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 .
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-11, drawn to a composition comprising an antimicrobial cationic amphipathic polypeptide (PAX), in addition to the species of SEQ ID NO: 31, in the reply filed on 4/9/2026 is acknowledged.
Upon further search and examination, the species election has been broadened to include polypeptides with at least 85% sequence identity to SEQ ID NO: 1, 21, 26, 31, 33, and 34; polypeptides with at least 90% sequence identity to SEQ ID NO: 14; and SEQ ID NO: 14, 39, and 48 in addition to the elected SEQ ID NO: 31.
Claim Status
Claims 1-30 are pending. Claims 10 and 12-30 are hereby withdrawn as non-elected inventions (claims 12-30) and species (claim 10). Claims 11, 22-23, and 27-30 are currently amended.
Priority
The instant application is the 371 national stage entry of PCT/US2022/016299, filed 2/14/2022, which claims priority to the provisional application 63/148,860, filed 2/12/2021. The priority date of 2/12/2021 is acknowledged.
Information Disclosure Statement
The IDS filed on 8/11/2023 and 12/26/2023 are under consideration.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - The Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) is missing or incomplete. See item 1) a) or 1) b) above.
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specification
The disclosure is objected to because of the following informalities: Table 6 is illegible.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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 3, 4, 5, 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 3 recites the PAX is 21-24 amino acids in length and comprises a sequence selected from several SEQ ID NO’s. The scope of this claim is indefinite because it is unclear whether the peptides of the claim are limited to peptides consisting of 21-24 amino acids that retain the amino acid sequence of one of the SEQ ID NO’s or is open to peptides comprising any one of the SEQ ID NO’s regardless of length.
Similarly, claim 4 recites the PAX is 16 amino acids in length and comprises a sequence selected from several SEQ ID NO’s. The scope of this claim is indefinite because it is unclear whether the peptides of the claim are limited to peptides consisting of 16 amino acids that retain the amino acid sequence of one of the SEQ ID NO’s or is open to peptides comprising any one of the SEQ ID NO’s regardless of length. By virtue of its dependency on claim 4, claim 5 is also hereby rejected for this same reasoning.
Similarly, claim 11 recites the PAX comprises a sequence selected the SEQ ID NO’s recited in claim 1 and is 8-24 amino acids in length. The scope of this claim is indefinite because it is unclear whether the peptides of the claim are limited to peptides consisting of 8-24 amino acids that retain the amino acid sequence of one of the SEQ ID NO’s or is open to peptides comprising any one of the SEQ ID NO’s regardless of length.
Each of the above claims are being interpreted as a peptide comprising any one of the recited SEQ ID NO’s, regardless of peptide length.
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 is rejected under 35 U.S.C. 101 because they are directed to a judicial exception.
The Supreme Court has given a three-part test for patent eligibility (see flowchart of MPEP 2106(III)):
Are the claims drawn to a process, machine, manufacture, or composition of matter?
2a) If the claims pass the first test, are the claims drawn to a judicial exception (a law of nature, a natural phenomenon (product of nature), or an abstract idea)?
2b) If a judicial exception applies, do the claims recite additional elements that amount to significantly more than the judicial exception?
Applying the three-part test to the instant claims:
Regarding 1), the claim is drawn to peptides, which are compositions of matter.
Regarding 2a), the peptides claimed are products of nature.
Claim 1 recites a composition comprising an antimicrobial cationic amphipathic polypeptide, wherein the sequence comprise one of SEQ ID NO: 1-87 or a sequence having at least 85% sequence identity with one of SEQ ID NO: 1-87. Polypeptides with at least 85% sequence identity to SEQ ID NO: 1 or 21; polypeptides with at least 93.1% sequence identity to SEQ ID NO: 26; polypeptides with at least 92.2% sequence identity to SEQ ID NO: 33; and polypeptides with at least 90.5% sequence identity to SEQ ID NO: 34 read on naturally-occurring peptides, for example:
SEQ ID NO: 1
CCHC-type domain-containing protein, UniProt ID A0A388M598_CHABU, 100% sequence identity
Glucose-methanol-choline oxidoreductase N-terminal domain-containing protein, UniProt ID A0AAW0TED5_SCYPA, 91% sequence identity
Capsid protein, UniProt ID A0AAU8H3Y7_9VIRU, 85.1% sequence identity
SEQ ID NO: 21
Pterin-binding domain-containing protein, UniProt ID A0A9Q0IRS5_9TELE, 100% sequence identity
Chlororespiratory reduction 42, UniProt ID A0AAV6HRX9_9ERIC, 88.8% sequence identity
Ground-like domain-containing protein, UniProt ID A0A6V7TJI5_MELEN, 85% sequence identity
SEQ ID NO: 26
FAD-dependent oxidoreductase, UniProt ID A0A3N6YZ83_9ACTN, 100% sequence identity
Hormogonium polysaccharide biosynthesis glycosyltransferase HpsE, UniProt ID A0ABV0K623_9CYAN, 93.1% sequence identity
SEQ ID NO: 33
PUM-HD domain-containing protein, UniProt ID A0AAV2IXR8_KNICA, 100% sequence identity
Alpha 1,6 mannopyranosyltransferase, UniProt ID A0A2W5KL62_9ACTN, 92.2% sequence identity
SEQ ID NO: 34
Uncharacterized protein, UniProt ID A0ACC2GPW5_DALPE, 100% sequence identity
Capsid protein, UniProt ID A0AAU8H5L4_9VIRU, 90.5% sequence identity
Regarding 2b), none of the claims above integrate the peptides into a practical application because there are no structural changes that would distinguish the claimed peptides from the naturally-occurring peptides. As such, they do not contain elements added to the judicial exception sufficient to render the claims significantly more than the exception.
Taken together, the claims are drawn to patent ineligible subject matter and are rejected here.
Claim Rejections - 35 USC § 102
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 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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
First rejection
Claim(s) 1-2, 4-5, 7, and 11 are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by Steckbeck (US 2020/0277334 A1, published 9/3/2020, effectively filed 3/3/2017).
Steckbeck teaches peptides with antimicrobial, antiviral, antifungal, or antitumor activity (Abstract). The peptides consist of Arg, Val, and Trp residues ([0005]; Sequence Listing).
Steckbeck teaches SEQ ID NO: 5, which comprises the instant SEQ ID NO: 14, in PBS buffer (composition; [0291-0292]). Thus, claims 1, 2, 4, 5, 7, and 11 are anticipated.
Steckbeck also teaches SEQ ID NO: 6 (Sequence Listing), which exhibits 90% sequence identity to the instant SEQ ID NO: 14. Thus, claim 1 is further anticipated by this teaching.
Second rejection
Claim(s) 1 is rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by Adami et al. (US20130231382A1, published 9/5/2013).
Adami teaches lipopeptide compounds for drug delivery enhancement as well as compositions and methods thereof (Abstract; [0003]).
Adami teaches SEQ ID NO: 164 (Sequence Listing), which exhibits 92.5% sequence identity to the instant SEQ ID NO: 1, thus meeting the limitations of claim 1.
Third rejection
Claim(s) 1 is rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by Fatora et al. (US20090053278A1, published 2/26/2009).
Fatora teaches anti-microbial compositions, devices and methods of using the same (Title; Abstract).
Fatora teaches SEQ ID NO: 184 and 185, which comprise the instant SEQ ID NO: 21 and 33 ([0084]; Sequence Listing). Thus, claim 1 is anticipated.
SEQ ID NO: 183 of Fatora also exhibits 92.2% sequence identity to the instant SEQ ID NO: 33, further meeting the limitations of claim 1.
Fourth rejection
Claim(s) 1 is rejected under 35 U.S.C. 102(a)(2) as being anticipated by Weinstein et al. (US20220040117A1, effectively filed 12/12/2018).
Weinstein teaches anellosomes and compositions and uses thereof (Title; Abstract).
Weinstein teaches SEQ ID NO: 908-910 and 938, which comprises the instant SEQ ID NO: 26. Thus claim 1 is anticipated.
Weinstein also teaches SEQ ID NO: 859-861, which exhibits 89.6% sequence identity to the instant SEQ ID NO: 1, further meeting the limitations of claim 1.
Weinstein also teaches SEQ ID NO: 900-902 and 932, which exhibit 90.5% sequence identity to the instant SEQ ID NO: 34, further meeting the limitations of claim 1.
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.
First rejection
Claim(s) 1, 6, 8, and 11 are rejected under 35 U.S.C. 103 as being unpatentable over Steckbeck (US 2020/0277334 A1, published 9/3/2020, effectively filed 3/3/2017) in view of Deslouches et al. (De novo generation of cationic antimicrobial peptides: influence of length and tryptophan substitution on antimicrobial activity. Antimicrob Agents Chemother. 2005 Jan;49(1):316-22.; cited on IDS filed 12/26/2023).
The teachings of Steckbeck have been set forth above. SEQ ID NO: 5 of Steckbeck exhibits 86.9% sequence identity to the instant SEQ ID NO: 39, shown below
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176
628
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. The difference between SEQ ID NO: 5 of Steckbeck and the instant SEQ ID NO: 39 is Val is substituted for Trp in the instant SEQ ID NO: 39 at position 3.
Deslouches teaches the impact of substituting Val residues for Trp residues and overall peptide length of antimicrobial peptides consisting exclusively of Arg, Val, and Trp residues (Title, Abstract). Deslouches teaches that substitution of Val for Trp in the hydrophobic face of AMPs consisting exclusively of Arg, Val, and Trp residues improves their antimicrobial potency (Figure 1; Pg 319, “Influence of Trp residues on antimicrobial potency of LBU peptides”; Table 1).
Thus, based on these teachings, regarding claims 1, 6, 9, and 11, it would be prima facie obvious to substitute the Val for Trp at position 3. One skilled in the art would be motivated to do so and have a reasonable expectation of success because Deslouches teaches that substitution of Val for Trp can improve antimicrobial potency.
Moreover, it would be obvious to try to substitute the Val at position 3 for Trp. As stated above, Deslouches teaches that the substitution of Val residues for Trp improves the potency of the antimicrobial peptide. SEQ ID NO: 5 taught by Steckbeck is an antimicrobial peptide that encompasses four Val residues total. Thus, it would be obvious to substitute each and every Val for Trp, thereby leading to the instant SEQ ID NO: 39. See MPEP 2143(I)(E).
Second rejection
Claim(s) 1-3, 9, and 11 are rejected under 35 U.S.C. 103 as being unpatentable over Montelaro (US20030036627A1, published 2/20/2003) in view of Deslouches et al. (De novo generation of cationic antimicrobial peptides: influence of length and tryptophan substitution on antimicrobial activity. Antimicrob Agents Chemother. 2005 Jan;49(1):316-22.; cited on IDS filed 12/26/2023).
Montelaro teaches antimicrobial peptides derived from the lentivirus lytic peptide 1 amino acid sequence (Abstract); the peptides can be in a physiological composition ([0067-0068]). One such peptide is SEQ ID NO: 5, which exhibits 67.7% sequence identity to the instant SEQ ID NO: 48, shown below
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184
616
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. The difference between SEQ ID NO: 5 of Monetlaro and the instant SEQ ID NO: 48 is Val is substituted for Trp in the instant SEQ ID NO: 48 at positions 7, 14, and 18.
Deslouches teaches the impact of substituting Val residues for Trp residues and overall peptide length of antimicrobial peptides consisting exclusively of Arg, Val, and Trp residues (Title, Abstract). Deslouches teaches that substitution of Val for Trp in the hydrophobic face of AMPs consisting exclusively of Arg, Val, and Trp residues improves their antimicrobial potency (Figure 1; Pg 319, “Influence of Trp residues on antimicrobial potency of LBU peptides”; Table 1).
Thus, based on these teachings, regarding claims 1-3, 9, and 11, it would be prima facie obvious to substitute the Val for Trp at positions 7, 14, and 18. One skilled in the art would be motivated to do so and have a reasonable expectation of success because Deslouches teaches that substitution of Val for Trp can improve antimicrobial potency.
Moreover, it would be obvious to try to substitute the Val at positions 7, 14, and 18 for Trp. As stated above, Deslouches teaches that the substitution of Val residues for Trp improves the potency of the antimicrobial peptide. SEQ ID NO: 5 taught by Montelaro is an antimicrobial peptide that encompasses 11 Val residues total. Thus, it would be obvious to substitute each and every Val for Trp, thereby leading to the instant SEQ ID NO: 48. See MPEP 2143(I)(E).
Prior Art Cited but not Referenced
The following is a subset of art that anticipates the following claimed polypeptides:
Polypeptides with at least 85% sequence identity to SEQ ID NO: 1
SEQ ID NO: 53045 of US20070039067A1, published 2/15/2007 (95.5% sequence identity)
SEQ ID NO: 238 of US20190211361A1, published 7/11/2019, (85.1% sequence identity)
Polypeptides with at least 85% sequence identity to SEQ ID NO: 21
SEQ ID NO: 44 of US20110258713A1, published 10/20/2011 (86.9% sequence identity)
SEQ ID NO: 27 of US20100184696A1, published 7/22/2010 (86.2% sequence identity)
Polypeptides with at least 85% sequence identity to SEQ ID NO: 26
SEQ ID NO: 88 of US20080207508A1, published 8/28/2008 (94.8% sequence identity)
SEQ ID NO: 79697 of US20120017292A1, published 1/19/2012 (87.9% sequence identity)
Polypeptides with at least 85% sequence identity to SEQ ID NO: 33
SEQ ID NO: 48 of US20110039760A1, published 2/17/2011 (95.3% sequence identity)
SEQ ID NO: 55 of US20150297742A1, published 10/22/2015 (87.5% sequence identity)
Polypeptides with at least 85% sequence identity to SEQ ID NO: 34
SEQ ID NO: 3 of US20070117746A1, published 5/24/2007 (85.1% sequence identity)
Allowable Subject Matter
Polypeptides comprising at least 85% sequence identity to SEQ ID NO: 31 or peptides comprising SEQ ID NO: 31 are free of the art. The closest art is Deslouches, 2005, cited above, which teaches the peptide WLBU3. The differences between WLBU3 and the instant SEQ ID NO: 31 are shown below:
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168
642
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. Deslouches teaches 1) substitution of Val residues to Trp residues in the hydrophobic face of the AMPs such as WLBU3 improves their antimicrobial potency and 2) the ideal length for such AMPs is ~24 residues. Regarding 1) it is not obvious to substitute the Val at position 8 for an Arg, which would introduce a residue typically presented on the external, hydrophilic face of the alpha helix of the AMP into the internal, hydrophobic face and alter the alpha helical structure. Regarding 2), although it is obvious to shorten WLBU3 because it is longer than the ideal length of ~24 residues, it is not obvious to delete “VRRV” at that specific location in the sequence. Consequently, the polypeptides are novel and non-obvious.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Sara Konopelski Snavely whose telephone number is (571)272-1841. The examiner can normally be reached Monday - Friday 9-6pm EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Melissa L 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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/SARA E KONOPELSKI SNAVELY/Examiner, Art Unit 1658
/Melissa L Fisher/Supervisory Patent Examiner, Art Unit 1658
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