DETAILED ACTION
Election/Restrictions
Applicants’ election with traverse of Group I and compound
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in the reply filed on August 10 2026 is acknowledged. The traversal is on the ground(s) that the examiner’s characterization of Group I is factually incorrect.. It is argued that the rationale in lack of unity does not apply claims 3-11. It is argued that the international searching authority expressly found that Wedekind do not fall within the scope of formulas I, IIa and IIb because they do not have nucleobases with alkyne and azide moieties or the corresponding triazole. It is argued that the cross-linked architecture is a special technical feature common to claims 1-11.
This is not found persuasive because the groups are in fact not incorrect. Firstly, as written, claim 3 depends from claim 1 and as such must be included in the same group. Thus, the independent claim of that group is claim 1 and structure of formula I. Secondly, the structure shown in Formula I is the precursor to those found in claim 3. The compounds in claim are the result of click chemistry between A1 and B1 as N3 and alkyne are the only choices for A1 and B1. Therefore, an election of a compound of formula I would necessarily result in the compound of formula IIa or IIb that is why the examiner did not require the compounds of claim 3 to be a separate group. While the examiner agrees that Wedekind does not teach compound of formula I, IIa and IIb because they do not contain an alkyne or azide moiety or the corresponding triazole, neither do the compounds of group II. Therefore, unity is lacking because the common structure amongst both groups is a structure that does not contain the alkyne or azide or triazole and this is the structure taught by Wedekind. The examiner recognizes that all of claim 1-11 require the azide and alkyne that is why they were not separated into separate groups. Furthermore, with regards to the species, Where a single claim defines alternatives of a Markush group, the requirement of a technical interrelationship and the same or corresponding special technical features as defined in Rule 13.2, is considered met when the alternatives are of a similar nature. When the Markush grouping is for alternatives of chemical compounds, the alternatives are regarded as being of a similar nature where the following criteria are fulfilled:
(A) all alternatives have a common property or activity; AND
(B)(1) a common structure is present, that is, a significant structural element is shared by all of the alternatives; OR
(B)(2) in cases where the common structure cannot be the unifying criteria, all alternatives belong to a recognized class of chemical compounds in the art to which the invention pertains.
The phrase “significant structural element is shared by all of the alternatives” refers to cases where the compounds share a common chemical structure which occupies a large portion of their structures, or in case the compounds have in common only a small portion of their structures, the commonly shared structure constitutes a structurally distinctive portion in view of existing prior art, and the common structure is essential to the common property or activity.
The phrase “recognized class of chemical compounds” means that there is an expectation from the knowledge in the art that members of the class will behave in the same way in the context of the claimed invention, i.e. each member could be substituted one for the other, with the expectation that the same intended result would be achieved.
The chemical compounds of claims 1-11 are not regarded as being of similar nature because: (1) the alternatives do not all share a common structure and (2) the alternatives do not all belong to a recognized class of chemical compounds. While the compounds all include an azide and alkyne, the corresponding sequence and components A and B are different. None of the claims require the sequence to correspond to a particular target or function. Therefore, the examiner cannot agree that within claim 1-11 unity isn’t lacking.
The requirement is still deemed proper and is therefore made FINAL.
Claims 1-15 are pending in the application. Claims 12-15 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 August 10 2026. Accordingly, claims 1-11 are being examined on the merits herein.
The elected species, identified above, is free of prior art. While Yoshimura et al. (Org. Biomol. Chem. 2010) teaches that nucleosides containing a carbazole can be used to form hairpin structure via crosslinking, Yoshimura et al. does not expressly teach click chemistry nor that this nucleoside can be used at a position other than the ends. While Saha et al. (Chem. Commun., 2019) teaches the use of carbazole derived triazole ligands (section 5.5) these are taught as targeting quadruplexes. Thus, the prior art does not teach with a reasonable expectation of success the formation of
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as elected (it is noted that this structure is represented on page 38 of the instant specification). In light of the elected species being free of prior art, the species election is expanded to include any ssDNA which targets APOBEC3 which the instant specification indicates is the desirable target, In of FdZ and dZ, and A/B include substituted A/T/C/G.
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 is a 371 of PCT/IB2022/050656 (01/26/2022) which claims FOR priority to AUSTRALIA 2021900164 (01/26/2021) as reflected in the filing receipt issued December 26 2023.
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on November 8 2023 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Drawings
The drawings are objected to for the following reasons: 37 CFR 1.84 (u)(1) states “View numbers must be preceded by the abbreviation "FIG."” In the current case, the view numbers for Figures 1-14 are preceded by the word "Figure" instead of the abbreviation "FIG.".
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - This application fails to comply with the requirements of 37 CFR 1.821 - 1.825 because it does not contain a "Sequence Listing" as a separate part of the disclosure or a CRF of the “Sequence Listing.”.
Required response - Applicant must provide:
A "Sequence Listing" part of the disclosure; together with
An amendment specifically directing its entry into the application in accordance with 37 CFR 1.825(a)(2);
A statement that the "Sequence Listing" includes no new matter as required by 37 CFR 1.821(a)(4); and
A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(a)(3).
If the "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
If the "Sequence Listing" part of the disclosure is submitted according to item 1) c) or d) above, applicant must also provide:
A CRF in accordance with 37 CFR 1.821(e)(1) or 1.821(e)(2) as required by 1.825(a)(5); and
A statement according to item 2) a) or b) above.
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings. Fig. 8 recites two sequences with 10 or more nucleotides that are not associated with a corresponding SEQ ID No.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Specifically pages 15 and 37-40 of the specification and claim 15.
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
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 of this title, 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 set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied 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 1-7 and 9-11 are rejected under 35 U.S.C. 103 as being unpatentable over Kvach et al. (ChemBioChem, first published October 21 2019) in view of Buisson et al. (Science, 2019), El-Sagheer et al. (Chemical Society Reviews, 2010).
Applicant Claims
The instant application claims a compound of formula I. The instant application claims a compound of formula IIa or Iib.
Determination of the Scope and Content of the Prior Art
(MPEP §2141.01)
Kvach et al. is directed to differential inhibition of APOBEC3 DNA-mutator isozymes by fluoro- and non-fluoro-substituted 2’-deoxyzebularine embedded in a single-stranded DNA.. Shown in scheme 1 are modified nucleotides as potential inhibitors of cytidine deamination. It is taught that incorporation of a known inhibitor of CDA (cytidine deaminase) specifically 2’-deoxyzebularine into ssDNA oligonucleotides. If incorporated into ssDNA, CDA becomes a low-micromolar inhibitor (page 1029, left column). Table 1 shows the synthesis of modified nucleosides. Table 2 shows the oligonucleotides used in the study and includes the use of dZ as well as 5Fdz in place of a C. An oligo containing 5Fdz exhibited an inhibition constant against APOBEC3B 3.5 times better than that of the comparable dz-containing oligo. A similar inhibition trend was observed for APOBEC3A. How the use of 5Fdz motif in an oligo designed for APOBEC3G inhibition resulted in an inhibitor that was less potent than the dZ-containing oligo (abstract). Future work focusing on the chemical optimization of the ssDNA-based A3 inhibitors is suggested. Nucleotides flanking the target dZ and 5FdZ motifs can be further modified to improve inhibitor potential and to enhance the lifetimes of oligonucleotides in biological media (page 1034, conclusions).
Ascertainment of the Difference Between Scope the Prior Art and the Claims
(MPEP §2141.02)
While Kvach et al. teaches ssDNA oligonucleotides which include a 2’-deoxyzebularine and/or a 5-fluoro-2’-deoxyzebularine and the nucleotides can be modified to improve inhibitor potential, Kvach et al. does not teach a connection between two nucleotides of the sequence to result in the claimed compound of formula I/II. However, this deficiency is cured by Buisson et al. and El-Sagheer et al.
Buisson et al. is directed to passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features. It is taught that APOBEC cytidine deaminase enzymes are prominent cause of mutations in cancer. Analysis of mutation patterns at the mesoscale level reveals that APOBEC3A strongly prefers “hairpin” substrates (page 1, left column). It is taught that A3A mutation frequency in hairpins depends on stem strength, loop size, position of the TpC site within the loop and the identity of the surround nucleotides (page 5, middle column). Fig. 3 shows data from in vitro enzymology and tumor bioinformatics to illustrate the substrate preference for APOBEC3A. It is shown that the natural 4 nt-loop is an efficient substrate. Increasing the loop size decreasing activity whereas decreasing to a 3 nt loop shows stronger activity (page 5; Fig. 3c). Also investigated sequence context where it was found that the globally optimal DNA substrate is a strongly based-paired hairpin with the 3 nt loop TTC and a C-G closing pair (Fig. 3E and 3F) though strong increases over baseline were seen for all possible contexts (page 5, middle column).
El-Sagheer et al. is directed to click chemistry with DNA. It is taught that click chemistry was developed to provide a simple method to join together organic molecules in high yields under mild conditions in the presence of a diverse range of functional groups. The best example is the extremely efficient azide-alkyne cycloaddition reaction (CuAAC). It is taught that azides and alkynes can be attached to nucleic acids without greatly disturbing their biophysical properties. Azides and unactivated alkynes are almost entirely unreactive towards the functional groups normally encountered in nature; they only react with each other. The formed triazole unit is extremely stable and is not toxic (page 1388, introduction). Fig. 1 shows the CuAAC reaction between an azide and a terminal alkyne to product a 1,4-triazole:
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. Fig. 3 shows nucleoside triphosphates, azide labels and triazole products:
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. Fig. 4 shows alkynyl Da, dG, dC and dU nucleosides. Scheme 13 a shows chemical ligation of two oligonucleotide strands, one with a 5’-alkyne and the other with a 3’-azide (page 1400, left column). Fig. 13 shows the linkages between the N3 atoms of thymine bases used to constrict cyclic dumbbell oligonucleotides (page 1403). It is taught that hairpin oligonucleotides were cyclized using the CuAAC reaction. The resultant cyclic constructs were designed as decoys for targeting the DNA binding site (page 1403, left column, first paragraph).
Finding of Prima Facie Obviousness Rationale and Motivation
(MPEP §2142-2143)
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to Kvach et al., Buisson et al. and El-Sagheer et al. and utilize a CuAAC reaction between two nucleotides in order to form a hairpin in the sequence designed to inhibit APOBEC3. One skilled in the art would have been motivated to form a hairpin as Buisson et al. teaches APOBEC3A strongly prefers “hairpin” substrates. One skilled in the art would have been motivated to utilize a CuAAC reaction as it is known to be utilized to cyclize nucleotides to form hairpins as taught by El-Sagheer et al. Since there are significant advantages, namely stability and ease of synthesis with CuAAC, and the corresponding functional groups, azide and alkyne, can be easily attached to nucleobases as taught by El-Sagheer et al. there is a reasonable expectation of success. Additionally, Kvach et al. expressly suggests work with optimizing the structure should be performed.
Regarding the claimed compounds, Kvach et al. teaches oligonucleotides with the following structure:
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, . Buisson et al. teaches oligonucleotides with the following structure:
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Kvach et al. teaches the importance of 5Fdz when targeting APOBEC3A. As taught by Buisson et al. the formation of a hairpin with 3 or 4 nt provides efficient activity. As taught by El-Sagheer et al. modified nucleosides include:
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and
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(figure 3). As shown in figure 4 the modification can be applied to any nucleoside:
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. Thus, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to Kvach et al., Buisson et al. and El-Sagheer et al. and utilize the A-T pair or G-C pair to form a covalent bond via click chemistry in order to form the desirable hairpin. Since Buisson et al. recognizes that optimization of not only the loop structure but also the stem strength plays a role in specificity, one skilled in the art would manipulate the location of the crosslink. Since El-Sagheer et al. shows that the alkyne/azide can be attached on any of the nucleobases, one skilled in the art would have a reasonable expectation of success in modifying either A/T or G/C with the appropriate alkyne/azide in order to afford the desired crosslinking. Additionally, since the sequences are taught as ssDNA, they possess the claimed β-D-2’-deoxyribofuranosyl unit.
The FdZ taught in Kvach et al. reads on the instantly claimed In in claim 1-3 and 9.
Regarding claims 1, 3, 5 and 10, as claimed X-6, X-5, X-4, X-2, X-1, X+1, X+2, X+4, X+5 and X+6 is absent or is independently selected from a nucleotide or a nucleotide derivative. Thus, the size of the claimed loop ranges from 1 (the required In) up to 5 (when X-2, X-1, X+1 and X+2 are all required to be present). Thus, the loop of 3 to 4 nt taught by Buisson et al. would meet these limitations. Regarding the remainder of X, these are not required to be present. Nonetheless, both Kvach et al. and Buisson et al. teach sequences have a corresponding number of nucleotides. Regarding ZA and ZB they are not required to be present (claim 1, 3 and 11).
Regarding A, B, LA and LB in claims 1, 3-4, 6-8, as set forth above, El-Sagheer et al. teaches a C5 alkylene connecting the nucleobase to N3 (Figure 3) and either the alkyne directly to the nucleobase (i.e. LA and LB are absent) or a C6 carbon chain linker to the alkyne (Fig. 3 and 4). Utilizing either A-T or G-C to form the click pair reads on A and B being a substituted 5-4 membered N-containing monocyclic or polycyclic heteroaryl group (claims 1 and 3). These also read on substituted purinyl and pyrimidnyl in claim 6-7.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Kvach et al. in view of Buisson et al., El-Sagheer et al. as applied to claims 1-7 and 9-11 above and in further view of Robinson et al. (WO2016168711).
Applicant Claims
The instant application claims a compound of claim 7 in which the A and B rings are independently selected from the group consisting of
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Determination of the Scope and Content of the Prior Art
(MPEP §2141.01)
The teachings of Kvach et al. in view of Buisson et al. and El-Sagheer et al. are set forth above.
Ascertainment of the Difference Between Scope the Prior Art and the Claims
(MPEP §2141.02)
While modifications to nucleobases are suggested for click chemistry reactions, attachment of an azide or alkyne to the N6 position of adenine is not expressly taught. However, this deficiency is cured by Robinson et al.
Robinson et al. is directed to methods for detecting agglutination and compositions for use in practicing the same. Taught are modified nucleotides which can be introduced into a polynucleotide by any convenient method. Modified nucleotides include those useful in click-chemistry (e.g. azide-functionalized, alkyne-functionalized). These include N6-(6-Azido)hexyl-3’-deoxyadenosine-5’-triphosphate and N6-Propargyl-adenosine-5 ’ -triphosphate (paragraph 00174).
Finding of Prima Facie Obviousness Rationale and Motivation
(MPEP §2142-2143)
Regarding claim 8, when the pairing is A-T this reads on the first two compounds recited. It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Kvach et al., Buisson et al., El-Sagheer et al. and Robinson et al. and utilize known modified nucleotides that contain functionality which includes an azide or alkyne. One skilled in the art would have been motivated to utilize azide and/or alkyne modified nucleotides in order to form hairpins as set forth above. Robinson et al. teaches that this functionality can be placed on the N6 position of adenine. Therefore, it would have been obvious to utilize the various T modified nucleotides taught in El-Sagheer et al. and the A modified nucleotides taught in Robinson et al. with a reasonable expectation of success as these are all taught as suitable modified nucleotides which can be used in click chemistry.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ABIGAIL VANHORN whose telephone number is (571)270-3502. The examiner can normally be reached M-Th 6 am-4 pm EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Neil Hammell can be reached on 571-270-5919. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/ABIGAIL VANHORN/Primary Examiner, Art Unit 1636
Prosecution Insights