DETAILED ACTION
The amendment filed on 01/08/2026 has been entered and fully considered. Claim 7 is canceled. Claims 1-6, 8-18 and 34-37 are pending, of which claim 1 is amended.
Response to Amendment
In response to amendment, the examiner maintains rejection over the prior art established in the previous Office 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 .
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim(s) 1-6, 8-18 and 34-37 is/are rejected under 35 U.S.C. 103 as being unpatentable over Xu et al. (US 2019/0345196, IDS) in view of Arora et al. (mAbs, 2015, IDA)(Arora).
Regarding claim 1, Xu teaches a method for identifying regions in a protein that contribute to self-association of the protein in high concentration and high viscosity sample (abstract), comprising:
microdialysing a high concentration (120 mg/ml) protein sample and a low concentration (15 mg/ml) protein sample in a microdialysis cartridge against a buffer comprising deuterium for at least two different time periods (Table 3, par [0010] [0065]);
subsequently quenching the microdialysis of the samples (par [0010]); and
analyzing the quenched samples in a hydrogen/deuterium exchange mass spectrometry system to determine surface charge distributions and hydrophobicity in regions of the protein by determining a differential deuterium uptake between the high concentration protein sample and the low concentration protein (Table 3, par [0010] [0065]), and
identifying regions of the protein that exhibit differential deuterium uptake of 10% or more contribute to the viscosity of the protein in the high concentration and high viscosity sample (Table 3, par [0010] [0065]),
wherein the protein in the high viscosity sample is at a concentration of 100 mg/mL or greater and at a viscosity of 80 centipoise (cP) or greater (Fig. 1A);
wherein the samples of protein in the microdialysing step are in 10 mM histidine buffer at pH between 5.0 and 7.5 (pH 6.0) (par [0062]).
Xu par [0065] and Table 3 explicitly present deuterium uptake values at 15 mg/mL and 120 mg/mL for various antibody peptides. The data show that multiple peptides in self-association regions exhibit differences exceeding 10% deuterium uptake between the high- and low-concentration samples. Thus, Xu directly teaches the step of determining differential uptake above the claimed threshold.
Xu does not specifically teach that wherein regions of the protein that exhibit reduced levels of deuterium contribute to self-association of the protein. However, Arora teaches that the reversible self-association (RSA) of the regions of protein (mAbs) gives rise to a network of the associated higher-order species that can affect the viscoelastic properties of the solution, resulting in increased viscosity (page 526, par 1). Arora also teaches the effects of reversible self-association (RSA) on hydrogen exchange of mAb-C (page 529). Arora teaches that regions of the protein that exhibit reduced levels of hydrogen exchange contribute to the self-association of the protein (page 533, par 3).
In summary, Xu teaches that regions of the protein that exhibit reduced levels of deuterium contribute to the increased viscosity of the protein in the high viscosity sample (par [0010]). The high concentration of a protein enhances self-association of the protein and therefore, increases the viscosity of the protein (Fig. 1A). Arora teaches that regions of protein self-association contribute to the viscosity of the protein solution (page 526, par 1), and the regions of the protein that exhibit the reduced levels of deuterium contribute to the self-association of the protein (page 533, par 3).
Thus, it would have been obvious to one of ordinary skill in the art to use Xu’s method to identify the regions of the protein that exhibit reduced levels of deuterium, and derives that the identified regions of the protein that exhibit reduced levels of deuterium contribute to self-association of the protein in the high viscosity sample. Because Arora teaches that the regions of the protein that exhibit the reduced levels of deuterium contribute to the self-association of the protein (page 533, par 3).
Xu is directed to systems and methods for identifying regions of proteins that contribute to viscosity in high-concentration protein formulations, using microdialysis in deuterated buffer followed by HDX-MS (Xu par [0010]). Xu expressly recognizes that high protein concentration enhances protein–protein interactions, which increase viscosity (Xu par [0005], Fig. 1A).
Arora is directed to reversible self-association (RSA) of monoclonal antibodies and explicitly teaches that RSA causes elevated viscosity, and that regions exhibiting reduced hydrogen/deuterium exchange correspond to self-association interfaces (Arora p. 526; p. 533).
Because both Xu and Arora address the same technical problem—identifying regions of antibodies responsible for concentration-dependent viscosity arising from protein–protein interactions—a person of ordinary skill in the art would have been motivated to combine Xu’s HDX-MS-based viscosity mapping method with Arora’s explicit teaching that reduced deuterium uptake corresponds to self-association regions. This represents a predictable use of prior art elements according to their established functions and is consistent with KSR Int’l Co. v. Teleflex Inc.
Neither the claims nor Xu require sulfate-induced self-association. Xu explicitly teaches microdialysis and HDX-MS analysis across a range of buffers, including histidine buffers at pH 5.0–7.5 (Xu par [0012]). Arora’s discussion of sulfate ions explains one mechanism by which self-association can be enhanced, but does not teach that self-association or viscosity mapping is limited to sulfate buffers.
A skilled artisan would have understood that buffer selection is a routine experimental variable and would reasonably apply Arora’s interpretation of HDX-MS data to Xu’s histidine-buffered system. Differences in buffer chemistry do not negate the motivation to combine nor render the combination unpredictable.
Regarding claim 2, Xu teaches that wherein the protein is a monoclonal antibody (par [0016]).
Regarding claim 3, An antibody's complementarity determining regions (CDRs) can "self-associate," meaning they can interact with each other on different antibody molecules, creating a phenomenon where antibodies bind to themselves due to specific amino acid sequences within the CDRs, Xu teaches that wherein the regions of the protein that exhibit differential deuterium uptake of 10% or more levels are complementarity determining regions (Table 3, par [0054][0065]).
Regarding claim 4, Xu fairly suggests that where the microdialysing is performed at a concentration used in subcutaneous delivery (par [0032]).
Regarding claim 5, Arora teaches that wherein surface charge distributions having positively charged patches contribute to self-association of the protein (page 537, par 0).
Both Xu and Arora disclose using HDX-MS to identify regions of reduced deuterium uptake, which is a well-established method for identifying buried, interacting, or solvent-shielded protein surfaces. Such regions inherently reflect electrostatic and hydrophobic interactions. Xu explicitly attributes viscosity-causing interactions to electrostatic and hydrophobic protein-protein interactions (Xu par [0005]), and Arora similarly discusses charge-mediated and hydrophobic interactions underlying RSA (Arora pp. 526, 532–534).
Thus, the claimed determination of surface charge distributions and hydrophobicity represents the inherent scientific interpretation of HDX-MS results and does not impart patentable distinction.
Regarding claim 6, Xu teaches that wherein the high concentration protein sample comprise between 100 mg/mL to 200 mg/mL of protein (120 mg/mL) (Table 3, par [0065]).
Regarding claim 8, Xu teaches that wherein the samples of protein in the microdialysing step are in 10 mM histidine buffer at pH 6.0 (par [0062]).
Regarding claim 9, Xu teaches that wherein the buffer comprising deuterium comprises 10 mM histidine buffer at pH 6.0 (par [0062]).
Regarding claim 10, Xu teaches that wherein the microdialysis is performed at 2 to 6 °C (par [0062]).
Regarding claim 11, Xu teaches that wherein at least one high concentration Protein sample and at least one low concentration protein sample is microdialysed for 4 hours and at least another sample is microdialysed for 24 hours (Table 3, par [0062] [0065]).
Regarding claim 12, Xu teaches that wherein the quenching step is performed at -2 to 2 °C for 1 to 5 minutes (par [0062]).
Regarding claim 13, Xu teaches digesting the protein into peptides before mass spectrometry analysis (par [0052]).
Regarding claim 14, Xu teaches that wherein the protein is selected from the group consisting of an antibody, a fusion protein, a recombinant protein, or a combination thereof (par [0016]).
Regarding claim 15, Xu teaches that wherein the protein is a concentrated monoclonal antibody (par [0016]).
Regarding claim 16, Xu teaches that wherein the monoclonal antibody is selected from the group consisting of abciximab, adalimumab, adalimumab-atto, ado-trastuzumab, alemtuzumab, alirocumab, atezolizumab, avelumab, basiliximab, belimumab, benralizumab, bevacizumab, bezlotoxumab, blinatumomab, brentuximab vedotin, brodalumab, canakinumab, capromab pendetide, certolizumab pegol, cemiplimab, cetuximab, denosumab, dinutuximab, dupilumab, durvalumab, eculizumab, elotuzumab, emicizumab-kxwh, emtansinealirocumab, evinacumab, evolocumab, fasinumab, golimumab, guselkumab, ibritumomab tiuxetan, idarucizumab, infliximab, infliximab-abda, infliximab-dyyb, ipilimumab, ixekizumab, mepolizumab, necitumumab, nesvacumab, nivolumab, obiltoxaximab, obinutuzumab, ocrelizumab, ofatumumab, olaratumab, omalizumab, panitumumab, pembrolizumab, pertuzumab, ramucirumab, ranibizumab, raxibacumab, reslizumab, rinucumab, rituximab, sarilumab, secukinumab, siltuximab, tocilizumab, tocilizumab, trastuzumab, trevogrumab, ustekinumab, and vedolizumab (par [0058]).
Regarding claim 17, Xu teaches that wherein the protein is an Fe-fusion protein (par [0059]).
Regarding claim 34, Xu teaches further comprising the step of modifying one or more of the regions identified as contributing to the self-association of the protein in the high concentration and high viscosity sample (par [0053] [0065]).
Regarding claim 35, Xu teaches further comprising the step of modifying one or more of the positively charged patches (regions) identified as contributing to the self-association of the protein in the high concentration and high viscosity sample (par [0053]). The self-association regions of a protein can be positively charged region, negatively charge region or hydrophobic region.
Regarding claim 36, Xu teaches that wherein the monoclonal antibody is dupilumab (par [0058]).
Regarding claim 37, Xu teaches that wherein the monoclonal antibody is cemiplimab (par [0058]).
Regarding claim 18, Xu teaches a protein produced by the method of claim 34 (par [0065]).
Response to Arguments
Applicant’s arguments filed 01/08/2026 have been fully considered but they are not persuasive.
Applicant argues that the Office Action fails to establish a motivation to combine Xu and Arora. This argument is not persuasive.
Xu is directed to systems and methods for identifying regions of proteins that contribute to viscosity in high-concentration protein formulations, using microdialysis in deuterated buffer followed by HDX-MS (Xu par [0010]). Xu expressly recognizes that high protein concentration enhances protein–protein interactions, which increase viscosity (Xu par [0005], Fig. 1A).
Arora is directed to reversible self-association (RSA) of monoclonal antibodies and explicitly teaches that RSA causes elevated viscosity, and that regions exhibiting reduced hydrogen/deuterium exchange correspond to self-association interfaces (Arora p. 526; p. 533).
Because both Xu and Arora address the same technical problem—identifying regions of antibodies responsible for concentration-dependent viscosity arising from protein–protein interactions—a person of ordinary skill in the art would have been motivated to combine Xu’s HDX-MS-based viscosity mapping method with Arora’s explicit teaching that reduced deuterium uptake corresponds to self-association regions. This represents a predictable use of prior art elements according to their established functions and is consistent with KSR Int’l Co. v. Teleflex Inc.
Applicant argues that neither Xu nor Arora teaches determining a differential deuterium uptake between high- and low-concentration protein samples. This argument is factually incorrect.
Xu explicitly discloses comparative HDX-MS analysis between low concentration (15 mg/mL) and high concentration (120 mg/mL) antibody samples (Xu par [0065]). Table 3 of Xu reports deuterium uptake values for both concentrations and shows that peptides identified as contributing to viscosity exhibit differences exceeding 10% deuterium uptake between the high- and low-concentration samples.
Accordingly, Xu alone teaches determining differential deuterium uptake between high- and low-concentration samples, including differences greater than the claimed 10% threshold. Arora further confirms that such reduced uptake regions correspond to self-association interfaces.
Applicant asserts that the “10% or more” limitation is not taught or suggested. This argument is not persuasive.
As noted above, Xu’s Table 3 expressly shows uptake differences greater than 10% between 15 mg/mL and 120 mg/mL samples in regions identified as contributing to viscosity and protein interactions (Xu par [0065], Table 3). Therefore, the claimed numerical threshold is expressly disclosed by Xu.
Even if Xu were viewed as not explicitly emphasizing the numerical cutoff, selecting a specific percentage threshold to define a “significant” uptake difference would have been an obvious matter of routine optimization of a known result, particularly where Xu and Arora already teach that uptake differences identify interaction regions.
Applicant argues that Xu and Arora do not teach protein samples having a viscosity of 80 cP or greater and that reaching such viscosity would require undue experimentation. This argument is not persuasive.
Xu teaches antibody concentrations up to 200 mg/mL (Xu par [0011]) and explicitly correlates increasing concentration with increasing viscosity (Xu Fig. 1A). Xu recognizes high viscosity as a limiting factor for administration and processing (Xu ¶[0005]), indicating that viscosities at or above the claimed threshold are inherently contemplated.
Arora reports viscosities up to approximately 75 mPa·s (≈75 cP) at 60 mg/mL under certain buffer and temperature conditions (Arora Fig. 3A), demonstrating that viscosities approaching the claimed value are achieved at substantially lower concentrations. A person of ordinary skill would have reasonably expected that increasing concentration into the range taught by Xu (≥100 mg/mL) would result in viscosities meeting or exceeding 80 cP.
Accordingly, the viscosity limitation does not patentably distinguish the claims.
Applicant argues that Arora’s use of sulfate or chloride buffers teaches away from the claimed histidine buffer and negates motivation to combine. This argument is not persuasive.
Neither the claims nor Xu require sulfate-induced self-association. Xu explicitly teaches microdialysis and HDX-MS analysis across a range of buffers, including histidine buffers at pH 5.0–7.5 (Xu par [0012]). Arora’s discussion of sulfate ions explains one mechanism by which self-association can be enhanced, but does not teach that self-association or viscosity mapping is limited to sulfate buffers.
A skilled artisan would have understood that buffer selection is a routine experimental variable and would reasonably apply Arora’s interpretation of HDX-MS data to Xu’s histidine-buffered system. Differences in buffer chemistry do not negate the motivation to combine nor render the combination unpredictable.
Applicant argues that Xu and Arora do not teach determining “surface charge distributions” or “positively charged patches.” This argument is not persuasive.
Both Xu and Arora disclose using HDX-MS to identify regions of reduced deuterium uptake, which is a well-established method for identifying buried, interacting, or solvent-shielded protein surfaces. Such regions inherently reflect electrostatic and hydrophobic interactions. Xu explicitly attributes viscosity-causing interactions to electrostatic and hydrophobic protein-protein interactions (Xu par [0005]), and Arora similarly discusses charge-mediated and hydrophobic interactions underlying RSA (Arora pp. 526, 532–534).
Thus, the claimed determination of surface charge distributions and hydrophobicity represents the inherent scientific interpretation of HDX-MS results and does not impart patentable distinction.
Conclusion
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to XIAOYUN R XU, Ph. D. whose telephone number is (571)270-5560. The examiner can normally be reached M-F 8am-5pm.
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/XIAOYUN R XU, Ph.D./ Primary Examiner, Art Unit 1797
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