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 the species SEQ ID NO: 1 in the reply filed on 23 June 2026 is acknowledged. All of SEQ ID NOs: 1-17 were searched. Therefore, the election of species requirement mailed 23 April 2026 is withdrawn.
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.
Claims 1-20 and 24 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon without significantly more.
Regarding claims 1 and 3-19, BRI of the claim is a peptide comprising the amino acid sequence of any one of SEQ ID NOs: 1-17:
PH domain-containing protein from Gossypium australe, which comprises instant SEQ ID NO: 1 at positions 30 to 35, as evidenced by Uniprot entry A0A5B6X339_9ROSI;
Receptor-like protein kinase from Saccharothrix ecbatanensis, which comprises instant SEQ ID NO: 2 at positions 21 to 26, as evidenced by Uniprot entry A0A7W9HLH2_9PSEU;
Hemoglobin from Saccharothrix algeriensis, which comprises instant SEQ ID NO: 3 at positions 44 to 49, as evidenced by Uniprot entry A0ABS2S0P7_9PSEU;
Protein BZR1 homolog from Salvia splendens (Scarlet sage), which comprises instant SEQ ID NO: 4 at positions 18 to 23, as evidenced by Uniprot entry A0A8X8ZWT9_SALSN;
NADH-quinone oxidoreductase from Thermus tengchongensis, which comprises instant SEQ ID NO: 5 at positions 110 to 115, as evidenced by Uniprot entry A0A7V4AMU4;
Inclusion body protein from Burkholderia ambifaria, which comprises instant SEQ ID NO: 6 at positions 116 to 120, as evidenced by Uniprot entry UPI00016D5996 · B1FIE0;
AzlC protein from Kingella negevensis, which comprises instant SEQ ID NO: 7 at positions 148 to 153, as evidenced by Uniprot entry A0A5B6X339_9ROSI;
3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabA from Paracoccus suum, which comprises instant SEQ ID NO: 8 at positions 94 to 99, as evidenced by Uniprot entry A0A344PPN4_9RHOB;
DUF3325 family protein from Sphingobium yanoikuyae, which comprises instant SEQ ID NO: 9 at positions 29 to 34, as evidenced by Uniprot entry UPI000F7EE54C · A0A430BQT3;
Reverse transcriptase from Gossypium australe, which comprises instant SEQ ID NO: 10 at positions 98 to 103, as evidenced by Uniprot entry A0A5B6U3E8_9ROSI;
Complex 1 LYR protein domain-containing protein from Aldrovandia affinis, which comprises instant SEQ ID NO: 11 at positions 128 to 133, as evidenced by Uniprot entry A0AAD7X2H7_9TELE;
DUF968 domain-containing protein from Brucella anthropi, which comprises instant SEQ ID NO: 12 at positions 81 to 86, as evidenced by Uniprot entry A0A6I0DVM0_BRUAN;
Beta/gamma crystallin 'Greek key' domain-containing protein from Coilia grayii (Gray's grenadier anchovy), which comprises instant SEQ ID NO: 13 at positions 30 to 35, as evidenced by Uniprot entry A0ABD1J4I0_9TELE;
Gtp-binding protein parf from Lynx pardinus (Iberian lynx) (Felis pardina), which comprises instant SEQ ID NO: 14 at positions 60 to 65, as evidenced by Uniprot entry A0A485P6N8_LYNPA;
N-acetyltransferase from Bacillus caldolyticus, which comprises instant SEQ ID NO: 15 at positions 15 to 20, as evidenced by Uniprot entry A0ABM6QMB2_BACCL;
Dihydrofolate reductase family protein from Microbacterium bandirmense, which comprises instant SEQ ID NO: 16 at positions 91 to 96, as evidenced by Uniprot entry A0ABU8LBB2_9MICO; and
GFA family protein from Aquincola tertiaricarbonis, which comprises instant SEQ ID NO: 17 at positions 57 to 62, as evidenced by Uniprot entry A0ABY4S578_AQUTE.
Step 1: Claims 1 and 3-19 are drawn to a composition of matter.
Step 2A, Prong 1: Claims 1 and 3-19 are directed to a product of nature, the peptides listed above. The closest counterparts to the nature-based products are the proteins listed above. The claimed peptides correspond to fragments of these proteins. The claimed peptides have a different structural characteristic than the natural peptides, i.e., the natural peptides have covalent bonds on their ends that connect them to the rest of the protein whereas the claimed peptide lacks these bonds. However, the claimed peptides are otherwise structurally identical to the natural peptides, e.g., they have the same peptide backbone and amino acid sequence as the proteins listed above in nature. This difference is not a marked difference in view of MPEP § 2106.04(c)(II)(C)(2) and the Supreme Court decision in Myriad. See, e.g., Myriad, 569 U.S. at 585, 106 USPQ2d at 1977. In addition, the function of the claimed peptides, immunoglobulin binding, is innate to the peptides themselves, and was not created or altered by the inventor. See Ambry Genetics, 774 F.3d at 760-61, 113 USPQ2d at 1244. In sum, the claimed peptides are different, but not markedly different, from their naturally occurring counterparts, and thus are natural phenomenon exceptions
Step 2A, Prong 2: The claim only recites the peptide, which is a natural phenomenon exception. Because there are no additional claim elements besides the judicial exception, the judicial exception is not integrated into a practical application (MPEP § 2106.04(d)(III)).
Step 2B: The claim only recites the peptide, which is a natural phenomenon exception. Because there are no additional claim elements besides the judicial exception, the claim does not amount to significantly more than the judicial exception (MPEP § 2106.05).
Therefore, claims 1 and 3-19 are patent ineligible.
Regarding claims 2 and 20, these claims recite a functional property of the claimed peptides. The claimed peptides are different, but not markedly different, from their naturally occurring counterparts for the same reasons above, and thus are natural phenomenon exceptions. The claim only recites the peptide, which is a natural phenomenon exception. Because the limitation reciting a function does not actually provide for the practice of this function, e.g., it is merely an intended use of the claimed invention or a field of use limitation, then it cannot integrate a judicial exception (MPEP § 2106.04(d)(2)). In addition, because only the peptide is claimed, the claims do not amount to significantly more than the judicial exception (MPEP § 2106.05).
Therefore, claims 2 and 20 patent ineligible.
Regarding claim 24, the rest of the proteins of which instant SEQ ID NOs: 1-17 are fragments, are detectable by molecular weight as well as other features. Therefore, claim 24 is patent ineligible.
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.
Claims 1-2, 20, 24, 26, and 30 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Shen et al. (Affinity interactions of human immunoglobulin G with short peptides: role of ligand spacer on binding, kinetics, and mass transfer. Anal Bioanal Chem 408, 1829–1841 (2016); hereafter “Shen”).
Shen teaches the synthetic peptide HWRGWV (p. 1831, col. 2, para. 1), which is 83% identical to instant SEQ ID NO: 16:
Shen HWRGWV
SEQ ID NO: 16 HWRGWW
The sequence identity of the prior art peptide falls within the claimed range “at least 80% sequence identity.” Therefore, Shen anticipates claim 1.
Regarding claim 2, Shen is silent regarding the claimed property of HCP LRV. Because the prior art peptide is structurally identical to the claimed peptide, this property is inherently met (MPEP § 2112.01(II)).
Regarding claim 20, Shen teaches that the synthetic peptide HWRGWV binds an immunoglobulin (p. 1832, col. 2, para. 2; Fig. 1; Table 1).
Regarding claim 24, Shen teaches that the synthetic peptide HWRGWV further comprises a solid support, a silica-coated QCM sensor (p. 1831, col. 1-2, bridging para.).
Regarding claim 26, Shen teaches an article, a sensor, comprising the synthetic peptide HWRGWV and a solid support, a silica-coated QCM sensor (p. 1831, col. 1-2, bridging para.).
Regarding claim 30, Shen teaches a method of detecting an immunoglobulin in a sample comprising contacting the sample and the synthetic peptide HWRGWV to provide a peptide-bound immunoglobulin, and detecting the peptide, thereby detecting the immunoglobulin. Specifically, Shen teaches that a QCM instrument was used to measure the changes in the resonance frequency (Δf) and energy dissipation (ΔD) of modified sensors upon human immunoglobulin (hIgG) adsorption (p. 1832, col. 2, para. 2; Fig. 1; Table 1).
Claims 1-2, 17, 20, 24, 26, and 30 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Yamada et al. (WO 2018/199337 A1, published 11 January 2018; citations are to the English-language equivalent, US 2020/0190165 A1; hereafter “Yamada”).
Yamada teaches the synthetic peptides SEQ ID NOs: 54-54, each of which comprise instant SEQ ID NO: 15 (underlined) ([2652]; Table 2; Examples 16-17):
Ac-DCKWHRGQLVWCT-NH2 (SEQ ID NO: 54)
DCKWHRGQLVWCT (SEQ ID NO: 55)
Therefore, Yamada anticipates instant claims 1 and 17.
Regarding claim 2, Yamada is silent regarding the claimed property of HCP LRV. Because the prior art peptide is structurally identical to the claimed peptide, this property is inherently met (MPEP § 2112.01(II)).
Regarding claim 20, Yamada teaches that the synthetic peptides comprising WHRGQL bind an immunoglobulin (Example 28).
Regarding claim 24, Yamada teaches that the synthetic peptides comprising WHRGQL further comprises a solid support, a resin for solid phase peptide synthesis ([2280]).
Regarding claim 26, Yamada teaches an article, a sensor, comprising the synthetic peptides comprising WHRGQL and a solid support, resin for solid phase peptide synthesis ([2280]).
Regarding claim 30, Yamada teaches a method of detecting an immunoglobulin in a sample comprising contacting the sample and the synthetic peptides comprising WHRGQL to provide a peptide-bound immunoglobulin, and detecting the peptide, thereby detecting the immunoglobulin. Specifically, Yamada teaches that ESI-TOFMS was used to measure mass changes upon human immunoglobulin (hIgG) binding to the peptide ([2289]).
Claims 1-20, 24, and 26 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Noren & Noren (Construction of High-Complexity Combinatorial Phage Display Peptide Libraries. METHODS 23, 169–178 (2001); hereafter “Noren”).
Noren teach a phage display heptapeptide library wherein a randomized segment is followed by a flexible linker and cleavage site and fused to the N-terminus of the M13 minor coat protein pIII (p. 170, col. 1, para. 2; Figures 1-2). Noren teach that the diversity of the library is greater than 109 unique sequences (p. 170, col. 1, para. 1), which is theoretically high enough to include all possible heptapeptide sequences comprising the twenty naturally-occurring amino acids.1 Therefore, the phage display heptapeptide library taught by Noren contains a heptapeptide comprising each of instant SEQ ID NOs: 1-17 and amino acid sequences having at least 80% identity to any one of SEQ ID NOs: 1-17, anticipating each of claims 1 and 3-19.
Regarding claims 2 and 20, Noren is silent regarding the claimed properties of HCP LRV and Igg binding. Because the prior art peptide is structurally identical to the claimed peptide, these properties are inherently met (MPEP § 2112.01(II)).
Regarding claim 24, the M13 phage to which the heptapeptides are fused in the phage display library of Noren are detectable moieties.
Regarding claim 26, the tube containing the phage display library of Noren is a solid support.
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.
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 32 is rejected under 35 U.S.C. 103 as being unpatentable over Carbonell et al. (US 7,408,030 B2; hereafter “Carbonell”) in view of Shen et al. (Affinity interactions of human immunoglobulin G with short peptides: role of ligand spacer on binding, kinetics, and mass transfer. Anal Bioanal Chem 408, 1829–1841 (2016); hereafter “Shen”) and Yamada et al. (WO 2018/199337 A1, published 11 January 2018; citations are to the English-language equivalent, US 2020/0190165 A1; hereafter “Yamada”).
The factual inquiries for establishing a background for determining obviousness under pre-AIA 35 U.S.C. 103(a) 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.
Determining the scope and contents of the prior art.
Carbonell teaches methods of purifying immunoglobulins present in a sample, comprising: contacting the sample and short peptide that bind to said immunoglobulins suitable conditions to provide a peptide-bound immunoglobulin; and releasing the immunoglobulin from the peptide, thereby purifying the immunoglobulin or fragment thereof from the sample (col 12, line 50 - col 14., line 11).
Ascertaining the differences between the prior art and the claims at issue.
Carbonell does not teach that the short peptide that bind to said immunoglobulins comprises any of instant SEQ ID NOs: 1-17 or peptides with at least 80% identity to any of instant SEQ ID NOs: 1-17.
Resolving the level of ordinary skill in the pertinent art.
Shen teaches the immunoglobulin-binding peptide HWRGWV (p. 1831, col. 2, para. 1), which is 83% identical to instant SEQ ID NO: 16 (p. 1832, col. 2, para. 2; Fig. 1; Table 1).
Yamada teaches the immunoglobulin-binding peptides SEQ ID NOs: 54-55, each of which comprise instant SEQ ID NO: 15 (underlined) ([2652]; Table 2; Examples 16-17, 28).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use the short peptides that bind to immunoglobulins taught by Shen (83% identical to instant SEQ ID NO: 16) and Yamada (SEQ ID NO: 15) in the method of purifying immunoglobulins taught by Carbonell. The rationale for obviousness is simple substitution of one known element for another to obtain predictable results (MPEP § 2143.01(B)). The relevant findings for this rationale are as follows.
(1) The prior art contained a device (method, product, etc.) which differed from the claimed device by the substitution of some components (step, element, etc.) with other components. In the instant case, the primary reference teaches a method of purifying immunoglobulins which differs from the claimed method by the substitution of one immunoglobulin-binding peptide for another. Therefore, prior art contained a device (method, product, etc.) which differed from the claimed device by the substitution of some components (step, element, etc.) with other components.
(2) The substituted components and their functions were known in the art. Shen teaches the synthetic peptide HWRGWV (p. 1831, col. 2, para. 1), which is 83% identical to instant SEQ ID NO: 16. Yamada teaches the synthetic peptides SEQ ID NOs: 54-55, each of which comprise instant SEQ ID NO: 15 (underlined) ([2652]; Table 2; Examples 16-17). The function of these peptides is known in the art because Shen (p. 1832, col. 2, para. 2; Fig. 1; Table 1) and Yamada (Example 28) teach that they bind to immunoglobulins. Therefore, the substituted components and their functions were known in the art.
(3) One of ordinary skill in the art could have substituted one known element for another, and the results of the substitution would have been predictable. One of ordinary skill in the art would expect that the peptides of Yamada and Shen perform the function of binding immunoglobulin in the combination because this is their function in isolation. Therefore, one of ordinary skill in the art could have substituted one known element for another, and the results of the substitution would have been predictable.
The rationale to support a conclusion that the claim would have been obvious is that the substitution of one known element for another yields predictable results to one of ordinary skill in the art. Therefore, claim 32 is obvious over the cited art.
Allowable Subject Matter
The following claims drafted by the examiner and considered to distinguish patentably over the art of record in this application, are presented to applicant for consideration:
1. (Currently Amended) An article comprising a solid support and a synthetic peptide comprising the amino acid sequence of any one of SEQ ID NOs: 1-14, 16, and 17;
wherein the solid support is a film, microtiter plate well, a channel in a microfluidic device, a particle, a chromatography column packing, a membrane, a biosensor a magnetic bead, a paramagnetic particle, a quantum dot, or a resin; and
wherein the synthetic peptide is conjugated to the solid support via a cysteine or a lysine residue at the N- or C-terminus of the synthetic peptide.
Amend the preamble of each of claims 2-16 and 18-20 to “The article synthetic peptide”.
Cancel claims 17 and 24.
30. (Currently Amended) A method of detecting an immunoglobulin or fragment thereof present in a sample, the method comprising:
contacting the sample anda peptide comprising the amino acid sequence of any one of SEQ ID NOs: 1-14, 16, and 17
detecting the peptide, thereby detecting the immunoglobulin or fragment thereof.
32. (Currently Amended) A method of purifying an immunoglobulin or fragment thereof present in a sample, comprising:
contacting the sample anda peptide comprising the amino acid sequence of any one of SEQ ID NOs: 1-14, 16, and 17
releasing the immunoglobulin or fragment thereof from the peptide, thereby purifying the immunoglobulin or fragment thereof from the sample.
The following is a statement of reasons for the indication of allowable subject matter:
Support for the proposed claims is found throughout the original specification, including at p. 13, lines 10-25, and p. 15, lines 9-34.
The proposed claims are patent eligible because the structures of the articles comprising a solid support conjugated to a peptide via an N- or C-terminal cysteine or lysine are markedly different from the corresponding peptides in nature.
The proposed claims are novel and unobvious over the prior art of Shen because they exclude peptides with less than 100% identity to the recited sequences.
The proposed claims are novel and unobvious over the prior art of Yamada because they exclude SEQ ID NO: 15.
The proposed claims are novel and unobvious over the prior art of Noren because although it may be obvious to screen the phage display libraries for sequences that bind to immunoglobulins, there is no reasonable expectation that instant SEQ ID NOs: 1-14, 16, or 17 would be selected.
Conclusion
The art made of record and not relied upon is considered pertinent to applicant's disclosure.
1) Reese et al. Novel peptide ligands for antibody purification provide superior clearance of host cell protein impurities. J Chromatogr A. 2020 Aug 16;1625:461237. doi: 10.1016/j.chroma.2020.461237. Epub 2020 M2
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CHRISTINA M MARCHETTI BRADLEY whose telephone number is (571)272-9044. The examiner can normally be reached Monday-Friday, 8:30 am - 5 pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Lianko G Garyu can be reached at (571) 270-7367. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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CHRISTINA M MARCHETTI BRADLEY
Primary Examiner
Art Unit 1654
/CHRISTINA M MARCHETTI BRADLEY/Primary Examiner, Art Unit 1654
1 A heptapeptide library limited to the twenty naturally occurring amino acids contains 207 unique sequences.
2 Reese et al. does not qualify as prior art because it was published after the earliest effective filing date of the claims. It is the post-filing date publication of the inventor’s work.
Prosecution Insights