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 .
Election/Restrictions
Applicant's election with traverse of Group I, claims 1-5, 17 and 18 and the following species: ABZ/ANB as the specific pair of C1/C2 in claim 3; the compound of formula 2 for claims 4, 8, 14, 18 and 28 and option (i) detection of primary liver cancer for claim 10 in the reply filed on 06/15/2026 is acknowledged. The traversal is on the ground(s) that (i) Poreba does not disclose, teach or suggest any diagnostic marker for liver cancer and Kang contains no teaching or suggestions that specific KSSD sequence has any diagnostic or biological sensitivity for liver cancer; (ii) that the special technical feature is the unexpected selectivity and utility of the KSSD substrate for liver cancer and (iii) Poreba and Kang do not suggest that the KSSD sequence would exhibit precise and exclusive selectivity for enzymes characteristic of liver cancer while remaining completely stable in healthy urine and other cancer types. This is not found persuasive because: (i) the same technical feature of Groups I-III is a compound having recited formula and comprising fluorescent donor and acceptor wherein compound undergoes enzymatic cleavage with generation of optical signal. The common technical feature does not include selectivity for liver cancer. (ii) The unexpected results argument is not applicable to a lack of unity restriction requirement, and for the reasons set forth in the restriction, it is maintained.
The requirement is still deemed proper and is therefore made FINAL.
Claims 6-16, 25 and 28 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 06/15/2026.
Claims 1-5, 17 and 18 (claim set filed 05/15/2024) are examined on the merits herein.
Priority
This application is a 371 of PCT/PL2022/050074 filed 11/02/2022. Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d) based on application POLAND P.439405 filed 11/03/2021. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 05/06/2024 complies with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Objections
Claims 1, 4 and 18 are objected to because of the following informalities:
Claim 1 recites “A compound having formula 1: X11-Lys2-Ser3-Ser4-Asp5-X26 (formula 1)”. Reciting “(formula 1)” in parenthesis seems to be redundant since the claim defines the structure of formula 1.
Claims 4 and 18 have the same issues. Reciting “(formula 2)” and “(formula 3)” limitations in parenthesis is redundant since the claims define the structures of formula 2 and formula 3.
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 1-5, 17 and 18 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 1 recites: “the pair of molecules C1 and C2 is a pair of a fluorescent donor and a fluorescent acceptor. It is not clear if C1 and C2 can be either fluorescent donor or fluorescent acceptor or C1 is a fluorescent donor and C2 is a fluorescent acceptor. The scope and boundaries of claim 1 are not certain, making claim 1 indefinite.
Claims 2-5, 17 and 18, dependent on claim 1, do not resolve the issues mentioned above and are rejected.
Regarding claims 2 and 3, a broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 2 recites the broad recitation “hydrolytic cleavage”, and the claim also recites “preferably proteolytic” which is the narrower statement of the range/limitation. Claim 3 recites the broad recitation of the group of C1 and C2 pairs, and the claim also recites “preferably” two alternatives of the group which is the narrower statement of the range/limitation. The claims are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims. The scope and boundaries of claims 2 and 3 are not certain, making claims 2 and 3 indefinite.
Claim 3 recites several acronyms for molecules C1 and C2 without reciting what it stands for, i.e. DNP, EDDNP, EDANS, DABCYL, TAM and DANZYL. The specification does not provide description for these abbreviations. The description is provided only to ABZ, ANB and pNA (p. 9, line 30 and p. 10, line 9). Without description of the chemical used for molecules C1 and C2 it is not clear what claim 3 is limited to. The scope and boundaries of claim 3 are not certain, making claim 3 indefinite.
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-3 and 17 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 1 is directed to a compound of formula 1: X11-Lys2-Ser3-Ser4-Asp5-X26, wherein X1 comprises molecule C1 and X2 comprises molecule C2 which are a pair of fluorescent donor and fluorescent acceptor. The compound is recited to undergo enzymatic cleavage to fragment 1 and fragment 2 with generation of optical signal. X1 and X2 are recited as comprising C1 and C2, respectively, and hence can have any additional structural parts. Thus, a compound of claim 1 represents a very broad genus of structures including genus of X1 and genus of X2 connected with a linker KSSD and the compound needs to be able to undergo the enzymatic cleavage with generation of optical signal.
The specification describes that X1 is an amino acid derivative or a peptide fragment comprising C1 or consisting of such a molecule C1 and X2 is an amino acid derivative or a peptide fragment comprising molecule C2 or X2 consisting of such a molecule C2 (p. 9, lines 1-3). The specification describes the fluorescent donor/acceptor pairs (p. 9, lines 29-31, p. 10, lines 1-2). However, the specification does not describe X1 and X2 other than consisting of C1 and C2, respectively, and does not provide structure function correlation for X1 and X2, does not describe the structures of X1 and X2 that will have function of being cleaved to fragment 1 and fragment 2 generating optical signal or structures of X1 and X2 that would lose the recited function. Further, applicants have not shown possession of the representative number of species for X1 and X2 since the working examples are provided only with compound with X1 consisting of C1, i.e. ABZ, and X2 consisting of C2, i.e. ANB (Examples 1 and 2). Examples of other variants of the compound are not provided.
Waugh (Waugh, Protein Expression and Purification, 2011, 80, 283-293) teaches that every affinity tags has the potential to interfere with the structure and function of its fusion partner (Abstract). Waugh discloses that the inability of a protease to cleave a fusion protein may also be caused by steric hindrance. For example, the cleavage site may be too close to ordered structure in the target protein (p. 288, right column, 2nd paragraph). Waugh describes overcoming steric hindrance by inserting "spacer" residues between a protease recognition site and the N-terminus of the protein of interest (p. 289, Figure 3). Waugh teaching points to possible interference of the structures of X1 and X2 with the cleavage of the compound and hence generation of optical signal.
Therefore, one of ordinary skill in the art would not be able to identify which X1 and X2 comprising C1 and C2, respectively, will be functional as required, i.e. provide compound undergoing enzymatic cleavage to fragments 1 and 2 with generation of optical signal. One of ordinary skill in the art would conclude based on the lack of representative number of species and the lack of describing the X1 and X2 structures critical for compound function that the applicant was not in possession of the claimed genus and the specification fails to satisfy the requirements of written description under 35 U.S.C. 112(a). Therefore, claim 1 is rejected.
Claims 2, 3 and 17, dependent on claim 1, do not resolve the issue discussed above and are rejected.
Claims 4, 5 and 18 define the formulas of compounds and are not rejected.
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.
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 1, 2 and 17 are rejected under 35 U.S.C. 103 as being unpatentable over Poreba (Poreba et al. Scientific Reports, 2017, 7, 43135, 1-13) in view of Kang (WO 2008084899 A1).
Regarding claim 1, Poreba teaches internally quenched fluorescent peptide substrates as a tool to examine activity and specificity of proteases (Abstract). Poreba describes developing a highly sensitive and adaptable donor/acceptor pair and applying it to investigation of various proteases, including caspase-3, caspase-7, caspase-8 and metalloproteases (Abstract). Poreba mentions that the developed probe can be used to design substrates for any group of endopeptidases (Abstract). Probes represent internally quenched peptidic substrate and contain fluorescent donor and fluorescent acceptor linked to the peptide. Upon cleavage with protease the peptide probe separates into two fragments one of which is linked to the fluorescent donor and the other to fluorescent acceptor. The distance between the donor and the acceptor increases, the fluorophore is no longer quenched, and an enhanced fluorescence signal is generated (p. 2, 1st paragraph, Figure 1). Poreba describes testing different caspases which have cleavage site at the C-terminus of aspartate (p. 5, Table 1).
Poreba does not teach a compound of formula 1.
Kang teaches identification of various peptides by phage display technique (Abstract). Kang mentions that peptides can target specific tissues (Abstract). Kang describes analysis of 852 peptide sequences from phage population recovered in liver, lung, kidney and spleen and found peptide "CSKSSDYQC" to appear with 9 times appearance frequency (paragraph 169). In a search of binding motif Kang extracted peptide motifs of each peptide sequence (paragraph 236). Kang describes peptide motif "SKSSD" identified with high appearing frequency (paragraph 243, Table 8). That motif includes the instant KSSD sequence.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to try using peptides identified in Kang teaching including SKSSD peptide and attach it to donor/acceptor pair as taught by Poreba for screening of substrates of proteases involved in different diseases or conditions. One would have been motivated to do so since Poreba provides a sensitive optical method of detection of various proteases by generation of optical signal upon cleavage of a peptide connecting fluorescent donor and acceptor and Kang suggests peptides with different tissue specificity and Poreba describes caspases cleaving peptides C-terminal to aspartate and Kang peptide SKSSD has aspartate as the C-terminal amino acid and hence may be cleaved by caspases. A skilled artisan would have reasonably expected success in the combination because Poreba provides method of detection of protease/caspase specificity and activity and Kang provides possible peptide substrate for protease/caspase.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to consider Ser of SKSSD attached to fluorescent donor of Poreba teaching as part of X1 of instant compound of formula 1 and fluorescent acceptor of Poreba teaching as X2 providing instant X1-KSSD-X2 compound. One would be motivated to do that with reasonably expected success since X1 in formula 1 is limited to comprising the fluorescent donor and therefore can also include additional structural components such as amino acid and that would leave KSSD as the peptide linker between X1 and X2.
Thus, Poreba and Kang teachings render claim 1 obvious.
Regarding claim 2, Poreba teaches the peptide probe to undergo hydrolytic cleavage of peptide bond (p. 2, 1st paragraph). Thus, Poreba and Kang teachings render claim 2 obvious.
Regarding claim 17, Poreba teaches testing activities of the proteases such as caspases with the peptide probes in specific measuring buffers (p. 10, 6th paragraph). It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention that the peptide probe and the measuring buffer can be included in a kit for testing activity or specificity of various proteases. One would have been motivated to expect that since Poreba provides highly sensitive method to determine activity of protease of diverse families. Thus, Poreba and Kang teachings render claim 17 obvious.
Claims 3-5 and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Poreba (Poreba et al. Scientific Reports, 2017, 7, 43135, 1-13) in view of Kang (WO 2008084899 A1) as applied to claims 1 and 17 above, and further in view of Gruba (Gruba et al. FEBS J., 2016, 283, 2929-2948).
The teachings of Poreba and Kang have been set forth above.
Poreba and Kang do not teach C1/C2 pair to be ABZ/ANB.
Regarding claim 3, Gruba teaches detection of bladder cancer using a specific peptide substrate of 20S proteosome (Abstract). Gruba describes that the peptide substrate of chymotrypsin-like subunit of proteosome 20S was converted into internally quenched substrate by attachment to its N and C termini of fluorescent donor-acceptor pair. Among tested substrates the highest proteolysis rate was observed for fluorescent pair ABZ/ANB-NH2 modified peptide (p. 2931, left column, 1st paragraph). The peptides were modified by replacing amino acid residues. The best substrate for the proteosome subunit with chymotrypsin-like activity was found to be ABZ-Val-Val-Ser-Tyr-ANB-NH2. The peptide was cleaved into two fragments of ABZ-Val-Val-Ser-Tyr-OH and ANB-NH2 as was confirmed by HPLC analysis (p. 2934, left column, 4th paragraph).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to follow Gruba teaching and use ABZ/ANB pair of fluorescent donor /acceptor for the peptide probe based on Poreba and Kang teachings for screening of substrates of proteases involved in different diseases or conditions. One would have been motivated to do so since Gruba showed ABZ/ANB fluorescent donor/acceptor pair to have the highest proteolysis rate, confirmed cleavage of the probe with the release of ANB fragment and used that approach to increase selectivity of the peptide substrate for specific protease. A skilled artisan would have reasonably expected success in the combination because Poreba and Gruba teach quenched peptide probes with fluorescent donor and acceptor that produce fluorescent signal after proteolytic cleavage. Thus, Poreba, Kang and Gruba teachings render claim 3 obvious.
Regarding claims 4 and 5, as described for claim 3 above, Gruba teaches the ABZ/ANB pair of fluorescent donor/acceptor that can be used for the peptide probe based on Poreba and Kang teachings in which Ser of SKSSD peptide of Kang is considered to be attached to fluorescent donor of Poreba teaching as part of X1 of instant compound of formula 1 and fluorescent acceptor of Poreba teaching is X2 providing instant X1-KSSD-X2 compound. Replacement of fluorescent donor/acceptor to ABZ/ANB pair would provide compound of formula: ABZ-SKSSD-ANB-NH2 similar to compound ABZ-Val-Val-Ser-Tyr-ANB-NH2 of Gruba teaching (p. 2934, left column, 4th paragraph). Gruba teaches that ABZ-Val-Val-Ser-Tyr-ANB-NH2 peptide was cleaved into two fragments of ABZ-Val-Val-Ser-Tyr-OH and ANB-NH2 as was confirmed by HPLC analysis (p. 2934, left column, 4th paragraph). Therefore, the ABZ-SKSSD-ANB-NH2 would similarly be cleaved into ABZ-Ser-Lys-Ser-Ser-Asp-OH and ANB-NH2.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention that compound ABZ-SKSSD-ANB-NH2 structure of which is based on combination of Poreba, Kang and Gruba teachings is an obvious variant of instant compound of formula 2 and that this compound can perform the same function of undergoing proteolytic cleavage into fragments ABZ-Ser-Lys-Ser-Ser-Asp-OH and ANB-NH2 with generation of optical signal. One would have been motivated to expect that since Poreba teaches generation of optical signal upon proteolytic cleavage of the peptide with C-terminal aspartate by caspases with generation of optical signal and Kang provides peptide with different tissue specificity with C-terminal aspartate that can be cleaved by caspases releasing ANB-NH2 fragment and Gruba showed ABZ/ANB fluorescent donor/acceptor pair to have the highest proteolysis rate and confirmed cleavage of the probe with the release of ANB-NH2 fragment. A skilled artisan would have reasonably expected success in the combination because Poreba and Gruba teach quenched peptide probes with fluorescent donor and acceptor that produce fluorescent signal after proteolytic cleavage and Kang provides peptide substrate for protease/caspase cleavage. Thus, Poreba, Kang and Gruba teachings render claims 4 and 5 obvious.
Regarding claim 18, Poreba teaches testing activities of the proteases such as caspases with the peptide probes in specific measuring buffers (p. 10, 6th paragraph) as described for claim 17 above. It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention that the peptide probe ABZ-SKSSD-ANB-NH2 structure of which is based on combination of Poreba, Kang and Gruba teachings is an obvious variant of instant compound of formula 2 and that this peptide probe and the measuring buffer can be included in a kit for testing activity or specificity of various proteases. One would have been motivated to expect that since Poreba provides highly sensitive method to determine activity of protease of diverse families by generation of optical signal upon peptide cleavage, Gruba teaches ABZ/ANB fluorescent donor/acceptor pair providing the highest proteolysis rate and Kang provides tissue-specific peptide for proteolytic cleavage with different tissue specificity. Thus, Poreba, Kang and Gruba teachings render claim 18 obvious.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to LIOUBOV G KOROTCHKINA whose telephone number is (571)270-0911. The examiner can normally be reached Monday-Friday: 8:00-5:30.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Sharmila G Landau can be reached at (571)272-0614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/L.G.K./Examiner, Art Unit 1653
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653
