DETAILED ACTION
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 . 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.
Election/Restrictions
Applicant’s election without traverse of SEQ ID 4 for invasive pneumococcal infection in the replies filed on 8 Oct, 2025 and 19 Dec, 2025 is acknowledged.
Applicants have elected SEQ ID 4 for invasive pneumococcal infection. A search was conducted for this invention, and a reference that anticipated it was found. As a result, claims 1, 4, 7, 10, 11, 17, 25, and 34 were examined and claims 5, 12-16, 19-22, 36, and 39 were withdrawn from consideration. Applicants state that they believe claims 36 and 39 read on their elected species, but the election of 19 Dec, 2025 explicitly stated the formulation comprised SEQ ID 4, not particles comprising that sequence. Thus, these claims are properly withdrawn.
Claims Status
Claims 1, 4, 5, 7, 10, 11-17, 19-22, 25, 34, 36, and 39 are pending.
Claims 5, 12-16, 19-22, 36, and 39 have been withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the replies filed on 8 Oct, 2025 and 19 Dec, 2025.
Drawings
The drawings are objected to because fig 2 requires color. The brief description of the drawings describes this figure using color, but the drawings are in greyscale. Applicants are required to replace the figure by a figure that is interpretable in greyscale (and the brief description of the drawings appropriately modified) or deleted. If applicants are unable to show what they need to demonstrate without color drawings, they can petition to allow color. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
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 1, 4, 10, 11, 17, 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 MPEP lists factors that can be used to determine if sufficient evidence of possession has been furnished in the disclosure of the application. These include "level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention. Disclosure of any combination of such identifying characteristics that distinguish the claimed invention from other materials and would lead one of skill in the art to the conclusion that the applicant was in possession of the claimed species is sufficient" (MPEP 2163).
A claimed genus may be satisfied through sufficient description of a representative number of species or disclosure of relevant, identifying characteristics such as functional characteristics coupled with a known or disclosed correlation between function and structure(MPEP 2163(3)a(II)). The number of species that describe the genus must be adequate to describe the entire genus; if there is substantial variability, a large number of species must be described.
The analysis for adequate written description considers (a) actual reduction to practice, (b) disclosure of drawings or structural chemical formulas, (c) sufficient relevant identifying characteristics in the way of complete/partial structure or physical and/or chemical properties or functional characteristics when coupled with known or disclosed correlation with structure and (d) representative number of samples.
The issue is what variants of SEQ ID 1 will still provide a meaningful effect.
(a and b) actual reduction to practice and disclosure of drawings or structural chemical formulas: Applicants have described 13 amino acid fragments of MCR1 that overlapped by 3 amino acids with the sequences prior and after. Two of these comprise the sequence YEN (table S1, p27). All these peptides were effective in in-vitro assays, including the ones without the sequence YEN (p26, 2nd paragraph), but the ones that had that sequence had higher potency (p26, 3d paragraph). Computational docking was used to assess which residues are important for binding (p25, 2nd paragraph).
(c) sufficient relevant identifying characteristics in the way of complete/partial structure or physical and/or chemical properties or functional characteristics when coupled with known or disclosed correlation with structure: Applicants are claiming a method of treating or preventing a bacterial infection, comprising administering a polypeptide or peptidomimietic of at least 7 residues of SEQ ID 1 comprising the sequence YEN, an allowing for no more than 2 insertions, deletions, and substitutions. This requires that the mutated sequences provide a benefit to patients. However, applicants have not provided any data showing what residues are required/important for binding, or any information how this sequence can be modified and retain activity. A person of skill in the art would not know what sequence/hydrophobicity/aromaticity is required to provide efficacy. In essence, applicants have claimed an important part of their invention by function. That is not sufficient to support the written description requirement.
As of applicant’s priority date, it was not possible to accurately predict if a given molecule bound to a receptor. Lowe (blog “In the pipeline” entry of 7 Sept, 2022) describes an experiment where that was attempted. 39K compounds, including known antibiotics, were screened against E. coli for growth inhibition, finding 218 active compounds (1st page, 3d paragraph). These were computer docked to a set of 296 essential bacterial proteins by multiple docking procedures (1st page, 3d paragraph), along with 100 random inactive compounds (2nd page, 1st paragraph). The number of strong binders predicted were essentially the same between the active compounds and the controls, and out of 142 compound/target interactions previously known, the methodology found only 3 (2nd page, 2nd paragraph). While a given docking program may accurately predict if compound A binds to protein B, it is impossible to a priori know if the prediction is accurate. In other words, several years after applicant’s priority date, it was not possible to predict if a given compound and target bound to each other. Note that, if it is not possible to accurately determine if a compound binds to another, the more difficult problem of calculating the structure of the two bound compounds is also reasonably expected to vary, depending on the parameters used. Note that this is essentially the same method that applicants have used to determine which residues are important for binding.
Nor is it possible to modify known sequences to reliably find new compounds. Guo et al (PNAS (2004) 101(25) p9205-9210) looked at the effect of random mutations (title). In a DNA repair enzyme, about one mutation in three killed the activity of the protein, consistent with studies with other proteins (abstract). Yampolsky et al (Genetics (2006) 170 p1459-1472), using a different methodology, found that even conservative substitutions were prone to problems (table 3, p1465, top of page). In other words, unless there is some information known about the binding, mutating the sequence is likely to be detrimental, making it a poor way to generate new compounds.
(d) representative number of samples: Applicants have tested a rolling array of fragments of the polypeptide, but have provided no real data, save that they bind. This is supported by computing the important residues, a method that is known to be of questionable utility. Given that mutating a sequence will frequently abrogate activity, and that there is no reliable way to predict where the sequence can be modified without causing problems, the claims lack written description.
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.
first rejection
Claims 10 and 11 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 10 mentions administration to a subject in need of prevention of a pneumococcal disease. It is not clear what this population is. For purpose of examination, as no one wants to be infected, this will be interpreted as any subject.
second rejection
Claim 11 is 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 11 has “including but not limited to” and “preferably” language. These turns of phrase render the claim indefinite, because it is not clear if the embodiments delineated by these phrases are limitations or not.
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) 1, 4, 7, 10, 11, 17, 25, and 34 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Brix et al (US 20110318380).
Brix et al discusses immunotherapy (abstract), which will allow for generation of T-cells that are reactive to bacteria or other infectious agents (paragraph 31). This can include SEQ ID 100117 (paragraph 164), which has the sequence VSYENWAYGEPNN (sequence listing). Note that this comprises SEQ ID 4 of applicants. While this reference does not specify that the pathogen expresses a CDC, administration of this sequence will necessarily prevent the disorder, anticipating claims 1, 4, 7, 10, 11, 25, and 34. Nasal administration is mentioned (paragraph 937), anticipating claim 17.
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.
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.
Claim(s) 1, 4, 7, 10, 11, 17, 25, and 34 are rejected under 35 U.S.C. 103 as being unpatentable over Brix et al (US 20110318380) in view of Farley et al (MMWR (2010) 59(9) 253-255), with evidentiary support from Shewell et al (PNAS (2014) pE5312-E5320).
Brix et al discusses immunotherapy (abstract), which will allow for generation of T-cells that are reactive to bacteria or other infectious agents (paragraph 31), presumably this allows for treatment and prevention. This can include SEQ ID 100117 (paragraph 164), which has the sequence VSYENWAYGEPNN (sequence listing). Note that this comprises SEQ ID 4 of applicants (underlined). Nasal administration is mentioned (paragraph 937).
The difference between this reference and applicant’s elected species is that it does not discuss applicant’s elected disorder, invasive pneumococcal disease.
Farley et al discuss invasive pneumococcal disease (title), caused by Streptococcus pneumoniae (p253, 1st column, 1st paragraph), which remains a leading cause of serious illness in children and adults (p253, 1st column, 1st paragraph). As evidenced by Shewell et al, this bacteria comprises a CDC (pE5312, 1st column, 1st paragraph). This reference shows that applicant’s elected disorder is caused by a subgenus of the disorders treated by Brix et al (bacteria or infectious agents).
Therefore, it would be obvious to treat the disorder of Farley et al with the therapy of Brix et al, as a substitution of one known element (the disorder of Farley et al) for another (the genus of disorders of Brix et al) yielding expected results (therapy). As the disorder of Farley et al is a species of the genus of Brix et al, an artisan in this field would attempt this therapy with a reasonable expectation of success.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FRED REYNOLDS whose telephone number is (571)270-7214. The examiner can normally be reached M-Th 9-3:30.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Melissa Fisher can be reached at 571-270-7430. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/FRED H REYNOLDS/Primary Examiner, Art Unit 1658