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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 12/16/2025 has been entered.
DETAILED ACTION
Claims 7 and 14 are canceled. Claims 1-6, 8-13, and 15 are pending.
The § 112(a) new matter rejection of claim 2 is withdrawn in light of the amendment on 11/26/2025.
The previous § 112(b) rejections of claims 1-6, 8-13, and 15 are withdrawn.
Drawings
The drawings received on 11/26/2025 are unacceptable, because in order to be compliant with 37 CFR 1.121 “[a]ny replacement sheet of drawings shall include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is amended”. The replacement sheet received on 11/26/2025 only includes amended figures 4 and 10.
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they do not include the following reference sign(s) mentioned in the description: 12a-i (line 17 on page 11, and line 21 on page 12); furthermore, figure 9 does not include reference sign 5 as described in the specification (page 5 line 2). 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. 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.
The specification filed 11/26/2025 recites “12(a-i)” in line 17 on page 11 and in line 21 on page 12, however Figure 10(a), a filed 11/26/2025, no longer includes reference characters 12a, 12b, 12c, 12d, 12e, 12f, 12g, 12h and 12i, because the reference characters were replaced with a, b, c, d, e, f, g, h and i respectively. Therefore, in the specification “12(a-i)” should be replaced with “a-i in figure 10(a)” or something to that effect. Note that figure 11(a) still recites 12i, so for consistency the 12i in figure 11(a) should be replaced with i.
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description: 3 as shown in figures 2(a) and in figure 3. Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) 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. 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.
The previous objection to the drawings under 37 CFR 1.83(a) is obviated in light of the replacement drawings filed 11/26/2025, which include reference character 10d.
Priority
All of the instant claims are entitled to the effective filing date of 04/22/2019.
Specification
The amendment filed 11/26/2025 is objected to under 35 U.S.C. 132(a) because it introduces new matter into the disclosure. 35 U.S.C. 132(a) states that no amendment shall introduce new matter into the disclosure of the invention. The added material which is not supported by the original disclosure is as follows:
On page 6 lines 7-8, the specification recites “hydrazide NHS ester functionalized cross-linked polysaccharide based resin such as sepharose resin 12”; and on page 6 lines 13-14 it recites “hydrazide functionalized NHS ester functionalized-cross linked polysaccharide based resin such as sepharose resin 12”. The original specification filed 10/22/2021 provides support for hydrazide functionalized resin (e.g. see example 5 on page 19), and it provides support for NHS SEPHAROSE™ resin, where SEPHAROSE™ is a cross-linked polysaccharide- based resin. However, SEPHAROSE™ is not inherently functionalized by hydrazide. Thus, the specification filed 11/26/2025 introduces the concept of a polysaccharide-based resin, such as SEPHAROSE™, that includes both NHS and hydrazide functionalization.
Applicant is required to cancel the new matter in the reply to this Office Action.
In the amended specification filed 11/26/2025, the use of the term “sepharose” (page 4 lines 4 and 18; page 5 line 2; page 6 lines 8, 14 and 25; page 11 line 10; page 12 line 14; page 20 lines 9 and 15; and page 22 line 15), “Sigma-Aldrich” (page 13 lines 2 and 5), “Merck”(page 13 lines 3 and 22), “Thermo Scientific” (page 13 line 4), “Millipore” (page 13 line 6), “Mettler Toledo” (page 13 line 11), “Agilent” (page 13 line 17), and “Bruker” (page 13 line 27), which are trade names or marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminologies; furthermore the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term(s).
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
The disclosure, as filed 11/26/2025, is objected to because of the following informalities:
Page 12 line 14 of the specification recites “sepharos”, which is a misspelling of SEPHAROSE™ .
The specification recites “resin 5a” (page 4 line 28), “N-terminus glycine capture reagent functionalized resin (5a) [Fig. 9]” (page 7 lines 5-6), and “SEPHAROSE™ beads 5a” (page 20 line 18). As such, the description of 5a is inconsistent. To obviate this objection, the description or reference character should be amended for consistency.
Appropriate correction is required.
Claim Objections
Claims 1 and 15 are objected to because of the following informalities:
Claim 1 recites “by C-C” in the fourth line from the bottom. The extra space between “by” and “C-C” should be deleted.
Claim 1 recites both “functionalized resin 5” (lines 4, 6, 9 and 13) and “functionalised resin 5” (line 10). For consistency, the term should either read “functionalized” in accordance with the American spelling or “functionalised” in accordance with the British spelling throughout the claim. If claim 1 is amended to recite “functionalised”, then claim 8 should also be amended to recite “functionalised resin 5”.
Claim 1 recites “with additive”, which should be replaced with “with an additive” because an article is required before the word additive.
Claim 15 recites “hydrazide functionalized resin 12” where functionalized is spelled in accordance with the American spelling, but claim 9 recites “hydrazide functionialised resin 12” in accordance with the British spelling. For consistency, the term should use the same spelling.
Appropriate correction is required.
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, 8-13 and 15 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 claims contain 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, at the time the application was filed, had possession of the claimed invention.
The claims are drawn to a genus of additives that enable resonance-associated electron density (RED) polarization to facilitate C-C bond dissociation for the separation of N-terminus glycine tagged proteins from a functionalized resin, and recovery and recycling of the functionalized resin without loss of activity. Specifically, claim 1 recites “separating the N-terminus glycine proteins 11d from the functionalized resin 5 under aqueous physiological conditions by C-C bond dissociation with additive, wherein the additive enables resonance-assisted electron density (RED) polarization to facilitate C-C bond dissociation, and recovery and recycling of the functionalized resin 5 without loss of activity”. Claim 9 and dependent claims require an additive that enables RED polarization to facilitate C-C bond dissociation for the separation of the N-terminus glycine tagged proteins [9] from the hydrazide functionalized resin 12 or a probe 10 under aqueous physiological conditions, and optionally recovering and recycling hydrazide functionalized resin 12 or probe 10 without substantial loss of activity. Claims 1-5, 8-12, and 15 do not limit the structure of the additive in anyway. Therefore, claims 1-5, 8-12 and 15 encompass any molecular structure capable of performing the required function. Claims 6 and 13 require the additive for C-C bond dissociation to be pyridoxal-5-phosphate (PLP). However, the specification does not disclose a representative number of species of the claimed genus by reduction to practice, and does not provide adequate guidance with regard to the structural features of the additive that is required to provide the recited properties. Therefore, one of skill cannot immediately envision which additives will have the required functional characteristics, and one could not conclude that Applicant was in possession of the claimed genus of additives at the time the filing, as discussed more fully below.
For claims drawn to a genus, MPEP § 2163(3)(a)(ii) indicates the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant identifying characteristics, i.e., structure or other physical and/ or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. A "representative number of species" means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus.
The instant specification reduces to practice one example of an additive that facilitates C-C bond dissociation, but the specification is silent as to whether the C-C dissociation was enabled by RED polarization. In example 3, native protein is dissolved in a solution containing Sepharose™ beads and sodium bicarbonate buffer. Binding is ensured using UV-Vis analysis. To elute the bound protein, pyridoxal 5’-phosphate (additive) in 0.1 M NaHCO3 is added to the resin and vortexed. See the last paragraph on page 18. In example 5, the specification teaches using phosphate buffer and KCl to remove adsorbed protein from [hydrazide functionalized] resin. To release the labeled protein from its immobilized derivative, aniline in phosphate buffer and coumarin or fluoro or biotin derivatives of O-hydroxylamine are added followed by vortex. After all the analysis, the probe is removed through C-C bond dissociation using PLP in NaHCO3 buffer by vortexting. See the paragraph spanning pages 19-20. Besides pyridoxal-5-phosphate, the specification indicates that the following compounds can serve as additives: 4-dimethyl amino pyridine (DMAP, i.e. 12a), 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU, i.e. 12b), 5-diazabicyclo[4.3.0]non-5-ene (DBN, i.e. 12c), 1,4-diazabicyclo[2.2.2] octane (DABCO, i.e. 12d), imidazole (i.e. 12e), N-methyl imidazole (i.e. 12f), and triethyl amine (i.e. 12g). See lines 10-14 of pages 10 and 11. However, the specification does not indicate that the additives enable the specifically claimed RED polarization for C-C bond dissociation commensurate in scope with the claims. Thus, the instant specification reduces to practice one example of an additive, i.e. pyridoxal 5’-phosphate, that facilitates C-C bond dissociation; yet, the instant specification is silent regarding the ability of pyridoxal 5’-phosphate to specifically enable RED polarization for the claimed separation, and its ability to enable the claimed recovery and recycling of without loss of activity.
MPEP 2163(3)(a)(ii) states that “the disclosure must adequately reflect the structural diversity of the claimed genus, either through the disclosure of sufficient species that are "representative of the full variety or scope of the genus," or by the establishment of "a reasonable structure-function correlation. Such correlations may be established "by the inventor as described in the specification," or they may be "known in the art at the time of the filing date”. Considering the lack of guidance provided in the specification, one would appraise support from the state of the art to extrapolate the correlation between additive structure and the RED polarization function for C-C bond dissociation.
With respect to the state of the art on additives, Purushottam, a post filing date reference (Chemical Science, 2020, 11(48), 13137-13142; as previously relied upon), teaches screening additives for C-C bond dissociation in an aminoalcohol under physiological conditions. Initially, Purushottam employed various organic bases and mixed them with labeled insulin. However, the additives were unable to initiate a release. Therefore, Purushottam hypothesized that transforming an amine to imine combined with an appropriate resonance-assisted electron density (RED) polarization might address the requirement for C-C bond dissociation in the aminoalcohol. Purushottam postulates that pyridoxal 5’-phosphate could provide the extended conjugation and activate the amino alcohol. Purushottam discloses that the feasibility depends on the additional pull effect provided by the that pyridoxal 5’-phosphate. See figures 5(a) and 5(b) and the paragraph spanning pages 13139 and 13140. Thus, Purushottam illustrates the unpredictability in the art to date because Purushottam merely hypothesizes the RED polarization effect of pyridoxal 5’-phosphate. Besides Purushottam, the art is silent regarding additives that are specifically capable of “resonance-assisted electron density polarization”.
In view of the art, the instant disclosure does not satisfy the written description requirement because the species disclosed do not adequately represent the substantial variation within the claimed genus. As discussed above, the breadth of potential structures embraced by the claims is substantial. As evidenced by Purushottam, to date the state of the art on additives that enable RED polarization for C-C bond dissociation is unpredictable. The instant specification reduces to practice one example of an additive capable of dissociating C-C bond dissociation; however, the specification does not disclose whether the additive can enable RED polarization C-C bond dissociation, recovery and recycling or functionalized resin without loss of activity. Moreover, the specification does not identify any relevant characteristic or structure associated with the additive that would allow one of skill to be able to determine, which additives will also satisfy the recited functional limitations. Consequently, one of skill could not conclude that Applicant was in possession of the claimed genus of additives at the time the application was filed.
Response to Arguments
Applicant's arguments filed 11/26/2025 have been fully considered but they are not persuasive.
§ 112(a) written description rejection of claims 1-6, 8-13 and 15
Applicant argues that the amendments carried out in claim 6 and claim 13 have been restricted only to the additive for which the exemplified embodiment is there in the application and in claims only one additive PLP have been retained. See the first paragraph on page 14 of the remarks.
This argument is not persuasive because claims 6 and 13, as filed 11/26/2025, have not been amended as compared to claims 6 and 13 filed 06/27/2025. To the extent that applicant is arguing that claims 6 and 13 should not be rejected under 112(a) because the claims limit the additive to PLP, it is unpersuasive. The specification does not clearly indicate that the observed C-C bond dissociation is the result of RED polarization. In example 3, the specification teaches using PLP in sodium bicarbonate to elute protein bound to Sepharose™ beads. The specific reaction for this elution is not disclosed. Claim 1 requires separating the N-terminus glycine proteins 11d from the functionalized resin 5 under aqueous physiological conditions by C-C bond dissociation with additive. However, instant figure 4 indicates that the resin is separated out prior to the introduction of PLP. Similarly, in example 5 the PLP is not used for the recovery of the resin. Rather, in example 5, the labeled proteins are released from the immobilized derivative using aniline in phosphate buffer and O-hydroxylamine derivatives; whereas the PLP is only used to remove the probe by C-C bond dissociation. Thus, the argument is unpersuasive because the specification does not adequately reflect the structural diversity of the claimed genus as the PLP species is not a sufficient representative of the full variety or scope of the genus, and there is no established reasonable structure-function correlation of record.
Applicant states Amended Claim 6 “The method as claimed in claim 1, wherein the additive for C-C bond dissociation is selected
For clarity of the record claim 6, as filed 11/26/2025, recites “The method as claimed in claim 1, wherein the additive for C-C bond dissociation is pyridoxal-5-phosphate (PLP).” Claim 13, as filed 11/26/2025, recites “The method as claimed in claim 9, wherein the additive for C-C bond dissociation is pyridoxal-5-phosphate (PLP).”
Applicant argues that, as outlined in figure 10b, the amine in amino alcohol reacts with the aldehyde of PLP, and subsequent elimination of water generates an imine. The sequence of curly arrows on the subsequent structure displays the movement of electrons for resonance-assisted electron density polarization. Applicant explains that in figure 10b the electron density of the C-C bond to be cleaved is polarized by the resonance-based pull of the heteroaromatic ring and push from lone pair on oxygen atom in hydroxyl group. The RED polarization is the key driving force that generates the enamine adduct (structure after the second reaction arrow). The re-aromatization drives the formation of subsequent imine (structure after third reaction arrow). Finally, hydrolysis completes the reaction sequence (structure after fourth reaction arrow; final structure in the scheme). The final product after C-C bond dissociation can form only through the given pathway. Hence, the formation of product (experimentally validated and given in disclosure) validates the resonance-assisted electron density polarization. See the paragraph spanning pages 15-16 and the last paragraph on page 25 of the remarks.
This argument is not persuasive because it is not commensurate in scope with the instant claims. Claim 1 requires separating the N-terminus glycine proteins 11d from the functionalized resin 5 under aqueous physiological conditions by C-C bond dissociation with an additive. Claim 9 requires separating the N-terminus glycine tagged proteins [9] from the hydrazide functionalised resin 12 or a probe 10 under aqueous physiological conditions by C-C bond dissociation with an additive. However, figure 10b does not show reference characters 11d, or 5, nor does figure 10b show reference characters 9, 12 or 10. As such, the scheme in figure 10b is not clearly commensurate in scope with claims 1 and 9. Figure 10b shows a scheme in which a PLP additive is used to separate a N-terminus glycine protein 1 (i.e. the last structure of figure 10b) from the N-terminus glycine capture reagent 2. The curved arrow notation in the second structure of figure 10b shows an elimination reaction in which the N-terminus glycine capture reagent 2 acts as the leaving group. Applicant indicates that these same curved arrows display RED polarization. However, it is unclear whether the claimed RED polarization is limited to the same electron delocalization pattern shown in the second structure of figure 10b.
Applicant argues that LC-MS data in figure 8 demonstrates a mass shift corresponding to C-C bond formation yielding the amino alcohol. See the first full paragraph on page 16 of the remarks. Applicant asserts that the supporting data confirms the formation of 1, 2-aminoalcohol. Applicant references the supporting experimental data for the reaction with Gly derivatives in the figures labelled as 13a, N-Gly capture reagent 13b, yielding 1,2-aminoalcohol 13c. See the last paragraph on page 16 and the figures spanning pages 17-24. Applicant asserts that the supporting analytical data evidently proves that Applicant in this patent application is not relying on unexpected results to overcome the rejection. The data is cited to clarify the reaction pathway and address Examiner’s mischaracterization of the chemistry (C-C bond formation vs C-C bond cleavage), not as a basis for secondary considerations. Because the prior art does not disclose or suggest PLP-mediated C-C bond formation at N-terminal glycine leading to amino alcohol products and because the mechanism and structural outcome differ fundamentally from the references cited, the rejection should be withdrawn. See the first paragraph on page 24 of the remarks.
This argument is not persuasive because the 112(a) rejection discussed above is a written description rejection and not an enablement or scope of enablement rejection. The reaction scheme on page 17 of the remarks shows the formation of a 1, 2 aminoalcohol 13c from N-Gly tag 13a and a N-terminus glycine capture reagent 13b in the presence of bicarbonate. The scheme appears similar to figure 2(a) in the instant disclosure. The data provided in the remarks supports such aminoalcohol formation. However, the way in which the information provided in the remarks relates the written description rejection above is unclear. Claim 1 requires “reacting N-terminus glycine containing proteins 11d from the protein mixture or cell lysate 6 with the functionalized resin 5 to form a C-C bond association and stable amino alcohol”. Yet, the rejection above focuses on the limitation that requires “separating the N-terminus glycine proteins 11d from the functionalized resin 5 under aqueous physiological conditions by C-C bond dissociation with additive, wherein the additive enables the [RED] polarization to facilitate C-C bond dissociation, and recovery and recycling of the functionalized resin 5 without loss of activity”. The scheme provided in the remarks does not support any such separation, nor does the data exemplify the use of any additive.
Applicant argues that Wang (2022 and 2024) submitted as exhibit A and exhibit B were provided to show that this RED is used in other research works as well. Thus, exhibit A and B were provided to counter the earlier arguments for objection against ‘unpredictability’ for RED polarization. See the second paragraph on page 26 of the remarks.
In response, Examiner posits that Wang (2022) and (2024) do not convey with reasonable clarity that the inventor was in possession of the claimed genus of additives at the time of filing. See the paragraph spanning pages 12-13 of the action mailed 08/26/2025 for a full response as to why the evidence of Wang (2022) and Wang (2024) is insufficient to overcome the written description rejection.
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 1-6, 8-13, and 15 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.
The term “stable” in claim 1 line 6 is a relative term which renders the claim indefinite. The term “stable” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Chemical stability may depend on a variety of factors, so the way in which amino alcohol is required to be stable is unclear. Consequently, there are multiple reasonable interpretations for a stable amino alcohol. In the first interpretation, the claim encompasses any amino alcohol that is formed by reacting N-terminus glycine containing proteins 11d from the protein mixture or cell lysate 6 with the functionalized resin 5. In the second interpretation, the amino alcohol is required to be stable in terms of its valence electrons.
Claim 1 recites “the additive enables the resonance-assisted electron density (RED) polarization to facilitate C-C bond dissociation, and recovery and recycling of the functionalized resin 5 without loss of activity”, which is indefinite because there are multiple reasonable interpretations. In the first interpretation, the claim requires the additive to enable RED polarization to facilitate C-C bond dissociation, and enable the recovery and recycling of the functionalized resin 5 without loss of activity. In the second interpretation, the claim requires the additive to enable the RED polarization to facilitate C-C bond dissociation, and the claim requires a step for the recovery and recycling of the functionalized resin 5 without loss of activity. Thus, the metes and bounds of the required additive are unclear. For compact prosecution, the claim is interpreted as require the additive to enable both the RED polarization to facilitate C-C bond dissociation and enable the recovery and recycling of the functionalized resin 5 without loss of activity. Support for this interpretation can be found in figure 11(a).
Claim 1 references 2, 5, 6, 11d and claim 9 references 2, 9, 10d, 10 and 12, which render the claims indefinite because it is unclear which objects are being referenced. MPEP 2173.05(b) states that a “claim may be rendered indefinite when a limitation of the claim is defined by reference to an object and the relationship between the limitation and the object is not sufficiently defined”. In the instant case, the specification filed 11/26/2025 does not provide consistent definitions for reference characters 2, 5, 6, 11d, 9, 10d, 10 and 12 so there are multiple reasonable claim interpretations. The specification describes reference character 2 as: a N-terminus glycine capture reagent on page 3 in line 5, glycine capture reagents on page 6 in line 9, in figure 2(a) it is shown as a structure with a R1 variable substituent, and in figure 10(a) it is shown as a structure with a R variable substituent. The specification describes reference character 5 as functionalized resin on page 2 in line 30, and “NHS ester functionalized cross-linked polysaccharide based resin such as sepharose resin 5” (page 5 lines 1-2). The specification describes reference character 6 as: protein mixture or cell lysate on page 3 line 1, cell lysate on page 4 line12, and in figure 5 the cell lysate 6 specifically includes SUMO1 (N-terminus Gly). The specification describes 11d as an N-terminus glycine containing protein on page 5 lines 28-29, but in figures 8 and 10(a) the 11d reference character specifically shows a labeled insulin. The specification describes 9 as an N-terminus glycine tagged protein on page 3 in line 7, and an aqueous bioconjugate on page 13 line 13. In claim 9, both reference characters 10d and 10 are used to describe a probe. See, in claim 9, line 8 for the recitation “probe 10d” and lines 10 and 14 for “probe 10”. It is unclear whether 10 and 10d refer to the same probe and it is further unclear whether this probe 10d is the specific structure shown in figure 4, as filed 11/26/2025. The specification describes 12 as: hydrazide functionalized resin on page 6 in line 5, “hydrazide NHS ester functionalized cross-linked polysaccharide based resin such as Sepharose resin 12” on page 6 in lines 7-8, and an additive in figure 10(a). As such, the disclosure provides inconsistent descriptions of the reference characters, so one of ordinary skill in the art cannot ascertain the metes and bounds of the required objects. Furthermore, claim 8 depends from claim 1 and recites 5. Claim 12 depends from claim 9 and recites 10. Claim 15 depends from claim 9 and recites 12. Thus, claims 8, 12 and 15 are indefinite because it is unclear which objects are being referenced.
Regarding claim 2, the phrase "such as, for example" in line 6 renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claims 2-3 recite “the N-terminus glycine capture reagent”, which render the claims indefinite because there are multiple reasonable interpretations for this limitation. In the first interpretation, the N-terminus glycine capture reagent of claims 2-3 reference the N-terminus glycine capture reagent 2 of claim 1. In the second reasonable interpretation, claim 2 references a separate N-terminus glycine capture reagent not recited in claim 1. Furthermore, claim 9 is indefinite because it requires the “N-terminus glycine capture reagent 2 as claimed in claim 2”, however claim 2 does not require a N-terminus glycine capture reagent 2. Thus, it is further unclear which reagent is being referenced in claim 9.
Claim 9 recites “the N-terminus glycine tagged proteins”, which renders the claim indefinite because it is unclear whether the N-terminus glycine tagged proteins is referring back to the earlier recited the N-terminus glycine tagged proteins 9 or separate N-terminus glycine tagged proteins.
Claim 9 recites “optionally recovering and recycling as hydrazide functionalised resin 12 or a probe 10 without substantial loss of activity”, which is indefinite because it is unclear how the term “as” modifies the limitation. Consequently, there are multiple reasonable interpretations for this limitation. In the first interpretation, the hydrazide functionalized resin 12 or probe 10 is optionally recovered or recycled without substantial loss. In the second interpretation, the limitation is incomplete. To clarify, the term “as” can be used as a preposition or conjunction. If the term “as” is being used as a preposition, then the limitation is incomplete because the subject that is to be recovered and recycled as hydrazide functionalized 12 or probe 10 is unclear. If the term “as” is being used as a conjunction, then the limitation is incomplete because clauses being conjoined by the term “as” are incomplete. To obviate this rejection, “as” can be deleted from the limitation.
Claims 2-6 depend from claim 1 whereas claims 10-13 depend from 9. These dependent claims are rejected for the reason set forth above.
Claim 11 recites “the resin”, which renders the claim indefinite because there are multiple reasonable interpretations for this limitation. In the first interpretation, claim 11 references the hydrazide functionalized resin 12 of claim 9. In the second interpretation, the claim references a separate resin not recited in claim 9.
Claim 12 recites “the probe 10 is selected from one of biotin, fluorophore, and biophysical probe 10”, which is indefinite because it is unclear whether reference character 10 represents any probe or specifically a biophysical probe.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 6 and 13 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claims 6 and 13 do not clearly include all the limitations of the claims upon which they depend. Claims 6 depends from claim 1, which requires the additive to enable the resonance-assisted electron density (RED) polarization to facilitate C-C bond dissociation, and recovery and recycling of the functionalized resin 5 without loss of activity. Claim 13 depends from claim 9, which requires the additive to enable the resonance-assisted electron density (RED) polarization to facilitate C-C bond dissociation. Claim 6 and 13 recite “the additive for C-C bond dissociation”. As such, claims 6 and 13 do not clearly include all of the same functional limitations for the additive. To obviate this rejection, “for C-C bond dissociation” can be deleted from claims 6 and 13, i.e. wherein the additive is pyridoxal-5-phosphate (PLP).
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Interpretation
For compact prosecution, the reference characters in the claims are interpreted as being synonymous with the structure recited immediately prior to the reference character, e.g. “functionalized resin 5” is interpreted as any functionalized resin. As such, claim 1 is a method that requires four active steps. First, a N-terminus glycine capture reagent is prepared. An example of an N-terminus glycine capture reagent is N-(3-(2-(2-(3-aminopropoxy)ethoxy)ethoxy)propyl)-2-(2-formylphenoxy)acetamide according to instant claim 3. Second, a functionalized resin is prepared with the N-terminus glycine capture reagent. The functionalized resin is interpreted as any resin that includes the N-terminus glycine capture reagent, such that the resin is functionalized by the incorporation of the N-terminus glycine capture reagent. Third, a protein mixture or cell lysate that includes N-terminus glycine containing proteins is reacted with the functionalized resin to form any C-C bond association and a stable amino alcohol. The C-C bond association is interpreted as an intended result inherent to the reaction; the “C-C bond association” encompasses any carbon interaction because the claim merely requires a bond “association”. As a result of the reaction, the N-terminus glycine containing proteins are immobilized in an ordered pattern from the protein mixture or cell lysate on the functionalized resin. The “ordered pattern” encompasses any immobilization because “an ordered pattern” is not defined in the claim or specification. Fourth, the N-terminus glycine proteins are separated from the functionalized resin under aqueous physiological conditions. The aqueous physiological conditions encompass any aqueous solution and the pH conditions encompass a pH of 7±1 according to instant claim 4. The separation is due to a C-C bond dissociation with an additive. An example of an additive is pyridoxal 5’-phosphate, according to instant claims 6 and 13. Therefore, for compact prosecution, pyridoxal 5’-phosphate is interpreted as being capable of enabling the RED polarization to facilitate C-C bond dissociation, and recover and recycling of the functionalized resin without loss of activity.
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.
Claims 1-6, 8-13, and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Rai (WO 2018/104962, as provided with the IDS filed 10/22/2021) in view of Witus (Curr Protoc Chem Biol. 2010 Jun 1;2(2):125-34), with evidence from LibreTexts (Chemistry LibreTexts, reference X on page 1 of the PTO-892 form) and CHEBI (CHEBI:73080, reference W on page 1 of the PTO-892 form). (n.d.). All references have previously been relied upon.
Regarding claims 1, 3, and 6, Rai teaches a method for metal free protein purification. See the abstract and line 5 of page 14. In example 4, Rai teaches preparing a resin-hydrogen bond promoter conjugate by adding N-(3-(2-(2-(3-aminopropoxy)ethoxy)ethoxy)propyl)-2-(2-formylphenoxy)acetamide (a N-terminus glycine capture reagent) in DMSO from freshly prepared stock to a solution with N-hydroxy succinimidyl resin beads to form a hydrogen bond promoter immobilized resin (functionalized resin). See the paragraph spanning pages 26-27. Rai teaches purifying unlabeled protein from a mixture of proteins by forming resin-hemiaminal conjugate. To the prepared hydrogen bond promoter immobilized resin (functionalized resin), a mixture of proteins is added. The protein with Gly at the N-terminus is immobilized selectively (an ordered pattern). See the first full paragraph on page 27 or paragraph [D]. Rai teaches washing beads with phosphate buffer, pH 7.3 (aqueous physiological condition), and KCl to remove the adsorbed protein from resin. The beads (resin) are further washed and re-suspended (recycled). To release labeled protein from its immobilized derivative, aniline in phosphate buffer and a O-hydroxylamine derivative of a tagging reagent are added followed by vortex. See page 26 lines 12-23. Evidentiary reference LibreTexts defines the term buffer as an aqueous solution. See the first paragraph of LibreTexts. As shown in figure 7(b), Rai teaches the structure of a hemiaminal. Evidentiary reference CHEBI discloses that hemiaminals are a form or amino alcohols. Rai teaches methods that operate under physiological conditions. See page 5 line 5. Rai teaches the synthesis of “stable hemiaminals”. See page 30 line 8 and figure 1. Rai teaches recovering and reusing resin in multiple cycles. See lines 14-15 of page 13.
In summation, Rai teaches a method for metal free purification of protein comprising preparing a N-terminus glycine capture reagent (i.e. the freshly prepared stock with N-(3-(2-(2-(3-aminopropoxy)ethoxy)ethoxy)propyl)-2-(2-formylphenoxy)acetamide). Rai teaches preparing a functionalized resin (i.e. the hydrogen bond promoter immobilized resin) with the N-terminus glycine capture reagent. Rai teaches reacting N-terminus glycine containing proteins from a mixture of proteins with the functionalized resin. Rai teaches forming stable amino alcohol (i.e. the stable hemiaminal). Rai implies that C-C bond association occurs because the compound structures in figure 7 include carbons. Rai teaches immobilizing N-terminus glycine containing proteins in an ordered pattern (i.e. the selective immobilization). Rai teaches separating proteins from resin with a phosphate buffer pH 7.3 wash, which is an aqueous solution at a physiological pH condition. Moreover, Rai suggests that the method can occur at physiological conditions. Rai suggests recovering and reusing a resin.
Rai does not teach C-C bond dissociation with an additive, wherein the additive enables the resonance-assisted electron density (RED) polarization to facilitate C-C bond dissociation.
Witus teaches a pyridoxal 5’-phosphate (PLP) mediated transamination reaction that is specific for the N-terminus of a protein. See the abstract. Witus teaches combining a protein solution with a PLP stock solution. See the first paragraph on page 4. The PLP stock solution is made in the same buffer in which the transamination reaction will be run, typically phosphate buffer at pH 6.5. In figure 1, Witus teaches a reaction scheme that includes a first step where the protein is incubated with PLP, which transaminates the N-terminus to form a ketone or an aldehyde. In the second step, the keto-protein reacts with an alkoxyamine probe to form an oxime-linked protein bioconjugate. Witus discloses that the protein is modified in a single specific location using this procedure. See page 12.
It would have been obvious to a person of ordinary skill in the art prior to the effective filing date of the instantly claimed invention to replace the phosphate buffer of Rai in the separation step with the PLP stock solution of Witus and to further reuse the hydrogen bond promoter immobilized resin of Rai. One would be motivated to replace the phosphate buffer of Rai with the PLP stock solution of Witus because Rai suggests that oxime formation is an intermediate during the release of a protein from the resin, and Witus teaches using PLP for site specific oxime-linked protein bioconjugation. There would be a reasonable expectation of success because Rai demonstrates releasing labeled protein from its immobilized derivative using an O-hydroxylamine (i.e. an alkoxyamine) derivative for transoximization, and Witus suggests that PLP can be used with an alkoxyamine probe to form an oxime-linked protein bioconjugate.
Regarding claim 2, Rai teaches synthesizing hydrogen bond promoters, such as 2-(2-formylphenoxy) acetic acid. See line 29 on page 14 and lines 13-15 on page 15 for the structure. Moreover, Rai illustrates the design of aldehyde with hydrogen bond promoters for stable hemiaminal formation with glycine in figure 2 scheme a. Thus, Rai teaches a structure that aligns with the instantly claimed structure wherein R1-5 are independently -H, X is O and n is 1.
It would have been obvious to a person of ordinary skill in the art prior to the effective filing date of the instantly claimed invention to replace the N-(3-(2-(2-(3-aminopropoxy)ethoxy)ethoxy)propyl)-2-(2-formylphenoxy)acetamide hydrogen bond promoter of Rai with the 2-(2-formylphenoxy) acetic acid hydrogen bond promoter of Rai. There would be a reasonable expectation of success because Rai demonstrates synthesizing the 2-(2-formylphenoxy) acetic acid hydrogen bond promoter and demonstrates preparing resin with a hydrogen bond promoter.
Regarding claim 4, Rai teaches washing beads with phosphate buffer, pH 7.3, and KCl to remove the adsorbed protein from resin. The beads are further washed with phosphate buffer, pH 7, and resuspended in phosphate buffer, pH 7. To release the labeled protein from its immobilized derivative, aniline in phosphate buffer, pH 7, and O-hydroxylamine derivative of a tagging reagent are added followed by vortex. See page 26 lines 12-26 and figure 7(b).
Witus teaches a PLP stock solution that is made in the same buffer in which the transamination reaction will be run, typically phosphate buffer at pH 6.5. See the “PLP Stock Solution” section on page 5.
Thus, Rai and Witus teach an aqueous physiological condition with a pH within the instantly claimed pH range of 7±1.
Regarding claim 5, Rai teaches NHS-SEPHAROSE (i.e. NHS ester functionalized cross-linked polysaccharide based resin) in figure 14. Figure 14 outlines the synthesis of hemiaminal precursor-resin conjugate. See page 4 line 10 for the description of the figure.
It would have been obvious to a person of ordinary skill in the art prior to the effective filing date of the instantly claimed invention to use the NHS-SEPHAROSE as the N-hydroxy succinimidyl resin beads in the method discussed above. One would be motivated to do so because Rai illustrates using NHS-SEPHAROSE in figure 14. There would be a reasonable expectation of success because Rai demonstrates forming a hydrogen bond promoter immobilized resin (e.g. functionalized resin) with N-hydroxy succinimidyl resin beads.
Regarding claim 8, Rai teaches recovering and reusing the hydrazide activated resin in multiple cycles. See lines 14-15 of page 13.
Rai does not teach using the recovered functionalized resin for 5-7 purification cycles.
It would have been obvious to a person of ordinary skill in the art prior to the effective filing date of the instantly claimed invention to optimize the number of cycles that the resin of Rai is reused. A person of ordinary skill in the art has good reason to pursue the known options within his or her technical grasp. One would be motivated to optimize the number of cycles in which the resin is reused in order to reduce waste. There would be a reasonable expectation of success because Rai suggests using resin for multiple cycles (e.g. at least 2). MPEP 2144.05(II) indicates that “[w]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955).
Regarding claims 9 and 13, Rai teaches a method for metal free protein purification. See the abstract and line 5 of page 14. Rai synthesizing hydrogen bond promoters, such as 2-(2-formylphenoxy) acetic acid (N-terminus glycine capture reagent), which aligns with the structure of instant claim 2 wherein R1-5 are independently -H, X is O and n is 1. See line 29 on page 14 and lines 13-15 on page 15 for the structure. Rai teaches reacting proteins with a hydrogen bond promoter to obtain a single site labelled protein with a stable hemiaminal formed. See claim 10. In example 4, Rai teaches single-site labeling of a protein where a solution containing protein and 2-(2-formyl phenoxy) acetic acid is diluted with acetonitrile: water (e.g. aqueous phase). See page 25 lines 13-24. Rai indicates that the single-site is an N-terminal glycine. See line 24 line 10. Rai teaches reacting labeled protein, 9, with hydrazide functionalized resin. See page 13 lines 9 and figure 7. As shown in figure 7, the labeled protein, “9”, is described as a hemiaminal (e.g. amino alcohol). Rai teaches releasing immobilized protein with O-hydroxylamine from resin through transoximization. Rai teaches recovering and reusing hydrazide activated resin in multiple cycles. See the first full paragraph on page 13. Rai teaches methods that operate under physiological conditions. See page 5 line 5. As shown in figure 12A resin is recovered with an aniline NaHCO3 buffer at pH 7 (e.g. aqueous physiological condition). See figure 12A and the description provided on page 3 lines 30-33.
Rai does not teach an additive that enables the RED polarization to facilitated C-C bond dissociation.
Witus teaches a pyridoxal 5’-phosphate (PLP) mediated transamination reaction that is specific for the N-terminus of a protein. See the abstract. Witus teaches a PLP stock solution that is made in the same buffer in which the transamination reaction will be run, typically phosphate buffer at pH 6.5. See the “PLP Stock Solution” section on page 5.
It would have been obvious to a person of ordinary skill in the art prior to the effective filing date of the instantly claimed invention to add the PLP of Witus to the aniline buffer of Rai where the transoximization reaction occurs. One would be motivated to do so because Rai indicates that transoximization involves the addition of an amino group (-NH2) in figure 12A, and Witus teaches transamination reaction specific to the N-terminus of a protein, where transamination is a transfer of an amino group. There would be a reasonable expectation of success because Witus demonstrates making a PLP stock solution and suggests that the stock solution may be made in the same buffer in which the transamination reaction will be run.
Regarding claim 10, Rai teaches synthesizing hydrogen bond promoters including N,N'-(((oxybis(ethane-2,1-diyl))bis(oxy))bis(propane-3,1-diyl))bis(2-(2-formylphenoxy)acetamide) (2i). See example 1 starting on page 14 and page 18 paragraph (i) for the specific synthesis. Rai teaches protein in sodium bicarbonate buffer. To this solution, N,N'-(((oxybis(ethane-2,1-diyl))bis( oxy))bis(propane-3,1-diyl))bis(2-(2-formylphenoxy)acetamide) 2i in DMSO is added and vortexed. After, the reaction mixture is diluted in acetonitrile: buffer. Unreacted N,N'-(((oxybis(ethane-2,1-diyl))bis(oxy))bis(propane-3,1-diyl))bis(2-(2-formylphenoxy)acetamide) is removed and the protein mixture is further washed with sodium bicarbonate buffer. To the concentrated sample in sodium bicarbonate buffer, derivatives of O-hydroxylamine in DMSO from freshly prepared stock solution is added to convert mono-labeled protein to its oxime derivative. See paragraph [B](i) spanning pages 25-26.
It would have been obvious to a person of ordinary skill in the art prior to the effective filing date of the instantly claimed invention to replace the 2-(2-formylphenoxy) acetic acid hydrogen bond promoter with the ,N'-(((oxybis(ethane-2,1-diyl))bis( oxy))bis(propane-3,1-diyl))bis(2-(2-formylphenoxy)acetamide) hydrogen bond promoter. Doing so is merely substituting known prior art equivalents. There would be a reasonable expectation of success because Rai demonstrates preparing a resin-hydrogen bond promoter conjugate.
Regarding claim 11, Rai teaches NHS-SEPHAROSE in figure 14, which outlines the synthesis of hemiaminal precursor-resin conjugate. See page 4 line 10 for the description of the figure.
It would have been obvious to a person of ordinary skill in the art prior to the effective filing date of the instantly claimed invention to replace the hydrazide activated resin with the NHS-SEPHAROSE . One would be motivated to do so because Rai illustrates using NHS-SEPHAROSE in figure 14. There would be a reasonable expectation of success because Rai demonstrates forming a hydrogen bond promoter immobilized resin (e.g. functionalized resin) with N-hydroxy succinimidyl resin beads (see the paragraph spanning pages 26-27 of Rai).
Regarding claim 12, Rai teaches late-stage tagging of N-terminus Gly with an affinity tag, 19F NMR, and a fluorophore. Rai teaches insulin tagged with an 19F NMR in figure 8 and biotin tagged insulin in figure 9. See page 3 line 17-21. Furthermore, in figure 12A, Rai depicts the 19F NMR probe as 11a, biotin as 11b, and a fluorophore as 11c. See the paragraph spanning pages 12-13 and figure 12A, which is included below.
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It would have been obvious to a person of ordinary skill in the art prior to the instantly claimed invention to replace the resin of Rai with the 19F NMR probe, the biotin or the fluorophore of Rai. Doing so is merely substituting known prior art equivalents. One would be motivated to tag the protein with 19F NMR probe, biotin or fluorophore because Rai suggests that the conversion for the 19F NMR probe was 85%, the conversion with biotin is 87% and with fluorophore is 87%. See the paragraph spanning pages 12-13. There would be a reasonable expectation of success because Rai demonstrates protein conjugated with resin (e.g. see figure 12A above) and Rai demonstrates protein conjugated with an 19F NMR probe, biotin and fluorophore.
Regarding claim 15, Rai teaches recovering and reusing the hydrazide activated resin in multiple cycles. See lines 14-15 of page 13.
Rai does not teach using the recovered functionalized resin for 5-7 purification cycles.
It would have been obvious to a person of ordinary skill in the art prior to the effective filing date of the instantly claimed invention to optimize the number of cycles that the resin of Rai is reused. A person of ordinary skill in the art has good reason to pursue the known options within his or her technical grasp. One would be motivated to optimize the number of cycles in which the resin is reused in order to reduce waste. There would be a reasonable expectation of success because Rai suggests using resin for multiple cycles (e.g. at least 2). MPEP 2144.05(II) indicates that “[w]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955).
Response to Arguments
Applicant's arguments filed 11/26/2025 have been fully considered but they are not persuasive.
§103 rejection over Rai in view of Witus, with evidence from LibreTexts, and CHEBI
Applicant argues that hemiaminal is a subclass of aminoalcohol, however this subcategory is completely different from the final aminoalcohol product in this disclosure. A hemiaminal falls under the sub-category of 1,1 aminoalcohol. On the other hand, the structure of the product falls under the sub-category of 1,2-aminoalcohcol. The differences between these two motifs are not limited to their bond architecture (N-C-O vs N-C-C-O) and structures alone, it makes hemiaminal unstable while 1,2-aminoalcohol stable. See the second to last paragraph on page 37 and the paragraph spanning pages 60-61 of the remarks.
This is not persuasive because a reference is presumed to be operable until applicant provides facts rebutting the presumption of operability. See MPEP 2121. In the instant case, Rai teaches the “stable” hemiaminal formation with native proteins or recombinant proteins or any peptide with Gly at the N-terminus. See page 4 lines 17-18. Therefore, the hemiaminal of Rai is presumed to be stable, absent evidence to the contrary. The claims do not limit the stable amino alcohol to 1,2-amino alcohol and the specification does not define stable amino alcohols as 1,2-amino alcohol. Thus, the argument is not commensurate in scope with the instant claims.
Applicant argues that Witus and Francis’s use of PLP leads to a completely different avenue. The additive PLP is reacted with N-terminus amine in this case and converted into amido-ketone or amido-aldehyde depending on the N-terminus residue. Whereas in the present application, the N-terminal glycine is converted into aminoalcohol in a residue-specific manner. There is no formation of amido-ketone or amido-aldehyde throughout the process. In the second step in this case, oxime formation, is a well-known chemistry that has been utilized to complete the process by them as well as in the instant application. See the last two paragraphs on page 41 of the remarks.
This argument is not persuasive because the reason or motivation to modify the reference may often suggest what the inventor has done, but for a different purpose or to solve a different problem. It is not necessary that the prior art suggest the combination to achieve the same advantage or result discovered by applicant. See, e.g., In re Kahn, 441 F.3d 977, 987, 78 USPQ2d 1329, 1336 (Fed. Cir. 2006). In the instant case, Rai teaches the single-site labeling of proteins (see page 1 line 9), and Witus teaches a basic protocol for protein labeling via a site-specific N-terminal transamination reaction (see the title on page 3). The instant specification, filed 10/22/2021, discloses that “the present invention addresses the problems of protein purification adopting single-site labelling” (page 2 lines 16-17). Thus, both Rai and Witus are in the same field of endeavor. The instant method claims are open-ended due to the transitional term “comprising”, so the claims do not exclude the presence of unrecited elements or reaction intermediates, such as an amido-ketone or an amido-aldehyde, as argued by Applicant.
Applicant argues that Witus does not teach or suggest substituting PLP stock solution for a phosphate buffer in a purification or separation step. Applicant asserts that Witus uses a PLP stock solution in aqueous medium only as a reagent for chemical modification. Applicant argues that the PLP was not used a reagent to enable any C-C bond dissociation or as a buffer substitute in any separation, washing or purification process. Additionally, the phosphate buffer by Rai has been used to wash the physically adsorbed protein on the resin by disturbing the non-covalent interactions between the two. Nowhere does Witus indicate that the PLP stock solution is appropriate for, compatible with, or interchangeable with the phosphate buffer conditions used by Rai for protein-resin interactions. Applicant asserts if the phosphate buffer used by Rai is replaced by PLP stock solution, it will do the transamination of all the proteins present in the mixture and will not result in a purified protein in its native form. Thus, one cannot hypothesize that a reagent designed for transamination chemistry could be used as a buffer in a resin-based protein purification where the purification step demands C-C bond dissociation of immobilized proteins in mild aqueous conditions to yield purified proteins in its native form. See the first two paragraphs on page 44 of the remarks. Applicant asserts that Witus does not teach the use of resin in their PLP chemistry, nor does it discuss the compatibility with PLP chemistry and Rai’s immobilized hydrogen-bond-promoter resin. Applicant asserts that there is no evidence or teaching that Rai’s resin will be stable, functional, or recoverable in the presence of PLP as a transamination reagent. See the last paragraph on page 44.
This argument is unpersuasive because the test for obvious is not whether the features of a secondary reference may be bodily incorporated into the structure of the primary reference; nor is it that the claimed invention must be expressly suggested in any one or all of the references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981). In the instant case, Witus provides motivation for using PLP stock solution that includes phosphate buffer. Rai teaches using phosphate buffer to wash the beads and to release labeled protein from its immobilized derivative (see page 26 lines 12-23, imaged below). Thus, the phosphate buffer of Rai is not only used to wash the physically adsorbed protein on the resin, as argued by Applicant. Instant claim 1 requires “separating the N-terminus glycine proteins 11d from the functionalised resin 5 under aqueous physiological conditions by C-C bond dissociation with additive” (instant claim 1 lines 10-11). The structure of the additive is not limited in claim 1, as discussed above. Furthermore, Applicant argues that if the phosphate buffer used by Rai is replaced by PLP stock solutions, it will do the transamination of all the proteins present. However, arguments of counsel cannot take the place of factually supported objective evidence (MPEP 2145 or 716.01(c)). See, e.g., In re Huang, 100 F.3d 135, 139-40, 40 USPQ2d 1685, 1689 (Fed. Cir. 1996); In re De Blauwe, 736 F.2d 699, 705, 222 USPQ 191, 196 (Fed. Cir. 1984).
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Applicant argues that Witus is cited for suggesting that PLP can mediate a transamination reaction specific to N-terminal glycine. However, Witus demonstrates N-terminus-selective transamination, irrespective of the residue at the termini. So, PLP-mediated transamination is not specific to N-termini glycine only. See the third paragraph on page 45 of the remarks. Applicant argues that the Witus transamination reaction demonstrates specificity only under its defined reaction conditions, not under Rai’s separation conditions. Additionally Rai does not involve any transamination chemistry. Therefore, there is no reason to assume the reaction selectivity of Witus would be preserved. Thus, one would not reasonably expect that simply replacing Rai’s phosphate buffer with a PLP stock solution would yield a functional or selective glycine-specific protein purification process. See the fourth paragraph on page 45 of the remarks and pages 65-66.
This argument is not persuasive because the rationale may be expressly or impliedly contained in the prior art or it may be reasoned from knowledge generally available to one of ordinary skill in the art, or established scientific principles (see MPEP 2144(I)). In the instant case, Rai suggests that an oxime is formed as an intermediate before the release of the labeled proteins from their immobilized derivative, i.e. the resin. Witus provides motivation to use PLP with an alkoxyamine for oxime formation. Although Rai does not explicitly teach transamination, Witus and Rai are in the same field of endeavor.
Applicant argues that the reasoning relies on hindsight reconstruction rather than the teachings of the prior art. See the last paragraph on page 45 of the remarks. Applicant argues that Rai teaches a hydrogen-bond promoter aldehyde, 2-(2-formylphenoxy)acetic acid, and that it would have been prima facie obvious to substitute the claimed N-(3-(2-(2-(3-aminopropoxy)ethoxy)ethoxy)propyl)-2-(2-formylphenoxy)acetaminde with Rai’s simpler 2-(2-formylphenoxy)acetic acid promoter. This conclusion is not supported by Rai’s teachings and critical structural and functional differences have been overlooked generating 1,2-amino alcohol on the resin rather than generating a hemiaminal solution. See paragraphs 2-3 on page 46 of the remarks. Applicant argues that the proposed combination [of Witus and Rai] is based on hindsight and lacks both evidence and motivation in the art. See page 53 of the remarks.
In response to applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it 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). In the instant case, every limitation is accounted for in the prior art, so nothing is gleaned from the instant disclosure. Specifically, Rai teaches hydrogen bond promoters including N-(3-(2-(2-(3-aminopropoxy)ethoxy)ethoxy)propyl)-2-(2-formylphenoxy)acetaminde and 2-(2-formylphenoxy)acetic acid in example 1. Therefore, Rai indicates that the two compounds are interchangeable as hydrogen bond promoters. Applicant argues that critical structural and functional differences have been overlooked in generating 1,2-amino alcohol on the resin. However, as discussed above, the instant claims do not require 1,2-amino alcohol.
Applicant argues that Rai does not teach the functional attributes of the claimed amide-linked, multivalent flexible spacer system. See the last two lines on page 46 of the remarks. Applicant asserts that the “claimed hydrogen-bond promoter is not a simple aldehyde with a hydrogen-bond-acceptor group, but it contains a PEG spacer, an amide hydrogen-bond acceptor, and a pendant primary amine” (first paragraph page 47 of the remarks). Applicant asserts that Rai does not teach or suggest the claimed amide-linked, multi-ether, amine-functionalized aldehyde structure for 1,2-aminoalcohol formation. Thus, substituting Rai’s simple aldehyde acid for the claimed extended scaffold is not a routine equivalent and would not be expected to retain function for N-terminus protein purification on resin. See page 47 of the remarks.
This argument is not persuasive because it is not commensurate in scope with the instant claims. The claims do not explicitly require: a hydrogen-bond promoter, a PEG spacer, a pendant primary amine, extended scaffold or an amide-linked, multi-ether, amine-functionalized aldehyde. To the extent that Applicant is arguing that Rai does not teach the claimed pyridoxal 5’ phosphate (i.e. an aldehyde containing compound), it is unpersuasive because Witus is relied upon for teaching that element, not Rai.
Applicant argues that replacing the Witus’s PLP stock solution with Rai’s phosphate buffer cannot render the transamination of proteins. Here, aqueous conditions have been maintained in both cases due to the suitable solubility of the substrate proteins. The cited references use phosphate buffers as solvent mediums in their procedures which are not related to each other. Applicant asserts that it does not teach that the specific pH range of 7±1 is critical, interchangeable, or functionally equivalent across the distinct procedures described. See the last paragraph on page 48 of the remarks.
This argument is not persuasive because the rejection discussed above does not rely on a rationale in which the PLP stock solution of Witus is replaced with Rai’s phosphate buffer, as argued. Rather, the rationale indicates that it would have been obvious to replace the phosphate buffer of Rai with the PLP stock solution of Witus. As discussed above, Witus and Rai are in the same field of endeavor, so the argument that their procedures are not related to each other is unpersuasive. Furthermore, both Rai and Witus teach pHs within the instantly claimed 7±1 range. For example, see the pH values throughout the reaction shown figure 7(b) of Rai and Witus indicates that the phosphate buffer is typically at pH 6.5 (“PLP Stock Solution” section on page 5).
Applicant argues that Rai does not teach that NHS-Sepharose is suitable for specific immobilization conditions required in the presently claimed method. The claimed process relies on mechanistically distinct chemistry for 1,2 amino alcohol formation which is not disclosed by Rai. See the middle paragraph on page 49 and page 55.
This argument is not persuasive because MPEP 2112.01(II) states that "products of identical chemical composition can not have mutually exclusive properties." In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990). The NHS-Sepharose of Rai is structurally indistinguishable from the claimed NHS-ester functionalized cross-linked polysaccharide-based resin. Rai may teach other resins. However, the argument is not persuasive because MPEP 2123 states that “[a] reference may be relied upon for all that it would have reasonably suggested to one having ordinary skill the art, including nonpreferred embodiments”. Merck & Co. v. Biocraft Laboratories, 874 F.2d 804, 10 USPQ2d 1843 (Fed. Cir.), cert. denied, 493 U.S. 975 (1989). See also Upsher-Smith Labs. v. Pamlab, LLC, 412 F.3d 1319, 1323, 75 USPQ2d 1213, 1215 (Fed. Cir. 2005).
Applicant argues that Rai discloses that resins activated with hydrazide could be reused in multiple cycles, but they have not provided any supporting data or suggestions for the reuse up to 5-7 times. See the paragraph spanning pages 50-51 and the paragraph spanning pages 57-58 of the remarks.
This argument is not persuasive because MPEP 2123 states that “[a] reference may be relied upon for all that it would have reasonably suggested to one having ordinary skill the art, including nonpreferred embodiments”. Merck & Co. v. Biocraft Laboratories, 874 F.2d 804, 10 USPQ2d 1843 (Fed. Cir.), cert. denied, 493 U.S. 975 (1989). See also Upsher-Smith Labs. v. Pamlab, LLC, 412 F.3d 1319, 1323, 75 USPQ2d 1213, 1215 (Fed. Cir. 2005). Claim 8 requires the recovered functionalized resin 5 to be used for 5-7 purification cycles, and claim 15 requires the recovered hydrazide functionalized resin 12 to be used for 5-7 purification cycles. Claims 8 and 15 are not rejected as being anticipated by Rai.
Applicant argues that Rai’s simple 2-(2-formylphenoxy)acetic acid promoter cannot be replaced with the far bulkier and structurally distinct N-(3-(2-(2-(3-aminopropoxy)ethoxy)ethoxy)propyl)-2-(2-formylphenoxy)acetaminde. Applicant assert that the Rai paper provides no teaching about function group tolerance with such major changes in steric and electronic character including conjugation with resin. See the last paragraph on page 54.
This argument is not persuasive because arguments of counsel cannot take the place of factually supported objective evidence (MPEP 2145 or 716.01(c)). See, e.g., In re Huang, 100 F.3d 135, 139-40, 40 USPQ2d 1685, 1689 (Fed. Cir. 1996); In re De Blauwe, 736 F.2d 699, 705, 222 USPQ 191, 196 (Fed. Cir. 1984). Instant claim 2 encompasses any N-terminus glycine capture regent that is selected from the compounds of the provided formula. The 2-(2-formylphenoxy)acetic acid of Rai aligns with the formula of instant claim 2. Instant claim 3 requires the N-terminus glycine capture reagent to be N-(3-(2-(2-(3-aminopropoxy)ethoxy)ethoxy)propyl)-2-(2-formylphenoxy)acetaminde. It is unclear, based on Applicant’s argument, how the 2-(2-formylphenoxy)acetic acid and N-(3-(2-(2-(3-aminopropoxy)ethoxy)ethoxy)propyl)-2-(2-formylphenoxy)acetaminde of Rai cannot be interchanged as hydrogen bond promoters, whereas the two may serve the same function as a N-terminus glycine capture regent in the instant claims.
Applicant argues that LC-MS data demonstrates a mass shift corresponding to C-C bond formation yielding the amino alcohol. See pages 67-68 of the remarks. Applicant asserts that the supporting data confirms the formation of 1, 2-aminoalcohol. Applicant references the supporting experimental data for the reaction with Gly derivatives in the figures labelled as 13a, N-Gly capture reagent 13b, yielding 1,2-aminoalcohol 13c. See pages 69-82. Applicant “at the moment is not relying on unexpected results to overcome the rejection”. The analytical data is cited to clarify the reaction pathway and address the Office’s mischaracterization of the chemistry C-C bond formation vs C-C bond cleavage. Because the prior art does not disclose or suggest PLP-mediate C-C bond formation at N-terminal glycine leading to aminoalcohol products. See page 83.
This argument is not persuasive because it is not commensurate in scope with the instant claims. The scheme provided on page 69 of the remarks (identical to the one provided on page 17 of the remarks and discussed above) is not commensurate in scope with the instant claims. The scheme does not include a protein mixture or cell lysate 6 or a functionalized resin 5. The scheme provided shows the formation of a 1,2 amino alcohol (present in 13c). However, the claims do not require a 1,2 aminoalcohol. Therefore, the argument is not persuasive.
Conclusion
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/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/K.C.B./Examiner, Art Unit 1657