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 group I (polypeptides) and SEQ ID 1 in the reply filed on 4 Dec, 2025 is acknowledged.
Applicants have elected SEQ ID 1. A search was conducted for this invention, and it was determined to be patent ineligible as a natural phenomenon. As a result, claims 1-6 were examined, and claims 8 and 9 have been withdrawn from consideration.
During examination, a reference was found that read on a non-elected species. That reference is discussed below.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code, note p22 of the specification as filed. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claims Status
Claims 1-6, 8, and 9 are pending.
Claims 8 and 9 have been withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 4 Dec, 2025.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim 1-6 are rejected under 35 U.S.C. 101 because the claims read on a judicial exception (natural phenomenon).
The Supreme Court has laid out a 3 part test for eligibility under this statute
1) Does the claim read on a process, machine, manufacture, or composition of matter?
2a) If the first test is passed, does a judicial exception apply?
2b) If a judicial exception applies, is there something beyond the judicial exception?
Applying the test
Applicants are claiming a polypeptide, a composition of matter.
2a) GenBank entry QTW43735 (2022) lists a polypeptide comprising SEQ ID 1 as a naturally occurring protein from Callistoctopus minor. The claims are open (“having”) so they read on the full length polypeptide. Alternatively, Ass’n for Molecular Pathology v Myriad Genetics stated that fragments of DNA excised from the chromosome can still be natural products under this statute. This is interpreted by the office to prevent fragments of biopolymers (such as proteins and nucleic acids) from being eligible if test 2b is not met. Claims 1 and 2 describe how much of SEQ ID 1 is required to meet the claim limitations, and competing claim 6 describes an antibacterial composition, all of which are met by the polypeptide itself. Competing claims 3-5 describe functional limitations related to antimicrobial activity, which are inherent to the polypeptide and do not introduce additional structural elements.
2b) The claims can be read by the protein alone. This means that there is nothing beyond the judicial exception and the claims lack eligibility.
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 1-6 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 question at issue is which fragments of SEQ ID 1 are antimicrobial
(a and b) actual reduction to practice and disclosure of drawings or structural chemical formulas: All examples use SEQ ID 1, which was derived by searching for proline rich sequences from O. minor. (p21, 2nd paragraph). The closest antimicrobial sequence that applicants could find had a sequence SIRDKGKTIAIDLAKSAGTGVLRTLMCKDKSC (p23, first paragraph and Wang et al (Mol. Biol. Rep. (2013) 40 p1097-1102, fig 2, p1101, top of page), which has little sequence identity to the claimed sequence.
(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 claims allow for antimicrobial fragments of SEQ ID 1. This means that the embodiments that read on the claims have a function limitation that the sequences be antimicrobial. However, applicants have not described what portions of SEQ ID 1 are required to meet this functional requirement. An artisan in this field, armed with applicant’s disclosure, would not know what portions of the sequence are required for activity. In essence, applicants have defined their invention by function. That is not sufficient to meet the written description requirement.
Ramesh et al (J. Peptide Sci. (2016) p438-451) mentions that antimicrobial peptides can be as short as 2 amino acids (abstract). This indicates that it is possible that the antimicrobial characteristics of SEQ ID 1 are due to a very small percentage of the amino acids in the sequence.
As of applicant’s priority date, it was not a priori possible to predict if a given molecule bound to another. 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 from the screen (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.
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, random truncations from either end are likely to abrogate activity.
(d) representative number of samples: As noted before, applicant’s examples all use SEQ ID 1. There is no information as to which portions of the sequence are important for activity. Applicants state that the closest sequence they can find has limited identity, indicating that they know of no prior art describing which portions of the sequence tolerate modification. Given that random changes often abrogate activity, it is impossible to extrapolate from applicant’s examples to all fragments that read on the claims. Thus, 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.
Claim 2 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 2 requires an antimicrobial peptide that has a sequence of 18-23 consecutive amino acids of SEQ ID 1. The issue is that a sequence with 24 or more consecutive amino acids of SEQ ID 1 will inherently have a sequence of 18-23 consecutive amino acids, yet the claim gives a range suggesting that there is an upper limit in the number of consecutive amino acids in the claim.
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 and 3-6 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by the GenBank entry MCC73228 (2018) (previously cited). Please note that this sequence does not read on applicant’s elected species.
The GenBank entry gives a partial sequence of the immunoglobulin light chain junction region of humans (title), which comprises the sequence RRLIR. As this sequence comprises the first 5 amino acids of SEQ ID 1 and has every structural feature that applicants have stated are required to meet the functional limitations of the claims, it anticipates claims 1 and 3-6.
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.
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