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
Applicants elected SEQ ID 4 for invasive pneumococcal infection without traverse in the replies filed on 8 Oct, 2025 and 19 Dec, 2025.
Claims Status
Claims 1, 4, 5, 7, 10, 11-17, 19-22, 25, 34, 36, 39, and 48-50 are pending.
Claims 1, 10, 34, and 36 have been amended.
Claims 5, 12-16, 19-22, 36, 39, and 50 have been withdrawn due to an election/restriction requirement.
Information Disclosure Statement
The information disclosure statement filed 22 June, 2026 fails to comply with the provisions of 37 CFR 1.98(a)(4) because it lacks the appropriate size fee assertion. It has been placed in the application file, but the information referred to therein has not been considered as to the merits.
Withdrawn Objections
The objection to the drawings due to color is hereby withdrawn due to amendment.
Withdrawn Rejections
The rejection of claim 11 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite due to the terms “preferably” and “including but not limited to” language is hereby withdrawn due to amendment.
Maintained/Modified Rejections
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, 34, 48, and 49 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.
response to applicant’s arguments
Applicants state that sequences comprising those allowed by the claims have been shown to be active.
Applicant's arguments filed 22 June, 2026 have been fully considered but they are not persuasive.
Applicants have demonstrated that sequences comprising those allowed by the claims are effective. But a person of skill in the art does not know what part(s) of those sequences is/are responsible for activity. There is no analysis of which residues are important, aside from a computer analysis which, as shown in the rejection, is not a reliable method.
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 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.
response to applicant’s arguments
Applicants argue that, because the terms “treating” and “preventing” are defined by applicants, the claim is clear.
Applicant's arguments filed 22 June, 2026 have been fully considered but they are not persuasive.
The issue is not the terms treatment and prevention, but rather the patient population. It is not clear if “prevention” is limited to patients that have been exposed, but are not showing symptoms, or to susceptible patients (such as immunocompromised individuals), or to humans or to all patients that can be infected with a sufficient exposure, or some other population.
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, 34, 48, and 49 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, 34, 48, and 49. Nasal administration is mentioned (paragraph 937), anticipating claim 17.
response to applicant’s arguments
Applicants argue that the reference discusses a large number of sequences, and that administering the complex would not necessarily prevent or treat the disorders of the claimed method, pointing to differences in the mechanism of activity described by Brix et al and that described by applicants.
Applicant's arguments filed 22 June, 2026 have been fully considered but they are not persuasive.
Applicants argue that there are a large number of sequences. However, that is not relevant; a reference that clearly names the claimed species anticipates the claims, no matter how many other species are named (MPEP 2131.02(II)).
Applicants point to differences in the mechanism described by Brix et al and that described by applicants to argue that prevention is not inherent. However, it is the same sequence administered to the same patient population (patients who do not want to catch a disease); it is unclear why it would not inherently work. Note that should this argument be persuasive, it would indicate that applicant’s invention is not enabled.
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, 34, 48, and 49 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.
response to applicant’s arguments
Applicants argue that Brix et al lists a large number of sequences, with no guidance as to which sequences are for which disorders, that there is no reasonable expectation of success, that the rejection is based on hindsight reasoning, and that Brix et al discusses a different mechanism of action than applicants.
Applicant's arguments filed 22 June, 2026 have been fully considered but they are not persuasive.
Applicants argue that Brix et al discusses a large number of sequences, with no guidance as to which sequences are for which disorders. This is a US patent document, which is required to give a written description to enable a person skilled in the art to make and use the invention (text of 35 USC 112(a)). This means that any of the sequences of the reference can be used for the disorders discussed, which is consistent with the mechanism of the reference (activation of the immune system). It is not clear how the fact that there are a lot of possible solutions renders the rejection invalid. Assume that a reference discussed one solution. The argument about the number of possible embodiments is moot. Then assume that the authors did additional research and found additional embodiments. In other words, applicant’s argument is stating that, because the problem is more thoroughly investigated, it cannot be solved. This is also the basis of the no expectation of success argument.
Applicants argue that the rejection is based on hindsight reasoning. The courts have ruled that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as the reconstruction takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971). Applicants have not pointed to any portion of the rejection that is not found in the cited references.
Applicants argue that the mechanism of action described by Brix et al is different than applicants. It is not clear why this renders the rejection invalid.
Conclusion
THIS ACTION IS MADE FINAL. 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 FRED REYNOLDS whose telephone number is (571)270-7214. The examiner can normally be reached M-Th 9-3:30.
Examiner interviews are available via telephone and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
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
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