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 .
Claim Objections
Claims 1-18 are objected to because of the following informalities:
Regarding claim 7, l. 1 recites “the chromatographic support a CSHTMC18 stationary phase”. Applicant may amend the claim to read “the chromatographic support comprises a C18 stationary phase”. See 112(b) rejection for the omission of “CSHTM”.
Claims 2-16 are rejected based on dependency of all of the limitations of claim 1.
Appropriate correction is required.
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 1-18 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.
Regarding claim 1, l. 6 recites “weak”. The term “weak” in claim 1 is a relative term which renders the claim indefinite. The term “weak” is not defined by the claim. Paragraph [0015] of the instant specification (publication US 20230314389 A1) defines a weak acid to have either a pH>3 or a pKa value of about 4.5. Not only are there two options to choose from, but the definition includes another indefinite term, “about”. Paragraph [0026] defines “about” to have many different meanings (e.g., 25%, 10%, 5%). The specification therefore 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. Applicant may correct the claim by including a definition for “weak” and omitting the term “about”.
Claims 2-16 are rejected based on dependency of all of the limitations of claim 1.
Regarding claim 16, l. 2 recites “about”. The term “about” in claim 1 is a relative term which renders the claim indefinite. The term “about” is not defined by the claim. Paragraph [0026] defines “about” to have many different meanings (e.g., 20%, 10%, 5%, 1%). The specification therefore 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. Applicant may correct the claim by omitting the term “about”.
Regarding claim 7, l. 1 recites the trademark/trade name “CSHTM” (Charged Surface Hybrid). Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe the properties listed below and, accordingly, the identification/description is indefinite. Applicant may amend the claim by omitting the trademark symbol and claiming general CSHTM properties such as hybrid material composition and pH ranges where positive surface charge is induced (See p. 4, col. 1, Important Notes and Table 2 of supporting reference Waters (“ACQUITY UPLC Peptide CSH C18 , 130 Å, 1.7 µm and XP 2.5 µm Columns and ACQUITY PREMIER Peptide CSH C18 , 130 Å, 1.7 µm Columns”; October 2020).
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.
Claims 1-10,13-18 are rejected under 35 U.S.C. 103 as being unpatentable over Wang (US 20190234964 A1), in view of Birdsall (US 20210255196 A1, entitled to the EFD of 20201013 by provisional application, US 63091169,) as evidenced by supporting reference Waters (“ACQUITY UPLC Peptide CSH C18, 130 Å, 1.7 μm and XP 2.5 μm Columns and ACQUITY PREMIER Peptide CSH C18, 130 Å, 1.7 μm Columns”; October 2020).
Regarding claim 1, Wang teaches a method for determining the relative distribution of glucuronylation (Emphasis Added), iduronidation, and galacturonidation of a population of polypeptides (“a method for identifying glucuronylation of a protein drug product,” wherein the drug product is a monoclonal antibody which is a population of polypeptides including Fc and Fab2 polypeptide fragments; [0007]; See relative abundances in Figs. 4B-7D which show a distribution of glucuronylation)(Under broadest reasonable interpretation the Examiner interprets the limitation of “determining” to be for at least one (Emphasis Added) of glucuronidation, iduronidation, and galacturonidation since step d) includes the optional “and/or” terminology)(The preamble has the import that the claim as a whole suggests for it (See MPEP 2111.02)), the method comprising:
a) contacting the population of polypeptides with a protease to generate peptides (“The dried and denatured acidic fractions are alkylated and then digested with trypsin to form a sample,” which would naturally generate peptides from Fc and Fab2 polypeptide fragments; [0007]);
b) contacting the peptides to a chromatographic support comprising a stationary phase (“samples are then subjected to reverse phase liquid chromatography,” using a WCX column which has a stationary phase; [0007];[0016])).
d) analyzing the separated peptides to determine the relative distribution of glucuronylation, iduronidation, and/or galacturonidation of the peptides (samples are then subjected to reverse phase liquid chromatography/mass spectroscopy analysis to identify glucuronylation of the protein drug product; [0007])(See relative abundances in Figs. 4B-7D which show a distribution of glucuronylation).
Wang is silent to teaching determining the relative distribution of glucuronidation (Emphasis Added), a chromatographic support comprising hydrophobic stationary phase and a positive surface charge (Emphasis Added), and c) contacting the chromatographic support with a weak acid mobile phase gradient to separate the peptides.
Wang instead teaches that glucuronylation (direct glucuronic acid addition) results in glucuronic acid attachment on the Lys residues and that it has been reported that glucuronidation (enzymatic addition) results in glucuronic acid attachment on the Ser and Thr residues ([0052]). However, Wang states that both modifications exhibit an accurate mass addition of 176.03 Da and are therefore believed to have the same elemental composition (C.sub.6H.sub.8O.sub.6)([0052]). Likewise, paragraphs [0004] and [0019] of the instant specification (US 20230314389 A1) teaches modification of the antibody through forced glucuronidation which would result in modification of lysine residues as taught by Wang. 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 modified the method taught by Wang by substituting glucuronidation for glucuronylation since both modifications result in the covalent attachment of glucuronic acid to a molecule thereby yielding the predictable results of confirming the identity of the modification (See MPEP 2143(I)(B)).
Wang is silent to teaching a chromatographic support comprising a hydrophobic stationary phase and a positive surface charge (Emphasis Added), and c) contacting the chromatographic support with a weak acid mobile phase gradient to separate the peptides. Although Wang uses an SCX column to separate the Fab and Fc fragments followed by formic acid quenching ([0053]), and uses a WCX column for subsequently carrying out the RPLC step ([0007][0053]).
Birdsall teaches a chromatographic support comprising a hydrophobic stationary phase and a positive surface charge (Emphasis Added) and c) contacting the chromatographic support with a weak acid mobile phase gradient to separate the peptides (“A commercially available lyophilized NIST mAb digest was used for all experiments. Samples were separated on a C18 reversed phase chemistry (CSH C18 columns) using a 50-min gradient at 0.68 %B/min with 0.1% formic acid as a mobile phase additive,” wherein Table 5 in paragraph [0182] shows a mobile phase of Acetonitrile, 0.1% Formic acid which has a pH of around 3.5 (>3) and is therefore a weak acid as described in paragraph [0015] of instant specification; [0090])(See 112(b) rejection above)(Coated ACQUITY Premier CSH C18 columns are positively charged when pH>6, which is satisfied when the mobile phase is Acetonitrile, 0.1% Formic acid; See supporting reference, Waters (“ACQUITY UPLC and ACQUITY Premier Peptide CSH C18 , 130 Å, 1.7 µm and XSelect XP and XSelect Premier 2.5 µm Columns”; February 2020) at p. 4, col. 1, last 3 ll.)(“The Examiner interprets a “weak acid mobile phase gradient” to have a ph>3 or a pKa value of 4.5,” wherein the instant specification teaches either formic acid or acetic acid be appropriate weak acids; See paragraphs [0015] and [0013])(See 112(b) rejection above);.
Birdsall is considered to be analogous to the claimed invention because it is in the same field of endeavor for detecting post translational modifications (PTMs) in mAbs using a CSH C18 column within an LC-MS-MS system. 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 modified the peptide separation method taught by Wang by substituting Birdsall’s coated ACQUITY CSH C18 column with a weak acid mobile phase gradient for Wang’s WCX column during the RPLC step in order to improve sample characterization. Birdsall compares the quality of separation between uncoated and coated ACQUITY CSH C18 columns using a PENNYK Fc peptide sample that is susceptible to deamidation, a PTM of mAbs that is correlated with drug efficacy (Table 5; [0156]-[0157]). Use of the uncoated column showed that the detection of the deamidation products (impurities) was prevented due to coelution with the starting residue (tailing). Conversely, use of the coated column greatly reduced tailing and assay variability while increasing detector response, analyte recovery, and peak shape. Wang encounters this same hurdle when describing an inability to achieve accurate results due to a glycation modification in the sample that eluted at the same time as the antibody variant ([0044]). A person of ordinary skill in the art would have recognized the benefits of a column substitution to yield the predictable results of improved separation during sample characterization (See MPEP 2143(I)(B and C)).
Regarding claim 2, The method of claim 1, wherein the protease is trypsin (trypsin; Wang, [0007]), lys-C, Glu-C, or Asp-N.
Regarding claim 3, Modified Wang teaches the method of claim 1, wherein the chromatographic support comprises a support material (130 Å particles…; Waters, p. 4, col. 1, Important Note, l. 2) with a positively charged surface modifier (…that undergo a surface modification by the addition of a low concentration of weakly basic ionizable silanes…provide frequently desired positive surface charge benefits; Waters, p. 4, col. 1, Important Note).
Regarding claim 4, Modified Wang teaches the method of claim 3, wherein the hydrophobic stationary phase (C18; Waters, p. 4, col. 1, Important Note) is linked to the surface modifier (130 Å particles that undergo a surface modification by the addition of a low concentration of weakly basic ionizable silanes, followed by C18 bonding and end capping; Waters, p. 4, col. 1, Important Note).
Regarding claim 5, Modified Wang teaches the method claim 4, wherein the hydrophobic stationary phase comprises an alkyl (C18; Waters, p. 4, col. 1, Important Note), alkenyl, alkynyl or aryl functional group.
Regarding claim 6, Modified Wang teaches the method of claim 5, wherein the hydrophobic stationary phase comprises a C18 functional group (C18; Waters, p. 4, col. 1, Important Note).
Regarding claim 7, Modified Wang teaches the method of claim 1, wherein the chromatographic support a CSHTMC18 stationary phase (ACQUITY ™ PREMIER Peptide CSH 130 Å C18 column (2.1 × 100 mm, 1.7 μm p/n 186009461; Birdsall, Table 5)(See 112(b) rejection).
Regarding claim 8, Modified Wang teaches the method of claim 1, wherein the separated peptides are analyzed by using mass spectrometry (subjected to reverse phase liquid chromatography/mass spectroscopy analysis to identify glucuronylation of the protein drug product; Wang, [0007]).
Regarding claim 9, Modified Wang teaches the method of claim 1, comprising the identification of glucuronidated peptides (Paragraphs [0050]-[0054] explain that mAb samples were subjected to peptide fragmentation followed by peptide mapping of the sequence. The results showed an unknown modification on Lys residues of the sequence suspected to be from glucuronidation. To confirm, forced glucuronylation was performed on the same mAb samples and confirmed the unknown modification to be from a glucuronidated peptide).
Modified Wang fails to teach the identification of iduronidated, and galacturonidated peptides. However, it is known that “the modification of polypeptides by glucuronic acid, iduronic acid, or galacturonic acid has the potential to impact the safety and/or efficacy of such recombinantly-expressed products “ ([0004] of the instant specification). A supporting reference, Liang (“Quantitation of protein post-translational modifications using isobaric tandem mass tags”; 2015) also states that post-translationally modified peptides contain uronic acids due to glycosylation. Furthermore, Wang acknowledges a need to “further characterize and discover PTMs that alter mAb activity and stability” ([0005]). 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 tried to apply the same forced glycuronidation and peptide mapping analysis steps taught by Wang to identify the other known uronic acids responsible for the PTMs of mAbs including iduronic and galacturonic acid (See MPEP 2143(I)(E)).
Regarding claim 10, Modified Wang teaches the method of claim 8, wherein the peptides are identified by their respective chromatographic retention time and mass spectra (an acidic shoulder peak was detected and attributed to a variant of the antibody with a mass increase of approximately 176 Da; Wang, [0044]; [0016]-[0019]); Figs. 5A, 6A, and 7A of Wang show 3 different samples with peaks at the same retention times as when the respective sample has undergone forced glucuronidation (See Figs. 5B, 6B, and 7B).
Regarding claim 13, Modified Wang teaches the method of claim 1, wherein the weak acid is formic acid (Birdsall, [0090]; Table 5) or acetic acid.
Regarding claim 14, Modified Wang teaches the method of claim 1, wherein the acidic mobile phase is at a pH where greater than 50% of the carboxylic acid moieties associated with glucuronidation, iduronidation, or galacturonidation are in a deprotonated state (Acetonitrile, 0.1% Formic acid which has a pH of around 3.5 which is at a pH greater than 50% of the carboxylic acid moieties associated with glucuronidation, iduronidation, or galacturonidation; Birdsall, Table 5).
Regarding claim 15, Modified Wang teaches the method of claim 1, wherein the weak acid mobile phase gradient has pH>3 (Acetonitrile, 0.1% Formic acid; Birdsall, Table 5).
Regarding claim 16, Modified Wang teaches the method of claim 1, wherein the weak acid mobile phase gradient has a pKa value of about 4.5 (Acetonitrile, 0.1% Formic acid; Birdsall, Table 5)(Formic acid has a pKa of around 3.75 which is within 20% of 4.5 as defined in paragraph [0026] of the instant publication for the term “about”)(See 112(b) rejection).
Regarding claim 17, Modified Wang teaches the method of claim 1.
Modified Wang fails to teach the mass spectrometry is electrospray ionization tandem mass spectrometry (ESI-MS/MS).
Wang instead uses HCD to run the MS/MS experiments.
Birdsall teaches mass spectrometry is electrospray ionization tandem mass spectrometry (ESI-MS/MS(Further Evaluation Including MS/MS; [0104])(Mass spectrometric (MS) data was also obtained for the three-peptide mixture as separated using the conditioned columns and performed with electrospray ionization and high sensitivity quadrupole time-of-flight instrumentation; [0134]).
Birdsall is considered to be analogous to the claimed invention because it is in the same field of endeavor for detecting post translational modifications (PTMs) in mAbs using a CSH C18 column within an LC-MS-MS system. 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 modified the peptide separation method taught by Wang in view of Birdsall by further substituting Wang’s HCD MS/MS technicqu with Birdsall’s electrospray ionization tandem mass spectrometry (ESI-MS/MS) technique in order to preserve fragile modifications and improve identification accuracy. ESI-MS/MS is well-known and routine in analysis instrumentation and the substitution would yield the predictable results of optimized sample result accuracy (See MPEP 2143(I)(B)).
Regarding claim 18, Modified Wang teaches the method of claim 1, wherein the polypeptide is an antibody (monoclonal antibody; Wang, [0007]).
Claims 11-12 are rejected under 35 U.S.C. 103 as being unpatentable over Wang (US 20190234964 A1) and Birdsall (US 20210255196 A1, provisional application, US 63091169) with supporting reference Waters (“ACQUITY UPLC Peptide CSH C18, 130 Å, 1.7 μm and XP 2.5 μm Columns and ACQUITY PREMIER Peptide CSH C18, 130 Å, 1.7 μm Columns”; October 2020), as applied to claim 1 above, in further view of Xu (US 20190237157 A1).
Regarding claim 11, Modified Wang teaches the method of claim 1 and monitored the liquid chromatography by UV absorbance (simultaneous UV detection; Wang, [0042]).
Modified Wang fails to teach the relative distribution of glucuronidation, iduronidation, and galacturonidation is determined by integrating the respective peaks of liquid chromatograms corresponding to the separated peptides.
Xu teaches determining the relative distribution of the PTMs in mAbs by integrating respective peaks of chromatograms corresponding to the separated peptides (spectra of peptide identification (FIG. 2A) and example extracted ion chromatograms for peptide peak integration and PTM quantitation; ([0030]; Figs. 2A-B; Abstract).
Xu is considered to be analogous to the claimed invention because it is in the same field of endeavor for detecting and quantitating post translational modifications (PTMs) in mAbs using LC-MS/MS. 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 modified the peptide separation method taught by Wang in view of Birdsall by further integrating the peaks associated with PTMs of liquid chromatograms since this is a routine and well-known technique to quantify analyte abundance. Wang already determines a relative distribution of glucuronidation through of liquid chromatograms showing defined peaks (See Figs. 5A, 6A, and 7A)(simultaneous UV detection; [0042]). Associating a true value with the modification would aide in Wang’s suggested implementation of removing glucuronylated proteins from a protein drug product to produce a purified protein drug product ([0009]). Knowing the peak concentrations associated with the modifications would help to determine the extent of removal needed to achieve this goal, yielding predictable results (See MPEP 2143(I)(A)).
Regarding claim 12, Modified Wang teaches the method of claim 1, wherein
Modified Wang fails to teach the relative distribution of glucuronidation, iduronidation, and galacturonidation is determined by integrating the respective peaks of ion chromatograms extracted from the mass spectrometry analysis.
Xu teaches determining the relative distribution of the PTMs in mAbs by integrating respective peaks of ion chromatograms extracted from the mass spectrometry analysis (MS/MS spectra of peptide identification (FIG. 2A) and example extracted ion chromatograms for peptide peak integration and PTM quantitation; ([0030]; Figs. 2A-B; Abstract).
Xu is considered to be analogous to the claimed invention because it is in the same field of endeavor for detecting and quantitating post translational modifications (PTMs) in mAbs using LC-MS/MS. 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 modified the peptide separation method taught by Wang in view of Birdsall by further integrating the peaks associated with PTMs since this is a routine and well-known technique to quantify analyte abundance. Wang already determines a relative distribution of glucuronidation through mass spectra showing defined peaks (See Figs. 5C-D, 6C-D, and 7C-D). Associating a true value with the modification would aide in Wang’s suggested implementation of removing glucuronylated proteins from a protein drug product to produce a purified protein drug product ([0009]). Knowing the peak concentrations associated with the modifications would help to determine the extent of removal needed to achieve this goal, yielding predictable results (See MPEP 2143(I)(A)).
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure:
Waters, October 2020 (instant PTO-892) teaches properties of CSHTMC18 stationary phase.
Liang et al. 2015 (instant PTO-892) teaches uronic acid as a reason for PTMs in glycopeptides.
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to VALERIE SIMMONS whose telephone number is (703)756-1361. The examiner can normally be reached M-F 7:30-4:00.
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, Maris Kessel can be reached on 571-270-7698. 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.
/V.S./Examiner, Art Unit 1758
/MARIS R KESSEL/Supervisory Patent Examiner, Art Unit 1758