DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Priority
This application claims benefit of priority to Provisional Application 63/221,436 filed on 07/13/2021.
Amendments and Claim Status
In the reply filed 12/22/2025, Applicant amended claim 1 and added new claim 18. Claim 8 was previously canceled.
Claims 1-7 and 9-18 are currently pending and under examination.
Claim Objections
Claim 1 is objected to because of the following informalities: Claim 1 recites “wherein said amount of target immobilized beads binds …” in line 7. The claim is missing a word. It appears as though the claims should recite “wherein said amount of target immobilized on beads binds …”. Appropriate correction is required.
Maintained Rejections (with modification as necessitated by amendment)
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-7 and 9-18 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1, as amended, recites the limitation "wherein the at least one product-related variant has compromised binding with said target" in lines 4-5. There is insufficient antecedent basis for this limitation in the claim. ‘Target’ is not recited prior to the just recited limitation. Therefore, there is insufficient antecedent basis for this limitation. For the purposes of compact prosecution, this limitation is being examined as if the claim recited "wherein the at least one product-related variant has compromised binding with a target".
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1, 4-6 and 9-18 are rejected under 35 U.S.C. 103 as being unpatentable over Bondarenko et al. (WO 2020/247790 A1, 10/12/2020) (Of Record).
Regarding claim 1, see 112b above. Bondarenko et al. disclose methods of identifying structures, e.g., attributes, of a therapeutic protein or a target that affect an interaction between the therapeutic protein and the target (See entire reference, more specifically, the Abstract).
The native structures of proteins adapt to changes within the protein's environment. Although this flexibility in structure is required for the biological function of most, if not all, proteins, it also presents many challenges during the development of therapeutic proteins for pharmaceutical applications. For example, therapeutic proteins endure various conditions during the many process steps that lead up to being administered to a patient. The many process steps include, for instance, one or more of protein production (e.g., recombinant production), harvest, purification, formulation, filling, packaging, storage, delivery, and final preparation immediately prior to administration to the patient. During each of these steps, a therapeutic protein is placed in one or more environments that may or may not lead to a change in its structure. The change in structure can lead to the formation of different species of the therapeutic protein that results in a heterogeneous product. While some species retain their ability to bind to their targets and therefore maintain therapeutic efficacy, others lose target binding ability and thus become functionally inactive. In order to maximize and maintain quality control of these pharmaceutical products, the biopharmaceutical industry has focused much effort to understand why some species lose activity while others retain activity. Current methodologies exist for analyzing species formation of therapeutic proteins.
However, current techniques are impractical with regard to time and cost, while others fail to mirror therapeutic proteins in a physiologically-relevant context. Also, some current techniques use a covalent cross-linking agent or a labeling agent which can negatively impact the results of the analysis. Accordingly, there is a need for methods of identifying the species of therapeutic proteins that lead to the loss of binding, as well as identifying the conditions that lead to the formation of such species (Paragraph [0003)].
Bondarenko et al. disclose a specific example, Example 3, utilizing affinity chromatography precipitation wherein beads labeled with the target are used (Paragraph [00125]). Specifically, in this example, affinity separation (affinity enrichment) of strongly-bound therapeutic protein-target complexes and unbound modified therapeutic protein is performed using binding targets immobilized onto resin beads and the beads are placed in an affinity chromatography column (Paragraph [00126]). Next, therapeutic proteins are stressed and mixed with the beads and an aliquot of the mixture is injected onto the affinity chromatography column (Paragraph [00127]). Fractions are eluted off the column with an appropriate elution buffer so that the bound fraction comprising the therapeutic protein-binding target complexes are retained on the column while the unbound fraction comprising therapeutic proteins not bound to the binding targets elute from the column (Paragraph [00127]). Thus, the fraction eluted does not contain the target as the target was immobilized on the beads and was retained on the column while the flow-through from the column contained therapeutic proteins that did not bind to the target.
Bondarenko et al. further disclose a competitive size exclusion chromatography (SEC) affinity separation for identification of antibody modifications impacting binding to target protein (Paragraph [00144]). More specifically, assessment of attributes by competitive affinity binding between an antibody and its target Her2, followed by SEC fractionation and LC-MS peptide mapping (Paragraph [00146]). In one iteration of the method, the critical quality attributes responsible for the loss of binding were identified (Paragraph [00150]). The method was applied to several antibody:target complexes by mixing them in a ratio defined by stoichiometry of interactions, typically 1:2 (Paragraph [00150]). When the smaller amount of target was provided, the 1:1 ratio, the antibody species with modifications that resulted in reduced binding eluted as unbound from the SEC (Paragraph [00150]). The disclosure of Bondarenko et al. of using the smaller amount of receptor, 1:1, leading to reduced binding among antibody species with modifications so the unbound would elute, reads on determining an amount of capture molecule immobilized on a solid surface to contact with the sample wherein the solid surface binds a determined percentage and the percentage is less than 100%.
Also, it would have been obvious to one of ordinary skill in the art that beads with a determined amount of target, a 1:1 or 1:2 ratio, would be used because as discussed above, affinity separation of strongly-bound therapeutic protein-target complexes and unbound modified therapeutic protein is performed using binding targets immobilized onto resin beads and the beads are placed in an affinity chromatography column (Paragraph [00126]). Next, therapeutic proteins are stressed and mixed with the beads and an aliquot of the mixture is injected onto the affinity chromatography column (Paragraph [00127]). Fractions are eluted off the column with an appropriate elution buffer so that the bound fraction comprising the therapeutic protein-binding target complexes are retained on the column while the unbound fraction comprising therapeutic proteins not bound to the binding targets elute from the column (Paragraph [00127]). Thus, before the SEC fractionation and LC-MS peptide mapping, beads would have been used to capture the protein-target complexes, the beads would be put in an affinity chromatography column, fractions would be eluted producing a flow-through, and the flow-through would be subjected to SEC fractionation and LC-MS peptide mapping. Additionally, absent evidence to the contrary, it would be expected that the flow-through, which contains therapeutic proteins that did not bind to the target, would contain protein of interest and at least one attribute as there is not enough target to bind everything, meaning protein of interesting and attributes of the protein of interest would be left unbound and would elute.
Bondarenko et al. further disclose the use of a control, wherein the control was just antibody, a completely unbound fraction (Paragraph [00114]). It is further evident the control did not contain any target due to Bondarenko et al. delineating a specific fraction as ‘completely unbound antibody’ based upon the fraction having the same elution time as the control (Paragraph [00114]). Bondarenko et al. go on to state the data obtained from LC-MS peptide mapping leads to the identification and quantification of the abundance of each species of each fraction (Paragraph [0068]).
Bondarenko et al. do not disclose each limitation present in claim 1 as instantly-claimed within one, single embodiment.
However, even though Bondarenko et al. do not disclose each limitation within one, single embodiment, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have combined the multiple methods of Bondarenko et al. because all of the methods are directed to identifying attributes of therapeutic proteins motivated by the desire to accurately identify the different attributes of the therapeutic proteins to determine if the attributes affect the interaction between the therapeutic protein and the target as taught by the prior art and discussed above.
Regarding claim 4, as disclosed above regarding claim 1, Bondarenko et al. disclose Example 3 utilizing affinity chromatography precipitation wherein beads labeled with the target are used (Paragraph [00125]). Specifically, in this example, affinity separation (affinity enrichment) of strongly-bound therapeutic protein-target complexes and unbound modified therapeutic protein is performed using binding targets immobilized onto resin beads and the beads are placed in an affinity chromatography column (Paragraph [00126]). Next, therapeutic proteins are stressed and mixed with the beads and an aliquot of the mixture is injected onto the affinity chromatography column (Paragraph [00127]). Fractions are eluted off the column with an appropriate elution buffer so that the bound fraction comprising the therapeutic protein-binding target complexes are retained on the column while the unbound fraction comprising therapeutic proteins not bound to the binding targets elute from the column (Paragraph [00127]). Thus, under the broadest reasonable interpretation, as enriching simply means concentrating the desired component, the flow-through containing only unbound therapeutic proteins reads on being enriched for at least one product related variant as the therapeutic protein variants are what was not binding/had reduced binding and the bound therapeutic protein target complexes were retained on the column, increasing the concentration of, or enriching, the therapeutic protein variants in the flow-through.
Regarding claim 5, Bondarenko et al. further disclose centrifuging to obtain a supernatant (i.e., flow-through) of the unbound and of the bound fraction (Claim 29 of Bondarenko et al.).
Regarding claim 6, Bondarenko et al. additionally disclose wherein the unbound fraction and bound fraction are subjected to a peptide digestion step prior to the quantifying step or identifying and quantifying step (Claim 33 of Bondarenko et al.).
Regarding claims 9 and 10, Bondarenko et al. do not disclose incubation for one hour or incubation at about room temperature.
However, Bondarenko et al. further disclose where therapeutic proteins are stressed and subsequently mixed with the beads covered with the binding targets. For the first subgroup, an aliquot of the mixture is injected onto the affinity chromatography column. For the second subgroup, the centrifuge tubes are gently rocked overnight. For the second group, the cells expressing the binding targets at the cell surface are mixed with the stressed therapeutic proteins and incubated in centrifuge tubes with gentle rocking. After the mixing, the centrifuge tubes are centrifuged to separate the beads comprising the bound fraction comprising therapeutic protein-binding target complexes from the unbound fraction comprising therapeutic proteins unbound to binding target (Paragraph [00127]).
Accordingly, from the above disclosure, Bondarenko et al. disclose incubation. Since it appears that incubation is a necessary step to obtain beads comprising therapeutic protein-binding target complexes, it would have taken no more than the relative skills of one of ordinary skill in the art through routine experimentation to have arrived at the claimed incubation time and temperature based on the degree of binding one desires. Where 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. See MPEP 2144.05(II)(A).
Regarding claim 11, Bondarenko et al. further disclose wherein the mixture is separated into at least two fractions using a technique that separates components of a mixture based on size (Claim 27 of Bondarenko et al.).
Regarding claim 12, Bondarenko et al. further disclose wherein the method is used for detecting fragmentation/clipping (Paragraph [0062]).
Regarding claim 13, Bondarenko et al. further disclose wherein the attribute forms as a result of a chemical modification and wherein the chemical modification is aggregation (Claims 51 and 52 of Bondarenko et al.).
Regarding claim 14, Bondarenko et al. further disclose wherein the attribute forms as a result of chemical modification and wherein the chemical modification alters the mass-to-charge ratio of charged ions of an amino acid of the therapeutic protein (Claim 51 of Bondarenko et al.).
Regarding claim 15, Bondarenko et al. further disclose wherein attributes include post-translational modifications of the therapeutic protein (Paragraph [00146]).
Regarding claim 16, Bondarenko et al. further disclose wherein the therapeutic protein can comprise an antibody, and the target can comprise an antigen for the antibody (Paragraph [0032]).
Regarding claim 17, Bondarenko et al. further disclose that when the abundance of a structure, e.g., attribute, in the unbound fraction is greater than the abundance of the structure, e.g., attribute, in the bound fraction, the structure, e.g., attribute, negatively affects the interaction between the therapeutic protein and the target (Paragraph [0005]).
Regarding claim 18, it is noted this limitation was previously recited in claim 1 but was moved to new claim 18. Bondarenko et al. disclose a stress that causes an about 10% to about 50% reduction in interactions, relative to interactions in corresponding conditions lacking the stress (Paragraph [0055]). Further, the stress causes an increase in the KD of the therapeutic protein for its target which KD is associated with weaker binding (Paragraph [0055]). Thus, assuming an initial binding interaction to be 100%, a reduction of about 10% to about 50% binding would result in about 50% to about 90% binding interaction, which overlaps with the claimed range of about 30% to about 80%. Therefore, given the broadest reasonable interpretation, Bondarenko et al. teach at least one product-related variant having compromised binding with the target and an amount of target capable of binding to about 30% to about 80% of the protein of interest.
Claim 2 is rejected under 35 U.S.C. 103 as being unpatentable over Bondarenko et al. (WO 2020/247790 A1, 10/12/2020) (Of Record) as applied to claims 1, 4-6 and 9-17 above, and further in view of Yan et al. (Analytical Chemistry, 10/03/2018) (Of Record).
The teachings of Bondarenko et al. are discussed above.
Regarding claim 2, Bondarenko et al. do not disclose wherein the liquid chromatography is strong cation exchange chromatography.
However, Yan et al. teach the use of strong cation exchange chromatography. Yan et al. disclose a method that combines a generic strong cation exchange (SCX) chromatography step with ultrasensitive online native MS analysis (SCX-MS) optimized for mAb separation and detection (Abstract). The combination of efficient upfront chromatographic separation and highly sensitive MS analysis allows the detection of minor variants present at very low levels (Results and Discussion).
As such, it would have been prima facie obvious for one of ordinary skill in the art to have used strong cation exchange chromatography with SCX-MS in the method of Bondarenko et al. motivated by the desire to detect a product-related variant that may be present only in low abundance as taught by Yan et al.
Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Bondarenko et al. (WO 2020/247790 A1, 10/12/2020) (Of Record) as applied to claims 1, 4-6 and 9-17 above, and further in view of Jooss et al. (US 2022/0162320, 05/26/2022) (Of Record).
The teachings of Bondarenko et al. are discussed above.
Regarding claim 3, Bondarenko et al. do not disclose wherein said beads are magnetic beads.
However, Jooss et al. teach the use of magnetic beads. Jooss et al. disclose a method where the antibody or binding partner is bound to a solid support or matrix, such as a magnetic bead or paramagnetic bead, to allow for separation of cells for positive and/or negative selection (Paragraph [0803]).
Generally, it is prima facie obvious to select a known material for incorporation into a composition, based on its recognized suitability for its intended use. See MPEP 2144.07. As such, it would have been prima facie obvious for one of ordinary skill in the art to have used magnetic beads in the method of Bondarenko et al. since the method does not require a particular type of bead and magnetic beads are known and effective beads for separation of components as taught by Jooss et al.
Claims 3 and 7 are rejected under 35 U.S.C. 103 as being unpatentable over Bondarenko et al. (WO 2020/247790 A1, 10/12/2020) (Of Record) as applied to claims 1, 4-6 and 9-17 above, and further in view of Polukhtin et al. (US 20160370376 A1, 12/22/2016).
The teachings of Bondarenko et al. are discussed above.
Regarding claims 3 and 7, Bondarenko et al. do not disclose wherein said beads are magnetic beads or coated with streptavidin resin.
However, Polukhtin et al. disclose a method for the detection and isolation of targets from heterologous mixtures (See entire reference, more specifically, Paragraph [0002]). Polukhtin et al. further disclose a method to detect a molecule by using binding molecules that have a specific affinity for another molecule, such as the binding of an antigen to an antigen-specific antibody, wherein either the antigen or antibody is immobilized on a solid support, such as a magnetic bead, and used to isolate the target molecule (Paragraph [0005]). More specifically, biotin or a biotin derivative is bound directly to a target molecule, such as a protein, and then interacted with streptavidin or avidin conjugated to an affinity medium like a magnetic bead and then used to isolate a target (Paragraph [0007]).
As such, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have utilized magnetic beads or beads coated with streptavidin resin in the method of Bondarenko et al. to effectively immobilize the target onto the bead as taught by Polukhtin et al. as this was a known and effective means of immobilizing a target onto a bead.
USC § 103 – Response to Arguments
Applicant's arguments filed 12/22/2025 have been fully considered but they are not persuasive.
The arguments presented by Applicant are all directed to the prior art not teaching the new limitations added to the amended claim set filed 12/22/2025. It is the Examiner’s position that the prior art does teach these limitation as set forth and explained in the modified rejection set forth above as necessitated by amendment.
Conclusion
Claims 1-7 and 9-18 are rejected
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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.
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/A.T.W./Examiner, Art Unit 1653
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653