The immunogenic composition comprises an immunoeffective amount of a hybrid of the peptide and the VP1. Such immunogenic composition may be formulated for mucosal or parenteral administration. Such immunogenic composition may comprise at least one other immunogenic or immunostimulating material, such as an adjuvant, which may be aluminum phosphate or aluminum hydroxide. Such immunogenic composition may be formulated as a vaccine for human administration wherein the hybrid picomavirus is attenuated or inactivated, or the isolated DNA molecule codes for an attenuated hybrid picomavirus. In an additional aspect, the present invention provides a method of immunizing a host, which may be a human, which comprises administering to' the host, the immunogenic composition provided herein. In the case of administration to a human host, the hybrid picomavirus is attenuated or inactivated, or the DNA codes for an attenuated strain of the hybrid picomavirus. Hybrid polio viruses express epitopes (given in AAR66356-63) from the major outer membrane protein of C. trachomatis ser. D and induce an immune response against both polio virus and C. trachomatis. The chlamydial epitope may be a serovar-specific epitope (AAR66356-59) of variable domain I (VDI) contained within a hybrid BC loop (AAR66364-65) of polio virus capsid protein VP1, or a species-specific epitope.
Matsuoka Toru et al (JP09031097; 2/4/1997) Chlamydia trachomatis L2 major outer membrane protein (aa 540-548 which is 100% identical to Applicants’ SEQ ID NO: 60) derived from the variable region IV of the C. trachomatis major outer membrane protein. Paragraph [0006] teaches that the present inventors have conducted extensive research aimed at developing a polypeptide useful in diagnosing Chlamydia trachomatis infection and a diagnostic method using said polypeptide. As a result, they have discovered that an antigenic determinant (hereinafter sometimes referred to as an "epitope") that specifically reacts with specimens from patients infected with Chlamydia trachomatis is located in the variable region IV of the major outer membrane protein (MOMP).
Accordingly, the prior art teaches that the peptide set forth in Applicant’s SEQ ID NO: 60 was a well-known and important epitope of MOMP and had been suggested in the prior art to be used in pharmaceutical compositions, as well as in diagnostics. It would have been prima facie obvious to one of ordinary skill in the art to use the compositions taught by Collar et al in a method to treat a Ct infection or raise an immune response as Murdin teaches a peptide epitope comprising SEQ ID NO: 60 teaches this epitope as a promising candidate. Additionally, the use of MS2 bacteriophage VLP to display antigens at the AB loop was known in the prior art as
Claim(s) 40-44, 45, 47 and 49 is/are rejected under 35 U.S.C. 103 as being unpatentable over Murdin et al (WO9426900-A2. 11/24/94) and Matsuoka Toru et al (JP09031097; 2/4/1997) in view of Peabody et al (J. Mol. Biol. Jun 2008. 380(1): 252-263).
Murdin et al (WO9426900-A2. 11/24/94) teaches a peptide which is 100% identical to Applicants’ SEQ ID NO: 60, e.g., 9 out of 10 amino acids of Murdin’s peptide is identical to Applicants’ SEQ ID NO: 60. Murdin’s peptide is a single amino acid longer. Murdin et al teaches this epitope as a promising candidate antigen for the development of an immunogenic composition useful as a vaccine is the chlamydial major outer membrane protein (MOMP) (refs. 6, 34). The MOMP, which is the predominant surface protein, is an integral membrane protein with a mass of about 40kDa. which, with the exception of four variable domains (VDs) designated I, II, III, and IV, is highly conserved amongst serovars. Antibodies capable of neutralizing chlamydial infectivity recognize the MOMP (refs. 21, 31, 33, 34, 42, 43) . Epitopes to which MOMP-specific neutralizing monoclonal antibodies bind have been mapped for serovars A, B and C (refs. 3, 8, 32, 42, 43), and may represent appropriate targets for the development of synthetic or subunit vaccines. The binding sites are contiguous sequences of six to eight amino acids located within VDs I or II, and IV, depending on the serovar. Subunit immunogens (e.g. isolated MOMP or synthetic peptides) expressing MOMP epitopes can induce antibodies capable of recognizing intact chlamydia (refs. 9, 33). the present invention, at least one chlamydial epitope is contained within a hybrid BC loop sequence of poliovirus capsid protein VP1 or other hybrid loop sequence of a poliovirus capsid protein, in particular a BC loop sequence extended by the chlamydial epitope, which may be a serovar-specific epitope. Murdin teaches the use of an adjuvant. See claim 57. The immunogenic composition comprises an immunoeffective amount of a hybrid of the peptide and the VP1. Such immunogenic composition may be formulated for mucosal or parenteral administration. Such immunogenic composition may comprise at least one other immunogenic or immunostimulating material, such as an adjuvant, which may be aluminum phosphate or aluminum hydroxide. Such immunogenic composition may be formulated as a vaccine for human administration wherein the hybrid picomavirus is attenuated or inactivated, or the isolated DNA molecule codes for an attenuated hybrid picomavirus. In an additional aspect, the present invention provides a method of immunizing a host, which may be a human, which comprises administering to' the host, the immunogenic composition provided herein. In the case of administration to a human host, the hybrid picomavirus is attenuated or inactivated, or the DNA codes for an attenuated strain of the hybrid picomavirus. Hybrid polio viruses express epitopes (given in AAR66356-63) from the major outer membrane protein of C. trachomatis ser. D and induce an immune response against both polio virus and C. trachomatis. The chlamydial epitope may be a serovar-specific epitope (AAR66356-59) of variable domain I (VDI) contained within a hybrid BC loop (AAR66364-65) of polio virus capsid protein VP1, or a species-specific epitope.
Matsuoka Toru et al (JP09031097; 2/4/1997) Chlamydia trachomatis L2 major outer membrane protein (aa 540-548 which is 100% identical to Applicants’ SEQ ID NO: 60) derived from the variable region IV of the C. trachomatis major outer membrane protein. Paragraph [0006] teaches that the present inventors have conducted extensive research aimed at developing a polypeptide useful in diagnosing Chlamydia trachomatis infection and a diagnostic method using said polypeptide. As a result, they have discovered that an antigenic determinant (hereinafter sometimes referred to as an "epitope") that specifically reacts with specimens from patients infected with Chlamydia trachomatis is located in the variable region IV of the major outer membrane protein (MOMP).
Accordingly, the prior art teaches that the peptide set forth in Applicant’s SEQ ID NO: 60 was a well-known and important epitope of MOMP and had been suggested in by Murdin to be used in pharmaceutical compositions, as well as in diagnostics. It would have been prima facie obvious to one of ordinary skill in the art to use the peptide epitope taught by Murdin and Toru in a method to treat a Ct infection or raise an immune response as Murdin teaches a peptide epitope comprising SEQ ID NO: 60 teaches this epitope as a promising candidate.
However, the use of MS2 bacteriophage VLP to display the epitope at the AB loop was not particularly exemplified by Murdin or Toru.
Peabody et al describes a platform for vaccine development based on the VLPs of RNA bacteriophage MS2. It serves for the engineered display of specific peptide sequences, using the AB loop display. Peptides were inserted into a surface loop of MS2 coat protein. The resulting VLPs displayed the V3 and ECL2 peptides on their surfaces where they showed the potent immunogenicity that is the hallmark of VLP-displayed antigens. Experiments with random-sequence peptide libraries show the single-chain dimer to be highly tolerant of six, eight and ten amino acid insertions. MS2 VLPs support the display of a wide diversity of peptides in a highly immunogenic format, and they encapsidate the mRNAs that direct their synthesis, thus establishing the genotype/phenotype linkage necessary for recovery of affinity-selected sequences. The single-chain MS2 VLP therefore unites in a single structural platform the selective power of phage display with the high immunogenicity of VLPs. See Abstract. Peabody teaches that VLPs of the RNA bacteriophage MS2 offer a number of advantages for peptide display. The icosahedral shell can assemble spontaneously from a single coat protein expressed from a plasmid in Escherichia coli. It is highly amenable to genetic manipulation, it is easily purified in large amounts, and the existence of detailed structural information facilitates genetic engineering. Moreover, it is a normal function of coat protein to encapsidate its own mRNA, which can be extracted from the assembled particle and amplified by reverse transcription and PCR. The so-called AB-loop of coat protein is a logical site for peptide display, because it protrudes prominently from the VLP surface. In summary, Peabody show that the single-chain dimer tolerates the insertion of a wide variety of peptides, that they are highly immunogenic when presented in the MS2 VLP format, and that the VLPs efficiently package the RNAs that direct their synthesis. See page 253, column 1.
Given that Peabody et al teaches that VLP MS2 bacteriophages with single chain dimer coat polypeptide are a great way to display peptide epitopes from 6-10 amino acids in length, e.g., SEQ ID NO: 60 is 9 amino acids in length. The so-called AB-loop of coat protein is a logical site for peptide display, because it protrudes prominently from the VLP surface. Peabody teaches that the single-chain dimer tolerates the insertion of a wide variety of peptides, that they are highly immunogenic when presented in the MS2 VLP format, and that the VLPs efficiently package the RNAs that direct their synthesis. Accordingly, it would have been prima facie obvious to one of ordinary skill in the art to use the peptide epitope in a VLP MS2 single chain dimer coat polypeptide, inserted at the AB loop, because Peabody teaches the VLPs are highly amenable to genetic manipulation, easily purified in large amounts, and the existence of detailed structural information facilitates genetic engineering. Peabody teaches the insertion of a wide variety of peptides, that they are highly immunogenic when presented in the MS2 VLP format.
Pertinent art, not presently relied upon:
Fu et al (Virus Res. 2015 Sep 28; 211:9–16)
A novel delivery platform based on Bacteriophage MS2 virus-like particles
Our objective here is to review the novel delivery platform based on Bacteriophage MS2 virus-like particles (VLPs), including introduction to their structure, their potential as a delivery platform, and their expected use in medicine and other fields. Bacteriophage MS2 VLPs are nanoparticles devoid of viral genetic material and can self-assemble from the coat protein into an icosahedral capsid. As a novel delivery platform, they possess numerous features that make them suitable and attractive for targeted delivery of RNAs or DNAs, epitope peptides, and drugs within the protein capsid. In short, as a novel delivery platform, MS2 VLPs are suitable for delivery of targeted agents and hold promise for use in diagnostics, vaccines, and therapeutic modalities.
Mastico et al (WO 92/13081; 8/6/92).
Mastico et al teach a protein, suitable for incorporation in a vaccine and capable of forming parts of a capsid assembly, comprises the amino acid sequence of the coat protein of phage MS-2, or a conservatively modified variant thereof, or sufficient of said sequence or variant to retain capsid-forming capability, which amino acid sequence has been modified by insertion of a foreign epitope in the region corresponding to a protuberant protein hairpin in the capsid assembly as shown in the crystal structure of the intact phage.
From the Claims section:
Claim 1: a chimeric MS2 (or related RNA phage) coat protein “modified by insertion of a foreign epitope…” at the N-terminal protruberant β-hairpin.
Claim 4: the MS2 coat protein with the insert specifically in the region of “glycine 14 and threonine 15.”
Claim 5: “Capsids assembled” from those chimeric proteins (i.e., VLPs/assembled capsids).
Claim 7: method steps: create a unique restriction site in the hairpin-coding region, insert oligos encoding the epitope, subclone into expression vector, express in host.
The spec teaches creating a restriction site at the codons for Gly14/Thr15, and says “Suitably a KpnI recognition site is created.”
It also notes the insertion ends up flanked by Gly/Thr (due to the KpnI site design), which they argue helps flexibility/presentation.
Concrete peptide-insertion examples (with sequences)
All of these are inserted at the KpnI site placed at Gly14/Thr15 (the AB-loop hairpin site described above):
Influenza HA epitope (9-mer)
Inserted peptide: YPYDVPDYA (HA tag epitope).
They state the KpnI strategy adds extra codons, giving 11 codons total inserted in that construct.
Human IgE-related decapeptide
Inserted peptide (10-mer): FGFFGSGKTK.
With KpnI-derived extra codons, they report 12 amino acids total inserted.
HIV-1 gp120 V3 loop-derived insert
Inserted peptide (24-mer): NNTRKSIRIQRGPGRAFVTIGKIG.
With the KpnI-derived additions, they report 26 amino acids total inserted.
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Any inquiry concerning this communication or earlier communications from the examiner should be directed to Jennifer E. Graser whose telephone number is (571) 272-0858. The examiner can normally be reached on Monday-Friday from 8:00 AM-4 PM.
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/JENNIFER E GRASER/Primary Examiner, Art Unit 1645 1/12/26