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 Claims
Claim 14 has been cancelled in the claim amendments filed 06/26/2025.
Claims 10 and 18 have been amended in the claim amendments filed 06/26/2025.
Claims 1-13 and 15-20, received 06/26/2025, are pending in this application
and have been examined.
Withdrawn and Maintained Rejections/Objections
The objections to the Drawings have been withdrawn in view of the amendments to the drawings filed 06/26/2025.
The rejection of claim 18 on the grounds of 35 USC § 112(b) has been withdrawn in light of the amendments filed 06/26/2025.
The maintained rejections and arguments can be found below.
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, 3-4, 6-7, 9-13, and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Hill et al. (Direct Proximity Tagging of Small Molecule Protein Targets Using an Engineered NEDD8 Ligase, J. Am. Chem. Soc. 2016, 138, 13123−13126 , published 2016-09-14) in view of Luo (US 20170283852 A1, published 2017-10-05) for reasons of record which are reiterated herein below.
Hill teaches a biomolecule sensor comprising a ubiquitin homolog, a linker, a self-labeling protein tag, a biotin-acceptor peptide, and ubiquitin homolog-ligating enzyme, as in claim 1 (see, e.g., ubiquitin homolog, self-labeling protein tag, and ubiquitin homolog-ligating enzyme - under “Figure 1”; biotin-acceptor peptide – under “Figure S2”; linker – under “Figure S4”). In addition, Hill teaches the linker comprises a peptide having 2 to 20 amino acids, as in claim 6 (see, e.g., under “Figure S4”). Also, Hill teaches the self-labeling tags selected from a group consisting of SNAP-tags, as in claim 7 (see, e.g., under “Figure 1”). Further, Hill teaches the biotin-acceptor peptide comprises 10 to 400 amino acids, as in claim 9 (see, e.g., under “Figure S2”). Finally, Hill teaches a system for proximity-based labeling of a biomolecule comprising a ubiquitin homolog, a self-labeling protein tag, a linker, a biomolecule derivative, and a ubiquitin homolog-ligating enzyme, as in claim 10 (see, e.g., ubiquitin homolog, self-labeling protein tag, and ubiquitin homolog-ligating enzyme - under “Figure 1”; biotin-acceptor peptide – under “Figure S2”; linker – under “Figure S4”).
Hill fails to teach the ADP-Ribosyltransferase (ART) domain of a SidE-ligase protein and the peptide comprising phosphodiesterase domain (PDE) of a SidE-ligase protein, as in claim 1 and 10. In addition, Hill fails to teach the SidE-ligase protein is from a species of Legionella, as in claim 3. Also, Hill fails to teach the peptides are of Legionella Pneumophila effector SdeA, as in claim 4. In addition, Hill fails to teach the self-labeling protein tags selected from the UV-cross-linking capable tags comprising aryl azides, fluorinated aryl azides, azido-methyl-coumarins, benzophenones, anthraquinones, diazo compounds, diazirines, psoralens, 5-halo-uridines, 5-halo-cytosines, 7-halo-adenosines, 2-nitro-5-azidobenzoyls, fluorinated aryl azides, amino-benzophenones, or derivatives thereof, as in claim 8. Further, Hill fails to teach the two full-length protein domains of SidE-ligase proteins, as in claims 10 and 11. Furthermore, Hill fails to teach the protein domains of a SidE-ligase protein comprises an ADP-Ribosyltransferase domain and a phosphodiesterase domain, as in claims 10 and 13. Also, Hill fails to teach the protein domains of the SidE-ligase protein are from Legionella Pneumophila, as in claim 15.
However, Luo rectifies these deficiencies by teaching the peptide comprising the ADP-Ribosyltransferase (ART) domain of a SidE-ligase protein and the peptide comprising the phosphodiesterase domain (PDE) of a SidE-ligase protein, as in claim 1 and 10 (see, e.g., under “Abstract”; and p. 1, col. 1, under claim 1). The examiner recognizes that the phosphodiesterase domain is inherent to the SidE-ligase protein based on “Fig. 1A” of the applicant’s specification, which illustrates a schematic representation of the domains of the SidE-ligase protein. In addition, Luo teaches the peptides from the SidE-ligase protein is from a species of Legionella, as in claim 3 (see, e.g., under “Abstract”; and p. 1, col. 1, under claim 1). Also, Luo teaches the peptides are of Legionella Pneumophila effector SdeA, as in claim 4 (see, e.g., under “Abstract”; and p. 1, col. 1, under claim 1). Further, Luo teaches the two protein domains comprise at least one full-length SidE-Ligase protein, as in claims 10 and 11 (see, e.g., under “Abstract”; and p. 1, col. 1, under claim 1). Furthermore, Luo teaches the two protein domains of a SidE-ligase protein comprises an ADP-Ribosyltransferase domain and a phosphodiesterase domain, as in claims 10 and 13 (see, e.g., under “Abstract”; and p. 1, col. 1, under claim 1). Also, Luo teaches a peptide fragment of Legionella Pneumophila, as in claim 15 (see, e.g., under “Abstract”; and p. 1, col. 1, under claim 1).
Hill and Luo are analogous to the field of the instant invention because they are all in the field of bioconjugation. One of ordinary skill in the art before the effective filing date of the instant application would have found it obvious to simply substitute the ubiquitin homolog-ligating enzyme of Hill with the ubiquitin-ligating enzyme of Luo. Doing so would allow ubiquitination that is independent of E1 and E2 enzymes and that “can be carried out by a single enzyme” (see, e.g., Luo, under “Abstract”). In addition, Hill does not disclose the biomolecular construct with the components arranged in the same order as the instant invention. However, it would have been prima facie obvious for one of ordinary skill in the art to perform routine optimization of the order of components in the claimed biosensor to make and use the claimed invention. As noted in In re Aller, 105 USPQ 233, 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 biosensor formula was anything other than routine, that the order of components in the biosensor formula resulting 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 Subsection II.A. The artisan would have had a reasonable expectation of success based on the cumulative disclosure of Hill and Luo.
Claims 2, 5, and 16 are under 35 U.S.C. 103 as being unpatentable over Hill (cited above) and Luo (cited above), as applied to claims 1, 3-4, 6-7, 9-13 and 15 above, and further in view of O'Connor et al. (Ubiquitin-Activated Interaction Traps (UBAITs): Tools for Capturing Protein-Protein Interactions, Springer Protocols, published 2018-09-22) for reasons of record which are reiterated herein below.
Hill and Luo teach as set forth above. In addition, they also add the at least one biotin-acceptor peptide, as in claim 16 (see, e.g., Hill, under “Figure S2”). However, they fail to teach the ubiquitin comprises at least one genetic modification in the C-terminal peptide region, as in claim 2. In addition, Hill and Luo fail to teach the epitope tags are selected from a group consisting of FLAG-tags, as in claim 5. Also, Hill and Luo fail to teach the epitope tags, as in claim 16.
However, O’Connor rectifies these deficiencies by teaching ubiquitin that has at least one genetic modification in the C-terminal peptide region, as in claim 2 (see, e.g., under “1 Introduction”, para. 3). In addition, O’Connor teaches an epitope tag selected from a group consisting of FLAG-tags, as in claim 5 (see, e.g., under “1 Introduction”, para. 4). Also, O’Connor teaches at least one epitope tag, as in claim 16 (see, e.g., under “1 Introduction”, para. 1).
Hill, Luo, and O’Connor are analogous to the field of the instant invention because they are all in the field of Bioconjugation. One of ordinary skill in the art before the effective filing date of the instant application would have found it obvious to add the epitope tag and ubiquitin modification of O’Connor to the biomolecular sensor of Hill and Luo. Doing so would allow an ordinary user “to create a [biomolecular sensor] by altering an endogenous chromosomal locus by a single-step gene modification” (see, e.g., O’Connor, under “1 Introduction”, para. 4). The artisan would have had a reasonable expectation of success based on the cumulative disclosures of these prior art references.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Hill (cited above) and Luo (cited above), as applied to claims 1, 3-4, 6-7, 9-13 and 15 above, and further in view of Farrell et al. (Photo-cross-linking interacting proteins with a genetically encoded benzophenone, Nature Methods, published 2005-05-01) for reasons of record which are reiterated herein below.
Hill and Luo teach as set forth above, but fail to teach the self-labeling protein tag being a UV-cross-linking capable tag comprising benzophenones, as in claim 8. Farrell rectifies this by teaching a method to measure protein interactions with a UV-cross-linking tag comprising benzophenones, as in claim 8 (see, e.g., under “Abstract”).
Hill, Luo, and Farrell are analogous to the field of the instant invention because they are all in the field of bioconjugation. One of ordinary skill in the art before the effective filing date of the instant application would have found it obvious to add the UV-cross-linking tag comprising benzophenones to the biomolecular sensor of Hill and Luo. Doing so would allow an ordinary artisan to “photo-cross-link the protein to its binding partner in vivo or in vitro” (see, e.g., Farrell, under “Abstract”). The artisan would have had a reasonable expectation of success based on the cumulative disclosures of these prior art references.
Claims 17 and 19-20 are rejected under 35 U.S.C. 103 as being unpatentable over O'Connor (cited above) in view of Luo (cited above) and Hill (cited above) for reasons of record which are reiterated herein below.
O’Connor teaches detecting a protein interaction with a target biomolecule by contacting a sample with a biomolecule sensor comprising a ubiquitin, a linker, an epitope tag, a target protein, and a ubiquitin-conjugating enzyme, wherein detection occurs when the target biomolecule is bound to the target protein, indicating protein interaction with a target biomolecule is present in the sample, as in claim 17 (see, e.g., under “Fig. 1A”). Also, O’Connor teaches the detecting a protein interaction wherein the target biomolecule is bound to the target protein by a linkage, as in claim 19 (see, e.g., under “Fig. 1A”). The examiner understands the “Interacting protein” and the “Protein of Interest” to be equivalent to the target biomolecule and the target protein, respectively. The examiner also understands that the amide bond indirectly binds the “Interacting protein” and the “Protein of Interest”.
O’Connor fails to teach the biotin-acceptor peptide, as in claim 17. In addition, O’Connor fails to teach the ADP-Ribosyltransferase (ART) domain of a SidE-ligase protein and the peptide comprising phosphodiesterase domain of a SidE-ligase protein, as in claim 17. Also, O’Connor fails to teach the linkage connecting the target biomolecule to the target is a phosphoribose linkage, as in claim 19. O’Connor fails to teach ubiquitin is ADP-ribosylated by an ADP-Ribosyltransferase (ART) domain of a SidE-ligase protein, as in claim 20. However, Luo and Hill rectify this by teaching the biotin-acceptor peptide, as in claim 17 (see, e.g., Hill, under “Figure S2”). In addition, Luo and Hill teach the peptide comprising the ADP-Ribosyltransferase (ART) domain of a SidE-ligase protein and the peptide comprising the phosphodiesterase domain of a SidE-ligase protein, as in claim 17 (see, e.g., Luo, under “Abstract”; and p. 1, col. 1, under claim 1). Furthermore, Luo and Hill teach the phosphoribose linkage, as in claim 19 (see, e.g., Luo, p. 1, col. 2, para. [0015]). Finally, Luo and Hill teach ubiquitin is ADP-ribosylated by an ADP-Ribosyltransferase (ART) domain of a SidE-ligase protein, as in claim 20 (see, e.g., Luo, p. 1, col. 2, para. [0015]).
O’Connor, Luo, and Hill are analogous to the field of the instant invention because they are all in the field of bioconjugation. One of ordinary skill in the art before the effective filing date of the instant application would have found it obvious to add the SidE-ligase protein that binds proteins by a phosphoribose linkage and the biotin-acceptor peptide of Luo and Hill to the biomolecular sensor of O’Connor. Doing so would allow ubiquitination that is independent of E1 and E2 enzymes and that “can be carried out by a single enzyme” (see, e.g., Luo, under “Abstract”). Also, the biotin tag “allows facile purification and target identification by LC-MS/MS” (see, e.g., Hill, under article body, para. 2). In addition, O’Connor does not disclose the biomolecular construct with the components arranged in the same order as the instant invention. However, it would have been prima facie obvious for one of ordinary skill in the art to perform routine optimization of the order of components in the claimed biosensor to make and use the claimed invention. As noted in In re Aller, 105 USPQ 233, 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 biosensor formula was anything other than routine, that the order of components in the biosensor formula resulting 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 Subsection II.A. The artisan would have had a reasonable expectation of success based on the cumulative disclosures of O’Connor, Luo, and Hill.
Response to Arguments
The applicant’s arguments filed 06/26/2025 have been considered.
Claims 1, 3-4, 6-7, and 9-15
The applicant states that the examiner has asserted without providing a clear rationale that one of ordinary skill in the art would have found it obvious to substitute the ubiquitin-ligating enzyme of Luo for that of Hill. In fact, the examiner’s rationale was that the substitution “would allow ubiquitination that is independent of E1 and E2 enzymes and that ‘can be carried out by a single enzyme’ (see, e.g., Luo, under ‘Abstract’)”. The simplification of the assay to a single enzyme would be seen as advantageous to an artisan of ordinary skill in the art.
The applicant asserts that Hill uses a ligating enzyme with a different mechanism of action than the claimed SidE-ligase enzyme, therefore, Hill arguably teaches away from using SidE-ligase proteins. However, the examiner acknowledged the difference in mechanism of action in the rationale for substituting the ubiquitin-ligating enzyme of Luo for that of Hill, specifically the mechanism of action of the SidE-ligase enzyme requires only one enzyme for ubiquitin-ligation. The decrease in the number of enzymes needed for the ligation reaction would be advantageous to an artisan because the simplicity of a reaction with only one enzyme decreases the number of factors that need to be optimized for the reaction to occur expeditiously. Indeed, the different mechanism of action would be a motivation for the substitution of the ubiquitination components of Hill for the ubiquitination components of Luo because simplifying the components to one enzyme would lead an artisan to have a higher expectation of success.
The applicant takes issue with the assertion that Hill and Luo are in the same field of bioconjugation. A reference is analogous art to the claimed invention if: (1) the reference is from the same field of endeavor as the claimed invention (even if it addresses a different problem); or (2) the reference is reasonably pertinent to the problem faced by the inventor (even if it is not in the same field of endeavor as the claimed invention). Note that “same field of endeavor” and “reasonably pertinent” are two separate tests for establishing analogous art; it is not necessary for a reference to fulfill both tests in order to qualify as analogous art. See Bigio, 381 F.3d at 1325, 72 USPQ2d at 1212. Luo recites, “The herein disclosed method demonstrates a method in which ubiquitination can be carried out by a single enzyme.” (see under “Abstract”). Ubiquitination is a form of bioconjugation. Hill recites a method for labeling target proteins with a small ubiquitin homolog with a covalent tag (see under “Abstract”). Labeling a target protein is a form of bioconjugation. The works of both Hill and Luo are directed at the same field of endeavor, bioconjugation, therefore, they are analogous art. Although references do not have to satisfy both tests discussed above to be considered analogous art, Hill and Luo are not only directed at the same field of endeavor, they are also reasonably pertinent to the problem faced by the inventor because they both disclose methods for ligating ubiquitin or ubiquitin homologs.
The applicant claims that Luo does not teach or suggest the phosphodiesterase domain of a SidE-ligase protein. However, as stated in page 6, paragraph 2 of the office action mailed 03/26/2025, “Fig. 1A” of the applicant’s specification shows that the phosphodiesterase domain is inherent to the SidE-ligase protein. An artisan of ordinary skill in the art would recognize that the SidE-ligase protein of Luo would be useful in a biosensor framework because Hill discloses a biosensor framework with enzymes that covalently label a target protein with the ubiquitin homolog, NEDD8. The artisan would understand the ubiquitination enzyme of Luo would be a better substitution for the enzymes of Hill because the ubiquitination of Luo is performed by only one enzyme. Simplifying the ubiquitin-ligation reaction to a single enzyme decreases the number of factors that must be optimized for the reaction to occur expeditiously. The applicant argues that there is no expectation of success, however, the success of Hill in creating a biosensor framework and the success of Luo in utilizing SidE-ligase proteins for one-enzyme ligation would motivate the artisan to integrate the teachings of the two references with a reasonable expectation of success.
The applicant claims the neither Hill nor Luo describe the arrangement of components of the instant claim elements in each claim as a whole. However, in making the claim, the applicant states that the two domains of SidE would have to be separated, but the claim as written does not require the separation of the two relevant domains of SidE. In response to the applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., the separation of the two relevant ) are not recited in the rejected claims. Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
The applicant asserts that modifying the disclosure of Hill with the teachings of Luo is not a simple substitution. The applicant asserts that the substitution of Hill’s ubiquitination components for Luo’s would produce a messy, low-sensitivity, high-background, and generally useless biosensor, but this cannot be accepted since the arguments of counsel cannot take the place of evidence in the record. In re Schulze, 346 F.2d 600, 602, 145 USPQ 716, 718 (CCPA 1965); In re Geisler, 116 F.3d 1465, 43 USPQ2d 1362 (Fed. Cir. 1997). Furthermore, while the integration of Luo’s ubiquitination components into the biosensor framework of Hill are non-trivial, one of ordinary skill in the art would have a reasonable expectation of being successful integrating the teachings of Luo. An artisan would have a reasonable expectation of success because the reference Hill discloses an effective biosensor framework and Luo discloses the SidE-ligase protein effectively ubiquitinates substrates with one enzyme. The artisan would be motivated to integrate the ubiquitination components of Luo into the framework of Hill because the simplification of the arrived assay to one enzyme decreases the number of factors that need to be optimized. Again, the applicant asserts that the ART domain and the PDE domain of the SidE enzyme must be separated, however, the claims as written do not necessitate the separation of these two domains. The other steps of modifying the biosensor with ADPRibose, purifying, and adding a lysate are not trivial, but they are well within the skills of an artisan of ordinary skill in the art. In fact, Hill discloses purification and adding a lysate in the cited journal article (see, e.g., purification – p. 13124, col. 1, para. 1; adding lysate – p. 13123, under “ABSTRACT:”). An artisan of ordinary skill in the art would understand that the ubiquitination components of Hill could be substituted for the ubiquitination components of Luo with a reasonable expectation of success. The ubiquitin and SidE-ligase protein of Luo integrated into the framework of Hill would allow for a proximity ligation assay with only one enzyme, a simplification that decreases the number of factors that must be optimized. The examiner has not been provided evidence that would indicate that the ubiquitination components of Luo are incompatible with the biosensor of Hill. The assertions of the applicant cannot be accepted since the arguments of counsel cannot take the place of evidence in the record.
The applicant argues that the SidE enzyme of Luo has inherent substrate specificity that would lead an ordinary artisan to not consider the enzyme for a proximity ligating tool. However, the Luo paragraph cited by the applicant merely states that the SidE enzyme ubiquitinates substrates such as Rab33b which is an exemplary embodiment, and does not disclose that the SidE enzyme has inherent substrate specificity that would prevent its use in a proximity ligating tool.
For all of the reasons above, the applicant’s arguments are found to not be persuasive and the rejections will be maintained.
Claims 2, 5, 8, 16-17, and 19-20
The applicant states that none of the cited disclosures describe or suggest the biosensor construct or system as claimed, i.e., a biosensor comprising a self-labeling tag, a biotin-acceptor peptide, and SideE-ligase domains. As stated above, Hill teaches a biomolecule sensor comprising a self-labeling protein tag, a biotin-acceptor peptide, and ubiquitin homolog-ligating enzyme (see, e.g., ubiquitin homolog, self-labeling protein tag, and ubiquitin homolog-ligating enzyme - under “Figure 1”; biotin-acceptor peptide – under “Figure S2”; linker – under “Figure S4”). Also, as stated above, Luo teaches the peptide comprising the ADP-Ribosyltransferase (ART) domain of a SidE-ligase protein and the peptide comprising the phosphodiesterase domain (PDE) of a SidE-ligase protein, as in claim 1 (see, e.g., under “Abstract”; and p. 1, col. 1, under claim 1). Hill and Luo together teach all the components of the claimed invention and are analogous to the field of the instant invention because they are both in the field of bioconjugation. One of ordinary skill in the art before the effective filing date of the instant application would have found it obvious to simply substitute the ubiquitin homolog-ligating enzyme of Hill with the ubiquitin-ligating enzyme of Luo. Doing so would allow ubiquitination that is independent of E1 and E2 enzymes and that “can be carried out by a single enzyme” (see, e.g., Luo, under “Abstract”).
The applicant states that O’Connor does not teach ubiquitin that has at least one genetic modification in the C-terminal peptide region. However, as stated above, O’Connor does teach ubiquitin that has at least one genetic modification in the C-terminal peptide region (see, e.g., under “1 Introduction”, para. 3 and p. 87, under “Fig. 1”, under panel “B.”). The ΔGG is the genetic modification of the C-terminal peptide region. Therefore, contrary to applicant’s argument, the combination of Hill, Luo, and O’Connor teaches each and every limitation as claimed and are analogous to the field of the instant invention because they are all in the field of bioconjugation. One of ordinary skill in the art before the effective filing date of the instant application would have found it obvious to add the epitope tag and ubiquitin modification of O’Connor to the biomolecular sensor of Hill and Luo. Doing so would allow an ordinary user “to create a [biomolecular sensor] by altering an endogenous chromosomal locus by a single-step gene modification” (see, e.g., O’Connor, under “1 Introduction”, para. 4). Also, “the C-terminal ubiquitin moiety of the UBAIT has the potential to form an amide linkage with lysine side chains of a protein that interacts transiently with the protein of interest, thereby covalently trapping the protein-protein interaction” (see, e.g., O’Connor, under “Abstract”).
For all of the reasons above, the applicant’s arguments are found to not be persuasive and the rejections will be maintained.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. 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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/MICHAEL CAMERON SVEIVEN/Examiner, Art Unit 1678
/BAO-THUY L NGUYEN/Supervisory Patent Examiner, Art Unit 1677 October 6, 2025