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 .
Status of the Claims
Claims 1-4, 42-43, and 45-57 are pending. Claims 1-4, 42-43, and 45-57 are the subject of this NON-FINAL Office Action. Applicant’s amendments to the claims necessitate a new grounds of rejection.
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 01/30/2026 has been entered.
Claim Interpretation
Applicant has amended claim 1 to recite “at least three different biological sensor peptides for each kinase.” The term “different” is not specifically defined in the specification.
Applicant’s Remarks, filed 1/30/2026, on pg. 8, states that the cited art does not teach a panel of sensor peptides comprising at least three different biological sensors. Applicant states that Kusalik in particular teaches a panel of sensor peptides wherein each peptide is represented by at least three replicates of a sensor peptide, while the claims require different peptides. Applicant refers to Fig. 8 and states that the use of three different peptides per kinase and not replicates provide a useful assay for determining activity of a kinase.
Furthermore, Applicant on pg. 8, par. 4, cites Kusalik’s definition of a replicate as “ ‘a peptide that has the same sequence and length as another peptide (e.g. two peptides having the same sequence and length are replicates of each other) treated under the same conditions (e.g. contacted with the same sample.’ Kusalik at [0090].” Applicant continues by contrasting Kusalik with claim 1’s use of at least three different biological sensor peptides.
The specification, particularly Table 1, indicates that the majority of the peptides used in the assay are unique peptides, each with a unique sequence.
In light of Applicant’s remarks and the specification, the limitation “at least three different peptides” will be interpreted as at least three unique biological sensor peptides for each kinase (e.g. at least three peptides with unique sequences for each kinase).
Response to Arguments
Applicant’s arguments with respect to claim(s) 1 have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument. The 103 rejections, presented below, do not rely on the teachings of Kusalik.
New Grounds - Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1-4, 45-46, 52, and 56 is/are rejected under 35 U.S.C. 103 as being unpatentable over by Parker et al. (US 2019/0302117 A1, filed 02/22/2019 with priority to 02/22/2018; previously cited) in view of Chen et al. (US 2011/0046018 A1; cited on the IDS filed 10/12/2020, previously cited) and Coppe et al. (Phospho-reactome profiling reveals the heterogenic, targetable kinase signature of breast cancer. Cancer Res. 74, 2014, 5309; cited on the IDS filed 10/12/2020; previously cited) and evidenced by Szafran et al. (High-content screening identifies Src family kinases as potential regulators of AR-V7 expression and androgen-independent cell growth. The Prostate. 77, 2017, 82-93).
Regarding claim 1, Parker teaches kinase substrates and methods comprising their use. Parker (Abstract). Parker teaches activity-based screen that assay phosphorylation of a substrate (par. 0003, 0151).
Parker does not teach the combination of ABL, AKT, HER, MAPK, and SFK kinase subfamilies. Parker does teach the panel comprises biological sensor peptides for members of at least two different kinase subfamilies, including ABL, BLK, BRK, CSK, EGFR, FGR, FRK, HCK, JAK2, LCK, SRC, SRMS, and YES1 subfamilies (par. 0073-0079, 0154).
Chen teaches methods for the detection and/or quantification of the presence and/or activity of one or more kinases and/or phosphatases (Abstract). Chen teaches a device comprising a surface with at least one attached kinase substrate molecule, wherein the kinase substrate molecules include peptides, contacting the sample with the device, and measuring the phosphorylation of the molecule (par. 0011-0014; claims 1-3, 30).
Chen teaches the panel comprises peptides for kinases that are members of the ABL, AKT, HER, SRC (par. 0049), and MAPK (par. 0046) kinase subfamilies (par. 0045-0046, 0049).
As evidenced by Szafran, SRC is encompassed by SFK (pg. 82, “Results”).
It would have been obvious to one of ordinary skill in the art to substitute the peptides of Parker for the peptides of Chen, as it would be a simple substitution of one group of peptides for another, with no evidence of unexpected results.
Parker does not teach that the panel comprises at least three biological sensor peptides for each kinase.
Coppe et al. (Coppe et al. (Phospho-reactome profiling reveals the heterogenic, targetable kinase signature of breast cancer. Cancer Res. 74, 2014, 5309; cited on the IDS filed 10/12/2020) teaches a library of peptide sensors from confirmed kinase substrate’s phosphorylation sites (par. 2). Coppe teaches that 228 peptides were developed into an ATP-consumption screen to identify the activity signatures of AKT, EGFR, MAPK, ABL, and SRC family kinases (par. 2).
As there are five peptide families and 228 peptides, this would be approximately 45 sensor peptides for each kinase. Coppe further teaches this allows to comprehensively measure the catalytic activity of a multitude of kinases at once (par. 4). It would be obvious to one of ordinary skill in the art to use at least three biological sensor peptides per kinase, as Coppe teaches the use of approximately 45 sensor peptides for each kinase and teaches that it allows for the measurement of the catalytic activity of a multitude of kinases at once, with no evidence of unexpected results.
Regarding claim 2, Chen teaches that the surface can include one or more positive and/or negative controls (par. 0078). Chen teaches that the negative control comprises one or more molecules of the same species as the kinase substrates, but lacking a phosphorylation site for a particular kinase expected to be present in the assay, and that the positive control comprises one or more molecules of the same species as the kinase substrates, but containing a phosphorylation site for a kinase known to be present in the assay (par. 0078).
It would have been obvious to one of ordinary skill in the art to include mutated control sensor peptides as taught by Chen, as it allows for the method of Parker to include a control for the assay, with no evidence of unexpected results.
Regarding claim 3, Parker teaches measuring phosphorylation activity by using radioactive ATP (par. 0151, 0274).
Regarding claim 4, Parker teaches the phosphorylation activity was normalized and was used to assign the activity to a subfamily or kinase (par. 0274-0276).
Regarding claim 45, Coppe teaches that 228 peptides were developed into an ATP-consumption screen to identify the activity signatures of AKT, EGFR, MAPK, ABL, and SRC family kinases (par. 2).
As there are five peptide families and 228 peptides, this would be approximately 45 sensor peptides for each kinase.
Regarding claim 46, Parker teaches the peptides can be 9 amino acids in length, and can be about 6 to about 15 amino acids in length (par. 0114).
Regarding claim 52, Parker teaches the kinase can be in a sample including in a cancer cell (par. 0214-0217).
Regarding claim 56, Parker teaches the cell is a cancer cell, wherein the cancer is leukemia (par. 0217).
Claim(s) 53-55 and 57 is/are rejected under 35 U.S.C. 103 as being unpatentable over Parker, Chen, and Coppe as applied to claim 1 above, and further in view of Labots et al. (Evaluation of a tyrosine kinase peptide microarray for tyrosine kinase inhibitor therapy selection in cancer. Experimental & Molecular Medicine. 48, 2016, pg. 1-11; previously cited).
Parker teaches that the sample can be from cancer cells, but does not teach that the cancer cells are from a solid tumor, from a breast tumor, colorectal tumor, melanoma, or lung tumors, that the sample comprises metastatic cancer cells, or that the cancer cells are from a patient that has been treated with a kinase inhibitor therapeutic agent.
Labots teaches an evaluation of a high-throughput tyrosine kinase peptide substrate array to determine its readiness as a selection tool for TKI therapy (Abstract).
Regarding claim 53, Labots teaches the cancer cells can be from a solid tumor (pg. 1, left col., par. 1; pg. 2, left col., par. 4).
Regarding claim 54, Labots teaches the solid tumor is a breast tumor, melanoma, colorectal tumor, or lung tumor (pg. 2, left col, par. 4).
Regarding claim 55, Labots teaches the sample comprises metastatic cancer cells (pg. 4, right col, par. 3).
Regarding claim 57, Labots teaches an evaluation of a high-throughput tyrosine kinase peptide substrate array to determine its readiness as a selection tool for TKI therapy (Abstract). It would have been obvious to one of ordinary skill in the art to use cancer cells from a solid tumor, where the solid tumor is a breast tumor, melanoma, colorectal tumor, or lung tumor, that the sample comprises metastatic cancer cells, or that the cancer cells are from a patient that has been treated with a kinase inhibitor therapeutic agent in the method of Parker, Chen, and Kusalik, as Labots teaches the use of these samples in an evaluation of a tyrosine kinase peptide substrate array, and it would be a simple substitution of one type of cancer cell for another, with no evidence of unexpected results.
Relevant Prior Art
Schutkowski et al. (Peptide arrays for kinase profiling. ChemBioChem. 2005, 6, 513-521.) is relevant to applicant’s disclosure. Schutkowski discusses the production principles, library types, and assay strategies used for kinase profiling on peptide arrays, and summarizes various peptide array applications in kinase research (pg. 513, left col., par. 1-2).
Claims Free of the Prior Art
Claims 42-43 and 47-51 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Claims 42-43 and 47-51 are free of the prior art. The prior art does not teach or suggest a panel comprising each of the recited kinase subfamilies of claims 42-43. The prior art does not make obvious the peptides in Fig. 4 or listed in Table 1 as SEQ ID NOs 1-574.
Coppe et al. (Coppe et al. (Phospho-reactome profiling reveals the heterogenic, targetable kinase signature of breast cancer. Cancer Res. 74, 2014, 5309; cited on the IDS filed 10/12/2020) teaches a library of peptide sensors from confirmed kinase substrate’s phosphorylation sites (par. 2). Coppe teaches that 228 peptides were developed into an ATP-consumption screen to identify the activity signatures of AKT, EGFR, MAPK, ABL, and SRC family kinases (par. 2).
Coppe does not teach the specific sequences as described in the claims.
The prior art does not make obvious the particular sequences as described in the claims, and does not provide or teach a reasoning or motivation for choosing the particular sequences described in claims 47-51.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Randi L Beil whose telephone number is (571)272-1147. The examiner can normally be reached M-F 8:00 am - 5:00 pm.
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/R.L.B./Examiner, Art Unit 1684
/AARON A PRIEST/Primary Examiner, Art Unit 1681
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