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 .
Please note that the correspondence information for this application has changed (see Conclusion section at the end of this Action).
Election/Restrictions
Applicant’s election without traverse of Group I (claims 18-31) in the reply filed on 12 December 2025 is acknowledged. Claims 32-37 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 12 December 2025. Claims 18-31 will be examined on the merits herein.
Priority
The instant application is a 371 of application PCT/EP2021/084054 (filed 2 December 2021) and claims priority to foreign application EP 20306480.3 (filed 2 December 2020). Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55. Therefore, the effective filing date of instant claims 18-31 is 2 December 2020.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 30 October 2023 are in compliance with the provisions of 37 CFR 1.97. Accordingly, each information disclosure statement is being considered by the examiner.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Claim Objections
Claim 18 is objected to because of the following informalities: “50 % of isolated, modified monomer” should read “50 % of isolated, modified monomers”. Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
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.
Claim 28 is 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 28 recites the limitation "at least one modified monomer as defined in claim 18" in line 5. There is insufficient antecedent basis for this limitation in the claim or the claim upon which it depends (i.e., claim 18) because claim 18 is not drawn to a modified monomer, but is instead drawn to a composition. Thus, it is unclear whether claim 28 (which is dependent upon claim 18 and thus comprises the whole of the composition recited in claim 18) is intended to comprise a composition of at least 50% of the isolated, modified monomers as recited in claim 18, or a composition with any concentration of modified monomers in which 50% of the total STxB pentamers comprise at least one modified monomer. It is suggested that claim 28 be amended to recite a specific structure of “at least one modified monomer.” Clarification is requested.
Claim Rejections - 35 USC § 103
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.
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 18-23 and 25-31 are rejected under 35 U.S.C. 103 as being unpatentable over Tobola et al. (2019, Interface Focus; cited in IDS; herein “Tobola”) in view of Billet et al. (WO 2020/245321 A1, effectively filed 4 June 2019; cited in IDS; herein “Billet”).
Regarding claims 18 and 28, Tobola teaches a composition comprising modified monomers of Shiga toxin B-subunit (i.e., Stx1B or StxB) comprising a substitution a reactive unnatural amino acid at position K8 (i.e., Lys 8) (pg. 2, right col., para. 2 and Figure 1), when numbered according to a Stx1B comprising a sequence identical to that of instant SEQ ID NO: 2 (Table S2; see Figure 1 below for alignment). Tobola also teaches that the modified Stx1B monomers form pentamers (Figure 1). However, Tobola teaches that the purified Stx1B[AzK] was highly contaminated with wild-type Stx1B and that the wild-type Stx1B species was the dominant species in the mixture, i.e., the Stx1B[AzK] species did not make up the majority of proteins (pg. 3-4, paragraph bridging pages).
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Figure 1: Alignment of instant SEQ ID NO: 2 (Qy) with the amino acid sequence of Stx1B taught by Tobola (Db).
Regarding claim 19, Tobola teaches that the monomer of the Stx1B protein does not comprise a substitution with an unnatural amino acid residue at positions 1, 6, and 26, when numbered according to a Stx1B comprising a sequence identical to that of instant SEQ ID NO: 2 (Table S2).
Regarding claims 20-21, Tobola teaches that the unnatural amino acid residue is L-azidolysine (i.e., AzK, an isomer of 6-azido-L-lysine), which comprises an azide functional group (pg. 2, right col., para. 2 and Figure 1).
Regarding claim 22, Tobola teaches a Stx1B protein comprising a substitution of Lys 8 into L-azidolysine (pg. 2, right col., para. 2 and Figure 1).
Regarding claim 23, Tobola teaches that the modified Stx1B protein comprises an amino acid sequence 98.6% identical to that of instant SEQ ID NO: 2 (Table S2 and Figure 1).
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Figure 2: Alignment of instant SEQ ID NO: 2 (Qy) with the modified Stx1B protein taught by Tobola (Db), where the X at position 8 of Tobola’s sequence represents the unnatural amino acid, L-azidolysine.
Regarding claims 26 and 29, Tobola teaches that the Stx1B[AzK] formed conjugates with Gal-1[Hpg] or RSL[Hpg] through the reactive unnatural amino acids incorporated within the sequences of Stx1B, Gal-1, or RSL (Figure 3), with or without a linker (Sections 2.3 and 2.4). Tobola also teaches that the Stx1B could be conjugated with effectors or drugs for the targeted delivery to specific cell types (pg. 7-8, paragraph bridging pages).
Regarding claim 31, Tobola teaches that substitution of unnatural amino acids at pre-defined locations in Stx1B allows for the selective, pre-defined, and site-specific conjugation of Stx1B with other modules (i.e., payload), which is beneficial because classical conjugation methods are often non-selective and the conjugation site is difficult to define, which leads to conjugation at random sites that can interfere with the natural protein function (Abstract). However, conjugation through the method taught by Tobola does not interfere with Stx1B protein function, so the Stx1B[AzK] protein can be used for targeted delivery of effectors or drugs to specific cell types (pg. 7-8, paragraph bridging pages).
However, Tobola does not teach a composition in which at least 50% of the StxB monomers are the modified StxB monomers, as in claim 18, modified StxB monomers of the StxB protein that are not a recombinant protein, as in claim 25, a payload as defined in claim 27, a composition wherein at least 50% of the total pentamers comprise at least one of the modified monomers, as in claim 28, or wherein the modified pentamers of the StxB protein comprise five of the modified StxB monomers, as in claim 30. Tobola is also silent on whether the modified Stx1B is capable of binding Gb3/CD77, as in claim 31.
Regarding claim 18, 28, and 30, Billet teaches a STxB protein produced by solid phase peptide synthesis, comprising an amino acid sequence shown in SEQ ID NO: 2, which is identical to instant SEQ ID NO: 2 (pg. 151-155; see Figure 3 below for alignment). Billet also teaches that the STxB produced by this method may comprise at least one non-proteinogenic (i.e., unnatural) amino acid residue at the C-terminus or substituted in place of a standard amino acid (pg. 27, lines 21-22 and pg. 28, line 21 – pg. 29, line 11). Billet teaches that UPLC-MS of the resulting product of solid phase synthesis shows a dominant peak corresponding with the expected mass of monomeric STxB, i.e., a majority of the product was the STxB monomer (pg. 159, lines 16-20), demonstrating that the STxB monomers produced had an amino acid sequence identical to SEQ ID NO: 2 and could be produced with no contaminants (pg. 159, lines 19-20), i.e., the entirety of the product was the STxB monomer. Because the method involves the addition of one amino acid at a time to the growing peptide (pg. 152-154), an unnatural amino acid may be used in the place of a natural amino acid at any given position to produce STxB monomers comprising that unnatural amino acid at only that position. Billet teaches that while STxB can be produced recombinantly, they contain exogenous impurities (pg. 3, lines 24-29), but peptides produced by solid phase peptide synthesis allows for large-scale production with pharmaceutical grade purity (pg. 5, lines 3-5).
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Figure 3: Alignment of instant SEQ ID NO: 2 (Qy) with Billet’s SEQ ID NO: 2 (Db).
Regarding claim 20, Billet teaches that the unnatural amino acids may be amino acids with azide, alkyne, aldehyde, keto, ester, boronate, or halide functional groups (pg. 30, lines 17-22).
Regarding claim 21, Billet teaches that the unnatural amino acid may be azido-lysine (i.e., an isomer of 6-azido-L-lysine) (pg. 30, line 10).
Regarding claim 25, Billet teaches that the STxB is produced by solid phase peptide synthesis (pg. 151-154) and therefore is not a recombinant protein (pg. 53, lines 23-28).
Regarding claim 26 and 29, Billet teaches that the monomer or oligomer of the STxB protein is conjugated to at least one payload (pg. 89, lines 9-10).
Regarding claim 27, Billet teaches that the payload may be selected from chemotherapeutic agents, targeted therapy agents, cytotoxic agents, antibiotics, antivirals, cell cycle-synchronizing agents, ligands for cellular receptor(s), immunomodulatory agents, pro-apoptotic agents, anti-angiogenic agents, cytokines, growth factors, antibodies or antigen-binding fragments thereof, antigens, hormones, coding or non-coding oligonucleotides, photodetectable labels, contrast agents, and radiolabels (pg. 89, lines 11-18).
Regarding claim 31, Billet teaches that STxB is capable of binding Gb3/CD77 receptors on target cells and is then transported from the plasma membrane of the target cell into the Golgi apparatus and endoplasmic reticulum via endosomes (pg. 2, lines 14-25). Billet teaches that Gb3 is expressed on malignant cells and that a prodrug inhibitor composition using topoisomerase I inhibitor SN38 coupled to STxB was designed to specifically target cancer cells (pg. 3, lines 15-23).
Therefore, it would have been prima facie obvious, before the effective filing date of the claimed invention, to a person of ordinary skill in the art, to modify the Stx1B protein product taught by Tobola by using the solid phase peptide synthesis method of producing STxB proteins taught by Billet, thereby arriving at the invention of claims 18-23 and 25-31. The person of ordinary skill in the art would have been motivated to make the modification because the modified Stx1B[AzK] taught by Tobola is capable of forming conjugates with other modules in a selective and site-specific manner through the incorporation of the unnatural amino acid and without disrupting natural protein function. This is beneficial because Billet teaches that STxB can be used to target Gb3/CD77 on cancer cells for detection or drug delivery. Therefore, the combination is also desirable (see MPEP 2144(II)). The person of ordinary skill in the art would have had a reasonable expectation of successfully producing the modified STxB protein because Billet teaches that their method may be used with unnatural amino acids, so one of ordinary skill in the art would predict that AzK could be incorporated into STxB at position 8. Therefore, the combination leads to expected results because each element performs the same function as is does individually.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that applying a known technique to a known device, method or product ready for improvement is obvious because a particular known technique is recognized as part of the ordinary capabilities of one skilled in the art. In the instant case, Tobola contains a “base” method of producing Stx1B monomers comprising an unnatural amino acid; and Billet contains a similar method for producing STxB monomers comprising an unnatural amino acids wherein the technique of solid phase peptide synthesis is taught as advantageous. Thus, one of ordinary skill in the art would have recognized that applying the known technique taught by Billet would have yielded predictable results (i.e., the same advantages) and an improved system. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Regarding claim 21, while neither of Tobola or Billet teach 6-azido-L-lysine, Tobola teaches the incorporation of L-azidolysine and Billet teaches the incorporation of azido-lysine, which each have the same chemical formula as 6-azido-L-lysine (C6H13N5O2). Both molecules contain the same functional groups (carboxyl, amine, and azide groups), the only difference is the position of the azide group. MPEP 2144.09(I) states: “A prima facie case of obviousness may be made when chemical compounds have very close structural similarities and similar utilities. ‘An obviousness rejection based on similarity in chemical structure and function entails the motivation of one skilled in the art to make a claimed compound, in the expectation that compounds similar in structure will have similar properties.’ In re Payne, 606 F.2d 303, 313, 203 USPQ 245, 254 (CCPA 1979).” In the instant case, Tobola demonstrates the successful integration of L-azidolysine into Stx1B, including at position 8, as in claim 22. Tobola also teaches that the Stx1B contains AzK is capable of conjugating to a payload by means of the azide group in the AzK residue, as is required in claims 26-27 and 28. Therefore, the art demonstrates that L-azidolysine has a similar function to the 6-azido-L-lysine, and one of ordinary skill in the art would predict that the isomers are of sufficiently close structural similarity that there is a presumed expectation that the compounds possess similar properties.
Claims 18-31 are rejected under 35 U.S.C. 103 as being unpatentable over Tobola (2019, Interface Focus; cited in IDS) in view of Billet (WO 2020/245321 A1, effectively filed 4 June 2019; cited in IDS) as applied to claims 18-23 and 25-31 above, and further in view of Xin et al. (2018, Org. Biomol. Chem.; herein “Xin”).
The combination of Tobola and Billet is set forth in para. 14-31 above and teaches all limitations of claims 18-23 and 25-31.
However, the combination of Tobola and Billet does not teach a STxB protein comprising a substitution of Met 48 with L-norleucine, as in claim 24.
Regarding claim 24, Xin teaches that, in proteins containing methionine residues, the thioether moiety in methionine is susceptible to oxidation into a sulfoxide or sulfone, which results in a significant loss of bioactivity of the synthesized protein (pg. 6307, left col., para. 1). To overcome this, Xin teaches that methionine may be substituted with norleucine without substantially affecting the protein structure and function (pg. 6307, left col., para. 1).
Therefore, it would have been prima facie obvious, before the effective filing date of the claimed invention, to a person of ordinary skill in the art, to modify the STxB protein produced by the combination of Tobola and Billet by substituting the methionine residues within the STxB protein (including that at position 48 when numbering according to instant SEQ ID NO: 2) with norleucine, as is taught by Xin, thereby arriving at the claimed invention. The person of ordinary skill in the art would have been motivated to make the modification because Xin teaches that substitution of methionine with norleucine prevents the oxidation of the methionine, thereby preventing the loss of protein activity caused by the oxidation. Therefore, the combination is also desirable (see MPEP 2144(II)). The person of ordinary skill in the art would have had a reasonable expectation of success because the method of producing proteins taught by Billet may be used with unnatural amino acids and Xin teaches that the incorporation of norleucine does not impact the structure or function of synthesized proteins. Therefore, the combination leads to expected results because each element performs the same function as is does individually.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that the simple substitution of one known element for another to obtain predictable results is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that "the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results". In the instant case, the prior art (Tobola and Billet) teaches a product (or method) that only differs from the claimed invention by the substitution of a single component (i.e., substitution of the methionine residue or analog used); the substituted element (i.e., the norleucine) was already known and already shown to function in the place of methionine in synthesized proteins, therefore no change in the function of the substituted element occurred; and one of ordinary skill in the art would be capable of substituting one amino acid residue for another with a reasonable expectation of success (i.e., the substitution of the element would lead to predictable results). Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BAILEY M MORGAN whose telephone number is (703)756-5388. The examiner can normally be reached M-F 9-5 ET.
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/BAILEY M MORGAN/Examiner, Art Unit 1645
/SAMIRA J JEAN-LOUIS/Supervisory Patent Examiner, Art Unit 1642
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