DETAILED ACTION
The amendment (03/23/2026) and RCE filed on 04/24/2026 has been entered and fully considered. Claims 5 and 11 are canceled. Claims 1-4, 6, 8-10, 12-18 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) 1-4, 6, 8-10, 12-18 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, IDS)(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]), wherein the two time points are between 4 hours and 24 hours (par [0012]);
subsequently quenching the microdialysis of the samples (par [0010]); and
analyzing the quenched samples in a hydrogen/deuterium exchange mass spectrometry system to determine a differential deuterium uptake between the high concentration protein sample and the low concentration protein (Table 3, par [0010] [0065]), and
identifying and comparing regions of the protein that exhibit differential deuterium uptake of 10% or more and regions of the protein with positive, negative, and/or hydrophobic patches, wherein regions of protein that exhibit differential deuterium uptake of 10% or more that overlap with regions of the protein that have positively charged patches 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 [0012]),
thereby identifying regions in a protein that contribute to the viscosity of the protein in a high concentration and high viscosity sample (Table 3, par [0010] [0065]).
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), and determining surface charge distribution of positive, negative, and/or hydrophobic patches of the protein by homology modelling (Fig. 7, page 530, par 3), and wherein regions of protein that exhibit differential deuterium uptake of 10% or more that overlap with regions of the protein that have positively charged patches contribute to self- association of the protein in the high concentration and high viscosity sample (page 532, par 0).
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 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 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 03/23/2026 have been fully considered but they are not persuasive.
Applicant argues that the Office Action fails to provide a motivation to combine Xu and Arora and therefore fails to establish a prima facie case of obviousness. The argument is not persuasive.
Xu is directed to identifying regions of proteins that contribute to increased viscosity in high-concentration protein formulations using hydrogen/deuterium exchange mass spectrometry (HDX-MS). Xu teaches that intermolecular interactions occurring at high protein concentrations lead to increased viscosity and that HDX-MS may be used to identify regions associated with such interactions (par [0010]).
Arora likewise investigates protein-protein interactions occurring in concentrated monoclonal antibody formulations. Specifically, Arora explains that reversible self-association (RSA) of monoclonal antibodies results in "increased viscosity" (page 526, par 1) and that HDX-MS may be used to identify protein regions involved in such self-association (page 533, par 3). Arora states that "Two specific sequences covering complementarity-determining regions CDR2H and CDR2L ... showed significant protection against deuterium uptake (i.e., decreased hydrogen exchange). These results define the major protein-protein interfaces associated with the concentration-dependent RSA of mAb-C." (abstract). Arora further explains that "significant decreases in hydrogen exchange (i.e., increased protection against deuterium uptake) were observed upon RSA of mAb-C" in the identified regions (page 530, par 1).
Accordingly, both Xu and Arora are directed to the same problem of identifying protein regions associated with concentration-dependent protein-protein interactions that contribute to elevated viscosity in concentrated protein formulations. One of ordinary skill in the art would have been motivated to apply Arora's express teaching that regions exhibiting reduced deuterium uptake correspond to self-association interfaces when interpreting the HDX-MS results generated by Xu in order to better identify regions responsible for concentration-dependent viscosity. Such a combination merely applies a known analytical interpretation from one HDX-MS study to another closely related HDX-MS study involving the same class of protein interactions and would have represented a predictable use of prior art elements according to their established functions.
Therefore, the rejection is not based on impermissible hindsight or a mere conclusory assertion that the individual claim elements were known independently. Rather, the combination is supported by the express teachings of the references and by the recognized relationship between self-association, reduced deuterium uptake, and increased viscosity in concentrated protein formulations as taught by Arora and Xu.
Applicant’s March 23, 2026 amendment added the 4- and 24-hour time points, homology modeling, charge/hydrophobic patches, and overlap with positively charged patches. Arora expressly compares high/low concentration samples by HX-MS and identifies RSA regions showing decreased deuterium uptake.
Applicant’s arguments regarding the newly added limitations have been fully considered but are not persuasive.
Regarding the limitation that the two time points are between 4 hours and 24 hours, Xu teaches microdialysis against deuterium-containing buffer for at least two different time periods, including 4 hours and 24 hours (par [0012]). Accordingly, the claimed time points are taught by Xu and do not patentably distinguish the claims.
Regarding the limitation requiring 10 mM histidine buffer at pH between 5.0 and 7.5, Xu expressly teaches that samples may be microdialyzed in a buffer having a pH between 5.0 and 7.5 and identifies 10 mM histidine at pH 6.0 as a preferred buffer (par [0012]). Thus, the claimed histidine buffer is taught by Xu. Applicant’s arguments concerning Arora’s sulfate-containing buffer are not persuasive because Arora is relied upon for its teaching that regions exhibiting reduced hydrogen/deuterium exchange correspond to self-association interfaces, not for the specific histidine buffer limitation.
Regarding the limitation requiring a high concentration protein sample at 100 mg/mL or greater, Xu teaches protein samples having concentrations between 10 mg/mL and 200 mg/mL (par [0011]) and specifically compares low concentration and high concentration antibody samples, including 15 mg/mL and 120 mg/mL samples (Fig. 3A-3F, par [0019][0065]). Therefore, Xu teaches a high concentration protein sample within the claimed range.
Regarding the limitation requiring a viscosity of 80 cP or greater, Xu teaches antibody concentrations up to 200 mg/mL (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 (par [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 (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. Thus, the claimed viscosity limitation would have been expected from the concentration-dependent viscosity behavior taught by Xu and Arora.
Regarding the limitation requiring determining surface charge distribution of positive, negative, and/or hydrophobic patches by homology modeling, this limitation does not overcome the rejection. Arora teaches mapping HX-MS results onto a homology model of the antibody to identify regions involved in RSA (Fig. 7, page 530, par 3). It would have been obvious to use known homology modeling to evaluate the surface properties of the same regions identified by HDX-MS, because Arora explains that electrostatic and hydrophobic interactions contribute to reversible self-association. Thus, determining surface charge and hydrophobic patch information by homology modeling is an obvious analytical step for interpreting the protein regions identified by HDX-MS.
Regarding the limitation requiring identifying and comparing regions having differential deuterium uptake of 10% or more with regions having positive, negative, and/or hydrophobic patches, Xu already teaches comparing deuterium uptake between low and high concentration samples and Table 3 shows uptake differences greater than 10% in regions associated with viscosity. Arora teaches that decreased hydrogen/deuterium exchange identifies regions involved in reversible self-association (Fig. 7, page 530, par 3). Therefore, comparing the HDX-MS-identified regions with modeled surface charge or hydrophobic patches would have been an obvious way to identify which interacting surface regions contribute to self-association.
Regarding the limitation that regions exhibiting differential deuterium uptake of 10% or more that overlap with positively charged patches contribute to self-association, the argument is not persuasive. Arora teaches that self-association of monoclonal antibodies is caused by weak, transient non-covalent interactions, including electrostatic and hydrophobic interactions, and further teaches that decreased hydrogen exchange identifies the RSA interface (page 526, par 2). Arora also discusses charge-mediated interactions in the context of RSA (page 532, par 0). Therefore, one of ordinary skill in the art would have had reason to identify whether the regions showing reduced deuterium uptake overlap with positively charged surface patches, because such overlap would indicate a charge-mediated self-association interface.
Accordingly, the amended limitations are taught or rendered obvious by Xu in view of Arora. Xu teaches the claimed microdialysis/HDX-MS protocol, histidine buffer, concentration range, time points, and differential uptake analysis, including uptake differences of 10% or more. Arora provides the reason to interpret reduced uptake regions as self-association interfaces and further teaches that charge-mediated and hydrophobic interactions contribute to reversible self-association. Therefore, Applicant’s arguments do not overcome the rejection.
Conclusion
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.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Lyle Alexander can be reached on 571-272-1254. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/XIAOYUN R XU, Ph.D./ Primary Examiner, Art Unit 1797
Prosecution Insights