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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 20 July 2026 has been entered.
DETAILED ACTION
Applicant’s amendment filed on 20 July 2026 is entered. Claims 176-177 are amended. Claims 176-196 are pending. Claims 194-195 remain withdrawn.
Claims 176-193 and 196 are under examination.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 20 July 2026 is being considered by the examiner.
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.
Claims 176-193 and 196 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 176 recites that (a)-(c) corresponding to a protease domain, a linker region, and a translocation domain, respectively, wherein (a)-(c) comprise an amino acid sequence that has at least 85% identity to SEQ ID NO: 2. It is unclear if each of the (a), (b), and (c) separately all comprise a sequence with at least 85% identity to SEQ ID NO: 2, or if the sequential combination of the sequences of (a), (b), and (c) into one sequence has at least 85% identity to SEQ ID NO: 2.
Claim 177 recites that the receptor binding domain comprises a substitution mutation at a position corresponding to C1240 in SEQ ID NO: 1. The claim does not limit the sequence of the receptor binding domain to be SEQ ID NO: 1 with a substitution at position C1240, rather it only limits the receptor binding domain sequence to comprise a substitution mutation. It is unclear how it can be determined whether or not a given sequence position in a receptor binding domain corresponds to C1240 in SEQ ID NO: 1. Furthermore, without the receptor binding domain limited to a particular sequence, it is unclear where the substitution mutation actually occurs in the domain sequence. The same issues are also recited in claims 178, 186, and 187.
Claims 177-193 and 196 depend from claim 176, and claims 188-193 depend from claim 186, so those dependent claims are indefinite for the same reasons.
Claim Rejections - 35 USC § 112
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.
Claims 176-179, 182-193, and 196 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 claims contain 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.
The MPEP states that the purpose of the written description requirement is to ensure that the inventor had possession, as of the filing date of the application, of the specific subject matter claimed. The MPEP lists factors that can be used to determine if sufficient evidence of possession has been furnished in the disclosure of the application. These include: (1) Actual reduction to practice, (2) Disclosure of drawings or structural chemical formulas, (3) Sufficient relevant identifying characteristics (such as: i. Complete structure, ii. Partial structure, iii. Physical and/or chemical properties, iv. Functional characteristics when coupled with a known or disclosed correlation between function and structure), (4) Method of making the claimed invention, (5) Level of skill and knowledge in the art, and (6) Predictability in the art. See MPEP §2163.
Claim 176 recites a chimeric Clostdridial Botulinum neurotoxin (BoNT) polypeptide comprising, from N-terminus to C-terminus: (a) a protease domain; (b) a linker region; (c) a translocation domain; and (d) a receptor binding domain, wherein (a)-(c) comprise an amino acid sequence that has at least 85% identity to SEQ ID NO: 2, and wherein (d) is a BoNT receptor binding domain of any one of BoNT serotypes A-G.”
Claim 179 limits the receptor binding domain to be from a serotype selected from the group consisting of: A, B, C, and D. Claim 196 limits the receptor binding domain to be from a serotype selected from the group consisting of: E, F, and G. Dependent claims 177-178 and 182-193 do not further limit the receptor binding domain to be from a specific serotype from the BoNT serotypes A-G, and none of the dependent claims limit the receptor binding domain to a specific subtype within the BoNT serotypes A-G, and so dependent claims 177-178 and 182-193 share the same written description issues of their parent claims as discussed below.
The genus of amino acid sequences that are at least 85% identical to SEQ ID NO: 2, and the genus of amino acid sequences that are at least 85% identical to any one of SEQ ID NOs: 22-24 are very large, encompassing many sequences that would not be expected by one of ordinary skill in the art to retain functionality. The disclosure has not described a representative number of species of this large genus such that one of ordinary skill in the art would conclude that the inventors had complete possession of the full genus as claimed.
The disclosure also lacks any particular guidelines on structural requirements, including required conserved sequence regions, that must be maintained that sufficiently shows one of ordinary skill in the art that all possible sequences within the claimed genera would be functionally equivalent to SEQ ID NO’s: 2 and 22-24, thus meeting the full breadth of the claims. The prior art also lacks sufficient description to show that the full breadth of the genus has the same or similar functionality as that of SEQ ID NO’s: 2 and 22-24. Applicant’s reference, Lam et al. (in the IDS filed 20 July 2026), only provides some guidance on conserved sequences of receptor binding domains, not the protease, linker, and translocation domains that SEQ ID NO: 2 corresponds to.
SEQ ID NO’s: 22-24 are full amino acid sequences for the entire BoNT polypeptide of claim 176, and suffer from the same issue of lack of guidance pertaining to their protease, linker, and translocation domains. The Lam reference does not provide sufficient description for the receptor binding domains of the BoNTs comprising sequences with at least 85% identity to any one of SEQ ID NOs: 22-24.
Although Lam discloses one chimeric “mosaic toxin” comprising a BoNT/D LC and HN domains (protease and translocation domains) and a BoNT/C HC domain (receptor binding domain) (Lam pg. 5 para. 1), there is no indication within Lam’s description that any BoNT amino acid sequence that has at least 85% identity to any one of SEQ ID NOs: 22-24 would be functionally identical or similar to that of SEQ ID NOs: 22-24.
It is important to consider the sheer number of sequence modifications that may be performed on SEQ ID Nos: 2 and 22-24 that would still allow those sequences to fall within the 85% identity threshold. For example, SEQ ID NO: 2 is 892 residues long. When considering only substitution mutations, of these 892 residues, 85% must be identical to those of SEQ ID NO: 2, leaving up to 133 residues that can possibly be different from their corresponding residues in SEQ ID NO: 2 (892-(892 x 85%)). When only considering the standard 20 natural amino acids used to make proteins, there are a total of 20133 different possible sequences. This calculation does not consider the possibility of substituting with non-natural amino acids, which increases the size of the genus even more. It is also important to consider that substitution mutations are not the only possible means of rendering a given sequence at least 85% identical to SEQ ID NO: 2, with other options such as insertions and deletions being possible, expanding the size of the genus even larger. This same concept can be seen with SEQ ID Nos: 22-24 as well. Both SEQ ID NO: 22 and 24 are 1316 residues long, leaving up to 198 residues that can be different. SEQ ID NO: 23 is 1324 residues long, leaving up to 199 residues that can be different.
Accordingly, one of ordinary skill in the art would not conclude that Applicant had possession of the full genus of amino acid sequences that are at least 85% identical to SEQ ID NO: 2, and the genera of amino acid sequences that are at least 85% identical to any one of SEQ ID NOs: 22-24 as claimed.
Regarding the genus of receptor binding domains of any one of BoNT serotypes A-G, the broadest reasonable interpretation of the chimeric BoNT polypeptide of claim 176 includes any chimeric BoNT polypeptide that has receptor binding domain that from any one of BoNT serotypes A-G. At the present moment, 7 other serotypes are known as BoNT serotypes A-G (Specification pg. 1 ln 14), and the chimeric BoNT polypeptide of claim 176 can have a receptor binding domain from any BoNT serotypes A-G. In addition to this, each of the BoNT serotypes A-G encompass many different subtypes (specification pg. 13-15). Thus, the broadest reasonable interpretation of the chimeric BoNT polypeptide of claim 176 includes chimeric BoNTs comprising any receptor binding domain from BoNT serotypes A-G and any of the subtypes within the BoNT serotypes A-G (specification pg. 13-15). This means that the genus of chimeric BoNT polypeptides recited in claim 176 is extremely large.
Although claims 179 and 196 limit the receptor binding domains to be from serotypes A, B, C, or D, or from serotypes E, F, and G, respectively, neither claim limits the subtypes of the serotypes. Thus, the broadest reasonable interpretation of the chimeric BoNT polypeptide of claim 179 includes a chimeric BoNT comprising a receptor binding domain from any of the subtypes within the BoNT serotypes A-D (specification pg. 13-15). Likewise, the broadest reasonable interpretation of the chimeric BoNT polypeptide of claim 196 includes a chimeric BoNT comprising a receptor binding domain from any of the subtypes within the BoNT serotypes E-G (specification pg. 13-15). The genus of chimeric BoNT polypeptides recited in claims 179 and 196 is also large.
The instant specification provides some broad suggestions in combining different BoNT receptor binding domains to the BoNT serotype X protease and translocation domains (specification pg. 28 lns. 6-20), and discloses additional specific embodiments that use the receptor binding domains of BoNT serotypes A1, B1, and C1, which are provided in SEQ ID Nos: 22-24, respectively (specification pg. 28 lns. 21-22). Of these sequences, only SEQ ID NO: 22 is reduced to practice and characterization within the instant disclosure (specification pg. 15-16 bridging para. and Fig. 8). However, the disclosure fails to adequately describe any other chimeric BoNTs with receptor binding domains from other BoNT serotypes A-G and their subtypes such that one of ordinary skill in the art would not be able to determine whether Applicant had possession of the entire genus of claimed invention at the time of filing.
The prior art recognized several challenges concerning fusion of proteins to each other. Yu et al. (Synthetic fusion protein design and applications, Biotechnology Advances 33 (2015) 155–164) teaches that the simplest form of fusion is tandem fusion, which involves joining together the coding genes of the proteins to be fused and expressing those joined genes as a single peptide chain in a suitable host organism (Yu pg. 156 sec. Tandem Fusion para. 1 sentence 5). Yu also teaches that the order of fusion partners in a polypeptide chain is often critical (Yu pg. 156 sec. Tandem Fusion para. 1 sentence 3). However, Yu teaches that this strategy fails when the free N- or C-terminus to be tethered is essential to the one of the protein’s function and/or is not flexible or long enough to avoid steric hindrance, which may give rise to undesirable outcomes such as protein misfolding, aggregation leading to inclusion body formation, low yield in protein production, and impaired bioactivity (Yu pg. 156 sec. Tandem Fusion para. 1 sentence 7). To remediate this, linker sequences, which serve to maintain necessary distance to reduce steric hinderance and/or permit favorable domain-domain interaction, are often used to link the two proteins together (Yu pg. 156 sec. Tandem Fusion para. 1 sentence 6 through para. 2 sentence 1). However, Yu then teaches that the selection of a linker is mostly ad hoc and still remains an underexplored area in fusion protein engineering, and admits that it is hard to assume that a linker suitable for one case will be applicable to others, as each type of linker has its specific characteristics (Yu pg. 156 sec. Tandem Fusion para. 3 sentences 3-4). Yu continues to another fusion technique called domain insertion, where functional fusion proteins can be reconstituted by inserting one domain into a host protein to achieve their chimerization (Yu pg. 157 sec. Domain Insertion para. 1 sentence 3). This approach appears to be the most applicable to the instant invention’s chimerization process described in the specification. However, Yu teaches that domain insertion is more difficult to design than tandem fusion since it is mandatory to find a “cut” site on the host protein to take the insert, which could disrupt domain folding if inappropriately selected, but generally surface loops or turns that are not in the catalytic sites are selected as insertion points (Yu pg. 157 sec. Domain Insertion para. 2 sentences 1-2). However, in most cases additional efforts are required to identify optimal insertion sites by directed evolution approaches (Yu pg. 157 sec. Domain Insertion para. 2 sentence 3). The combination of Yu’s teachings indicate that there are many challenges when fusing proteins or functional domains together to form a chimeric protein, and that these challenges can lead to unpredictable results, such as protein misfolding, aggregation leading to inclusion body formation, low yield in protein production, and impaired bioactivity. In light of these known challenges and the lack of adequate written description in the disclosure, one of ordinary skill in the art would find it unpredictable to successfully fuse any given receptor binding domain from serotypes A-G or their subtypes to the C-terminus of a translocation domain from BoNT serotype X.
In conclusion, the invention recited in instant claims 176-193 and 196 lacks sufficient written description to reasonably convey to one of skill in the art that Applicant had possession of the entire genus of claimed invention.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 176, 179, 182-185, and 196 are rejected under 35 U.S.C. 103 as being unpatentable over Steward et al. (US 8052979 B2, published 08 November 2011) in view of Hosomi et al. (putative botulinum neurotoxin, GenBank Accession number BAQ12790.1, publicly available 21 February 2015), as evidenced by Zhang et al. (Identification and characterization of a novel botulinum neurotoxin, Nature Communications, 8:14130, DOI: 10.1038/ncomms14130, published 03 August 2017) and David et al. (The Receptor Binding Domain of Botulinum Neurotoxin Serotype A (BoNT/A) Inhibits BoNT/A and BoNT/E Intoxications In Vivo, Clinical and Vaccine Immunology, p. 1266–1273, August 2013, Volume 20, Number 8).
Regarding claims 176, 179 and 196, Steward teaches a modified Clostridial toxin comprising an enzymatic domain (protease domain), a translocation domain, a targeting domain that is a glucagon like hormone (hormone receptor binding domain), and a protease cleavage site (linker region), which is equivalent to instant claim 176 (a)-(d) (Steward claim 1), and that the amino-to-carboxyl polypeptide order of the domains is the enzymatic domain, the protease cleavage site, the translocation domain, and the targeting domain (Steward claim 2). The enzyme domain (protease domain) and the translocation domain are taught to be from any BoNT serotype A-G (Steward claims 8-9). Steward also teaches that the targeting domain (receptor binding domain) can be the natural sequences of BoNT A-G, which meets the limitations of instant claims 179 and 196 (Steward col. 122 lns. 42-55).
However, Steward does not teach that the enzymatic domain (protease domain) and the translocation domain are from BoNT serotype X.
Hosomi teaches the sequence of GenBank accession number BAQ12790.1 is the putative botulinum neurotoxin from the whole genome sequence of Clostridium botulinum strain 111, which was considered to be a serotype B strain at the time (Hosomi lns. 27-29). However, this sequence was later characterized and determined to be the new BoNT serotype X, as evidenced by Zhang (Pg. 2 sec. Results para. 1 sentence 3), but the sequences are from the same accession number, BAQ12790.1, and thus are equivalent to each other. Therefore, the polypeptide of BAQ12790.1 would have had an enzyme domain (protease domain) and a translocation domain from a sequence that is equivalent to a BoNT serotype X, which would meet the limitations of instant claim 176 (a) and (c). Furthermore, BAQ12790.1 is 100% identical to SEQ ID NO: 2. See below alignment with “Query” being SEQ ID NO: 2 and “Sbjct” being BAQ12790.1.
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950
729
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Therefore, it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the present invention to substitute the Clostridium botulinum strain 111 serotype B polypeptide of sequence of BAQ12790.1 for the modified Clostridial toxin of Steward, and to replace the targeting (receptor binding) domain with one from a BoNT serotype A-G as suggested by Steward, because one of ordinary skill in the art would have considered BAQ12790.1 to be a BoNT serotype B, and thus would have understood that the polypeptide of BAQ12790.1 was applicable in the modified Clostridial toxin of Steward since Steward teaches that the enzyme domain (protease domain) and the translocation domain can be from any BoNT serotype A-G (Steward claims 8-9). Furthermore, the very same polypeptide sequence BAQ12790.1 is now considered to be BoNT serotype X, as evidenced by Zhang (Pg. 2 sec. Results para. 1 sentence 3). Therefore, the polypeptide of BAQ12790.1 would have had an enzyme domain (protease domain) and a translocation domain from a sequence that is equivalent to a BoNT serotype X, which would meet the limitation “wherein (a) and (c) are from BoNT serotype X” of instant claim 176. One of ordinary skill in the art would have been motivated to replace the targeting (receptor binding) domain of BAQ12790.1 described above with one from a BoNT serotype A-G as suggested by Steward, because changing the targeting domain of a BoNT would reduce undesirable dispersal of the toxin to areas not targeted for treatment, thereby reducing undesirable side effects associated with diffusion of a Clostridial toxin to an unwanted location (Steward col. 3 lns. 21-24 and 31-33) in order to adapt the modified Clostridial toxin of Steward to target different receptor proteins because different serotypes bind to different receptors, as evidenced by David (Pg. 1272 para. 2 sentence 2).
Regarding claims 182, Steward teaches that artificial flexible spacers (or several in tandem) can be placed between the different domains which can be used to adjust the length of a polypeptide region in order better expose a protease cleavage site to facilitate cleavage of that site (Steward col. 133 lns. 9-16), and the flexible spacers can be adjacent to the protease cleavage site, thereby linking the two into one region (Steward col. 134 lns. 16-20).
Regarding claims 183-185, Steward teaches the exogenous protease cleavage site is a thrombin cleavage site (Steward claim 12), which is presented as SEQ ID NO: 94 of Steward (Steward table 9), which aligns 100% to SEQ ID NO: 50 of instant claim 185 (see Sequence Search Results dated 27 February 2025).
Response to Arguments
Applicant's arguments filed 20 July 2026 have been fully considered but they are not persuasive.
Regarding Applicant’s arguments that one of ordinary skill in the art recognizes that receptor binding domains from BoNT serotypes share conserved overall fold and functional architecture such that any receptor binding domain from any one of the serotypes A-G and their subtypes could be used in the claimed invention, pointing to fig. 1 of Lam et al. as evidence (Remarks pg. 6-7 bridging para.), the receptor binding domains are not present by themselves in the claimed invention, but are rather fused to the protease and translocation domains from a completely different serotype X with a different amino acid sequence than that of the other serotypes. Any conserved overall fold and functional architecture among the receptor binding domains of the different serotypes as Lam teaches is in the context of the receptor binding domains still naturally bound to their protease and translocation domains of the same serotype, but this does not consider the very real possibilities of misfolds and elimination of enzymatic activity that accompanies protein fusion, as taught by Yu. Regardless, neither the instant disclosure nor the prior art teaches a representative number of fusion examples that demonstrates to one of ordinary skill in the art the predictability and reasonable expectation of success of fusing different receptor binding domains to form the claimed genus of chimeric BoNTs.
Regarding Applicant’s arguments that Lam discloses modular structures of BoNTs that show one of ordinary skill in the art that any given receptor binding domain from serotypes A-G or their subtypes may be able to fuse to the C-terminus of a translocation domain from BoNT serotype X, and that Yu is directed to fusing unrelated non-homologous proteins that have not co-evolved to interact (Remarks pg. 7 para. 2), Lam teaches that BoNTs are typically trimodular, meaning they comprise three modules: protease, translocation, and receptor binding domains. Just because BoNTs are typically comprised of three modules does not mean that those modules can be independently substituted between the different BoNT serotypes. It cannot be extrapolated that there is a reasonable expectation that one receptor binding domain may be readily replaced with a different serotype and still retain its functionality. Yu teaches the challenges of fusing proteins in general, and it is important to note that serotypes are formed because of divergent evolutions through sequence mutations over time. It is therefore not convincing to state that the different BoNT serotypes are homologous proteins and have co-evolved to interact. The individual modules within a single serotype of BoNTs have are homologous and have co-evolved to interact, but a mix and match of the individual modules from different serotypes have not co-evolved to interact, so there is no expectation that fusing them would maintain functionality.
Regarding Applicant’s arguments that cited reference Zhang does not qualify as prior art because it was published after the effective filing date (Remarks pg. 9 para. 1), MPEP §2124 states “In certain circumstances, references cited to show a universal fact need not be available as prior art before the effective filing date of applicant’s claimed invention. In re Wilson, 311 F.2d 266, 135 USPQ 442 (CCPA 1962). Such facts include the characteristics and properties of a material or a scientific truism. Some specific examples in which later publications showing factual evidence can be cited include situations where the facts shown in the reference are evidence.” Zhang is used in the 103 rejection as an evidentiary reference providing evidence that Hosomi’s sequence BAQ12790.1 is actually characterized as being BoNT serotype X, not serotype B as Hosomi had originally suggested. Since Zhang is used to describe characteristics of the BoNT polypeptide it does not need to antedate the effective filing date.
Regarding Applicant’s arguments that at the time of filing one of ordinary skill in the art would understand that Hosomi’s BAQ12790.1 does not have a functional enzymatic domain and/or translocation domain (Remarks pg. 9 para. 2), Hosomi’s BAQ12790.1 clearly indicates that the sequence comprises an enzymatic domain “Peptidase_M27” at amino acids 5-404, and a translocation domain “Toxin_trans” at amino acids 559-871 (Hosomi lns. 40-48). Therefore, one of ordinary skill in the art would recognize that Hosomi’s BoNT would have enzymatic and translocation domains. Thus, one of ordinary skill in the art would understand that modifiying Steward’s chimeric BoNT with Hosomi’s would not render the resultant modified chimeric BoNT inactive.
Conclusion
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/Alexander M Duryee/Examiner, Art Unit 1657 /LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
