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 .
Response to Amendment
The amendment received on 01/14/2026 is acknowledged. Claims 1 and 17 have been amended. Claims 16 and 24 have been cancelled. Claims 1-3, 5-15, and 17-23 are currently pending and have been treated on the merits.
Applicant’s amendment had necessitated a new grounds of rejection based on the prior art of record outlined below. Applicant’s arguments to the previous rejection are addressed below.
Response to Arguments
Applicant’s arguments have been fully considered, but they are not persuasive.
Applicant argues that one of ordinary skill in the art would find the term “pre-selected” as definite based on the specification. This argument has been fully considered and is not persuasive. Applicant argues that surrogate peptides could be selected through in silico digestion and analysis prior to the use of the peptide; however, applicant does not claim a method of performing in silico digestion to determine a surrogate peptide. Applicant’s arguments highlights the indefiniteness of this term as they suggest it implies that in silico digestion is used to pre-select the peptide to quantify the protein. However, no method steps are performed, how does this abstract designation of pre-selected, different than selecting a peptide for this purpose. How does one differentiate this abstract designation, from identifying this peptide via different methods, or detecting the same peptide previously identified in experiments, or most mass spectrometers can detect multiple peaks simultaneously, how does pre selection limit the peak which was already going to be detected. If applicant intends for “pre-selected” to mean identified by in silico digestion and analysis, amendment to do so might provide clarity. Such an amendment would be analyzed to see if it differentiates from a method which performs the same non-abstract method steps, and further compared to the prior art of proteomic analysis in which such steps might be performed, such as described in Jiang (In Silico Digestion and the Basic Local Alignment Search Tool (BLAST) Search, Page 9861)
Applicant argues that there was no motivation to combine Xu and Jiang. The following motivation has been given " One or ordinary skill in the art would be motivated to do so to ensure the analytes were a sufficient size for LC-MS as taught by Xu (Page 20 [0073]), and would further be motivated to do so to create more peptides which may be analyzed.”. Applicant argues that there is not reasonable expectation of success; however, the following reasons have been given “One or ordinary skill in the art would further have a reasonable expectation of success in doing so as Jiang already teaches the digestion of antibodies and detection of peptides and Xu teaches that samples may be digested by one or more proteases. One of ordinary skill in the art would further have a reasonable expectation of success as the pool of peptides for analysis will now contain some smaller peptides where a cleavage site was present.” Applicant further argues that further digestion may remove uniqueness; however, as has been noted in the rejection and above many fragments will not have a sequence of the additional protease and would remain unchanged and in the majority of cases the unique portion of a peptide would remain in which ever fragment contains the unique sequence, except when a cut occurs within the unique sequence. One of ordinary skill in the art would readily be able to select the proteases which create peptides that have unique sequences though in silico digestion or routine experimentation.
Applicant argues that the use of digestive enzymes alone may not necessarily lead to surrogate peptides. However, Jiang has already found surrogate peptides for the administered antibodies. Jiang teaches that the unique peptides identified may be used for humans, (Page 9866, 1st paragraph). Jiang further teaches that these methods are general and can be applied to other systems (Page 9865-9866, Results and Conclusions). Further a prima facie case of obviousness does not require certainty, rather a reasonable expectation of success that one of ordinary skill in the art could do it. In the instant case one of ordinary skill in the art would readily be able to use more than one protease to digest samples and find unique peptides for the antibodies as described through routine experimentation in the event that 2 specific proteases did not successfully make a unique peptide, one of ordinary skill would be able to select different combinations of enzymes.
Applicant argues that Jiang or Xu do not teach peptides that match the requirements of the claims. The peptides of Jiang for the drugs however teach finding peptides which are unique from human sequences and Jiang teaches that the methodology can be adapted for other species including humans. The GLEW and ASGI peptides segment are specific to the drugs and can be used in humans, i.e. it is not found in humans, and thus Jiang clearly demonstrates it is within the ability of one of ordinary skill to select peptides that are unique to the human genome. Jiang further teaches that these methods are general and can be applied to other systems (Page 9865-9866, Results and Conclusions). Jiang teaches methodology for determining and finding unique peptides compared to genomes and limits their size to fewer than 30 amino acids which will include all those shorter than 20 amino acids (Page 9861, Results, Method development). It is well within the ability of one of ordinary skill to apply the general validated method of Jiang to additional antibody drugs and species such as humans. The newly added limitation regarding methionine is addressed below.
Applicant further argues that some digests may not produce satisfactory fragments for some antibodies demonstrating unpredictability and unexpectedness in the art. This is not found persuasive as Jiang already teaches peptides for use from the CDR of two antibodies that meet the requirements. Further Jiang teaches methodology for determining and finding unique peptides (Page 9861, Results, Method development), which one of ordinary skill in the art could further apply. In addition, Jiang further teaches that these methods are general and can be applied to other systems (Page 9865-9866, Results and Conclusions). It is well within the ability of one of ordinary skill to apply the general validated method of Jiang to additional antibody drugs and species such as humans, to find proteases which produce unique peptide for detection.
Applicant argues that Jiang nor Xu teach possible issues that might arise such as failure to generate surrogate peptides. Jiang already teaches the production of unique peptides that are unique to human proteome. Further identifying potential surrogate peptides using one or two enzymes is well within the ability of one of ordinary skill based on the guidance of Jiang. The entire section of method development provides for modeling digestions and searching for unique short peptides relative to the genome. Jiang further teaches the method may be developed and used in other organisms such as Human (Page 9866, 1st paragraph, Page 9861, Results, Method development). In addition Jiang further teaches that these methods are general and can be applied to other systems (Page 9865-9866, Results and Conclusions). It is well within the ability of one of ordinary skill to apply the general validated method of Jiang to additional antibody drugs and species such as humans. The newly added limitation to methionine is addressed below.
Applicant argues that Xu does not adequately teach the use of multiple enzymes to digest more than one protein, and only exemplifies one analyte being digested with one protease. It is unclear exactly what argument is made; however, this is statement is not found persuasive as the use of digestive enzymes on complex samples is standardly performed in the field of proteomics. For example, Jiang digests samples containing two antibodies being monitored along with all of the proteins found in the serum. The detection of peptides, especially ones that can be the same peptides after digestion with 2 proteases, is well within the ability of one of ordinary skill in the art as thy are detecting the peptides in complex mixtures already. It is further noted that in the instant specification the general description for performing digestions is as follows “[0059] As used herein, the term “digestive enzyme” refers to any of a large number of different agents that can perform digestion of a protein. Non-limiting examples of hydrolyzing agents that can carry out enzymatic digestion include protease from Aspergillus Saitoi, elastase, subtilisin, protease XIII, pepsin, trypsin, Tryp-N, chymotrypsin, aspergillopepsin I, LysN protease (Lys-N), LysC endoproteinase (Lys-C), endoproteinase Asp-N (Asp-N), endoproteinase Arg-C (Arg-C), endoproteinase Glu-C (Glu-C) or outer membrane protein T (OmpT), immunoglobulin-degrading enzyme of Streptococcus pyogenes (IdeS), thermolysin, papain, pronase, V8 protease or biologically active fragments or homologs thereof or combinations thereof. For a recent review discussing the available techniques for protein digestion see Switazar et al., “Protein Digestion: An Overview of the Available Techniques and Recent Developments” (Linda Switzar, Martin Giera & Wilfried M. A. Niessen, Protein Digestion: An Overview of the Available Techniques and Recent Developments, 12 JOURNAL OF PROTEOME RESEARCH 1067-1077 (2013)).” The descriptions of the art in Jiang, Xu and the instant specification all suggest that the use of one or more proteases in creating a sample in well within the ability of one of ordinary skill in the art.
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.
Claim 23 is 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 23, it is unclear what is meant by the term “pre-selected” and how this limits the method. Once a peptide has been selected as usable for quantifying a peptide and used to do so it can be considered to have been preselected as it has been selected previously. Further it is unclear how the steps of c and d could be practices prior to selecting as the describe steps of selecting a peptide.
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 1-3, 6-16, and 23 are rejected under 35 U.S.C. 103 as being unpatentable over Jiang et al. (Analytical Chemistry 2013; 85:9859-9867/previously) in view of Xu (WO 2021/211939 A1; Priority Date 17 April 2020/previously cited).
Regarding claim 1 and the limitation “A method for simultaneously quantitating at least two therapeutic proteins, comprising:(a) obtaining a sample including a first therapeutic protein and a second therapeutic protein, wherein said first and second therapeutic proteins are selected from the group consisting of an antibody, a monoclonal antibody, a bispecific antibody, an antibody fragment, a Fab region of an antibody, and an antibody-drug conjugate; ;(b) contacting said sample with at least two digestive enzymes, thereby generating at least one unique surrogate peptide for each of said first and second therapeutic proteins,wherein: the at least one unique surrogate peptide for the first therapeutic protein is a peptide that is specific to only a digest of the first therapeutic protein and is absent from the digestive enzyme digest in the absence of the first therapeutic protein, has a peptide length shorter than 20 amino acid residues, has no identical match in a human proteome database, and does not contain methionine; and the at least one unique surrogate peptide for the second therapeutic protein is a peptide that is specific to only a digest of the second therapeutic protein and is absent from the digestive enzyme digest in the absence of the second therapeutic protein, has a peptide length shorter than 20 amino acid residues, has no identical match in a human proteome database, and does not contain methionine; and(d) quantitating said first and second therapeutic proteins using the quantitated surrogate peptides.” Jiang teaches an LC-MS/MS assay for the” simultaneous quantitation of two coadministered human monoclonal antibodies” in monkey serum wherein “[t]he total serum proteins were digested with trypsin” and “a unique peptide for each mAb and two confirmatory peptides from different antibody domains, were simultaneously quantified by LC-MS/MS in the multiple reaction-monitoring mode” (page 9859, Abstract). The digestion of the antibodies generates unique peptides, or surrogate peptides. Jiang teaches coadministering two antibodies (mAb-A and mAb-B) to monkeys once weekly for four weeks and harvesting the serum from the monkeys. Jiang teaches quantitating surrogate peptides for both antibodies generated from trypsin digestions of the whole proteins in serum. Finally, Jiang teaches the simultaneous quantitation of mAb-A and mAb-B from the serum samples using the surrogate peptides by LC-MS/MS. Jiang further teaches the method may be developed and used in other organisms such as Human (Page 9866, 1st paragraph, Page 9861, Results, Method development). In addition Jiang further teaches that these methods are general and can be applied to other systems (Page 9865-9866, Results and Conclusions). It is well within the ability of one of ordinary skill to apply the general validated method of Jiang to additional antibody drugs and species such as humans. Jiang teaches in silico digestion of the antibodies and comparison of the calculated digests with the proteome of the organism using databases Blast and Expasy, and specifically analyzes peptides under 30 amino acids due to difficulties in LC-MS/MS for larger peptides (Page 9861, Method Development). Less than 30 includes less that 20, and less than 20 amino acids comprises the majority of the range claimed and thus renders obvious the instantly claimed range. Jiang further teaches that one of the peptides selected in the reference had reduced signal likely do to oxidation of methionine (Page 9865, Left hand column, last 10 lines).
Jiang does not teach that the unique peptide should lack methionine, this difference however would have been obvious to one of ordinary skill in the art as Jiang teaches that methionine in the unique peptide can lead to signal reduction. As Jiang identifies this property, one of ordinary skill in the art would find it obvious that a unique peptide lacking a methionine could be selected for. One of ordinary skill in the art would be motivated to do so, so that the peptide being detected for quantification produced a similar amount regardless of oxidative conditions or damage which may occur to the sample. One of ordinary skill in the art would further have a reasonable expectation of success in doing so as they can search for such peptides while searching for unique peptides using in silico digestion.
Jiang does not teach the use of two digestive enzyme to generate the peptides which are used for quantification of the administered antibodies. This difference however would have been obvious to one of ordinary skill in the art as it is taught in the same field of endeavor as preparation and analysis of biological samples for antibodies using digestion and mass spectrometry.
In the same field of endeavor, Xu teaches a targeted two-dimensional tandem mass spectrometry (2D-LC-MS/MS) system used for assaying presence of large molecule analytes such as antibodies (page 1, paragraph [001]), wherein “the proteases used for the cleavage [of serum proteins] comprise one or more of: trypsin, endoproteinase LysC, endoproteinase ArgC, staph aureus V8, endoproteinase GluC, chymotrypsin, or papain” (page 5, paragraph [0012]). Xu teaches the detection of large molecule analytes such as proteins from serum samples wherein “the sample is treated with one or more enzymes to at least partially digest the analyte so that it is sufficient size for the liquid chromatography and mass spectrometry detection” (page 20, paragraph [0073]). Xu teaches the digestion by one or more proteases on the sample may be performed directly on the sample or purified samples and teaches the use of LysC, GluC, Arg-C, chymotrypsin, trypsin, AspN, (Page 20, [0073]-[0074]).
It would have been obvious to one of ordinary skill in the art prior to the effective filing date of the instant invention that the method of Jiang could be combined with the method of Xu as both are methods of analyzing the presence of antibodies in biological samples via the digestion of the antibody and detection of produced peptide. One of ordinary skill in the art would find it obvious that the method of Jiang could include digestion by more than one protease, as Xu teaches such steps for the analysis of large analytes such as antibodies. One or ordinary skill in the art would be motivated to do so to ensure the analytes were a sufficient size for LC-MS as taught by Xu (Page 20 [0073]), and would further be motivated to do so to create more peptides which may be analyzed. One or ordinary skill in the art would further have a reasonable expectation of success in doing so as Jiang already teaches the digestion of antibodies and detection of peptides and Xu teaches that samples may be digested by one or more proteases. One of ordinary skill in the art would further have a reasonable expectation of success as the pool of peptides for analysis will now contain some smaller peptides where a cleavage site was present.
Regarding claims 2 and 3 and the limitations “wherein said digestive enzymes are chosen from the group consisting of trypsin, chymotrypsin, LysC, LysN, AspN, GluC and ArgC.” , Xu teaches “the proteases used for the cleavage [of serum proteins] comprise one or more of: trypsin, endoproteinase LysC, endoproteinase ArgC, staph aureus V8, endoproteinase GluC, chymotrypsin, or papain” (page 6, paragraph [0012]). Xu further teaches that It would have been obvious to one of ordinary skill in the art to use the digestive enzymes trypsin and LysC. Xu teaches the digestion by one or more proteases on the sample may be performed directly on the sample or purified samples and teaches the used of LysC, GluC, Arg-C, chymotrypsin, trypsin, AspN, (Page 20, [0073]-[0074]). One of ordinary skill in the art would thus find it obvious that combinations of these proteases could be used with the trypsin of Jiang.
Regarding claims 6-8 and the limitations “wherein said mass spectrometer is an electrospray ionization mass spectrometer, nano-electrospray ionization mass spectrometer, or a triple quadrupole mass spectrometer”, “wherein said mass spectrometer is coupled to a chromatography system”, and “wherein said chromatography system comprises reverse phase liquid chromatography, ion exchange chromatography, size exclusion chromatography, affinity chromatography, hydrophobic interaction chromatography, hydrophilic interaction chromatography, mixed-mode chromatography, or a combination thereof “”, Jiang teaches that the sample analysis was done by loading serum digest into a HPLC system using a C18, i.e. reversed phase column, and the eluent of the HPLC eluent was ionized in positive electrospray mode (page 9860, column 2, LC-MS/MS Analysis). Xu teaches “performing high pH reversed phase liquid chromatography (RPLC) survey scan with detection by mass spectrometry” (page 50, claim 1). Jiang thus teaches the use of electrospray mass spectrometer coupled to a reversed phase chromatographic system. And further the use of reversed phase chromatography is taught by Xu.
Regarding claim 9 and the limitation “wherein said sample includes human serum”, Jiang teaches the intravenous administration of two therapeutic antibodies followed by the collection of the serum for quantification (Abstract). Jiang further teaches the pharmaceutical industry to develop bioanalytical methods for measuring mAbs in biological fluids (Page 9859). Jaing further teaches that the sample other matrices may be used with other species, and indicates that only two of the peptides detected were human IgG specific and that those two can only be used with non humans (9866). Jiang thus teaches that that analytical methods taught can be used with humans and the analysis set up is specifically for developing techniques for the pharmaceutical industry, i.e. humans. Xu further teaches the detection of target proteins in human serum (Figures 6-8, Table 2). One would thus find it obvious that the method of Jiang could be practiced with humans and human serum.
Regarding claim 10 and the limitation “further comprising selecting said digestive enzymes using in silico analysis of potential surrogate peptides”, Jiang teaches “[i]n silico trypsin digestion was used to predict complementary determining region (CDR) peptides and confirmatory peptides, based on the known amino acid sequences and functional structures of the mAb drugs. Then the online protein BLAST was used to predict the selectivity of each tryptic peptide in monkey serum by querying the protein databases” (page 9861, Results, paragraph 2). It would have been obvious to one of ordinary skill in the art that this in silico analysis could be utilized with different digestive enzymes such as those disclosed by Xu.
Regarding claims 12 and 13 and the limitations “wherein said method has a dynamic range of about 10 to about 2000 μg/mL of the first therapeutic protein in the sample.” and “wherein said method has a dynamic range of about 10 to about 2000 μg/mL of the second therapeutic protein in the sample”, Jiang teaches “[t]he LC-MS/MS assay showed lower limit of quantitation (LLOQ) at 5 μg/mL for mAb-A and 25 μg/mL for mAb-B” (Abstract). The upper limit of quantification is not explicitly taught, but Figure S6 in the supplement clearly shows the measurement of the GLEW peptide (for mAb-A) being quantitated well over 2,000 μg/mL and the ASGI peptide (for mAb-B) being quantitated to around 2,000 μg/mL. Therefore, the dynamic range of detection of mAb-A is around 5-5,000 μg/mL and the dynamic range of detection of mAb-B is around 25-2000 μg/mL as taught by Jiang. The range of Jiang comprise nearly the entirety of the claimed range and is rendered obvious by the teaching of Jiang. The method of Jiang and Xu would further be expected to detect other identified peptides with similar sensitivity.
Regarding claim 14 and the limitation “wherein said mass spectrometer is capable performing a multiple reaction monitoring or parallel reaction monitoring”, Jiang teaches “a unique peptide for each mAb and two confirmatory peptides from different antibody domains, were simultaneously quantified by LC-MS/MS in the multiple reaction-monitoring mode” (Abstract). Jiang thus teaches multiple reaction-monitoring.
Regarding claims 15 and 16, and the limitations “further comprising the steps of conducting peptide mapping of said surrogate peptides, selecting unique peptides and fragment ions of the surrogate peptides to generate multiple reaction monitoring transitions, selecting the top two or top three transitions of the surrogate peptides, optimizing collision energy of the surrogate peptides, subsequently generating a calibration curve, and determining a LLOQ (lower limit of quantification) according to the calibration curve. ”, and “, further comprising selecting said at least one surrogate peptide specific to said first or said second therapeutic protein, wherein the at least one surrogate peptide is pre-selected by determining that: i. the surrogate peptide is specific to a digest of the therapeutic protein to be quantified; ii. the surrogate peptide is specifically absent from the protease digest of the preparation in the absence of the at least one therapeutic protein; iii. the surrogate peptide produces a strong signal in a mass spectrometric analysis; and iv. the surrogate peptide produces a distinguishable signal in a mass spectrometric analysis.”, Jiang teaches the use of the PeptideMass tool for mapping and selecting potential surrogate peptides of mAb-A and mAb-B, and the BLAST tool was used to predict the selectivity of each tryptic peptide in the monkey serum to ensure the surrogate peptides would be absent without the mAbs present. After selection, the peptides with significant mass spectrometry responses were identified for each mAb, the MRM ion transitions were selected, and the LC-MS/MS parameters were then optimized (page 9861, Method Development, Figures 3-4). In doing so calibration curves were generated with the peptides and the LLOQ were determined. One of ordinary skill in the art would have been found it obvious that these steps could be used with a product digested by a second enzyme to determine peptides in the combined method of Jiang and Xu.
Regarding claim 23 and the limitations “wherein the at least one surrogate peptide is pre-selected in the CDR regions of the variable domains of said first or said second therapeutic protein” , Jiang specifically teaches the production and detection of unique sequences and highlights that the CDR region is a good region for finding these peptides in an antibody (Sample analysis and Incurred Sample Reanalysis (ISR), Confirmatory Peptides, Figures 3-4, Discussion). Jiang teaches “[i]n silico trypsin digestion was used to predict complementary determining region (CDR) peptides and confirmatory peptides, based on the known amino acid sequences and functional structures of the mAb drugs. Then the online protein BLAST was used to predict the selectivity of each tryptic peptide in monkey serum by querying the protein databases” (page 9861, Results, paragraph 2).
Claims 5, 17-22 and 24 are rejected under 35 U.S.C. 103 as being unpatentable over Jiang and Xu as applied to claims 1-2, 4, and 6-16 and 23 above, and further in view of Weinrich et al. (N Engl J Med 2021; 384: 238-251/previously cited) as evidenced by Babb et al. (US 10,787,501 B1; Published 29 Sept 2020/Previously cited)
Regarding claim 5 and the limitation “wherein said first therapeutic protein is casirivimab and said second therapeutic protein is imdevimab”, For a description of what Jiang and Xu teach, see the above sections.
Jiang teaches “a fully validated LC-MS/MS method for the simultaneous quantitation of two codosed human mAbs drugs” and “[t]he method development strategy, sample processing protocol, and the LC-MS/MS conditions are general and may be applicable for quantification of other monoclonal antibodies in biological measures” (page 9866, Conclusions).
Jiang does not teach specifically using the method for detecting the antibodies casirivimab and imdevimab in humans, this difference however would have been obvious as Jiang teaches that the other sample matrices may be used with other species, and indicates that only two of the peptides detected in the assay were human IgG specific and that those two can only be used with non-humans (9866). Jiang thus teaches that that analytical methods taught can be used with humans and the analysis set up is specifically for developing techniques for the pharmaceutical industry, i.e. humans. And in the same field of endeavor as pharmaceutical treatments involving the administration of two antibodies, it is known to administer a combination cocktail of these two antibodies.
In the same field of endeavor Weinreich teaches the use of the REGN-COV2 antibody cocktail comprised of casirivimab (REGN10933) and imdevimab (REGN10987) administered together for the treatment of non-hospitalized COVID-19 in patients (Abstract) who were given either a placebo, 2.4 g, or 8.0 g of REGN-COV2 (Abstract). The REGN-COV2 contains equal doses of casirivimab and imdevimab (page 239, column 2, Trial Design).
One of ordinary skill in the art prior to the effective filing date of the instant invention would have found it obvious to use the method of Jiang and Xu on the antibody cocktail of Weinreich as Jiang contemplates the method for use in pharmaceutical industry for other pharmaceuticals and further describes design features contemplating use in human. One of ordinary skill in the art would have been motivated to do so to monitor the amount of pharmaceutical treatment present in the serum and detect the two therapeutic mAbs in an accurate, precise, and timely manner. One of ordinary skill in the art would further have a reasonable expectation of success in doing so as Jiang contemplates the method for use in pharmaceutical industry for other pharmaceuticals and further describes design features contemplating use in human.
Regarding claims 17, the limitations “A method for simultaneously quantitating casirivimab and imdevimab from an administered antibody cocktail, comprising:(a) obtaining a serum sample including casirivimab and imdevimab;(b) generating at least one unique surrogate peptide for each of casirivimab and imdevimab by contacting said sample to trypsin and AspN;(c) quantitating said surrogate peptides using a mass spectrometer; and(d) quantitating casirivimab and imdevimab using the quantitated surrogate peptides”,
As noted above the combination of Jiang and Xu teaches these steps for use with the antibodies administered to monkeys including, Jiang teaches simultaneously administering two mAbs to cynomolgus monkeys, obtaining a serum sample, generating one unique surrogate peptide for each mAb, quantitating the surrogate peptides, and quantitating each of the mAbs using the quantitated surrogate peptides via LC-MS/MS (Abstract). Jiang teaches the use of trypsin and Xu teaches the use of one or more enzymes for obtaining surrogate peptides including trypsin and Xu teaches the digestion by one or more proteases on the sample may be performed directly on the sample or purified samples and teaches the use of LysC, GluC, Arg-C, chymotrypsin, trypsin, AspN, (Page 20, [0073]-[0074]). Further, Jiang teaches the use of electrospray ionization of the effluent that was then analyzed by multiple reaction monitoring (page 9860, column 2, LC-MS/MS Analysis). The act of performing the method steps of Jiang and Xu on the antibody cocktail of Weinreich will result in the claimed method being practiced.
Regarding claim 18 and the limitation “wherein said surrogate peptides comprise the amino acid sequences LLIYAASNLETGVPSR (SEQ ID NO: 1) and DTAVYYCASGS (SEQ ID NO: 2).”, Xu makes obvious the digestion of samples with trypsin and AspN. As evidenced by Babb, the sequence casirivimab (SEQ ID NO: 210) and imdevimab (SEQ ID NO: 654) are known and when these sequences are analyzed using the PeptideMass Tool (http://web.expasy.org/peptide_mass/) as taught by Jiang, SEQ ID NO: 210 from Babb is entered into the tool with the enzyme Trypsin selected, a peptide with 100% identity to SEQ ID NO: 1 is generated. When SEQ ID NO: 654 from Babb is entered into the tool with the enzyme Trypsin selected, a peptide containing 100% identity to SEQ ID NO: 2 is generated. When this trypsin-digested product is reassessed with the additional AspN digestive enzyme selected, a peptide with 100% identity to SEQ ID NO: 2 is generated. The method of Jiang, Xu and Weinreich will thus produce the claimed fragments which will be detected via the method of Jiang, Xu, and Weinreich and be found unique in the analysis of Jiang, Xu and Weinreich as the same steps and fragments are being taken and produced.
Regarding claims 19, 20, and 22, and the limitations “wherein said mass spectrometer is coupled to a liquid chromatography system”, “wherein said mass spectrometer is an electrospray ionization mass spectrometer, nano-electrospray ionization mass spectrometer, or a triple quadrupole mass spectrometer”, “wherein said mass spectrometer is capable performing a multiple reaction monitoring or parallel reaction monitoring”, Jiang teaches that the sample analysis was done by loading serum digest into a HPLC system using a C18, i.e. reversed phase column, and the eluent of the HPLC eluent was ionized in positive electrospray mode (page 9860, column 2, LC-MS/MS Analysis). Xu teaches “performing high pH reversed phase liquid chromatography (RPLC) survey scan with detection by mass spectrometry” (page 50, claim 1). Jiang thus teaches the use of electrospray mass spectrometer coupled to a reversed phase chromatographic system. And further the use of reversed phase chromatography is taught by Xu. Jiang teaches “a unique peptide for each mAb and two confirmatory peptides from different antibody domains, were simultaneously quantified by LC-MS/MS in the multiple reaction-monitoring mode” (Abstract). Jiang thus teaches multiple reaction-monitoring.
Regarding claim 21 and the limitation “further comprising administering casirivimab and imdevimab to a subject” Weinreich teaches the administration of these antibodies (Abstract). In addition, one of ordinary skill in the art would find it obvious that additional antibodies could be administered if the amount found in serum were below effective amounts.
Regarding claim 24 and the limitation “wherein the at least one surrogate peptide is pre-selected to further meet the following criteria: (1) no identical match in Uniprot human proteome database; (2) peptide length shorter than 20 amino acid residues; (3) sequence does not contain sites prone to missed cleavages during enzymatic digestion; and (4) sequence does not contain sites susceptible to in vivo biotransformation or residues prone to partial modification during sample processing.” Jiang specifically teaches the production and detection of unique sequences and highlights that the CDR region is a good region for finding these peptides in an antibody (Sample analysis and Incurred Sample Reanalysis (ISR), Confirmatory Peptides, Figures 3-4, Discussion). Jiang teaches “[i]n silico trypsin digestion was used to predict complementary determining region (CDR) peptides and confirmatory peptides, based on the known amino acid sequences and functional structures of the mAb drugs. Then the online protein BLAST was used to predict the selectivity of each tryptic peptide in monkey serum by querying the protein databases” (page 9861, Results, paragraph 2). Jaing further teaches that the sample other matrices may be used with other species, and indicates that only two of the peptides detected were human IgG specific and that those two can only be used with non-humans (9866). Jiang thus teaches that that analytical methods taught can be used with humans and the analysis set up is specifically for developing techniques for the pharmaceutical industry, i.e. humans. The method of Jiang and Xu will result in the selection of peptides which match these parameters when applied to these antibodies or to other antibodies. In the case of the enzyme cocktail of Weinriech the method of Jiang and Xu will result in at least the peptide fragments of claim 18 which further match the claimed properties.
Conclusion
No claim is 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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/CHARLES Z CONSTANTINE/Examiner, Art Unit 1657
/ROBERT J YAMASAKI/Primary Examiner, Art Unit 1657
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