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 .
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 28 April 2025 has been entered.
Restriction/Election Response
Applicant’s election without traverse of Group I (i.e., claims 1, 4-8, 10, 12, 16, 20-22, 40, 51, and 56-58), Species A (i.e., cell surface protein as the binding target), and Species B (i.e., O-GlcNAc transferase (OGT)) in the reply filed on 17 May 2024 is acknowledged.
Status of the Claims
Claims 1-59 were originally filed 28 April 2021. The preliminary amendment filed 15 November 2021 has been acknowledged and entered.
Claims 12, 16, 22, 29, 30, 35, and 36 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected Group or Species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 17 May 2024.
Currently, claims 1, 8, 10, 20, 21, 40, 51, 56-58, and 60 are under consideration.
Withdrawn Objections
In view of Applicant amending claim 40 the claim objection is hereby withdrawn.
Withdrawn Rejections
In view of the Declaration under 37 C.F.R. § 1.130(a) on 28 April 2025 the 35 U.S.C. 102(a)(1) rejection of claims 1, 8, 20, 21, and 51 over Ramirez (as cited on the PTO-892 dated 08/01/2024) and the 35 U.S.C. 103 rejection of claims 56-58 over Ramirez and Khan (as cited on the PTO-892 dated 08/01/2024) are hereby withdrawn.
In view of Applicant’s arguments the U.S.C. 103 rejections of i. claims 1, 8, 10, 20, 21, 58, and 60 are rejected under 35 U.S.C. 103 as being unpatentable over Schumacher (as cited on the PTO-892 dated 08/01/2024) and Ong (see Ong et al. (2018) as cited on the IDS mailed 17 May 2024), ii . claims 56 and 57 over Schumacher, Ong and in further view of Khan, and iii. Torgov (see Torgov as cited on the PTO-892 dated 01/28/2025) and Smolarek (as cited on the PTO-892 dated 01/28/2025) are hereby withdrawn.
Maintained Objections
Specification
The amendment filed 1 November 2024 is objected to under 35 U.S.C. 132(a) because it introduces new matter into the disclosure. 35 U.S.C. 132(a) states that no amendment shall introduce new matter into the disclosure of the invention. The added material which is not supported by the original disclosure is as follows:
The specification now recites, “NANOBODY® (single, variable domain, heavy chain antibody)” throughout the specification (e.g. see specification para [0006 and 0007]). A single, variable domain, heavy chain expands the scope of the original disclosure. The specification defines a “nanobody” as a small protein recognition domain, the smallest antigen binging fragment or single variable domain derived from naturally occurring heavy chain antibody from camelids or sharks (see specification dated 04/28/2021 pg. 9 para [0046]). In addition, the specification discloses single variable domain heavy chain antibody is a nanobody or a VHH antibody (see specification dated 04/28/2021, pg. 9 para [0046]). A single, variable domain, heavy chain antibody broadens the scope of the original disclosure as the term includes, for example, heavy chain only variable domains derived from humans. The original disclosure did not contemplate single domain antibodies beyond single heavy chain only variable domains derived from camelids and sharks.
In is noted the specification sets forth a “common rigid linker (EAAAK)4” (see specification pg. 72 para [00156]) without a corresponding sequence identifier.
Applicant is required to cancel the new matter in the reply to this Office Action.
Maintained Claim Rejections
Claim Rejections - 35 USC § 112(a)
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.
New Matter
Claims 1, 8, 10, 20, 21, 40, 51, 56-58, and 60 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 has been amended to recite, “a single, variable domain, heavy chain antibody” in lines 1-2.
Claims 1, 10, and 20 are drawn to a fusion protein comprising a single, variable domain, heavy chain antibody and a glycan modifying enzyme.
The specification does not disclose or contemplate a genus of fusion proteins comprising a single, variable domain, heavy chain antibody (see specification pg. 10 para [0048]). A single, variable domain, heavy chain antibody expands the scope of the original disclosure. The specification defines a “nanobody” as a small protein recognition domain, the smallest antigen binging fragment or single variable domain derived from naturally occurring heavy chain antibody from camelids or sharks (see specification dated 04/28/2021 pg. 9 para [0046]). In addition, the specification discloses single variable domain heavy chain antibody is a nanobody or a VHH antibody (see specification dated 04/28/2021, pg. 9 para [0046]). The original disclosure did not contemplate single, variable domain, heavy chain antibodies beyond those derived from camelids and sharks. A single, variable domain, heavy chain antibody broadens the scope of the original disclosure as the term includes, for example, heavy chain only variable domains derived from humans. Therefore, reciting a genus of single, variable domain, heavy chain antibodies is new matter that reaches beyond the specification as originally filed because the specification never contemplated the particular subgenus encompassed by the claim language.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim 1 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of copending Application No. 18/030,245 (referred to herein as ‘245 application). Although the claims at issue are not identical, they are not patentably distinct from each other.
Applicant's arguments filed 28 April 2025 have been fully considered but they are not persuasive.
Applicant argues as the non-statutory obviousness-type double patenting rejection is the only remaining rejection and in light of a later filing date the rejection should be withdrawn (see Remarks pg. 14, last para). However, the non-statutory obviousness-type double patenting rejection is not the only remaining rejection. Therefore the non-statutory obviousness-type double patenting rejection of claim 1 is hereby maintained.
Claims 56 and 57 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of copending Application No. 18/030,245 (referred to herein as ‘245 application) in view of Schumacher and Ong.
Applicant's arguments filed 28 April 2025 have been fully considered but they are not persuasive.
Applicant argues as the non-statutory obviousness-type double patenting rejection is the only remaining rejection and in light of a later filing date the rejection should be withdrawn (see Remarks pg. 15, 2nd para). However, the non-statutory obviousness-type double patenting rejection is not the only remaining rejection. Therefore the non-statutory obviousness-type double patenting rejection of claims 56 and 57 is hereby maintained.
The following are new grounds of rejection.
Claim Rejections - 35 USC § 112(a)
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 1, 8, 10, 20, 21, 40, 51, 56-58, and 60 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Factors to be considered in determining whether undue experimentation is required to practice the claimed invention are summarized in In re Wands (858 Fed 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988)). The factors most relevant to this rejection are the scope of the claim, the amount of direction or guidance provided, limited working examples, the unpredictability in the art and the amount of experimentation required to enable one of skill in the art to make and use the claimed invention.
Breadth of the Claims
Claim 1 is drawn to a fusion protein comprising any single, variable domain, heavy chain antibody that binds to any target in any location on said target and either OGT or OGA. Dependent claims 8, 20, 21, 51, 56-58, and 60 further limit the structure to the catalytic domain, number of TPR domains present, polynucleotides encoding, vector comprising, and a cell comprising the same.
Claim 10 is drawn to a single, variable domain, heavy chain antibody which binds a “cell surface protein”. The specification does not provide a limiting definition for “a cell surface protein”. The broadest reasonable interpretation of “a cell surface protein” includes proteins anchored to the plasma membrane (i.e., cell surface) as evidenced by (see Cooper GM. (2000) The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates; Chapter 12, The Cell Surface; see MPEP § 2111).
Claim 40 is drawn to a method of administering a fusion protein comprising a single, variable domain, heavy chain antibody fused to OGT or OGA to a subject.
Amount of Direction or Guidance Provided
Applicant’s disclosure teaches over 15% of the cellular proteome is post-translationally modified by O-GlcNAc (see specification pg. 1 para [0003]). This post-translational modification O-GlcNAc consists of a single glucosamine monosaccharide attached to serine or threonine residues of nuclear, cytosolic, and mitochondrial proteins (see specification pg. 1 para [0003]). O-GlcNAc modification is regulated via two enzymes OGT and OGA (see specification pg. 2 para [0005]). OGT has a catalytic domain connected to a TPR domain which is the primary mechanism for substrate selection (see specification pg. 2 para [0005]). The specification discloses the “parameters that dictate how these enzymes dynamically regulate thousands of O-GlcNAc modification sites on various substrates is still under investigation” (see specification pg. 3 para [0005]). Global changes in O-GlcNAc are challenging to relate to specific glycoproteins whereas protein-specific studies prevent analysis of competing post-translational modification pathways, require knowing the exact glycosite, and are laborious (see specification pg. 2 para [0004]). Protein-specific studies are possible by mutagenesis of transfected proteins to remove the glycosite or via total synthesis of the O-GlcNAcylated protein in vitro (see specification pg. 2 para [0004]). There is an ongoing need for a general method to control glycosylation on specific target proteins in order to systematically evaluate O-GlcNAc function in cells (see specification pg. 2 para [0004]).
Working Examples
Applicant demonstrates a GFP or EPEA NANOBODY® (i.e., nGFP, nEPEA (4 amino acid tag)) fused to full-length OGT with 13 (i.e., nGFP(13), nEPEA(13)) or 4 (i.e., nGFP(4), nEPEA(4)) TPRs fused via a rigid linker (i.e., Seq ID No: (EAAAK)4) were transfected into cell lines (e.g., HEK293T) expressing a GFP fused JunB (e.g., GFP-Flag-JunB-EPEA) (see specification pg. 3 para [0007], pg. 72 para [00156], figure 2A). Applicant’s measured changes in O-GlcNAc via the metabolic reporter, Ac4GalNAz, which leads to glycan-specific enrichment and quantification by Western blot, determination of O-GlcNAc protein occupancy by mass-shift PEG-5kDa assays (see specification pg. 73 para [0158]). Using the nGFP(13)-FLAG-JunB-EPEA resulted in increases in O-GlcNAc levels on the target protein that was dependent on the co-transfected with nGFP(13) (see specification pg. 3 para [0007], pg. 72 para [00156], figure 2A pg. 73 para [00158, 00159] figure 2C). Applicant notes, nGFP(13) targeting JunB also equivalently elevated global O-GlcNAc levels and suggests the selectivity for the target protein could be further improved (see specification pg. 73 para [00159], figure 2F). The nGFP(4) and nEPEA(4) (i.e., 4 TPRs) constructs significantly increased the O-GlcNAcylated target relative to the untargeted controls (see specification pg. 73 para [00160], Figure 3C). Truncation of the number of TPRs attenuated the global increase in O-GlcNAc while the single, variable domain, heavy chain antibody improved proximity direction for the desired target protein (see specification pg. 74 para [00161], Figure 3F). Similarly, increases in O-GlcNAcylated target proteins, JunB-Flag-EPEA, cJun-Flag-EPEA, and Nup62-Flag-EPEA were also observed (see specification pg. 74 para [00162]). Applicant’s demonstrate the fusion proteins can target various classes of intracellular targets (e.g., transcription factors, kinases, oxidoreductase) (see specification pg. 75 para [00165]). Applicant also demonstrates particular glycosylation sites may be affected by the particular number of TPRs (see specification para spanning pgs. 77-78). For example, glycosite S85 of the JunB-Flag-EPEA was identified using only the nGFP(13) and not nEPEA(4) (see specification pg. 78 para [00170]). In a second example, Applicant’s show the number of TPRs affect the subcellular localization of TET3 wherein nEPEA-OGT(13) showed a distinct transition of TET-3-Flag-EPEA from the nucleus to the cytoplasm while coexpression with nEPEA-OGT(4) localized in the nucleus (see specification pg. 81 para [00177]). It is noted the nEPEA was originally developed against α-synuclein and recognizes the c-terminal region (see specification pg. 72 para [00157], pg. 80 para [00175]). Applicant’s demonstrate HEK273T cells transfected with nEPEA-OGT(4.5) reduces endogenous α-synuclein and similar results were observed with nEPEA(13), nEPEA(4), and nEPEA with the TPR domain alone (see specification pg. 82 para [00179, 00180, figures 7-10).
With respect to claim 1, there is no evidence from the disclosure that fusion proteins that bind i. an extracellular target, ii. the extracellular region of a membrane bound target, iii. a location on the endogenous protein aside from the c-terminal region of α-synuclein, iv. proteins not already confirmed binding partners of OGT, nor v. comprising flexible, cleavable, nor alternative rigid linkers were made and used. Applicant has not provided guidance nor a representative number of species of binding to any location on the breadth of targets without affecting glycosylation nor downstream protein-protein interactions aside from the single example of reduced aggregation of α-synuclein which naturally comprises the EPEA amino acid sequence in the c-terminal region. For example, Applicant shows increased glycosylation of TET3 resulted in changes in localization; however, it was known in the art that antibodies do not release their target antigen and thus unclear how the single complex comprising both the TET3::EPEA and nEPEA::OGT may affect downstream TET3 protein interactions.
With respect to claim 40, there is no evidence from the disclosure that fusion proteins of claim 1 nor any kind were administered to any subject by any means.
The State of the Art/Predictability
The state of the art teaches it would be highly unpredictable to target the following: i. an extracellular target an ii. any location on any target.
First, there is “no evidence for O-GlcNAc on the regions of polypeptides that reside on the outside of the cells or within luminal compartments” (see Hart and Akimoto (2009) Chapter 18: The O-GlcNAc Modification. Essentials of Glycobiology 2nd Edition. Cold Springs Harbor (NY), in particular pg. 2, purple highlight). Second, OGT catalyzes the addition of N-acetylglucosamine from UDP-GlcNAc to specific serine or threonine residues to form a β-glycosidic linkage (see Hart and Akimoto pg. 8, 1st para). UDP-GlcNAc is generated through the intracellular hexosamine biosynthetic pathway (see Hart and Akimoto pg. 8, 2nd para; see Sunden et al. (2023) Enzymatic assay for UDP-GlcNAc and its application in the parallel assessment of substrate availability and protein O-GlcNAcylation. Cell Reports Methods 3, 100518, graphical abstract; see Ong pg. 1 last para). Thus, the substrate for glycosylating is produced intracellularly and there are no known extracellular targets, bound or unbound, with this particular type of glycosylation.
The state of the art and Applicant’s own working examples teach it would be highly unpredictable to use the claimed invention given accessory proteins and TPRs can effect whether a target protein is glycosylated at a particular site or at all.
Hart and Akimoto disclose OGT has only a single catalytic subunit yet exists within the cell as a multitude of different holoenzymes in which the catalytic subunit is noncovalently bound to a myriad of accessory proteins which, in turn, control the targeting specificities (see Hart and Akimoto pg. 7 last para). This is in line with Applicant’s results which demonstrate changes in the number of TPRs can affect the particular sites glycosylated by OGT (see specification pg. 78 para [00172]). Furthermore, the TPRs act as a scaffold for interacting substrates with substantial binding plasticity and are susceptible to posttranslational modifications that can effect activity (see Ong pg. 3, 1st col. 3rd para). Ong teaches,
“Comparatively, the functions and implications of OGA posttranslational modifications have been less well-studies. OGA can be O-GlcNAcylated at serine 405 and act as a substrate of OGT; however, the implications of O-GlcNAcylation of OGA are unexplored” (see Ong pg. 3, 2nd col. 2nd para).
A person of ordinary skill in the art would understand OGT activity is affected by both the structure of OGT and the accessory proteins present.
The state of the art also teaches targeting OGT to specific proteins is highly unpredictable.
All of O-GlcNAcylation is dependent on two enzymes alone OGT and OGA and global increases in OGT activity would have far reaching consequences for cellular activity. Applicant’s own work suggests even with a targeted OGT there can still be global increases in glycosylation making it difficult to protein specific consequences (see specification pg. 73 para [00159]). Specifically the state of the art teaches,
“A better understanding of the mechanisms of OGT/OGA action would enable us to derive therapeutic benefits of resetting cellular O-GlcNAc levels within an optimal range” (see Ong abstract),
“Up to 4,000 and potentially more proteins have been found to be O-GlcNAcylated” (see Ong pg. 1, 1st para),
“O-GlcNAcylation uses the substrate UDP-GlcNAc, the final product of nutrient flux through the hexosamine biosynthetic pathway (HBP) which integrates amino acid, carbohydrate, fatty acid, nucleotide, and energy metabolism. The HBP fluctuates with cellular metabolism and may be dramatically altered under physiological and pathological conditions. The extent of O-GlcNAcylation can reflect metabolic dynamics in the cell. This sets up the OGT/OGA pair to be an “all-in-one” metabolic and nutrient sensor and has been understood to alter diverse cellular processes such as apoptosis, gluconeogenesis, calcium signaling, insulin signaling, and mitochondrial homeostasis. Physiologically, disruption of OGT and OGA function has been implicated in the pathogenesis of several major health problems, such as diabetes, cancer and neurodegenerative diseases” (see Ong para spanning pgs. 1-2; see also Hart and Akimoto pg. 8, 2nd para).
Currently, therapeutic compounds targeting OGT and OGA are not limited to interactions with specific substrates but rather universally effect function (see Cheng et al. (2024) Opportunities for Therapeutic Modulation of O-GlcNAc. Chem Rev 124, 12918-13019, in particular, pg. 12978, 1st col. section 4.7.1-pg. 12979, 1st col. section 4.7.5). Furthermore, six years post filing the only disclosed utility of the instantly claimed invention is in studying the impact of O-GlcNAc on specific substrates within cells (see Cheng pg. 12981, 1st col. 1st para).
The state of the art teaches antibody binding can affect both the structure and function of the target.
Regarding the specificity of the antibody binding site, it was known in the art at the time of filing that antibodies can alter both structure and function of its target.
“The interaction of enzymes with their specific antibodies generally leads to a reduction in their enzymatic activity. The mechanism of this inhibition is rarely a direct combination of the antibodies with the catalytic site, but is rather due to steric hindrance, namely, barring the access to the active site. In several systems the mechanism of the antibody effect is by conformational changes which it induces on the enzyme. In these cases, the interaction with the antibody may result either in inhibition or in enhancement of the enzymatic activity” (see Arnon (1975) Enzyme inhibition by Antibodies. Acta Endocrinologica, Volume 80, Issue 2_Supplement, Dec 1975, Pages S133–S153, in particular abstract).
“As they provide access to conformational epitopes in concave and hinge regions, nanobodies are also increasingly applied in structural biology to freeze dynamic proteins into single functional conformations” (see Uchanski et al. (2020) Nanobodies to study protein conformational states. Current Opinion in Structural Biology. Vol. 60, pgs. 117-123, abstract),
“nanobodies have emerged as exquisite tools to freeze dynamic proteins into single functional conformations” (see Uchanski pg. 117, 2nd col. 2nd para), and
“Importantly, nanobodies were identified that inhibit LRRK2 kinase activity while binding to a site that is topographically distinct from the active site and thus act through an allosteric inhibitory mechanism that does not involve binding to the AP pocket or even to the kinase domain” (see Singh et al. (2022) Nanobodies as allosteric modulators of Parkinson’s disease–associated LRRK2, Proc. Natl. Acad. Sci. U.S.A. 119 (9) e2112712119, abstract).
An ordinary artisan would understand an antibody binding to a target protein can affect both the 3D structure of target protein potentially affecting the presentation of a glycosylation site or the ability of the target protein to interact with subsequent binding partners. Furthermore, conventional antibodies are known to bind with sub-nanomolar affinity and remain in complex with the target for a long time (see Klaus and Deshmukh (2021) pH responsive antibodies for therapeutic applications. J Biomed Sci 28, 11 pgs. 1-14, in particular pg. 3, 2nd col. 2nd para).
The state of the art teaches the presence of a linker and the specific linker chosen can impact the function of a fusion protein.
“the selection of a suitable linker to join the protein domains together can be complicated and is often neglected in the design of fusion proteins. Direct fusion of functional domains without a linker may lead to many undesirable outcomes, including misfolding of the fusion proteins, low yield in protein production, or impaired bioactivity. Therefore, the selection or rational design of a linker to join fusion protein domains is an important, yet underexplored, area in recombinant fusion protein technology” (see Chen et al. (2013) Fusion protein linkers: property, design and functionality. Adv Drug Deliv Rev. 65(10): 1357-1369, in particular pg. 2, 2nd para) and
“With the rapid advancement of protein science and biotechnology, the design of linkers in fusion proteins has become more important than ever before. With a thorough understanding of their structures, conformations, and functions via future biomedical research, the incorporation of linkers will greatly facilitate the construction of stable and bioactive recombinant fusion proteins for drug delivery applications” (see Chen pg. 16, last para).
Amount of Experimentation Required
The language of claim 1 requires undue experimentation to make and use the genus of antibodies encompassed by the current language. A person of ordinary skill in the art would recognize glycosylation both in general and at specific sites on any given target would require first identifying both the necessary accessory proteins and minimal OGT structure (e.g., number of TPRs) required for glycosylation that do not also globally increase glycosylation. The ordinary artisan would then have to develop a nanobody which binds to a location on said target that does not affect said glycosylation (e.g., binding to a potential glycosylation site) nor prevent OGT activity on the respective target in order to determine what if any consequences of said glycosylation. It is noted it would be even more highly unpredictable how the fusion protein would function with an extracellular target given the substrate required for glycosylation is intracellular and there are no known extracellular domains glycosylated by OGT. Furthermore, the ordinary artisan would then have to determine the functionality of the targeted protein in the disclosed use of altering glycosylation.
The state of the art teaches the breadth in the antibody repertoire is vast,
“genetic diversity of these adaptive immune receptors is generated through a somatic recombination process that acts on their constituent V, D, and J segments. During the gene rearrangement process, additional sequence diversity is created by nucleotide deletion and addition, resulting in a potential diversity of >1013 unique B- and T-cell immune receptor sequences” (see Miho et al. (2018) Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires. Front. Immunol. 9:224, in particular pg. 1 last para),
“Immune repertoires are highly dynamic. They are constantly evolving within the repertoire sequence space, which is defined as the set of all biologically achievable immune receptor sequences. Repertoire dynamics and evolution span several orders of magnitude in size (germline gene to clonal diversity), physical components (molecular to cellular dynamics), and time (short-lived responses to immunological memory that can persist for decades)” (see Miho pg. 2, 1st col. 1st para), and
“Theoretically, under physiological conditions, the human immune system can generate BCRs with 1026 distinct sequences, an astronomical number that is far greater than the calculated number of all B cell clones that can be generated during the lifespan of a healthy human (estimated to be 4×1014)3” (see Kanyavuz et al. (2019) Breaking the law: unconventional strategies for antibody diversification. Nature Reviews: Immunology, Vol 19, pgs. 355-368, in particular pg. 355, 2nd col. 1st para).
The state of the art also teaches designing antibodies requires optimizing several key attributes including binding affinity and specificity, folding stability, solubility, pharmacokinetics, and compatibility with the attachment of additional antibody domains (see Tiller and Tessier (2015) Advances in antibody design, Annu. Rev. Biomed. Eng. Vol. 17, pgs. 191-216, in particular abstract).
“there are many challenges in generating mAbs for therapeutic applications. At the discovery stage, immunization affords limited control over antibody affinity and specificity due to the difficulty in controlling antigen presentation to the immune system. In vitro methods, such as phage and yeast surface display, enable improved control over antigen presentation. However, these display methods are limited by their need to screen large libraries, their typical use of antibody fragments instead of full-length antibodies, and their reduced quality-control mechanisms relative to mammalian systems. Moreover, antibodies identified via either immunization or display methods have variable and difficult-to-predict solubilities and viscosities at the high concentrations required for subcutaneous delivery. Antibody aggregation is particularly concerning due to the potential immunogenicity of such aggregates” (see Tiller and Tessier pg. 193, 1st para), and
“Attempts to optimize each antibody property sequentially are limited by the fact that improving one antibody attribute (such as binding affinity) can lead to defects in other attributes (such as solubility). Attempts to simultaneously optimize multiple antibody properties using mutagenesis and screening methods require libraries that are prohibitively large” (see Tiller and Tessier pg. 193, last para).
The two embodiments reduced to practice in the instant specification using antibodies that bind GFP and nEPEA are not representative of the genus of antibody fusion proteins claimed.
Conclusion
Accordingly, regarding claims 1, 8, 10, 20, 21, 40, 51, 56-58, and 60 in the absence of substantive direction or guidance in the instant specification, the entire scope of experimentation required raise antibodies to each potential target (e.g., known, unknown, extracellular) in a location that does not impact OGT activity for said target or functionality of the target in general, construct a fusion protein, and determine functionality (e.g., localization, protein-protein interactions) in the disclosed use of altering glycosylation amounts to little more than a research assignment which would be highly unpredictable given the current state of the art. See Amgen Inc. v. Sanofi, 598 U.S. 594 (2023). The present claims and disclosure amounting to nothing more than an invitation to the skilled artisan to develop such embodiments. Given the resource- intensive nature of the required experimentation, the skilled artisan would reasonably conclude that such experimentation would be unnecessarily, and improperly, extensive and undue.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1, 8, 10, 20, 21, 40, 51, 56-58, and 60 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 1 is drawn to “a single, variable domain, heavy chain antibody” (lines 1-2). The scope of the antibody is unclear. For example, is a single drawn to a numerical number as in a monoclonal or alternatively is single drawn to an antibody with a singular variable domain wherein the variable domain is a heavy chain antibody. In addition, it is unclear what is meant by “glycosyl transferase is O-GlcNAc transferase (OGT) or O-GlcNAcase (OGA)”. Examiner recommends amending the claim to recite “and ii. a glycosyl transferase wherein the glycosyl transferase is either O-GlcNAc transferase (OGT) or O-GlcNAcase (OGA)” to address the latter.
Claim 20 recites the limitation "the glycan modifying enzyme" in line 2. There is insufficient antecedent basis for this limitation in the claim.
Claim 40 recites both “a method of administering a protein to a subject which glycosylates a target protein or removes a sugar from a target protein” and “the method comprising administering the fusion protein of claim 1 to a subject”. It is unclear if the protein in the preamble is the same as the fusion protein of claim 1 or alternatively a separate protein given a protein which glycosylates a target protein or removes a sugar from a target protein is broader than the fusion protein of claim 1.
Claim 60 is drawn to wherein the OGT further comprises a TPR domain. The scope of the OGT is unclear. The state of the art teaches OGT comprises a TRP domain comprising up to 13.5 TRP repeats (see Ong pg. 3, 1st col. 3rd para). Therefore, it is unclear if “further comprises a TRP domain” is in addition to the TRP domain present in OGT (i.e., 14.5-27 TRPs) or alternatively is drawn to the 1 TPR domain present in OGT.
Claim Rejections - 35 USC § 112
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 8 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 8 is drawn to wherein the OGT comprises a catalytic domain and depends from claim 1 wherein the fusion protein comprises OGT. Given claim 1 is draw to a fusion protein comprising OGT it necessarily follows the catalytic domain of OGT is present; therefore, claim 8 does not further limit claim 1.
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 claim allowed.
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/H.A.P./Examiner, Art Unit 1644 /AMY E JUEDES/Primary Examiner, Art Unit 1644