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 .
Priority
This application, Serial No. 17/553,725 was filed on 12/16/2021, claims benefit under 35 U.S.C 119(e) to provisional application Serial Nos. 63/126,991, filed on 12/17/2020 and 63/287,008, filed on 12/07/2021.
Status of the Claims
Claims 1, 5–9, 12–16, 20, 24, 30, 37, 44, and 47–48 are currently pending. Claims 2–4, 10–11, 17–19, 21–23, 25–29, 31–36, 38–43, 45–46, and 49–61 are canceled. Claims 1, 5, 8-9, 15-16, and 20 are amended. Claims 16 and 47-48 are withdrawn from further consideration. The withdrawals of claims 9, 13, and 24 are withdrawn because these claims are readable on the elected species SEQ ID NO: 2. Accordingly, 1, 5–9, 12–15, 20, 24, 30, 37, and 44 are examined herein.
Claim Objections
Claims 6 and 7 are objected to because of the following informalities: Claims 6 and 7 recites “The opioid sensor of claim 5,” while claim 5 recites an “opioid biosensor.” Appropriate correction would be: “The opioid biosensor of claim 5.”
Claim 8 is objected to because of the following informalities: Claim 8 recites “position 1-75,” which should be corrected for consistency and clarity. Appropriate correction would be: “positions 1-75.”
Claim 14 is objected to because of the following informalities: Claim 14 appears to omit the article “The” before “opioid biosensor.” Appropriate correction would be: “The opioid biosensor of claim 5.”
Claim 15 is objected to because of the following informalities: Claim 15 recites “N11V” twice in the Markush group. Appropriate correction would be to delete the duplicate recitation of N11V.
Maintained 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.
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.
The rejection of claims 1, 5–9, 12–15, 20, 24, 30, 37, and 44 under 35 U.S.C. 112(a) is maintained. However, the rejection has been updated in view of Applicant’s claim amendments and is set forth below to address the amended claim language.
Claims 1, 5–9, 12–15, 20, 24, 30, 37, and 44 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.
Claim 1 recites a broad genus of polypeptides comprising a first mutated PBP domain and a second PBP domain connected to the first PBP domain, wherein at least one of the first and second PBP domains comprises at least one amino acid substitution mutation at one or more positions positionally equivalent to K10, N11, Q15, T43, T68, T325, K330, D341, Y357, A360, E391, R395, V405, F436, H455, and D490 in SEQ ID NO: 29. Claim 1 further recites that the first PBP domain need only be at least 93% identical to positions 1–75 of SEQ ID NO: 29 and the second PBP domain need only be at least 93% identical to positions 325–521 of SEQ ID NO: 29.
Although amended claim 1 now includes a 93% sequence identity limitation, the claim still encompasses a large genus of polypeptides defined principally by percent identity and the presence of at least one listed substitution, rather than by the specific engineered biosensor sequences, specific mutation combinations, or demonstrated structure-function relationships disclosed in the specification.
The specification does not demonstrate possession of this broad genus. The specification provides general identity ranges and variant language, but that type of disclosure does not identify which members across the full 93% identity genus would actually be possessed. For example, the specification states: a variant of a polypeptide can have deletions, substitutions, additions of one or more amino acids in comparison to the reference polypeptide and further states that a variant can have at least, or at least about, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more sequence identity to the reference polypeptide ([0064], pp. 12-13). This is broad variant language, not a representative disclosure of the claimed genus. The written description requirement is not satisfied merely because one skilled in the art could make or obtain additional variants; rather, the specification must reasonably convey that Applicant had possession of the claimed genus as of the filing date. The specification also confirms that sequence variation can affect biosensor properties. The specification states: the sequence variation are within the binding pocket of the PBP domains. Such variation may affect the selectivity and/or specificity of an opioid biosensor ([0080], pp. 18-19). This supports the rejection because the claims permit sequence variation within a genus where changes can affect the very properties relevant to the claimed biosensor function.
Claim 5 recites the genus of claim 1 in functional form as an opioid biosensor capable of undergoing a detectable conformational change upon binding to an opioid. Thus, claim 5 is broader and more problematic because it requires not only structural features, but also functional performance across the claimed genus. The specification does not reasonably convey possession of all polypeptides within the 93% identity genus that would also undergo the required detectable conformational change upon opioid binding. The specification shows that opioid biosensor function was obtained through directed evolution, screening, and optimization of particular biosensor-opioid pairs, not by merely selecting any sequence within a 93% identity genus having at least one listed substitution. The specification states: directed evolution was performed to convert OpuBC from a cholinergic to an opioid binding protein and further states that the work describes an exemplary workflow for developing opioid biosensors from amine binding periplasmic binding proteins such as OpuBC ([0152], p. 44). The specification further states that a hit is defined for a biosensor-opioid pair with ΔF/F0 > 0.5 at 200 uM, and that this criterion filters out biosensors that will not likely be evolvable in ~5 rounds of site-saturation mutagenesis (SSM) to yield the desired affinity and dynamic range ([0161], p. 45). This disclosure confirms that opioid biosensor performance was not predictable from the broad structural genus alone; instead, candidate biosensor-opioid pairs had to be screened and then evolved. Thus, the specification shows possession of particular screened and optimized biosensors, not possession of all polypeptides within the claimed 93% identity genus that contain at least one listed substitution.
The specification also states that optimization may include identifying sites or amino acid positions in the binding moiety which are involved in the conformational change and that various types of mutagenesis can be used including site-saturation mutagenesis ([0137], pp. 38-39). This supports the conclusion that Applicant had possession of specific screened and evolved biosensors, not the full genus now claimed. The working examples also show possession of particular species and mutation combinations rather than the full scope of claims 1 and 5. Table 2 lists specific mutation sets for exemplary opioid biosensors, including iFentanylSnFR1.0, iFentanylSnFR2.0, iTapentadolSnFR1.0, iS-methadoneSnFR1.0, and iLevorphanolSnFR1.0. The disclosed examples contain multiple coordinated mutations, not merely one substitution at any positionally equivalent listed position. For example, Table 2 identifies iFentanylSnFR2.0 as having K10A, Q15G, T43G, T68H, T325S, K330G, D341R, Y357G, A360T, E391F, R395A, V405L, F436W, H455A, D490G (Table 2, pp. 25-26). This evidence is important because claims 1 and 5 are not limited to those specific combinations. Applicant’s amendments reduce the numerical identity range, but they do not restrict the claims to the specific engineered biosensors actually disclosed, the disclosed coordinated mutation combinations, or any demonstrated subset shown to possess the claimed opioid biosensor function. The claims cover polypeptides and biosensors having only at least one amino acid substitution mutation at one or more listed positions and 93% identity over the PBP domains. The specification does not identify representative species across that full scope, nor does it provide a sufficient structure-function correlation showing that the broad universe of claimed variants would possess the claimed polypeptide structure or opioid biosensor function.
The specification further confirms that substitutions can materially change biosensor selectivity and binding. It states: the substitution mutations described herein can shift the biosensor selectivity from one opioid ligand to another opioid or non-opioid ligand or vice versa and the substitution mutation in an opioid biosensor can substantially alter the binding affinity between the biosensor and an opioid ligand. The specification also states: the substitution mutation can increase the binding affinity between the biosensor and one opioid ligand and decrease the binding affinity between the biosensor and another opioid or non-opioid ligand ([0103], pp. 26-27). Accordingly, the specification itself shows that the claimed mutation positions are functionally significant and that substitutions at those positions can change ligand binding and selectivity. This weighs against finding possession of a broad genus defined by 93% identity and at least one substitution, especially where claim 5 requires opioid biosensor function. These disclosures indicate that whether a particular variant functions as an opioid biosensor cannot be predicted solely from the sequence identity or from the presence of one recited mutation; functionality depends on the particular mutation combination and its effect on binding, selectivity, and conformational response.
Claims 6 and 7 depend from claim 5 and further define the opioid or opioid class to be detected. These claims do not cure the deficiency because they still rely on the broad genus of claim 5 and still encompass opioid biosensors across the 93% identity genus without requiring the specific mutation combinations shown to work in the specification.
Claim 8 further broadens the genus by permitting the first PBP domain to be at least 93% identical to positions 1–75 of a sequence selected from SEQ ID NOs: 1–27 and the second PBP domain to be at least 93% identical to positions 325–521 of a sequence selected from SEQ ID NOs: 1–27. The specification’s disclosure of specific SEQ ID NOs and broad identity ranges does not reasonably convey possession of all 93% identity variants across SEQ ID NOs: 1–27 that would also retain opioid biosensor function.
Claim 9 similarly fails because it merely recites 93% identity to positions 1–75 of SEQ ID NO: 29 and 94% identity to positions 325–521 of SEQ ID NO: 29. These percent-identity limitations narrow the genus somewhat, but they still do not limit the claim to disclosed species or disclosed mutation combinations and do not provide possession of all variants within that scope.
Claim 12 recites exact PBP-domain regions selected from SEQ ID NOs: 1–25, but because claim 12 depends from claim 5, the biosensor must still be capable of undergoing a detectable conformational change upon opioid binding. The specification provides specific examples of biosensors and ligands, but does not establish that every selected SEQ ID NO: 1–25 PBP-domain combination within the claim would possess the claimed opioid biosensor function.
Claims 13, 14, 15, 20, and 24 recite particular mutation features, including F436, N11, selected N11 substitutions, N11E or N11V, and Gly at position 357. These dependent claims do not overcome the written description deficiency because the specification shows that individual mutation positions are not generally interchangeable across the entire claimed genus. The specification provides specific mutation sets for specific opioid ligands, and further explains that substitutions can shift selectivity and alter binding affinity. Thus, reciting one mutation or one residue does not demonstrate possession of the full genus of opioid biosensors having that mutation within the broad 93% identity framework.
Claim 30 recites a reporter connected to the first PBP domain and the second PBP domain on either end. Claim 37 recites a nucleic acid encoding the opioid biosensor of claim 5. Claim 44 recites a device comprising the opioid biosensor of claim 5. These claims remain deficient because they depend from and incorporate the unsupported genus of claim 5. Adding a reporter, encoding nucleic acid, or device context does not provide written description support for the underlying broad opioid biosensor genus.
Therefore, the specification reasonably conveys possession of certain specific engineered opioid biosensors and specific mutation combinations disclosed in the examples and tables, but it does not reasonably convey possession of the full scope of claims 1, 5–9, 12–15, 20, 24, 30, 37, and 44. The written description rejection is therefore maintained.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim 1 is rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Marvin et al. (US 2019/0376964 A1).
Marvin teaches genetically encoded recombinant peptide biosensors comprising analyte-binding framework portions and signaling portions (Abstract, p. 1).
Regarding the limitation a polypeptide, Marvin teaches recombinant peptides for use as biosensors ([0032], p. 100). Marvin also discloses SEQ ID NO: 185 as a synthetic polypeptide (Sequence Listing, p. 225).
Regarding the limitation a first mutated periplasmic binding protein (PBP) domain and a second PBP domain connected to the first PBP domain, Marvin teaches an analyte-binding framework portion and a signaling portion, wherein the signaling portion is present within the framework portion at a site or amino acid position that undergoes a conformational change ([0004], p. 99). Marvin further teaches that the framework portion has first structure in the absence of an analyte and a second structure, that is detectably distinct from the first structure, in the presence of the analyte. In some embodiments, the framework portion is a periplasmic binding protein (PBP) or a variant of a PBP ([0007], p. 99).
Regarding the limitation requiring at least one amino acid substitution mutation at one or more positions positionally equivalent to the listed positions of SEQ ID NO: 29, Marvin teaches this limitation at least by the substitution N11I. The alignment (below) of Marvin’s SEQ ID NO: 185 against SEQ ID NO: 29 positions 1–75 shows that the residue positionally equivalent to N11 of SEQ ID NO: 29 is I in Marvin SEQ ID NO: 185. Thus, Marvin discloses a substitution mutation at the position positionally equivalent to N11, namely N11I. Marvin also discloses additional substitutions in the first PBP domain, including K10I, Q15G, T43V, and T68H, based on the alignment result.
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Regarding the limitation that the first PBP domain comprises an amino acid sequence at least 93% identical to amino acid residues 1–75 of SEQ ID NO: 29, the alignment (above) for Marvin’s SEQ ID NO: 185 shows 70/75 identical residues, i.e., 93.3% identity, satisfying the claimed at least 93% identity requirement.
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Regarding the limitation that the second PBP domain comprises an amino acid sequence at least 93% identical to amino acid residues 325–521 of SEQ ID NO: 29, the alignment (below) for Marvin’s SEQ ID NO: 185 shows 188/197 identical residues, i.e., 95.4% identity, satisfying the claimed at least 93% identity requirement.
Accordingly, Marvin discloses, expressly or inherently, each and every limitation of claim 1. Accordingly, claim 1 is anticipated under 35 U.S.C. 102.
Response to Arguments
Applicant’s arguments filed 11/14/2025 have been fully considered but they are not persuasive. The rejections under 35 U.S.C. § 112(a) are maintained for the reasons set forth below.
Election/Restriction
Applicant’s arguments with respect to claims 9, 13, and 24 have been fully considered and are persuasive. Claims 9, 13, and 24 are returned to examination. Specifically, Applicant argues that claim 9 reads on the elected species SEQ ID NO: 2 because SEQ ID NO: 2 has 94.67% identity to positions 1-75 of SEQ ID NO: 29 and 94.42% identity to positions 325-521 of SEQ ID NO: 29. Applicant further argues that claim 13 reads on the elected species because SEQ ID NO: 2 contains a substitution at the F436 position, and that claim 24 reads on the elected species because SEQ ID NO: 2 contains Gly at position 357. These arguments have been considered and are persuasive. Accordingly, claims 9, 13, and 24 are returned to examination.
Claims 16 and 47-48 remain withdrawn from further consideration. Claim 16 remains withdrawn because it is directed to a non-elected species. Claims 47-48 remain withdrawn because they are directed to the non-elected method group.
Claim Rejections under 35 U.S.C. § 112(a) — Written Description
Applicant argues that the amendments to claims 1 and 5 overcome the written description rejection because the claims now recite that the first PBP domain is at least 93% identical to positions 1-75 of SEQ ID NO: 29 and the second PBP domain is at least 93% identical to positions 325-521 of SEQ ID NO: 29. Applicant further argues that the specification provides a well-defined structure-function correlation, identifies functional determinants, describes preferred mutation positions in the binding pocket, and discloses a representative number of species. These arguments are not persuasive.
The amendments narrow the claims to some extent, but they do not limit the claims to the specific disclosed biosensor sequences or to the specific disclosed mutation combinations. Claims 1 and 5 still encompass a broad genus of polypeptides having only 93% identity over the recited PBP-domain regions and at least one substitution at one or more positionally equivalent listed positions. The claims therefore continue to encompass numerous undisclosed variants.
Applicant’s reliance on paragraph [0084], Table 2, and SEQ ID NOs: 1-27 and 29 is not persuasive because the cited disclosure describes particular species and particular mutation sets, not the full scope of the claimed genus. A disclosure of specific examples does not necessarily provide written description support for a broad genus unless the disclosed species are representative of the entire claimed genus or the specification provides sufficient identifying characteristics correlating structure with function across the full scope of the genus. Here, the specification shows that opioid biosensor function depends on particular mutations, particular positions, and particular ligand-specific optimization. The disclosed examples are not commensurate in scope with claims 1 and 5 because the claims are not limited to any disclosed full-length sequence, any disclosed complete mutation set, or any specific ligand-binding profile.
Applicant argues that paragraph [0096] explains that mutations can be introduced at the binding pocket where the opioid ligand interacts with the opioid binding domain. This is not persuasive because identifying a general region where mutations may be introduced does not show possession of all claimed 93% identity variants having at least one substitution at the listed positions. The claimed genus still permits numerous sequence changes outside the specifically exemplified combinations, and the specification does not establish that those variants would retain the claimed structure or biosensor function.
Applicant also argues that paragraph [0097] identifies residues that should not be mutated, such as F12, Y65, and/or Y460. This argument is not persuasive because identifying certain residues that should not be mutated does not affirmatively identify which of the many remaining variants within the claimed 93% identity genus are possessed. Excluding some residues from mutation does not provide written description support for all other possible variants encompassed by the claims.
Applicant further argues that 27 sequences having about 93%-99% identity to positions 1-75 of SEQ ID NO: 29 and about 94%-97% identity to positions 325-521 of SEQ ID NO: 29 were tested and described. This argument is not persuasive because even if certain tested sequences fall within the claimed identity ranges, the claims are not limited to those tested sequences. The claims cover any sequence meeting the identity thresholds and the recited substitution-position language. The specification does not demonstrate that the disclosed tested sequences are representative of the full genus now claimed.
Applicant also argues that one of ordinary skill in the art would understand that the mutations are in particular locations where mutations can be introduced. This argument is not persuasive because written description requires that the specification reasonably convey possession of the claimed invention, not merely that one of ordinary skill could perform additional alignment, mutation, screening, or optimization after reading the disclosure. The specification describes screening and optimization of particular biosensor candidates, which indicates that functional opioid biosensors were obtained through empirical selection rather than predictable possession of the entire claimed genus.
Further, claim 5 recites not merely a polypeptide structure but an opioid biosensor capable of undergoing a detectable conformational change upon binding to an opioid. Applicant’s arguments do not establish that the specification reasonably conveys possession of all 93% identity variants that would also satisfy this functional requirement. The specification supports possession of specific biosensors and specific mutation combinations, but not every structurally permitted variant that would be capable of the claimed opioid-binding conformational response.
Applicant’s arguments regarding claims 6-9, 12-15, 20, 24, 30, 37, and 44 are also not persuasive because these claims depend directly or indirectly from claim 5 and do not cure the written description deficiency. The dependent claims add opioid classes, identity ranges, particular mutation positions, reporters, nucleic acids, or devices, but they still rely on the unsupported broad genus of opioid biosensors recited in claim 5.
Accordingly, the written description rejection of claims 1, 5-9, 12-15, 20, 24, 30, 37, and 44 is maintained.
Claim Rejections under 35 U.S.C. § 112(b) — Indefiniteness
Applicant’s arguments with respect to claims 1, 5, 15, and 20 have been fully considered and are persuasive. The rejection of claims 1, 5, 15, and 20 under 35 U.S.C. § 112(b) has been withdrawn.
Specifically, claims 1 and 5 were amended to recite positions positionally equivalent to the listed positions of SEQ ID NO: 29, and claims 15 and 20 were amended to remove the term homologous. Accordingly, the prior indefiniteness concerns have been addressed.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/E.O./Examiner, Art Unit 1677
/BAO-THUY L NGUYEN/Supervisory Patent Examiner, Art Unit 1677 July 10, 2026
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