DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Claims
Claims 1-20 are currently pending.
Election/Restrictions
Applicant’s election of Group I, Claims 1-10 and 12-20, in the reply filed on 12/22/2025 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.03(a)).
The requirement is still deemed proper and is therefore made FINAL.
Claim 11 has been withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to nonelected inventions and species, there being no allowable generic or linking claims.
Claims 1-10 and 12-20 are being examined in this application.
Claim Objections
Applicant is advised that should claims 2-10 be found allowable, claims 12-20 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 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 of this title, 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 1-3, 5-9, 12-13, and 15-19 are rejected under 35 U.S.C. 103 as being unpatentable over Zheng et al (US 2021/0109107 A1; 4/15/2021.) in view of Zhang et al (US 2021/0008199 A1; 1/14/2021.).
The instant claims recite a method for identifying at least one host cell protein in a sample matrix including a protein of interest, comprising: (a) adding a digestion agent under native conditions to obtain a native digested sample; and (b) analyzing the native digested sample using a triple quadrupole mass spectrometer to identify a peptide specific to said at least one host cell protein, wherein said triple quadrupole mass spectrometer is run to obtain multiple reaction monitoring for at least one precursor-product ion for said peptide.
Zheng teaches a method for characterizing host cell proteins in a sample matrix (Abstract), comprising subjecting the sample matrix having host cell proteins to non-denaturing (native, para 0229) digestion conditions to form a mixture, enriching host cell proteins in said mixture (para 0075), and characterizing at least one of the host cell proteins using a mass spectrometer (para 0079, 0206), wherein the sample matrix comprises a protein of interest (para 0078), the enrichment step comprises adding a hydrolyzing agent including trypsin to the sample to produce peptides (para 0077, 0187), the enrichment step further comprises washing (para 0076), the mass spectrometer is a tandem mass spectrometer coupled with a liquid chromatography (para 0079), and the characterizing comprises identifying the peptides (para 0207, 0211). The method further comprising performing depletion of protein of interest (Example 2, for example).
Zheng does not teach the method wherein the mass spectrometer is a triple quadrupole mass spectrometer, said triple quadrupole mass spectrometer is run to obtain multiple reaction monitoring for at least one precursor-product ion for said peptide (claim 1), said triple quadrupole mass spectrometer is coupled to liquid chromatography (claims 5 and 15), said triple quadrupole mass spectrometer is run in a positive mode (claims 6 and 16), and the host cell protein is liver carboxylesterase (claims 9 and 19).
However, Zheng does teach the method wherein the mass spectrometer is used for characterizing at least one of the host cell proteins (para 0206), the characterizing comprises identifying the peptides (para 0207), the mass spectrometer is a tandem mass spectrometer (para 0209), tandem mass spectrometry methods include a tandem-in-space mass spectrometer involving precursor ion selection and product ion analysis (para 0210), and the tandem mass spectrometer is coupled with a liquid chromatography (para 0079).
Zhang teaches a method comprising analyzing a digested sample (hydrolysis of one or more peptide bonds of a protein, para 0158) using a mass spectrometer that is coupled to a liquid chromatography – multiple reaction monitoring (MRM) system (para 0029), wherein MRM refers to a mass spectrometry-based technique that can precisely quantify small molecules, peptides, and proteins within complex matrices with high sensitivity, specificity and a wide dynamic range, MRM is typically performed with triple quadrupole mass spectrometer involving select a precursor ion in the first quadrupole and select specific product ion for detection in the third quadrupole (para 0177), and the mass spectrometer is run in a positive mode (para 0191, 0195). In addition, Zhang teaches reduction of host cell proteins can be an important step in a drug formulation development (para 0007), porcine liver esterase (liver carboxylesterase) is reported to be able to specifically hydrolyze polysorbate 80 and lead the formation of PS85 over time in mA drug product, it can be essential to evaluate the effect of a host cell protein copurified with a drug product on polysorbates to ensure stability of the drug formulation, and this can require identification of the host cell protein and its ability to degrade polysorbates (para 0077).
Thus, before the effective filing date of the claimed invention, it would have been obvious to one of ordinary skill in the art to incorporate a triple quadrupole mass spectrometer to identify a peptide specific to a host cell protein, since Zheng and Zhang both disclose a method comprising identifying a peptide obtained from a sample matrix having host cell proteins using a tandem mass spectrometer coupled with a liquid chromatography, and Zhang specifically discloses that a tandem mass spectrometer that is coupled to a liquid chromatography – multiple reaction monitoring (MRM) can precisely quantify small molecules, peptides, and proteins within complex matrices with high sensitivity, specificity and a wide dynamic range, and that MRM is typically performed with triple quadrupole mass spectrometer. In addition, before the effective filing date of the claimed invention, it would have been obvious to one of ordinary skill in the art to use liver carboxylesterase as host cell protein, since liver carboxylesterase has been used as host cell protein in the art as evidenced by Zhang. Moreover, before the effective filing date of the claimed invention, one of ordinary skill in the art would have been motivated by the cited reference and routine practice to incorporate a triple quadrupole mass spectrometer with a reasonable expectation for successfully characterizing host cell proteins in a sample matrix.
References cited above do not teach the method wherein the digestion agent is about 0.4 µg of trypsin (claims 3 and 13).
However, Zheng and Zhang both teach the method wherein trypsin is used as a digestion agent. Zheng does teach the sample is digested with trypsin, 1:20 w/w enzyme:substrate ratio (para 0250, for example), and Zhang does teach the sample is digested with 50 µl 0.01 µg/L trypsin (para 0198). In addition, Zheng does teach the term ratio of hydrolyzing agent to the protein and the time required for digestion can be appropriately selected to obtain a digestion of the protein, when the enzyme to substrate ratio is unsuitably high, it can cause a non-specific cleavage thereby limiting the ability to identify proteins as well as reducing sequence coverage, on the other hand, a low E/S ratio would need long digestion and thus long sample preparation time (para 0188).
Thus, before the effective filing date of the claimed invention, it would have been obvious to one of ordinary skill in the art to optimize the concentration of trypsin, since Zheng discloses that the term ratio of hydrolyzing agent to the protein and the time required for digestion can be appropriately selected to obtain a digestion of the protein. Generally, differences in concentration will not support patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration is critical. (MPEP 2144.05 II) Moreover, before the effective filing date of the claimed invention, one of ordinary skill in the art would have been motivated by the cited reference and routine practice to optimize the concentration of trypsin, with a reasonable expectation for successfully characterizing host cell proteins in a sample matrix.
Claims 4 and 14 are rejected under 35 U.S.C. 103 as being unpatentable over Zheng et al (US 2021/0109107 A1; 4/15/2021.) in view of Zhang et al (US 2021/0008199 A1; 1/14/2021.) as applied to claims 1-3, 5-9, 12-13, and 15-19 above, further in view of Huang et al (Anal. Chem. 2017;89:5436-5444.).
References cited above do not teach the method wherein the native conditions include using said digestion agent such that said protein of interest is digested less than said host cell protein (claims 4 and 14).
However, Zheng and Zhang both teach the method wherein trypsin is used as a digestion agent, and Zheng does teach non-denaturing (native) digestion conditions. Huang teaches antibodies are very stable and resistant to trypsin digestion in their native state (p.5439 col left – para 2), utilizing trypsin digestion under non-denaturing (native) conditions, proteins of interest are less likely to be digested, while host cell proteins are preferentially digested (p.5443 col left – last para).
Thus, before the effective filing date of the claimed invention, it would have been obvious to one of ordinary skill in the art to incorporate native conditions with trypsin such that protein of interest is digested less than host cell protein, since Zheng and Zhang both disclose a method wherein trypsin is used as a digestion agent, Zheng discloses non-denaturing (native) digestion conditions, and Huang discloses that under non-denaturing (native) digestion conditions, protein of interest is digested less than host cell protein. Moreover, before the effective filing date of the claimed invention, one of ordinary skill in the art would have been motivated by the cited reference and routine practice to incorporate native conditions with trypsin such that protein of interest is digested less than host cell protein with a reasonable expectation of success.
Claims 10 and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Zheng et al (US 2021/0109107 A1; 4/15/2021.) in view of Zhang et al (US 2021/0008199 A1; 1/14/2021.) as applied to claims 1-3, 5-9, 12-13, and 15-19 above, further in view of Ma et al (J. Proteome Res. 2020;19:3396-3404.).
References cited above do not teach the method wherein the lower limit of quantification of the method is less than about 1 ppm (claims 10 and 20).
However, Zheng does teach a key criterion in developing biopharmaceutical products can be to monitor impurities in the product (para 0004). Zhang does teach one of the major challenges for protein biotherapeutics development is to overcome the limited stability of the proteins which can be affected by the presence of host cell protein, evaluation of its effect on the drug formulation and reduction of such host cell proteins can be an important step in a drug formulation development (para 0007). Ma teaches there is a growing industry and regulatory need to detect host cell protein impurities in the production of protein biopharmaceuticals, as certain host cell proteins can impact product stability, safety, ad efficacy, even at low levels (Abstract). Ma teaches detecting peptides at levels as low as 0.1 ppm with respect to the original mAb concentration support purification process development (p.3403 col left – para 2).
Thus, before the effective filing date of the claimed invention, it would have been obvious to one of ordinary skill in the art to achieve a lower limit of quantification that is less than about 1 ppm, since Zheng, Zhang and Ma all discloses that detecting host cell protein impurities is critical in biopharmaceutical development to ensure safety, efficacy, and stability, and Ma discloses that peptides can be detected at levels as low as 0.1 ppm with respect to the original mAb concentration, which support purification process development. Moreover, before the effective filing date of the claimed invention, one of ordinary skill in the art would have been motivated by the cited reference to achieve a lower limit of quantification that is less than about 1 ppm with a reasonable expectation of success.
Conclusion
No claims are allowed.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to LYNN Y FAN whose telephone number is (571)270-3541. The examiner can normally be reached on M-F 7am-4pm.
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/Lynn Y Fan/
Primary Examiner, Art Unit 1759