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 .
Priority
This application claims benefit of priority to Provisional Application 63/187,965 filed on 05/13/2021. Support for the instant claims can be found in the Provisional Application, therefore, for examination purposes, the effective filing date of the claimed invention is 05/13/2021.
Drawings
The Drawings filed 04/06/2026 are accepted by the Examiner.
Amendment and Claim Status
In the reply filed on 04/06/2026, Applicant amended claims 13, 15-18 and 20. Claims 1-12 remain withdrawn as they are not encompassed by Applicant’s election made 08/20/2025.
Claims 1-20 are currently pending.
Claims 1-12 are withdrawn.
Claims 13-20 are under examination.
Non-Compliant Amendment
Claim 15 does not have the required markings for an amended claim. Claim 15 recites: “wherein the detects a presence of …” in lines 1-2 of the claim. Claim 15 as originally examined recited: “wherein the system determines the presence of the substrate in a sample, …” The addition of the phrase, “detector at least one of:” should be underlined as it is new text not present within the claims as originally presented. See MPEP § 714(c)(2). Appropriate correction is required.
Claim Objections
Claim 13 is objected to because of the following informalities: Claim 13 has been amended to recite:
A system for detecting kinase activity in vivo, comprising:
A well and a detector positioned to detect an analyte in the well, wherein the well comprises live cells that comprise one or more mutated kinases, and wherein the one or more mutated kinases comprise a mutation that enlarges an ATP binding pocket of the kinase,
An ATP analog-nanoparticle conjugate capable of intracellular delivery of the ATP analog-nanoparticle conjugate,
Wherein the ATP analog comprises a detectable label, and after a predetermined period of time, a detectable label on a substrate from the ATP analog-nanoparticle conjugate when it contacts the one or more mutated kinases in cellulo is capable of being detected, and
The detectable label is capable of being transferred from the ATP analog-nanoparticle conjugate to the substrate of the one or more mutated kinases;
Wherein the detector is capable of measuring the detectable label being transferred from the ATP analog-nanoparticle conjugate to the substrate of the one or more mutated kinases in the live cells.
The claim is grammatically awkward and would be easier to read and understand if re-written. For example, Applicant removed the verb, being ‘detecting,’ from line 8 of the claim, leaving just “… a detectable label on a substrate from the ATP analog-nanoparticle conjugate when it contacts …” The limitation does not make sense after the removal of the verb. Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 13-20 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 13, as-amended, recites “wherein the detector is capable of measuring the detectable label being transferred from the ATP analog-nanoparticle conjugate to the substrate of the one or more mutated kinases in the live cells” in lines 12-14. This new limitation contradicts the limitation from lines 7-8 of claim 13 which recites “the ATP analog comprises a detectable label, and after a predetermined period of time, a detectable label on a substrate.” Thus, it is unclear how many detectable labels are present and what the detectable label is present on. Therefore, claim 13 and all claims dependent upon claim 13 are rendered indefinite.
Claims 17-18, even as-amended, remain rejected because Applicant has not clarified the structural components required by the system. Therefore, it appears the limitations of claims 17-18 are directed to intended use steps. For example, it is unclear if the binding agent is a structural component of the system or if it is for use in the system because the binding agent is only referring to when using the system. Thus, claims 17-18 remain indefinite.
Claim 20, as amended, recites “and an ATP analog-nanoparticle conjugate capable of intracellular delivery of the ATP analog-nanoparticle conjugate, a detectable label capable of being detected in the live cells” in lines 4-8 of the claim. The claim is missing a word after “conjugate” and before “a detectable label.” It is unclear what word the claim is missing, leaving it unclear exactly what the kit comprises. For example, it is unclear if the missing word is ‘and,’ meaning the kit comprises the ATP analog-nanoparticle conjugate and a detectable label or if the missing word is ‘comprising,’ meaning the kit comprises the ATP analog-nanoparticle conjugate which comprises a detectable label, or something else. Overall, it is unclear exactly what the kit comprises. Thus, claim 20 is indefinite.
USC § 112 – Response to Arguments
Applicant's arguments filed 04/06/2026 have been fully considered but they are not persuasive.
Applicant argued the amended claims presented in the claim set of 04/06/2026 overcome the 35 USC § 112 rejections of record.
A modified rejection, as necessitated by amendment, has been set forth above to address the amended claims.
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.
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.
Claims 13-20 are rejected under 35 U.S.C. 103 as being unpatentable over Sicinski et al. (WO 2018035296 A1, 02/22/2018) (Of Record) in view of Huang et al. (US 20120201872 A1, 08/09/2012) (Of Record).
Regarding claim 13, it is reiterated that claim 13 is directed to a product, being a system. Therefore, patentable weight is being given to the limitations that structurally limit the product. As such, claim 13 is being interpreted as a system, comprising: a well, a detector, live cells comprising a mutated kinase and an ATP analog-nanoparticle conjugate. The ‘capable of’ limitations are interpreted as intended uses.
Sicinski et al. disclose:
methods for in situ detection of protein substrates of an analog-sensitive kinase. The methods are particularly useful for identification of kinase activity in cells in culture and within tissues at subcellular levels at various physiological and pathological conditions, or for quantification of overall kinase activity at cellular or subcellular levels. Kits comprising agents for using the methods are also provided.
An aspect of the invention provides a method for in situ visualization of kinase activity in a sample comprising a kinase, the method comprising: (a) incubating the sample with a fixative; (b) incubating the sample with an ATP analog, such that the kinase accepts the ATP analog as a phosphate donor substrate, such that the γ-phosphate of the ATP analog- comprises a transferrable label; and (c) detecting the transferrable label (Page 2, Lines 8-17).
Sicinski et al. go on to disclose a specific example, Example 2, where a murine kinase, CDK1, was engineered with two substitution, M32V and F80G (Page 22, Lines 3-4), reading on a mutated kinase with a mutation that enlarges the ATP binding pocket of the kinase. Cells comprising the mutated kinases were cultured on glass coverslips (Page 22, Lines 7-8) and incubated with furfuryladenosine-5’-O-(3-thiotriphosphate) (Page 22, Lines 10-11), furfuryladenosine-5’-O-(3-thiotriphosphate) reads on an ATP analog, allowing thiophosphorylation of substrates of the mutated kinase (Page 22, Lines 13-14). The thiophosphorylated residues of the substrates were alkylated with PBBM (Page 22, Lines 15-16) and subsequently visualized with an antithiophosphoester antibody and a secondary antibody coupled with AlexaFluor 594 (Page 22, Lines 18-19). Thus, the glass coverslip, reading on a system, comprising the mutated kinase and the furfuryladenosine-5’-O-(3-thiotriphosphate) that contained the label that was passed to the substrate, reads on a system comprising one or more mutated kinases with a mutation that enlarges the ATP binding pocket and an ATP conjugate with a detectable label.
Sicinski et al. further disclose the Shokat method, introducing a mutation of a bulky gatekeeper residue in the ATP-binding pocket of a kinase which allows the kinase to utilize a bulky ATP analog that is not usable by wild-type kinases (Page 1, 17-18), requires a membrane permeabilization step due to the impermeability of the bulky ATP analogs which disrupts cellular and intracellular architecture, leading to the model not be representative of the cell in its native state (Page 1, Lines 26-28). Therefore, there is a need for methods that can be used in situ for detecting kinase activity while maintaining the natural state of the cell (Page 2, Lines 4-5).
Regarding the new limitation of the well comprising live cells, as stated above, Sicinski et al. specifically state their methods are particularly useful for identification of kinase activity in cell in culture (Page 2, Lines 9-10). Sicinski et al. further disclose wild-type or AS mutant stem cells were cultured on glass coverslips and processed according to the steps in Figure 5 (Page 22, Lines 7-8). Figure 5 of Sicinski et al. shows cells or organisms expressing the kinase of interest are generated, the cells or tissue sections are mildly fixed, endogenous SH groups are quenched, targets are labeled on the kinase, the kinase reaction is stopped, thiophosphorylated resides are alkylated and quenched and then the targets are detected via immunofluorescence (Figure 5 of Sicinski et al.). Thus, it appears the ‘mild fixation’ step that occurs before the reactions occur is simply fixing the cell in place as evidenced by the kinase reaction occurring after the mild fixation step. It is further noted the step where the kinase reaction is stopped occurs due to a second fixation step wherein the cells are incubated in EDTA and formaldehyde for 10 minutes (Page 22, Lines 13-14). It is interpreted that the second fixation, being a longer fixation process, is what ‘kills’ the cells.
Regarding the ‘capable of’ limitations, including capable of being detected and capable of being transferred, the cells of Sicinski et al. are ‘capable of’ these reactions as shown in Figure 5 of Sicinski et al. as multiple reactions occur after the mild fixation step (See Figure 5 of Sicinski et al.).
Regarding the new limitation of a detector, Sicinski et al. disclose detecting the transferrable label comprises fluorescent microscopy (Page 14, Lines 6-7). The fluorescent microscope reads on a detector as it is detecting the fluorescence. Regarding ‘positioned to detect an analyte,’ this is interpreted as an intended use of the detector.
Sicinski et al. further disclose in some embodiments the sample is a monolayer of cells mounted on a support material, such as a coverslip, a tissue section, or a population of cells in suspension (Page 15, Lines 23-25).
Sicinski et al. do not disclose the system comprises a well comprising the live cells or an ATP analog-nanoparticle conjugate.
However, as discussed above, Sicinski et al. disclose the cells can be in suspension, and cells in suspension are very commonly in wells, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have utilized cells in suspension in wells as the system in Sicinski et al. because utilizing wells for culturing cells is well-known in the art. It is well-known in the art that culturing cells can be carried out in wells, for example, in a multi-well plate.
Additionally, Huang et al. disclose methods and compositions for delivering bioactive compounds to a cell, tissue or physiological site (See entire document, Abstract). Compositions include delivery system complexes comprising a biodegradable ionic precipitate comprising a bioactive compound, wherein the precipitate is encapsulated by a liposome, wherein the bioactive compound can comprise any type of bioactive compound and wherein the delivery system complexes can be formulated into liposome/calcium phosphate (LCP) nanoparticles (Paragraph [0005]).
As such, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have utilized a liposome/calcium phosphate nanoparticle (LCP), reading on a lipid/calcium/phosphate (LCP) nanoparticle which is the elected species of nanoparticle, to form an ATP analog-nanoparticle conjugate in the system of Sicinski et al. because Sicinski et al. disclose there is a need for in situ detection of kinase activity where the natural state of the cell is maintained and utilizing an LCP nanoparticle was a known and effective means of delivering a bioactive compound, of which ATP analogs are, to a cell as taught by Huang et al.
Regarding claim 14, as disclosed above regarding claim 13, Sicinski et al. disclose mutating CDK1. CDK1 is a serine/threonine kinase, which is the specific kinase elected by Applicant.
Regarding claim 15, the limitations of this claim do not structurally limit the product and are interpreted as intended uses.
Regarding claim 16, it is noted Applicant elected AKT. Sicinski et al. disclose the kinase can be any kinase selected from a Markush group which includes AKT (Claim 34 of Sicinski et al.).
Regarding claims 17-18, see 112b above. The limitations of these claims do not structurally limit the product and are interpreted as intended uses.
Regarding claim 19, as discussed above regarding claim 13, Sicinski et al. disclose incubating mutant murine stem cells comprising a CDK1 with an M32V substitution and an F80G mutation on a glass coverslip. Sicinski et al. further disclose murine CDK5 was engineered with an F80G substitution and substituted from the wild type CDK5 in mice (Page 23, Line 16-17). Brain sections from the mice were mounted on glass coverslips (Page 23, Lines 20-21). It is noted ‘each well is used to detect an activity of a different mutated kinase on the one or more substrates’ is an intended use and the use of a well does not materially change or alter any characteristic of the instantly-claimed components. Thus, Sicinski et al. disclose two glass coverslips wherein each comprises a different mutated kinase.
Sicinski et al. do not explicitly disclose wells.
However, as discussed above regarding claim 13, Sicinski et al. do disclose the cells can be in suspension, and cells in suspension are well-known in the art to be in wells. Wells provide the ability to simultaneously examine multiple samples, while keeping the samples separated. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have utilized cells in suspension in wells as the system in Sicinski et al. because of the ability to examine multiple samples at once and utilizing wells for culturing cells is well-known in the art.
Regarding claim 20, see 112b above. Claim 20 is being interpreted as: a kit, comprising: a well that comprises live cells that comprise a mutation that enlarges the ATP binding pocket of a kinase, an ATP analog-nanoparticle conjugate and a detectable label.
Sicinski et al. disclose, as discussed above regarding claim 13, kits comprising agents for using the methods are also provided. Sicinski et al. further disclose the kit comprises a fixative; an ATP analog, wherein the γ-phosphate of the ATP analog comprises a transferrable label; and one or more agents for detecting the transferrable label (Page 17, Lines 2-4). The transferrable label is a thiophosphate that comprises a detectable moiety (Page 3, Lines 8-11), reading on a detectable label. Sicinski et al. go on to disclose the Shokat method, introducing a mutation of a bulky gatekeeper residue in the ATP-binding pocket of a kinase which allows the kinase to utilize a bulky ATP analog that is not usable by wild-type kinases (Page 1, 17-18), requires a membrane permeabilization step due to the impermeability of the bulky ATP analogs which disrupts cellular and intracellular architecture, leading to the model not be representative of the cell in its native state (Page 1, Lines 26-28). Therefore, there is a need for methods that can be used in situ for detecting kinase activity while maintaining the natural state of the cell (Page 2, Lines 4-5). The methods are particularly useful for identification of kinase activity in cells in culture (Page 2, Lines 9-10), reading on live cells.
Sicinski et al. do not disclose the kit comprising a well comprising live cells, a mutated kinase or an ATP analog-nanoparticle conjugate.
However, Sicinski et al. do disclose the cells can be in suspension, and cells in suspension are very commonly in wells. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have utilized a well to contain the components of the kit of Sicinski et al.
Further, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to include live cells in the kit because the methods are particularly useful for cells in culture. Cells in culture are live cells. Thus, it would be obvious to include cells in the kit that the methods are useful for identifying kinase activity in.
Additionally, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have included one or more of the mutated kinases disclosed by Sicinski et al. in the kit because Sicinski et al. disclose the kit comprising agents for using the methods. To fully utilize the method, one would need the mutated kinase used in the method. Thus, it would have been obvious to include one or more of the mutated kinases in the kit of Sicinski et al. so that the kit would provide the ability to fully utilize the method disclosed by Sicinski et al.
Moreover, Huang et al. disclose methods and compositions for delivering bioactive compounds to a cell, tissue or physiological site (See entire document, More specifically, the Abstract). Compositions include delivery system complexes comprising a biodegradable ionic precipitate comprising a bioactive compound, wherein the precipitate is encapsulated by a liposome, wherein the bioactive compound can comprise any type of bioactive compound and wherein the delivery system complexes can be formulated into liposome/calcium phosphate (LCP) nanoparticles (Paragraph [0005]).
As such, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have utilized a liposome/calcium phosphate nanoparticle (LCP), reading on a lipid/calcium/phosphate (LCP) nanoparticle which is the elected species of nanoparticle, to form an ATP analog-nanoparticle conjugate in the kit of Sicinski et al. because Sicinski et al. disclose there is a need for in situ detection of kinase activity where the natural state of the cell is maintained and utilizing an LCP nanoparticle was a known and effective means of delivering a bioactive compound, of which ATP analogs are, to a cell as taught by Huang et al.
USC § 103 – Response to Arguments
Applicant's arguments filed 04/06/2026 have been fully considered but they are not persuasive.
On the bottom of page 11, Applicant argued Sicinski et al. do not teach measuring living cells because Applicant states in each instance of Sicinski the cells that are visualized have been fixed with 4% formaldehyde for 5 minutes.
The Examiner respectfully disagrees. This argument was addressed in the modified rejection set forth above as necessitated by amendment. It is the Examiner’s position that Sicinski et al. do disclose live cells as evidenced by Figure 5 of Sicinski et al. See the bottom of Page 8 – top of Page 9 for the discussion over live cells.
Applicant further argued on page 12 that Huang et al., the secondary reference, does not teach the measurement of kinase activity in living cells.
Huang et al. was not utilized to teach measuring kinase activity in living cells.
It is the Examiner’s position that the modified rejection set forth above, as necessitated by amendment, renders obvious the amended claims.
Conclusion
Claims 13-20 are rejected.
No claims are 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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/A.T.W./Examiner, Art Unit 1653 /SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653
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