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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 04/01/2026 has been entered.
Oath/Declaration
The declaration under 37 C.F.R. 1.132 filed 04/01/2026 has been considered by the examiner.
Status of Claims
Claims 3, 10-12, and 16 are cancelled by the applicant.
Claims 1-2, 4-9, 13-15, and 17-20 are pending and examined herein.
Withdrawn Rejections/Objections
The objections to claims 1, 2, and 4 have been withdrawn, necessitated by amendments filed 04/01/2026.
The rejection of claim 12 on the grounds of 35 U.S.C. 112(b) has been withdrawn, due to the claim being cancelled in amendments filed 04/01/2026.
The rejections of claim 11 on the grounds of 35 U.S.C. 103 has been withdrawn, due to the claim being cancelled in amendments filed 04/01/2026.
Modified rejections, necessitated by amendment filed 04/01/2026, are discussed below.
New Objections
Claim Objections
Claims 1-2, 9, and 13 are objected to because of the following informalities:
Claim 1 recites “wherein each of the first supernatant and the second supernatant independently contains a residual amount of the first protein” when it should recite “wherein each of the first supernatant and the second supernatant independently contain a residual amount of the first protein”. Emphasis added.
Claim 1 recites “wherein the solvent is an ascorbic acid solution, and the concentration of ascorbic acid in both the first mixture and the second mixture being 1-12 mM” when it should recite “wherein the solvent is an ascorbic acid solution, and the concentration of ascorbic acid in both the first mixture and the second mixture is 1-12 mM”. Emphasis added.
Claim 1 recites “the solvent is a citric acid solution, and the concentration of citric acid in both the first mixture and the second mixture being 1-5 mM” when it should recite “the solvent is a citric acid solution, and the concentration of citric acid in both the first mixture and the second mixture is 1-5 mM”. Emphasis added.
Claim 1 recites “the solvent is a mixture of acetone, ethanol and acetic acid at a volumetric ratio of acetone: ethanol: acetic acid=50: 50: 0.1, and a volumetric percentage of the mixture of acetone, ethanol and acetic acid in both the first mixture and the second mixture being 9%-22%” when it should recite “the solvent is a mixture of acetone, ethanol and acetic acid at a volumetric ratio of acetone: ethanol: acetic acid=50: 50: 0.1, and a volumetric percentage of the mixture of acetone, ethanol and acetic acid in both the first mixture and the second mixture is 9%-22%”. Emphasis added.
Claim 2 recites “identifying, among the first protein to the Nth protein, one or more target proteins when the difference in abundance thereof satisfy a predefined criterion” when it should recite “identifying, among the first protein to the Nth protein, one or more target proteins when the difference in abundance thereof satisfies a predefined criterion”. Emphasis added.
Claim 9 recites “wherein each of the first ligand sample to the Nth ligand sample has a concentration of the ligand that is same or different from one another” when it should recite “wherein each of the first ligand sample to the Nth ligand sample has a concentration of the ligand that is the same or different from one another”. Emphasis added.
Claim 13 recites “step b) is carried out by mixing the solvent and the first control sample under at 20-30°C for 20- 40 min or at 30-40°C for 10-20 min” when it should recite “step b) is carried out by mixing the solvent and the first control sample at 20-30°C for 20-40 min or at 30-40°C for 10-20 min”. Emphasis added.
Appropriate correction is required.
Modified Rejections
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.
Claims 1, 2, 4, 5, 7-9, 13-15, 18, and 19 are rejected under 35 U.S.C. 103 as being unpatentable over Meng, et al. (“Chemical Denaturation and Protein Precipitation Approach for
Discovery and Quantitation of Protein−Drug Interactions”, published 2018-07-11, cited in PTO-892 dated 2025-06-12) in view of Wang, et al. (“A new chromatographic approach to analyze methylproteome with enhanced lysine methylation identification performance”, published 2019-03-20) as evidenced by the compound summary of guanidine hydrochloride from PubChem (https://pubchem.ncbi.nlm.nih.gov/compound/Guanidine-
Hydrochloride, cited in PTO-892 dated 2025-06-12). The following rejections have been modified, necessitated by amendments filed 04/01/2026.
Meng teaches a method for detecting the interaction between a ligand and a protein based on solvent-induced protein precipitation, comprising: A) mixing a solvent and a ligand sample containing a protein and a ligand to form a first mixture, denaturing the first protein in the first mixture, and precipitating the denatured first protein to obtain a first precipitated protein then separating the mixture to obtain the precipitated protein and the supernatant; B) mixing the solvent with a control sample to form a second mixture, denaturing the first protein in the second mixture, and precipitating a second precipitated protein from the second mixture then separating the mixture to obtain the second precipitated protein and the second supernatant, wherein the control sample contains the protein without the ligand; C) measuring the protein concentration in the precipitated protein or the supernatant of step A) ; D) measuring the protein concentration in the precipitated protein or the supernatant of step B); E) comparing the measurement from step C) to the measurement of step D), wherein each of the first supernatant and the second supernatant independently contains a residual amount of the first protein, as in claim 1 (see, e.g., solvent-induced protein precipitation - p. 9250, col. 2, under “CPP Analysis.”; with and without a ligand - p. 9250, col. 2, under “CPP Analysis.”; equal amount of solvent is added to the protein samples with and without a ligand to denature and partially precipitate the proteins, the protein abundances in supernatant and/or precipitate in the ligand group and control group are measured – p. 9252, col. 1, under “Figure 1.”; comparing the differences of protein abundances in the ligand group and the control group – p. 9251, col. 2 para. 3: “Protein hits were selected using the following criteria: (i) the normalized protein intensities in the (−) and (+) ligand groups were significantly different”; wherein each of the first supernatant and the second supernatant independently contain a residual amount of the first protein - p. 9252, col. 1, under “Figure 1.”). The application’s specification clarifies that “The solvent includes but not limited to one or more of solvents, acidic agents, alkaline agents, metal ions or salts” (see, e.g., p. 4, lines 20-21). The denaturing agent, guanidine hydrochloride (GdmCl), of Meng is equivalent to a solvent because it is a salt and a protein denaturant as evidenced by the compound summary of GdmCl from PubChem (https://pubchem.ncbi.nlm.nih.gov/compound/Guanidine-
Hydrochloride).
Meng teaches the first ligand sample is a member of a ligand group comprising a N number of ligand samples each containing the ligand and one of a second protein to a Nth protein, respectively, wherein the first protein to the Nth protein are different from one another, and the first control sample is a member of a control group comprising the N number of control samples, each containing one of the second protein to the Nth protein without the ligand, the method further comprising: carrying out step a) to step e) for each of remaining members of the ligand group and the control group to obtain a second protein abundance to a Nth protein abundance and a second corresponding protein abundance to a Nth corresponding protein abundance; obtaining a second difference in abundance to a Nth difference in abundance corresponding to the second to the Nth protein, respectively; and identifying, amongst the first protein to the Nth protein, one or more target proteins when the difference in abundance thereof satisfy a predefined criterion, wherein N is an integer of 2 or more, as in claim 2 (see, e.g., protein solution incubated with ligand group and control
group - p. 9250, col. 2, under “CPP Analysis.”; add equal amount of denaturing solvent - p.
9250, col. 2, under “CPP Analysis.”; quantify the abundance of each protein in supernatant
and/or precipitate of the ligand and control group - p. 9249, under “ABSTRACT:”; compare the
abundance difference of each protein in the ligand group and the control group to determine
the target(s) of a ligand - p. 9251, col. 2 para. 3: “Protein hits were selected using the following
criteria: (i) the normalized protein intensities in the (−) and (+) ligand groups were significantly
different”).
Meng teaches separating the mixtures are by centrifugation, as in claim 4 (see, e.g., p. 9252, col. 1, under “Figure 1.”).
Meng teaches each ligand sample or each control sample contains a plurality of proteins derived from a human, as in claim 5 (see, e.g., p. 9249, under “ABSTRACT”: “The technique was
also used to identify protein targets of sinefungin, a broad-based methyltransferase inhibitor, in a human MCF-7 cell lysate”). It is understood that the human cell lysates used in the approach contain a plurality of proteins.
Meng teaches the ligand sample proteins are in natural conformation, as in claim 7 (see, e.g., p. 9250, under “Cell Culture and Lysis”, col. 2, para. 2: “Cell lysis was accomplished using zirconia/silica beads (1 mm) at 4 °C with 20 s of disruption 20 times with 1 min intervals on ice in between. The cell lysate was centrifuged at 14 000g and 4 °C for 10 min, and the supernatant was saved for subsequent analysis”).
Meng teaches the ligand is a drug, as in claim 8 (see, e.g., p. 9249, under “ABSTRACT:”).
Meng teaches each of the ligand samples has a concentration of ligand that is the same as one another, as in claim 9 (see, e.g., p. 9250, under “CPP Analysis.”: “The final concentration of drug was 100 μM in the CsA-binding experiment”).
Meng teaches that step A) is carried out by mixing the solvent and the ligand sample at 20-30° for 20 minutes and that step B) is carried out by mixing the solvent and the control sample at 20-30° for 20 minutes, as in claim 13 (see, e.g., p. 9250, under “CPP Analysis.”: “In all experiments, the (+) and (−) ligand containing lysate samples were distributed into a series of
GdmCl-containing buffers (PBS pH 7.4) with the final GdmCl concentrations ranging from 0 to 2.5 M. The final volume in each buffer was 20 μL. The final concentration of drug was 100
μM in the CsA-binding experiment, 20 μM in the geldanamycin binding experiment, and 0.2, 1.2, or 2.5 mM in the sinefungin binding experiments. The solutions were equilibrated at room temperature for 10 min before 480 μL of deionized water was added into each solution to initiate protein precipitation. After 10 min, the samples were centrifuged”). It is understood that the GdmCl-containing buffer, the solvent in Meng, is incubated with the lysate samples with and without the ligand for a total time of 20 minutes at room temperature (between 20-30°), which is equivalent to steps A) and B).
Meng teaches the protein is measured by label quantification, wherein the label quantification is TMT, as in claim 14 (see, e.g., p. 9250, under “CPP Analysis.”: “The TMT-10plex labeling scheme involved labeling the protein samples derived from each of the denaturant concentrations in the (−) ligand samples with the reagents from one TMT-10plex and labeling each of the denaturant concentrations in the (+) ligand samples with the reagents from another TMT-10plex”).
Meng teaches quantifying the protein abundance in the ligand group and the control group after solvent treatment utilizing mass spectrometry with Data Dependent Acquisition, as in claim 15 (see, e.g., p. 9251, col. 1, para. 1).
Meng teaches identifying a protein as the target protein when the difference between the measurement with and without the ligand satisfies a predefined criterion, as in claim 18 (see, e.g., p. 9251, col. 2 para. 3: “Protein hits were selected using the following criteria: (i) the normalized protein intensities in the (−) and (+) ligand groups were significantly different (i.e., different by at least 1.645σ or 3σ, depending on the experiment)”).
Meng teaches the ligand sample contains a plurality of proteins that includes the target protein and the control sample contains the same plurality of protein that include the first protein, as in claim 19 (see, e.g., p. 9250, under “CPP Analysis.”: “In all experiments, the (+) and (−) ligand containing lysate samples were distributed into a series of GdmCl-containing buffers (PBS pH 7.4) with the final GdmCl concentrations ranging from 0 to 2.5 M”). Again, it is understood that cell lysates contain a plurality of proteins.
Meng fails to teach wherein the solvent is a mixture of acetone, ethanol and acetic acid at a volumetric ratio of acetone: ethanol: acetic acid=50: 50: 0.1, and a volumetric percentage of the mixture of acetone, ethanol and acetic acid in both the first mixture and the second mixture is 9%-22%, as in claim 1.
However, in a journal article on proteome analysis, Wang rectifies these deficiencies. Wang discloses, “5 mL of solvent (acetone: ethanol: acetic acid = 50:50:0.1) was added for precipitation” to cell lysates, as in claim 1 (see, e.g., p. 112, under “2.2. Cell lysis and protein digestion”).
It would have been prima facie obvious to the person of ordinary skill in the art to make
and use the claimed invention from the disclosures of Meng and Wang. Such would have
been considered a simple substitution of equivalent elements as Meng teaches the use of the solvent GdmCl in deionized water for denaturing and precipitating proteins and Wang teaches the solvent acetone: ethanol: acetic acid at a volumetric ratio of 50:50:0.1 for denaturing and precipitating protein. As is stated in MPEP §2144.06, substituting one equivalent element for another known for the same purpose renders an invention obvious and an “express suggestion to substitute one equivalent component or process for another is not necessary to render such substitution obvious. In re Fout, 675 F.2d 297, 213 USPQ 532 (CCPA 1982)." The person of ordinary skill in the art would have had a reasonable expectation of success based on the cumulative disclosures of these prior art references.
While Meng and Wang do not explicitly teach the volumetric percentage of the mixture of acetone, ethanol, and acetic acid in both the first and the second mixture is 9%-22%, it would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to perform routine optimization of the components in the claimed invention to make and use the claimed invention. As noted in In re Aller, 105 USPQ 233 at 235, more particularly, 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. Routine optimization is not considered inventive and no evidence has been presented that arriving at the claimed solvent volumetric percentage was anything other than routine, that the properties of the solvent volumetric percentage from the optimization has any unexpected properties, or that the results should be considered unexpected in any way as compared to the closest prior art. Optimization of parameters is a routine practice that would be obvious for the artisan to employ. See MPEP § 2144.05. An artisan would have understood that the solvent volumetric percentage of Wang can be optimized for use in the method of Meng. The artisan would have understood that the solvent volumetric percentage of the acetone, ethanol, and acetic acid mixture would need to be optimized for use with the invention of Meng because Meng teaches, “In the CPP approach, the soluble protein fraction decreases as a function of the GdmCl [solvent] concentration in the original buffers and the precipitated protein fraction increases as a function of the GdmCl [solvent] concentration in the original buffers” (see, p.9252, col. 1, para. 2). The artisan would have had a reasonable expectation of success based on the cumulative disclosure of Meng and Wang.
Claims 1, 2, 4, 5, 7-9, 13-15, 18, and 19 are newly rejected under 35 U.S.C. 103 as being unpatentable over Meng, et al. (cited above) in view of Zhao, et al. (“Simultaneous determination of six isoflavonoids in rat plasma after administration of total flavonoid from Gegen by ultra-HPLC-MS/MS”, published 2012-05-15, cited in PTO-892 dated 12/04/2025) as evidenced by the compound summary of GdmCl from PubChem (https://pubchem.ncbi.nlm.nih.gov/compound/Guanidine-
Hydrochloride). The following rejections have been modified, necessitated by amendments filed 04/01/2026.
Meng teaches a method for detecting the interaction between a ligand and a protein based on solvent-induced protein precipitation, comprising: A) mixing a solvent and a ligand sample containing a protein and a ligand to form a first mixture, denaturing the first protein in the first mixture, and precipitating the denatured first protein to obtain a first precipitated protein then separating the mixture to obtain the precipitated protein and the supernatant; B) mixing the solvent with a control sample to form a second mixture, denaturing the first protein in the second mixture, and precipitating a second precipitated protein from the second mixture then separating the mixture to obtain the second precipitated protein and the second supernatant, wherein the control sample contains the protein without the ligand; C) measuring the protein concentration in the precipitated protein or the supernatant of step A) ; D) measuring the protein concentration in the precipitated protein or the supernatant of step B); E) comparing the measurement from step C) to the measurement of step D), wherein each of the first supernatant and the second supernatant independently contains a residual amount of the first protein, as in claim 1 (see, e.g., solvent-induced protein precipitation - p. 9250, col. 2, under “CPP Analysis.”; with and without a ligand - p. 9250, col. 2, under “CPP Analysis.”; equal amount of solvent is added to the protein samples with and without a ligand to denature and partially precipitate the proteins, the protein abundances in supernatant and/or precipitate in the ligand group and control group are measured – p. 9252, col. 1, under “Figure 1.”; comparing the differences of protein abundances in the ligand group and the control group – p. 9251, col. 2 para. 3: “Protein hits were selected using the following criteria: (i) the normalized protein intensities in the (−) and (+) ligand groups were significantly different”; wherein each of the first supernatant and the second supernatant independently contain a residual amount of the first protein - p. 9252, col. 1, under “Figure 1.”). The application’s specification clarifies that “The solvent includes but not limited to one or more of solvents, acidic agents, alkaline agents, metal ions or salts” (see, e.g., p. 4, lines 20-21). The denaturing agent, guanidine hydrochloride (GdmCl), of Meng is equivalent to a solvent because it is a salt and a protein denaturant as evidenced by the compound summary of GdmCl from PubChem (https://pubchem.ncbi.nlm.nih.gov/compound/Guanidine-
Hydrochloride).
Meng teaches the first ligand sample is a member of a ligand group comprising a N number of ligand samples each containing the ligand and one of a second protein to a Nth protein, respectively, wherein the first protein to the Nth protein are different from one another, and the first control sample is a member of a control group comprising the N number of control samples, each containing one of the second protein to the Nth protein without the ligand, the method further comprising: carrying out step a) to step e) for each of remaining members of the ligand group and the control group to obtain a second protein abundance to a Nth protein abundance and a second corresponding protein abundance to a Nth corresponding protein abundance; obtaining a second difference in abundance to a Nth difference in abundance corresponding to the second to the Nth protein, respectively; and identifying, amongst the first protein to the Nth protein, one or more target proteins when the difference in abundance thereof satisfy a predefined criterion, wherein N is an integer of 2 or more, as in claim 2 (see, e.g., protein solution incubated with ligand group and control
group - p. 9250, col. 2, under “CPP Analysis.”; add equal amount of denaturing solvent - p.
9250, col. 2, under “CPP Analysis.”; quantify the abundance of each protein in supernatant
and/or precipitate of the ligand and control group - p. 9249, under “ABSTRACT:”; compare the
abundance difference of each protein in the ligand group and the control group to determine
the target(s) of a ligand - p. 9251, col. 2 para. 3: “Protein hits were selected using the following
criteria: (i) the normalized protein intensities in the (−) and (+) ligand groups were significantly
different”).
Meng teaches separating the mixtures are by centrifugation, as in claim 4 (see, e.g., p. 9252, col. 1, under “Figure 1.”).
Meng teaches each ligand sample or each control sample contains a plurality of proteins derived from a human, as in claim 5 (see, e.g., p. 9249, under “ABSTRACT”: “The technique was
also used to identify protein targets of sinefungin, a broad-based methyltransferase inhibitor, in a human MCF-7 cell lysate”). It is understood that the human cell lysates used in the approach contain a plurality of proteins.
Meng teaches the ligand sample proteins are in natural conformation, as in claim 7 (see, e.g., p. 9250, under “Cell Culture and Lysis”, col. 2, para. 2: “Cell lysis was accomplished using zirconia/silica beads (1 mm) at 4 °C with 20 s of disruption 20 times with 1 min intervals on ice in between. The cell lysate was centrifuged at 14 000g and 4 °C for 10 min, and the supernatant was saved for subsequent analysis”).
Meng teaches the ligand is a drug, as in claim 8 (see, e.g., p. 9249, under “ABSTRACT:”).
Meng teaches each of the ligand samples has a concentration of ligand that is the same as one another, as in claim 9 (see, e.g., p. 9250, under “CPP Analysis.”: “The final concentration of drug was 100 μM in the CsA-binding experiment”).
Meng teaches that step A) is carried out by mixing the solvent and the ligand sample at 20-30° for 20 minutes and that step B) is carried out by mixing the solvent and the control sample at 20-30° for 20 minutes, as in claim 13 (see, e.g., p. 9250, under “CPP Analysis.”: “In all experiments, the (+) and (−) ligand containing lysate samples were distributed into a series of
GdmCl-containing buffers (PBS pH 7.4) with the final GdmCl concentrations ranging from 0 to 2.5 M. The final volume in each buffer was 20 μL. The final concentration of drug was 100
μM in the CsA-binding experiment, 20 μM in the geldanamycin binding experiment, and 0.2, 1.2, or 2.5 mM in the sinefungin binding experiments. The solutions were equilibrated at room temperature for 10 min before 480 μL of deionized water was added into each solution to initiate protein precipitation. After 10 min, the samples were centrifuged”). It is understood that the GdmCl-containing buffer, the solvent in Meng, is incubated with the lysate samples with and without the ligand for a total time of 20 minutes at room temperature (between 20-30°), which is equivalent to steps A) and B).
Meng teaches the protein is measured by label quantification, wherein the label quantification is TMT, as in claim 14 (see, e.g., p. 9250, under “CPP Analysis.”: “The TMT-10plex labeling scheme involved labeling the protein samples derived from each of the denaturant concentrations in the (−) ligand samples with the reagents from one TMT-10plex and labeling each of the denaturant concentrations in the (+) ligand samples with the reagents from another TMT-10plex”).
Meng teaches quantifying the protein abundance in the ligand group and the control group after solvent treatment utilizing mass spectrometry with Data Dependent Acquisition, as in claim 15 (see, e.g., p. 9251, col. 1, para. 1).
Meng teaches identifying a protein as the target protein when the difference between the measurement with and without the ligand satisfies a predefined criterion, as in claim 18 (see, e.g., p. 9251, col. 2 para. 3: “Protein hits were selected using the following criteria: (i) the normalized protein intensities in the (−) and (+) ligand groups were significantly different (i.e., different by at least 1.645σ or 3σ, depending on the experiment)”).
Meng teaches the ligand sample contains a plurality of proteins that includes the target protein and the control sample contains the same plurality of protein that include the first protein, as in claim 19 (see, e.g., p. 9250, under “CPP Analysis.”: “In all experiments, the (+) and (−) ligand containing lysate samples were distributed into a series of GdmCl-containing buffers (PBS pH 7.4) with the final GdmCl concentrations ranging from 0 to 2.5 M”). Again, it is understood that cell lysates contain a plurality of proteins.
Meng fails to teach the solvent is an ascorbic acid solution, and the concentration of ascorbic acid in both the first mixture and the second mixture is 1-12 mM, as in claim 1.
However, in a journal article on a HPLC-MS/MS method, Zhao rectifies these deficiencies. Zhao discloses, “After the addition of methanol containing 0.1% formic acid and 10% ascorbic acid, the analytes and rutoside were obtained by protein precipitation”, as in claims 1 and 11 (see p. 984, under abstract).
It would have been prima facie obvious to the person of ordinary skill in the art to make
and use the claimed invention from the disclosures of Meng and Zhao. Such would have
been considered a simple substitution of equivalent elements as Meng teaches the use of the solvent GdmCl in deionized water for denaturing and precipitating proteins and Zhao teaches the solvent is 10% ascorbic acid for denaturing and precipitating protein. As is stated in MPEP §2144.06, substituting one equivalent element for another known for the same purpose renders an invention obvious and an “express suggestion to substitute one equivalent component or process for another is not necessary to render such substitution obvious. In re Fout, 675 F.2d 297, 213 USPQ 532 (CCPA 1982)." The person of ordinary skill in the art would have had a reasonable expectation of success based on the cumulative disclosures of these prior art references.
While Meng and Zhao do not explicitly teach the concentration of ascorbic acid is 1-12 mM, the applicant admits that Zhao teaches ascorbic acid at 16.2 mM on p. 13 of the applicant’s remarks filed 04/01/2026. Therefore, it would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to perform routine optimization of the components in the claimed invention to make and use the claimed invention. As noted in In re Aller, 105 USPQ 233 at 235, more particularly, 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. Routine optimization is not considered inventive and no evidence has been presented that arriving at the claimed solvent concentration was anything other than routine, that the properties of the solvent concentration from the optimization has any unexpected properties, or that the results should be considered unexpected in any way as compared to the closest prior art. Optimization of parameters is a routine practice that would be obvious for the artisan to employ. See MPEP § 2144.05. An artisan would have understood that the solvent concentration of Zhao can be optimized for use in the method of Meng. The artisan would have understood that the solvent concentration of ascorbic acid would need to be optimized for use with the invention of Meng because Zhao teaches, “In the CPP approach, the soluble protein fraction decreases as a function of the GdmCl [solvent] concentration in the original buffers and the precipitated protein fraction increases as a function of the GdmCl [solvent] concentration in the original buffers” (see, p.9252, col. 1, para. 2). The artisan would have had a reasonable expectation of success based on the cumulative disclosure of Meng and Zhao.
Claim 6 is rejected under 35 U.S.C. 103 as being unpatentable over Meng (cited above) and Wang (cited above), as applied to claims 1, 2, 4, 5, 7-9, 13-15, 18, and 19, and further in view of Trainor (“The importance of plasma protein binding in drug discovery”, published 2007-01-16, cited in PTO-892 dated 2025-06-12). The following rejections have been modified, necessitated by amendments filed 04/01/2026.
Meng and Wang teaches as set forth above, but fail to teach the protein solution includes blood or plasma, as in claim 6. However, Trainor rectifies this deficiency in a journal article on the role of plasma protein binding in drug discovery. Trainor recites, “Plasma protein binding of drugs is a well-recognised phenomena, but it is only recently that the implications for drug action in vivo have been fully appreciated” (see, e.g., p. 51, under abstract).
Meng, Wang, and Trainor are analogous to the field of the claimed invention because they are both in the field of protein-drug binding. One of ordinary skill in the art before the effective filing date of the application would have found it obvious to incorporate the teachings of Trainor into the methods of Meng and Wang by measuring the affinity of proteins and ligands, specifically drugs, in blood or plasma samples. An artisan would have been motivated to do so because “[p]lasma proteins, by virtue of their high concentration, control the free drug concentration in plasma and in compartments in equilibrium with plasma, thereby, effectively attenuating drug potency in vivo” (see, e.g., Trainor, p. 51, under abstract). An artisan would have had a reasonable expectation of success based on the given disclosures.
Claim 6 is newly rejected under 35 U.S.C. 103 as being unpatentable over Meng (cited above) and Zhao (cited above), as applied to claims 1, 2, 4, 5, 7-9, 13-15, 18, and 19, and further in view of Trainor (cited above). The following rejections have been modified, necessitated by amendments filed 04/01/2026.
Meng and Zhao teaches as set forth above, but fails to teach the protein solution includes blood or plasma, as in claim 6. However, Trainor rectifies this deficiency in a journal article on the role of plasma protein binding in drug discovery. Trainor recites, “Plasma protein binding of drugs is a well-recognised phenomena, but it is only recently that the implications for drug action in vivo have been fully appreciated” (see, e.g., p. 51, under abstract).
Meng, Zhao, and Trainor are analogous to the field of the claimed invention because they are both in the field of protein-drug binding. One of ordinary skill in the art before the effective filing date of the application would have found it obvious to incorporate the teachings of Trainor into the methods of Meng and Zhao by measuring the affinity of proteins and ligands, specifically drugs, in blood or plasma samples. An artisan would have been motivated to do so because “[p]lasma proteins, by virtue of their high concentration, control the free drug concentration in plasma and in compartments in equilibrium with plasma, thereby, effectively attenuating drug potency in vivo” (see, e.g., Trainor, p. 51, under abstract). An artisan would have had a reasonable expectation of success based on the given disclosures.
Claims 17 and 20 are newly rejected under 35 U.S.C. 103 as being unpatentable over Meng (cited above) and Wang (cited above), as applied to claims 1, 2, 4, 5, 7-9, 13-15, 18, and 19, and further in view Lomenick, et al. (“Target identification using drug affinity responsive target stability (DARTS)”, published 2009-12-22, cited in PTO-892 dated 12/04/2025). The following rejections have been modified, necessitated by amendments filed 04/01/2026.
Meng and Wang teach as set forth above, especially that target proteins are identified by a predetermined criterion (see, e.g., p. 9251, col. 2 para. 3: “Protein hits were selected using the following criteria: (i) the normalized protein intensities in the (−) and (+) ligand groups were significantly different (i.e., different by at least 1.645σ or 3σ, depending on the experiment)”). But, the references fail to teach the predefined criterion is determined according to a fold change of protein abundance ≥ 2, as in claims 17 and 20.
However, in a journal article on target identification using drug affinity responsive target stability, Lomenick rectifies this deficiency. Lomenick teaches the predefined criterion is determined according to a fold change of protein abundance ≥ 2, as in claims 17 and 20 (see, e.g., p. 21985, under “Fig. 2.”, under panel “B”, under figure caption).
Meng, Wang, and Lomenick are analogous to the field of the claimed invention because they are all in the field of biological assays. One of ordinary skill in the art before the effective filing date of the application would have found it obvious to incorporate the predefined criterion of Lomenick into the method of Meng and Wang. An artisan would have been motivated to do so because Lomenick disclosed that a known drug target, EF-1α, is identified by their predetermined criterion (see, e.g., p. 21985, col. 1, para. 1-2). An artisan would have a reasonable expectation of success based on the given disclosures.
Claims 17 and 20 are newly rejected under 35 U.S.C. 103 as being unpatentable over Meng (cited above) and Zhao (cited above), as applied to claims 1, 2, 4, 5, 7-9, 13-15, 18, and 19, and further in view Lomenick, et al. (cited above). The following rejections have been modified, necessitated by amendments filed 04/01/2026.
Meng and Zhao teach as set forth above, especially that target proteins are identified by a predetermined criterion (see, e.g., p. 9251, col. 2 para. 3: “Protein hits were selected using the following criteria: (i) the normalized protein intensities in the (−) and (+) ligand groups were significantly different (i.e., different by at least 1.645σ or 3σ, depending on the experiment)”). But, the references fail to teach the predefined criterion is determined according to a fold change of protein abundance ≥ 2, as in claims 17 and 20.
However, in a journal article on target identification using drug affinity responsive target stability, Lomenick rectifies this deficiency. Lomenick teaches the predefined criterion is determined according to a fold change of protein abundance ≥ 2, as in claims 17 and 20 (see, e.g., p. 21985, under “Fig. 2.”, under panel “B”, under figure caption).
Meng, Zhao, and Lomenick are analogous to the field of the claimed invention because they are all in the field of biological assays. One of ordinary skill in the art before the effective filing date of the application would have found it obvious to incorporate the predefined criterion of Lomenick into the method of Meng and Zhao. An artisan would have been motivated to do so because Lomenick disclosed that a known drug target, EF-1α, is identified by their predetermined criterion (see, e.g., p. 21985, col. 1, para. 1-2). An artisan would have a reasonable expectation of success based on the given disclosures.
Declaration under 37 C.F.R. § 1.132
The declaration under 37 C.F.R. § 1.132 filed 04/01/2026, i.e., the Zhang Declaration, is insufficient to overcome the outstanding rejections under 35 U.S.C. 103. The declarant asserts that both Wang (cited above) and Zhao (cited above) teach precipitating all the proteins in the sample (see, para. 4 of Zhang). Zhang asserts that Zhao precipitates all proteins in the sample by centrifugation at a high speed, a low temperature, and for a long time (see, para. 7 of Zhang). Zhang further asserts that Zhao uses a large amount of strong reagent, which precipitates all proteins in the sample (see, para. 9 of Zhang). Zhang also asserts that Wang’s objective is maximizing protein precipitation for global methylproteome analysis (see, para. 10 of Zhang). Zhang additionally asserts that Wang uses a large volume of the acetone: ethanol: acetic acid mixture (see, para. 12 of Zhang). The declarant, Dr. Xiaolei Zhang, concludes that both references are limited to the use of protein precipitation for either protein removal or protein purification purposes, which are distinct purposes from the claimed invention (see, para. 13 of Zhang). Zhang contrasts Zhao and Wang to the claimed invention which teaches partial precipitation of the protein in the mixture, leaving a residual amount of proteins in the supernatant. In the newly amended claims filed 04/01/2026, the applicant has added the following limitation to claim 1: “wherein each of the first supernatant and the second supernatant independently contains [sic] a residual amount of the first protein”. However, the claim amendments filed 04/01/2026 have necessitated modifications to the 35 U.S.C. 103 rejection of claim 1 (discussed above). Meng (cited above) is currently relied upon in part because they teach the partial precipitation of proteins for the same purpose as the claimed invention, the discovery and quantitation of protein-drug interaction (see, e.g., p. 9249, under “Abstract”). Zhao and Wang are relied upon for the substitution of functionally equivalent solvents, as discussed above. The partial precipitation and objective is taught by the primary reference Meng instead. The solvents of Zhao and Wang are disclosed as precipitating solvents, and Meng teaches that the degree of protein precipitation is a function of the concentration of the precipitating solvent (see, p.9252, col. 1, para. 2). Therefore, the partial precipitation of proteins with the solvents of Zhao and Wang would have been obvious to one of ordinary skill in the art and a reasonable expectation of success is provided in the disclosures above.
Response to Arguments
The arguments filed 04/01/2026 have been fully considered but they have not been found persuasive.
Rejections under 35 U.S.C. 103
The applicant begins arguments on p. 10 of the applicant’s remarks by pointing to the Zhang Declaration under 37 CFR 1.132, which indicates that references Wang (cited above) and Zhao (cited above) teach precipitating all the proteins in the sample and use a large amount of strong reagents to achieve that goal. The declarant, Dr. Xiaolei Zhang, concludes that both references are limited to the use of protein precipitation for either protein removal or protein purification purposes, which are distinct purposes from the claimed invention. The applicant continues by contrasting the claimed invention which teaches partial precipitation of the protein in the mixture, leaving a residual amount of proteins in the supernatant. In the newly amended claims filed 04/01/2026, the applicant has added the following limitation to claim 1: “wherein each of the first supernatant and the second supernatant independently contains [sic] a residual amount of the first protein”. However, the claim amendments filed 04/01/2026 have necessitated modifications to the 35 U.S.C. 103 rejection of claim 1 (discussed above). Meng (cited above) is relied upon in part because they teach the partial precipitation of proteins for the same purpose as the claimed invention, the discovery and quantitation of protein-drug interaction (see, e.g., p. 9249, under “Abstract”). Wang and Zhao are relied upon for the substitution of functionally equivalent solvents, as discussed above. The partial precipitation and purpose is taught by the primary reference Meng instead.
The applicant then turns the argument’s focus to Meng. The applicant argues that Meng requires a large amount of water to initiate protein precipitation from the GdmCl-containing buffer. The GdmCl in the buffer of Meng causes the protein to unfold and dissolve, in other words to denature. The applicant argues that according to claim 1, no water is added and the precipitation is from the first mixture. However, the amended claim 1 recites, “mixing a solvent and a first ligand sample containing a first protein and a ligand to form a first mixture, denaturing the first protein in the first mixture, and precipitating the denature first protein to obtain a first precipitated protein from the first mixture”. The broadest reasonable interpretation of the amended claim 1 encompasses methods like the one disclosed in Meng where a denaturing solvent, such as GdmCl, is added to a ligand sample containing a protein and a ligand then water is added to precipitate the protein in the ligand sample. In other words, Meng teaches the amended limitation of claim 1 under the broadest reasonable interpretation of the claim.
The applicant continues by pointing to the amended claim 1 limitation that further defines the solvent. The amended claim 1 limitation is distinct from the limitation previously set forth in claims 11 and 12. The amended claim 1 necessitated modified 35 U.S.C. 103 rejection, set forth above.
Conclusion
No claims are allowed.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
The compound summary of GdmCl from PubChem (https://pubchem.ncbi.nlm.nih.gov/compound/Guanidine-Hydrochloride) discloses guanidine hydrochloride (GdmCl) is equivalent to a solvent because it is a salt and a protein denaturant.
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/MICHAEL CAMERON SVEIVEN/Examiner, Art Unit 1678
/GREGORY S EMCH/Supervisory Patent Examiner, Art Unit 1678
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