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 .
DETAILED ACTION
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 of RCE on October 9, 2025 and amendment after final filed October 9, 2025 has been entered. Claims 9-11, 14-15, 17 were canceled, claim 7 was amended and claims 1-8, 12-13, 16 are pending in the instant application.
The restriction requirement was deemed proper and made FINAL in a previous office action. Claims 1-6, 12-13 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention/species, there being no allowable generic or linking claim. After further review, claim 16 is hereby rejoined. Claims 7-8, 16 is examined on the merits of this office action.
Withdrawn Rejections
The sequence compliance objection is hereby withdrawn in view of amendment of claim 7 in the response filed October 9, 2025.
The objection to the specification is withdrawn in view of amendment of the specification filed October 9, 2025.
The objection to claim 7 is withdrawn in view of amendment of claim 7 filed October 9, 2025.
The rejection of claims 7-8 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or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention is withdrawn in view of amendment of the claims filed October 9, 2025.
Maintained/Revised Rejections
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 7-8, 16 are/remains rejected under 35 U.S.C. 103 as being unpatentable over Albert US20160178627 A1 (effective filing date 12/19/2014 (62/094495) and 11/25/2015 (62/260162), cited in Applicant’s IDS) in view of Andres (WO2012150321, cited previously) and Wenfang (WO2000043492 A2, cited previously).
*Please note, given the language of “at least partially replaced” the insert-in-flap domain can be completely replaced with the “Q-tag” or replaced in part (i.e. as little as one amino acid replaced with the sequence).
Albert discloses a kutzneria albida substrate comprising the sequence YRYRQ which is identical to instant SEQ ID NO: 1 (see Table 3). Albert Further discloses substrate peptide GGGYRYRQGGGG (see paragraph 0105, 0109, see also paragraph 0113). *Please note that claim 7 was amended to include “wherein the Q-tag comprises an amino acid sequence of 11 to 20 amino acid and comprises the peptide sequence G1-YRYR1-G2….wherein G1 and G2 are Gly Gly Gly”. The Q-tag and peptide sequence is open given the comprising language and thus, the Qtag can have greater than three glycine residues and is not limited to only three glycine residues on each terminus.
Albert further discloses a chimeric protein comprising the FKBP domain and the KalbTG recognition sequence (see paragraph 0106, lines 7-9, paragraph 0113). Albert further discloses labeling with a 10 fold excess of KalbTG K-tag-Cy3 and the substrate for labeling (see paragraph 0106, lines 1-11, which comprises an alkyl amine group). Albert further teaches grafting the Q-tag sequence into the FKBP domain of SlyD (see paragraph 0112) and wherein the SlyD is from E.coli (see SEQ ID NO:11, 0093). Regarding claim 7, Albert teaches wherein the QTAG was grafted on the FKBP domain of SlyD from Thermus thermophilus thus meeting the limitations of wherein the FKBP domain is from Thermus thermophilus (see SEQ ID NO:97) and is identical to instant SEQ ID NO:29 (of which SEQ ID NO:29 is identical to instant SEQ ID NO:54 found in instant claim 16). The sequence of Albert comprising SEQ ID NO:97 contains the Q-tag sequence within the Insert-in-flap domain (See SEQ ID NO:97). Albert further teaches wherein the label is biotin (see claim 4). Albert further teaches wherein the KalbTg comprises SEQ ID NO: 6 (see claim 16) which is identical to instant SEQ IDNO:23. Albert teaches that “These results confirm that KalbTG and S. mobaraensis MTG constitute a semi-orthogonal labeling system with unparalleled ease of use, yield, and efficiency. Accordingly, KalbTG may be useful for the industrial-scale synthesis of complex protein conjugates of interest in therapeutic or diagnostic applications” (see paragraph 0107, last 5 lines). Albert additionally teaches wherein the detectable label is biotin moiety, a fluorescent dye, a ruthenium label, a radiolabel, and a chemiluminescent label (see paragraph 0016 and claim 4). Albert further teaches that “The molecular chaperone SlyD is a useful scaffold for labeling approaches as epitope-containing loops can be grafted onto the FKBP domain for presentation to binders or enzymes” (see paragraph 0106).
Albert is silent to (i) attaching/grafting a peptide of interest to the TG substrate and at the c-terminus and then labeling with ruthenium containing chemiluminescent label and achieving a 1:1 ratio.
However, Andres teaches grafting a peptide immunogen to thermus thermophilus SlyD FKBP domain (see page 6 lines 10-15). Andres teaches that “The amino acid graft is presented by the Thermus thermophilus SlyD FKBP domain in a constrained, enthalpically favored way, which retains the native-like secondary structure of the IGF-1 insertion motif. This chimeric polypeptide is used as an immunogen for the immunization” (see page 6, lines 10-21). Take together, Andres teaches that grafting peptide sequences into the FKBP domain of Thermus thermophilus SlyD presents the inserted sequence in a constrained, native like conformation thereby retaining function and structural integrity. Furthermore, Andres additionally teaches that recombinant SlyD FKBP fusion constructs in which the insert in flap domain is replaced and additional sequences, including tags and heterologous protein inserts, are fused at the C-terminus of the SlyD scaffold (see page 24 for example, peptide tags at the c-terminus).
Wenfang teaches of modifying a protein to comprise a transglutaminase substrate for adding a detectable label via using a TG enzyme (see claims 1). Wenfang teaches “These methods modify proteins which have been labeled at a particular site by the reaction of a transglutaminase with a glutamine peptide sequence which has been engineered into the protein. The site-specific modification methods of the invention are useful for producing reagents useful in high throughput screening methods and in producing protein delivery vehicles for specifically targeting cellular and non-cellular targets. Also described are improved biotinylation reagents” (see abstract). Wenfang teaches wherein the label can be incorporated at the N or C-terminus of the protein (See Page 19, paragraph 0004 for example) and wherein the label can be Ruthenium tris bipyridyl which is luminescent label. Wenfang teaches wherein the protein of interest is an antibody. Taken together, Wenfang teaches that proteins engineered to comprises a transglutaminase substrate can be site specifically labeled with detectable labels, including ruthenium containing chemiluminescent labels, thereby providing a motivation to apply transglutaminase labeling chemistry to engineered substrates such as those taught by Albert.
It would have been obvious before the effective filing date of the claimed invention to include a protein of interest (including an immunogenic peptide or antibody) to the TG substrate of Albert (the SlyD FKBP domain of SEQ ID NO:97/98) as taught by Andres for labeling of the protein of interest with a ruthenium containing label.
One of ordinary skill in the art would have been motivated to do so given that incorporation of a TG substrate to a protein of interest is an easy, effective way of labeling a protein of interest for therapeutic/diagnostic purposes. One of ordinary skill in the art would have been further motivated giving that attaching the immunogenic peptide to SlyD in a constrained, enthalpically favored way, which retains the native-like secondary structure of immunogenic protein and affective at creating an immune response. There is a reasonable expectation of success given that Albert specifically teaches use of the KalbTG substrates for labeling via a KalbTG reaction and states that including immunogenic peptides are encompassed by the invention and Wenfang teaches effective labeling of a fusion peptide of interest comprising a substrate for TG (see Examples 1 and 2).
Furthermore, one of ordinary skill in the art would have been further motivated to attach the protein of interest at the C-terminal end of the SlyD FKBP domain of Albert. Andres teaches slyD fusion constructs in which heterologous sequences are appended at the C-terminus, including constructs in which internal regions (IF domains) are modified are replaced. These teaching demonstrate that C-terminal fusion to SlyD scaffolds is a conventional structurally compatible configuration.
Albert teaches placement of the Q tag within the IF domain of the FKBP scaffold, thereby localizing the site of TG mediated labeling internally within the SlyD domain. In view of this teaching, one of ordinary skill in the art would have recognized that attaching the protein of interest at the C-terminus spatially separates the site of labeling from the site of protein attachment, thereby reducing interference and enabling labeling efficiency. Selecting the C-terminus as the attachment site thereof represents a predictable design choice that works with Albert’s internal Qtag labeling strategy with the established C-terminal fusion approaches taught by Andres (see MPEP 2141 III(A) and (E)), KSR int’l Co. V. Teleflex Inc. 550 US 398 (2007)). Accordingly, attaching the protein of interest/heterologous peptide to the C-terminus of the SlyD FKBP domain would have been obvious to one of ordinary skill in the art with a reasonable expectation of success.
Furthermore, claim 7 does not require that the protein of interest be positioned at the C-terminus of the FKBP domain. The recited general formula (F*-L)y-X is open-ended and does not preclude additional FKBP domain sequence following X, nor does it require that X be terminally positioned. Accordingly, the claim encompasses embodiments in which the protein of interest is positioned downstream of the Q-tag within an FKBP domain context, including constructs in which FKBP domain sequence remains present after the protein of interest. Such arrangements are rendered obvious by the combined teachings of Albert, Andres, and Wenfang, which collectively demonstrate that FKBP domains tolerate insertions and fusions and that transglutaminase-mediated labeling occurs predictably at the Q-tag.
Regarding claim 8, Albert teaches wherein the KalbTG is recombinantly produced (see paragraph 0059).
Regarding the ratio of label and protein of interest in instant claim 7, Albert teaches that “Factors that can be varied for labeling experiments include the ratio of substrate to transglutaminase enzyme, the ratio of one substrate to another substrate, the labelling time, pH, or the like. Notably, a substrate refers to any peptide, protein, or other structure including one or more amine-donor or acyl-donor substrates sequences” (see paragraph 0075). The ratio of the substrate-protein of interest and label is considered a result effective variable. Therefore, it would be obvious to one of ordinary skill in the art to optimize the ratio of the label and the substrate comprising the protein of interest to achieve optimal labeling. The MPEP states the following: Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical. “[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.” In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955) (Claimed process which was performed at a temperature between 40°C and 80°C and an acid concentration between 25% and 70% was held to be prima facie obvious over a reference process which differed from the claims only in that the reference process was performed at a temperature of 100°C and an acid concentration of 10%.); see also Peterson, 315 F.3d at 1330, 65 USPQ2d at 1382 (“The normal desire of scientists or artisans to improve upon what is already generally known provides the motivation to determine where in a disclosed set of percentage ranges is the optimum combination of percentages.”); In re Hoeschele, 406 F.2d 1403, 160 USPQ 809 (CCPA 1969) (Claimed elastomeric polyurethanes which fell within the broad scope of the references were held to be unpatentable thereover because, among other reasons, there was no evidence of the criticality of the claimed ranges of molecular weight or molar proportions.). For more recent cases applying this principle, see Merck & Co. Inc. v. Biocraft Laboratories Inc., 874 F.2d 804, 10 USPQ2d 1843 (Fed. Cir.), cert. denied, 493 U.S. 975 (1989); In re Kulling, 897 F.2d 1147, 14 USPQ2d 1056 (Fed. Cir. 1990); and In re Geisler, 116 F.3d 1465, 43 USPQ2d 1362 (Fed. Cir. 1997). There is a motivation to optimize since it is normal desire of scientists or artisans to improve upon what is already generally known with a reasonable expectation that optimization would at least work the same. Furthermore, Wenfang teaches a ratio of about 1:1 when labeling the peptide (see Examples 2 and 4). Furthermore, the combined references of Albert, Andres and Wenfang teach the same method of the instant claims, including labeling via a transglutaminase reaction and Albert teaches successful labeling of the SlyD Q-tagged construct and thus, the effects of 1:1 ratio of label to protein of interest would be achieved inherently.
Response to Applicant’s Arguments
Applicants argue “ It is Applicant's understanding that the Office Action is of the opinion that the present formula (I) recited in claim 7 does not reflect the differentiating features on which Applicant's last response relies. Applicant respectfully traverses. As previously argued, the cited references do not teach the recited formula (I) in claim 7. Primary reference Albert references secondary reference Andres for teaching a method of grafting. However, Andres teaches that a protein of interest is grafted into the IF domain of the Thermus thermophilus SlyD having a structural representation as FN-ter -X-FC-ter. In contrast, the structure of formula (I) in claim 7 is (F*-L)y-X. The technique taught by Andres and Albert results in a different protein-substrate attachment than that required in amended claim 7, which a person skilled in the art would have no motivation to deviate from. Further, Neither Albert nor Andres suggest or provide motivation to one of ordinary skill in the art to modify their respective teachings to arrive at Applicant's formula (I). Turning to Wenfang does not cure the deficiencies of Albert and Andres.
For the reasons discussed herein, Applicant respectfully submits the Office Action has failed to establish that the cited references render claim 7 and 8 unpatentable under the standard set forth above. Applicant respectfully requests the Examiner withdraw this Section 103 rejection of claims 7 and 8.
Applicants arguments have been fully considered but not found persuasive.
In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., peptide of interest being at the C-terminus, i.e. a different protein attachment) is not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
It is important to note that the general formula I is open. Thus, there is no requirement that the protein of interest be at the c-terminal end of the FKBP domain. The requirement is that the FKBP domain (F*) with an IF region at least partially replaced with a X-tag is attached to X, optionally through a linker. Thus, the protein of interest being embedded within the IF domain of the FKBP domain along with the Q-tag in this order meets the limitations of claim 7 (i.e. FKBP- (part of the IF domain)Q-tag-protein of interest-further FKBP sequence).
Nevertheless, as stated in the above rejection, it would have been obvious before the effective filing date of the claimed invention to include a protein of interest (including an immunogenic peptide or antibody) to the TG substrate of Albert (the SlyD FKBP domain of SEQ ID NO:97/98) as taught by Andres for labeling of the protein of interest with a ruthenium containing label.
One of ordinary skill in the art would have been motivated to do so given that incorporation of a TG substrate to a protein of interest is an easy, effective way of labeling a protein of interest for therapeutic/diagnostic purposes. One of ordinary skill in the art would have been further motivated giving that attaching the immunogenic peptide to SlyD in a constrained, enthalpically favored way, which retains the native-like secondary structure of immunogenic protein and affective at creating an immune response. There is a reasonable expectation of success given that Albert specifically teaches use of the KalbTG substrates for labeling via a KalbTG reaction and states that including immunogenic peptides are encompassed by the invention and Wenfang teaches effective labeling of a fusion peptide of interest comprising a substrate for TG (see Examples 1 and 2).
Furthermore, one of ordinary skill in the art would have been further motivated to attach the protein of interest at the C-terminal end of the SlyD FKBP domain/Qtag of Albert. Andres teaches slyD fusion constructs in which heterologous sequences are appended at the C-terminus, including constructs in which internal regions (IF domains) are modified are replaced. These teaching demonstrate that C-terminal fusion to SlyD scaffolds is a conventional structurally compatible configuration.
Albert teaches placement of the Q tag within the IF domain of the FKBP scaffold, thereby localizing the site of TG mediated labeling internally within the SlyD domain. In view of this teaching, one of ordinary skill in the art would have recognized that attaching the protein of interest at the C-terminus spatially separates the site of labeling from the site of protein attachment, thereby reducing interference and enabling labeling efficiency. Selecting the C-terminus as the attachment site thereof represents a predictable design choice that works with Albert’s internal Qtag labeling strategy with the established C-terminal fusion approaches taught by Andres (see MPEP 2141 III(A) and (E)), KSR int’l Co. V. Teleflex Inc. 550 US 398 (2007)). Accordingly, attaching the protein of interest/heterologous peptide to the C-terminus of the SlyD FKBP domain would have been obvious to one of ordinary skill in the art with a reasonable expectation of success.
Furthermore, claim 7 does not require that the protein of interest be positioned at the C-terminus of the FKBP domain. The recited general formula (F*-L)y-X is open-ended and does not preclude additional FKBP domain sequence following X, nor does it require that X be terminally positioned. Accordingly, the claim encompasses embodiments in which the protein of interest is positioned downstream of the Q-tag within an FKBP domain context, including constructs in which FKBP domain sequence remains present after the protein of interest. Such arrangements are rendered obvious by the combined teachings of Albert, Andres, and Wenfang, which collectively demonstrate that FKBP domains tolerate insertions and fusions and that transglutaminase-mediated labeling occurs predictably at the Q-tag.
New Objections
Claim 7 is objected to for the following informality: the limitation of “an insert in flap” (IF) domain should be replaced with “the [[an]] “insert-in-flap” (IF) domain” in line 7.
Claim 7 is objected to for the following informality: the limitation of “an FKBP domain” should be replaced with “the [[an]] FKBP domain” in line 13.
Claim 7 is objected to for the following informality: the limitation of “(SEQ IDNO. 29)” should be replaced with –(SEQ ID NO: 29)-.
Claim 7 is objected to for the following informality: the limitation of “providing an effective amount of the transglutaminase of Kutzneria albida, according to SEQ ID NO:23” should be replaced with -“providing an effective amount of the transglutaminase of Kutzneria albidacomprising SEQ ID NO:23”
Claim 7 is objected to for the following informality: the limitation of “wherein said transglutaminase attaches said label to said substrate…” should be replaced with - wherein said transglutaminase attaches said label to said recombinant TG substrate…
Claim 8 is objected to for the following informality: the limitation of Kutzneria albida should be replaced with Kutzneria albida.
New Rejection-Reinstated rejection
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.
Claims 7-8, 16 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
MPEP § 2163 states that the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus.
Scope of the claims
The claims are “An in vitro method for labelling a protein of interest, comprising
a) providing a recombinant transglutaminase (TG) substrate being attached to a protein of interest, wherein the recombinant transglutaminase (TG) substrate is according to the following general formula I (F*-L)y-X Formula (I)
wherein F* is an FKBP domain of a Thermus thermophilus SlyD polypeptide, wherein an "insert-in-flap" (IF) domain of the FKBP domain of the Thermus thermophilus SlyD polypeptide is at least partially replaced with a Q-tag, wherein the Q-tag comprises an amino acid sequence of 11 to 20 amino acids, and comprises the peptide sequence G1-YRYRQ (SEQ ID NO: 30) -G2,wherein sections of the FKBP domain of the Thermus thermophilus SlyD polypeptide of F* that are not replaced with the Q-tag comprise an amino acid sequence that is at least 95% identical to the corresponding sections of an amino acid sequence of an FKBP domain of a thermus thermophilus SlyD polypeptide (SEQ ID NO. 29),
L is absent or is a linker amino acid sequence; and X is a protein of interest attached thereto selected from the group consisting of an enzyme, an antigen, an antibody or fragment thereof and other immunological binding partners; y is an integer of between 1 and 100; G1 is Gly Gly Gly; and G2 is Gly Gly Gly b) providing an effective amount of the transglutaminase of Kutzneria albida, according to SEQ ID NO: 23,c) providing a suitable label comprising an alkyl-amine group, wherein said label is a Ruthenium containing chemiluminescent label, and contacting said components according to a) to c), whereby said transglutaminase attaches said label to said substrate, wherein said labelling is achieved in a stoichiometric ratio of label and protein of interest at about 1:1.
Given the language of “at least partially replaces” the insert-in-flap domain can be completely replaced with the “Q-tag” thus the peptide not having an insert-in-flap domain. With the FKBP peptide having an “insert in flap” domain, the Q-tag can partially replace the insert in flap domain meaning that domain can be completely replaced (missing) or the Q-tag can be replaced part of the sequence (an amino acid stretch of the domain as low as one amino acid missing with the Q-tag inserted). Thus, the requirements of the claim are that the FKBP has at least 95% identical to Thermus Thermophilus SlyD SEQ ID NO:29 it the sequence that is not replaced by the Q-tag.
The possibilities are vast for Thermus Thermophilus SlyD polypeptides given the claim encompasses any sequence 95% identical to Thermus Thermophilus SlyD polypeptide and applicants provide little guidance regarding what structure/amino acid sequence is required of the SlyD peptide for having activity as a substrate of specifically Kutzneria albida TG (SEQ ID NO :23). For example, the SlyD FKBP domain of Thermus Thermophilus is 149mer peptide (of which the insert in flap domain is 20-30 amino acids). If one amino acid is replaced with the Q-tag, the remaining sequence having at least 95% sequence identity could be up to 7 amino acids different (plus the inclusion of the Q-tag).
Applicants have not shown that ANY sequence of the FKBP domain (including variants of FKBP of Thermus Thermophilus SlyD) and what portions of the insert-in-flap domain of SlyD would have the desired function. The Q-tag defined embedded into the Thermus Thermophilus SlyD peptide is not sufficient structure to show that any peptide having at least 95% sequence identity (outside the Qtag) to the peptide having this tag would be a substrate for kutzneria albida/ TG and be capable of labeling a protein of interest. Importantly, the phrase “at least partially replaced” encompasses a broad continuum of embodiments including but not limited to: replacement of a single amino acid of the IF domain, replacement of multiple contiguous or non contiguous residues, replacement of majority of the domain and complete replacement. The claim further recites “immunological binding partners”. As claimed, this term encompasses a broad genus of molecules that bind on another in the context of the immunes system, potentially including, but not limited to antibodies, antibody fragments, antigens, immune receptors, ligands involved in immune recognition and immune derived binding pairs. However, the specification does not demonstrate possession of this full genus. The disclosure is limited, at most, to specific exemplary binding proteins and odes not described or exemplify a representative number of immunological binding partner across the scope encompassed by the claims Nor does the specification identify common structural features or provide a disclosed correlation between structure and immunological binding function that would allow a person of ordinary skill in the art to recognize that the inventors were in possession of all immunological binding partners encompassed by the claims.
Therefore, to meet the written description requirement of 35 U.S.C. § 112, first paragraph, the specification must disclose a representative number of species that meet both the structural and functional limitations of the genus or the specification and/or the prior art must identify the structural elements that correlate to the claimed function in a manner that demonstrates to one of ordinary skill in the art that Applicant was in possession of the claimed genus at the time the application was filed. In the instant case, the specification must establish which of the vast number of peptide sequences encompassed by the claims that satisfy the structural limitations of the claim are also able to be a substrate specifically for Kutzneria albida TG for attaching a label to said substrate and a scaffold for a protein of interest.
Actual Reduction to Practice
MPEP § 2163 states that the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice. A “representative number of species” means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus.
The specification demonstrates reduction to practice for only a narrow subset of the claimed scope. In particular, Applicants disclose specific FKBP scaffolds derived from Thermus thermophilus SlyD (no variants); Insertion or replacement of a substantial portion of the IF domain with a defined Q-tag sequence (e.g., YRYRQ-based motifs); Q-tag insertions that are flanked by long glycine-rich linker sequences, a limited set of fusion architectures, such as SlyD-Q-tag-gp21 and SlyD-Q-tag-SlpA constructs; and demonstrated TG-mediated labeling (e.g., biotin or ruthenium labels), often achieving approximately 1:1 labeling stoichiometry.
The examples consistently involve large, contiguous insertions replacing a substantial portion of the IF domain and do not demonstrate minimal or incremental IF-domain replacements or variants of the FKBP with less than 100% sequence identity to SEQ ID NO:29.
One of ordinary skill in the art would not consider the examples provided in the instant specification to be representative of the full scope of the claimed genus.
Therefore, the instant specification has failed to meet the written description requirement by actual reduction to practice of a representative number of species alone.
Sufficient relevant identifying characteristic
MPEP § 2163 states that the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination thereof.
As stated above, the complete structure of SlyD FKBP domain from specific bacterial species with the Q-tag YRYRQ is disclosed.
The sequence RYRQ was grafted into the SlyD sequence of SEQ ID NO: 29 (see pages 17-18) yielding instant SEQ ID NO: 52. A similar Q-tag construct was tested comprising slyD Q-Tag gp21 fusion (see figure 3B, insertion between 65-122 of SlyD). A further labeling assay was done with a recombinant fusion between the chaperone SlyD and gp21 and SlpA (see page 19). Figures 5-6 shows labeling efficacies with these constructs. Thus, all the examples reduced to practice where using the slyD FKBP domain from Thermus thermophilus with insertion of the Q-tag (RYRQ) which is not representative of the scope of the claims which encompasses any sequence having at least 95% sequence identity to SEQ ID NO:29 (Thermus Thermophilus SlyD polypeptide). The specification does not identify which residues outside the IF domain may be substituted while retaining function, how many substitutions are tolerated, any structural rules correlating substitutions outside the Q-tag region with preserved folding or labeling activity. Although the claims can permit FKBP domains having as low as 95% sequence identity outside the Qtag region, the specification provides no examples, guidance or representative species demonstrating possession of said variants.
Physical and/or chemical properties:
The data do not suggest the physical basis for the claimed activity and therefore do not describe which substitutions, deletions or additions could be made while preserving the ability to be a Kutzneria albida substrate, labeling of a protein of interest and be capable of being labeled using a Kutzneria albida substrate. Understanding the physical basis for the claimed activity is critical to determining which of the sequences that meet the structural requirements of the genus also meet the functional requirements of the genus. Given the size of the FKBP domain, the greater than equal 95% identity limitation permits multiple amino acid substitutions outside the Q-tag region. Even a small number of substitutions (5-7) may significantly affect folding, stability and enzymatic presentation. The specification does not provide structural analyses, stability data, comparative functional data or even biophysical characterization for FKBP variants having substitutions outside the Q-tag region. Thus, the physical properties of the claimed variants have not been described.
Functional characteristics when coupled with a known or disclosed correlation between function and structure:
The specification does not describe a general correlation between structure and function for the claimed genus. The role of the amino acids in the Thermus Thermophilus SlyD polypeptide regarding TG substrate activity is not sufficiently described. As a result, it is impossible to predict, based on the specification, how changing any position of the domain will affect the ability of the peptide to be an effective substrate of specifically Kutzneria albida TG and labeling reactions.
The specification asserts that the IF-domain modification “does not substantially interfere” with FKBP structure or function. However, these statements are supported only for constructs in which: the FKBP sequence outside the Q-tag region is unchanged, and the Q-tag insertion is buffered by glycine rich spacers. The specification does not disclose any structure function correlation demonstrating that FKBP domains with additional amino acid substitutions outside the Qtag region retain folding, transglutaminase accessibility or labeling efficiency. The specification does not demonstrate possession of FKBP variants having less than 100% sequence identity outside the Q-tag region that achieve the claimed function.
Method of Making
The specification teaches methods for making specific exemplified FKBP-Q tag constructs, including recombinant expression and insertion of Q tag sequences at defined IF domain locations. However, the specification does not teach how to make FKBP variants having substitutions outside the Qtag region, up to 5% divergence from the native FKBP sequence while retaining the claimed function. Accordingly the disclosed methos does not demonstrate possession of the full scope of the claimed genus.
Conclusion
In conclusion, the specification demonstrates possession of specific FKBP-Q tag fusion constructs in which the FKBP domain outside the Q-tag region remains 100% identical to the native Thermus Thermophilus SlyD FKBP sequence. However, the claims encompass a broader genus of FKBP variants permitting up to 5% sequence divergence outside the Q tag region, as well as any degree of partial IF domain replacement. Because the specification provides lack of examples, guidance or representative species demonstration possession of FKBP variants having less than 100% identity outside the Q tag region, it does not reasonably convey to a person or ordinary skill in the art that the invention was in possession of the full scope of the claimed invention at the time of filing as require by 35 U.S.C. 112(a). Furthermore, regarding immunological binding partners, while the claims broadly encompass any two molecules that binding and are associated with the immune system, the specification fails to reasonably convey possession of the full scope of immunological binding partners as claimed.
New Rejection
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 16 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 16 is indefinite. SEQ ID NO:54 is identical to SEQ ID NO:29 which is recited in instant claim 7 as the FKBP domain prior to insertion of the Q-tag. It is unclear whether SEQ ID NO:54 represents the FKBP domain prior to insertion of the Q-tag,the FKBP domain after insertion of the Q-tag or the FKBP domain sequence outside of the Q-tag. As a result the scope of the FKBP domain recite in claim 16 cannot be determined with reasonable certainty.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 16 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 16 is dependent on claim 7. Claim 16 claims an FKBP domain comprised by SEQ ID NO:54 (which is identical to instant SEQ ID NO:29), which does not include the Q-tag insertion required by claim 1. Claim 16 therefore fails to further limit claim 7 and instead removes a limitation required by the base claim.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Conclusion
No claims are allowed.
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/ERINNE R DABKOWSKI/Examiner, Art Unit 1654