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 .
Claims 1 and 3-20 are pending.
Claims 13-15 and 17-20 are withdrawn from further consideration by the examiner, 37 C.F.R. 1.142(b) as being drawn to non-elected inventions.
Claims 1, 3-12 and 16, drawn to an adapter that read on (A) SpyCatcher and SpyTag as the first binding pair, (B) photoreactive pZ domain derived from protein A and a photoreactive B1 domain of protein G (HTB1) as the pair of photoreactive antibody binding domain (pAbBDs), are being acted upon in this Office Action.
Priority
Applicant’ claim priority to provisional application 62/160,130, filed May 12, 2015, is acknowledged.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on December 1, 2025 has been considered by the examiner and an initialed copy of the IDS is included with this Office Action.
Specification
The amendment to the specification filed on November 14, 2025 has been entered.
Objection and Rejection Withdrawn
The objection to claim 5 is withdrawn in light of the claim amendment.
The rejection of claims 1-12 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph is withdrawn in view of the claim amendment.
The rejection of claims 1, 7 and 8 under 35 U.S.C. 102 (a)(1) as being anticipated by Jung et al (Anal. Chem 81: 936-942, 2009; PTO 892) is withdrawn in view of the claim amendment.
The rejection of claims 1-10 and 16 under 35 U.S.C. 103 as being unpatentable over Tsourkas et al (WO2016183387, published November 17, 2016; PTO 1449) in view of Jung et al (Anal. Chem 81: 936-942, 2009; PTO 892) is withdrawn in view of the argument that the present application claims priority to PCT/US2016/032221 published as WO2016183387.
The rejection of claims 11 and 12 under 35 U.S.C. 103 as being unpatentable over Tsourkas et al (WO2016183387, published November 17, 2016; PTO 1449) in view of Jung et al (Anal. Chem 81: 936-942, 2009; PTO 892) as applied to claims 1-10 and 16 and further in view of Collier et al (WO2017035507, published March 2, 2017; PTO 892) or Evnin et al (US20200115461, published April 16, 2020; PTO 892) is withdrawn in view of the addition of Collier or Evnin does not cure the deficiency of Jung.
Claim rejections under - 35 U.S.C. 112
The following is a quotation 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 35 U.S.C. 112 (pre-AIA ), first paragraph:
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, 3-12 and 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 lists factors that can be used to determine if sufficient evidence of possession has been furnished in the disclosure of the Application. These include: (1) Actual reduction to practice, (2) Disclosure of drawings or structural chemical formulas, (3) Sufficient relevant identifying characteristics (such as: i. Complete structure, ii. Partial structure, iii. Physical and/or chemical properties, iv. Functional characteristics when coupled with a known or disclosed, and correlation between function and structure), (4) Method of making the claimed invention, (5) Level of skill and knowledge in the art, and (6) Predictability in the art. “Disclosure of any combination of such identifying characteristics that distinguish the claimed invention from other materials and would lead one of skill in the art to the conclusion that the applicant was in possession of the claimed species is sufficient.”
An adequate written description must contain enough information about the actual makeup of the claimed products – “a precise definition, such as structure, formula, chemic name, physical properties of other properties, of species falling with the genus sufficient to distinguish the gene from other materials”, which may be present in “functional terminology when the art has established a correlation between structure and function” (Amgen page 1361).
Claim 1 encompasses any adapter comprising a first binding pair member and a pair of photoreactive antibody binding domains (pAbBDs) that site-specifically bind and photo-crosslink to an immunoglobulin, wherein said first binding pair member and a second binding pair member comprise two moieties that form a heterodimer, wherein the pair of pAbBDs and the first binding pair member are connected via linkers and wherein the two moieties that form a heterodimer are any two protein or peptide moieties that form a heterodimer, two moieties that can undergo a click reaction, or a pair of complementary oligonucleotides.
Claim 3 encompasses the adapter of claim 1, wherein the two moieties form a covalently-linked heterodimer.
Claim 4 encompasses the adapter of claim 1, wherein each of said pair of pAbBDs in the adapter site-specifically bind and photo-crosslink to the two heavy chains of a single immunoglobulin.
Claim 5 encompasses the adapter of claim 1, wherein the two protein or peptide moieties that form a heterodimer are selected from the group consisting of SpyCatcher and SpyTag; two complementary halves of a split intein; c-Jun and c-Fos; leucine zippers; split adhesin domains; SnoopCatcher and SnoopTag; S-protein and S-Tag; Streptavidin/Streptactin or variants thereof and Strep-tag or Strep-tag II; calmodulin and calmodulin binding peptide; a leader peptide and a B1 protein pair from a lasso peptide biosynthesis system and a binding pair of a dock-and-lock system.
Claim 6 encompasses the adapter of claim 5, wherein the binding pair members are SpyTag and SpyCatcher.
Claim 7 encompasses the adapter of claim 1, wherein the immunoglobulin is an IgG molecule.
Claim 8 encompasses the adapter of claim 1, wherein the adapter is a fusion protein comprising in series a first pAbBD connected via a first linker to the first binding pair member connected via a second linker to a second pAbBD.
Claim 9 encompasses the adapter of claim 1, wherein the adapter is a fusion protein comprising in series a first pAbBD connected via a first linker to the second pAbBD, and the first binding pair member is connected via a second linker to either the first or the second pAbBD.
Claim 10 encompasses the adapter of claim 8, wherein the first pAbBD and the second pAbBD site-specifically bind and photo-crosslink to the two heavy chains of a single immunoglobulin.
Claim 11 encompasses the adapter of claim 8, wherein the first and the second linkers are flexible GS-rich linkers and wherein the flexible GS-rich linkers have from 1 to 8 GGS repeats (SEQ ID NO: 44).
Claim 12 encompasses the adapter of claim 9, wherein the first linker is between 35 and 100 amino acids in length.
Claim 16 encompasses a composition comprising: (a) a first adapter comprising a first binding pair member and a first pair of any photoreactive antibody binding domains (pAbBDs) that site-specifically bind and photo-crosslink to any first antibody, and wherein the first pair of pAbBDs and the first binding pair member are connected via linkers; and (b) a second adapter comprising any second binding pair member and any second pair of photoreactive antibody binding domains (pAbBDs) that site-specifically bind and photo-crosslink to a second antibody, wherein the second pair of pAbBDs and the second binding pair member are connected via linkers; wherein the first and second binding pair members comprise two moieties that form a heterodimer.
Regarding adapter, the specification discloses:
[0187] Bispecific antibodies (BsAb) refer to a class of biomacromolecules that are capable of binding two antigens or epitopes simultaneously. This can elicit unique biological effects that cannot be achieved with either individual antibody or with two unlinked antibodies. Bispecific antibodies have been used for targeting effector cells to tumor cells, preferential targeting of cells expressing two target biomarkers over cells expressing either target biomarker individually, or to couple two molecular targets on the same cell surface to trigger unique intracellular signaling pathways. In this Example, two related methods are presented that allow direct, rapid assembly of bispecific antibodies from any two “off-the-shelf” Immunoglobulin G (IgG) antibodies, in as little as one day. Both workflows can be summarized into two steps: 1) attach a small photoreactive antibody binding domain (pAbBD) fused to SpyCatcher or SpyTag (peptide-protein partners derived from the S. pyrogenes fibronectin-binding protein FbaB) to each component IgG, respectively; 2) assemble the BsAb through the spontaneous isopeptide bond formation that occurs between SpyTag and SpyCatcher. These approaches allow production of BsAbs from any two IgG molecules without the need to elucidate their amino acid sequences or genetically alter their structure. Binding assays and T cell-mediated cytolysis assays were performed to validate the binding and functional properties of Trastuzumab×Cetuximab BsAb and Cetuximab×OKT3 BsAb, respectively. This approach allows rapid, low-cost production of highly homogenous tetravalent BsAbs in a modular fashion, presenting an opportunity to quickly evaluate antibody pairs in a BsAb format for unique or synergistic functionalities.
[0190] In this Example, two methods are presented for rapid, in vitro assembly of tetravalent, bispecific antibodies from two full-length IgGs. Both methods use small photoreactive antibody binding domains (pAbBDs) fused to SpyCatcher (SC) or SpyTag (ST) to steer full-length IgG molecules into forming heterodimers (FIG. 31). pAbBDs are composed of IgG-binding domains derived from the bacterial protein G or protein Z and allow highly-efficient photocrosslinking to the heavy chains of nearly any IgG, from a diverse range of hosts and subclasses. pAbBDs can be expressed as a fusion protein in series with other proteins of interest to label IgGs covalently and in a site-specific manner. Here, pAbBDs are used to label IgGs with either SpyCatcher or SpyTag. This protein-peptide binding pair was originally developed from the S. pyrogenes fibronectin binding protein FbaB domain and can spontaneously form a covalent isopeptide bond. Therefore, once SpyCatcher and SpyTag are covalently attached to two different antibodies via the pAbBDs, they can drive the formation of a stable BsAb. This eliminates the need for genetic engineering of the component antibodies and allows the use of an off-the shelf IgG to create BsAbs in a modular fashion. Thus, this represents a powerful new approach to test any combination of antibodies in a BsAb format for unique or synergistic functionalities.
However, the specification does not describe the structure-identifying information, e.g., amino acid sequence about the claimed first binding pair member and the pair of photoreactive antibody binding domain (pAbBDs) that correlated with functions, e.g., photo-crosslinking to all immunoglobulin. The specification does not describe a representative number of species falling with the scope of the genus of adaptor or structural common to the members of the genus so the one of skill in the art can visualize or recognize the member of the genus of the actual claimed adapter themselves.
Regarding any pair of photoreactive antibody binding domains (pAbBDs) that site-specifically bind and photo-crosslink to any immunoglobulin, the specification discloses:
[0080] “Protein Z” refers to a Z domain based on the B domain of Staphylococcal aureus Protein A. The wild-type Protein Z amino acid sequence is: VDNKFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAP KMRM (SEQ ID NO: 1). Photoreactive Protein Z includes those where an amino acid in protein Z has been replaced with benzoylphenylalanine (BPA), such as F13BPA and F5BPA (underlined amino acids in bold in SEQ ID NO: 1). Examples of other BPA-containing Protein Z mutants include, but are not limited to, Q32BPA, K35BPA, N28BPA, N23BPA, and L17BPA. Examples of Protein Z variants or mutants include, F5I, such as F5I K35BPA. The Protein Z amino acid sequence may also include homologous, variant, and fragment sequences having Z domain function. In some embodiments, the Protein Z amino acid sequence includes an amino acid sequence which is 60, 65, 70, 75, 80, 85, 90, 95, or 99% identity to the sequence set forth in SEQ ID NO: 1.
[0081] “Protein G” refers to a B1 domain based on Streptococcal Protein G. Preferably, the Protein G is a hyperthermophilic variant of a B1 domain based on Streptococcal Protein G. The Protein G amino acid sequence preferably is: MTFKLIINGKTLKGEITIEAVDAAEAEKIFKQYANDYGIDGEWTYDDATKTFTVTE (SEQ ID NO: 2). Nine Protein G variants were successfully designed and expressed, each with an Fc-facing amino acid substituted by BPA: V21, A24, K28, I29, K31, Q32, D40, E42, W42 (underlined and bold in SEQ ID NO: 23). Only variants, A24BPA and K28BPA, allowed ˜100% of all human IgG subtypes to be labeled. The Protein G amino acid sequence may also include homologous, variant, and fragment sequences having B1 domain function. In some embodiments, the Protein G amino acid sequence includes an amino acid sequence which is 60, 65, 70, 75, 80, 85, 90, 95, or 99% identity to the sequence set forth in SEQ ID NO: 2.
Even assuming the pAbBDs is Protein Z, the specification does not teach which amino acid within the full-length sequence of SEQ ID NO: 1 to be substituted, deleted, added or a combination thereof such that the modified variant having 60, 65, 70, 75, 80, 85, 90 to SEQ ID NO: 1 maintains binding to all immunoglobulin, e.g., immunoglobulin of different isotype, e.g., IgG1, Ig2, IgG3, IgG4, IgM, IgA and from other species, e.g., human, mouse, rat, monkey, etc.
Likewise, the specification does not teach which amino acid within the full-length sequence of SEQ ID NO: 2 to be substituted, deleted, added or a combination thereof such that the variant having 60, 65, 70, 75, 80, 85, 90 to SEQ ID NO: 2 maintains binding to human Fc of IgG, much less to any and all immunoglobulin, other than A24BPA and K28BPA substitution in SEQ ID NO: 2.
Hui (of record, Bioconjugate Chemistry 25: 1709-1719, 2014; PTO 892) teaches that amino acid substitution in domain Z of protein A at position Q32 for benzoylphenylalanine (BPA) has maximum cross-linking of mIgG1 with 50% of heavy chains. However, mouse IgG2a, mIgG2b, mIgG3 isotypes were not appreciably cross-linked by Q32BPA, see p. 1712, left col. Hui further teaches while the utility of photoreactive Protein Z has been previously demonstrated, it is very challenging to produce such as a recombinant protein with multiple modifications, see p. 1715, Discussion, in particular. Thus, the prior art teaches binding specificity and crosslinking ability of bacterial protein Z and protein G to a target, i.e., immunoglobulin is necessarily determined empirically.
Regarding two peptide moieties that form a heterodimer, the specification does not describe the structure of peptide moieties that form a heterodimer.
Regarding two protein moieties that form a heterodimer, the specification discloses
SpyCatcher and SpyTag; two complementary halves of a split intein; c-Jun and c-Fos; leucine zippers; split adhesin domains; SnoopCatcher and SnoopTag; S-protein and S-Tag; Streptavidin/Streptactin, Strep-tag or Strep-tag II; calmodulin and calmodulin binding peptide, see para. [0057].
However, the specification does not describe the structure of protein binding pair members other than SpyCatcher and SpyTag; two complementary halves of a split intein; c-Jun and c-Fos; leucine zippers; split adhesin domains; SnoopCatcher and SnoopTag; S-protein and S-Tag; Streptavidin/Streptactin, Strep-tag or Strep-tag II; calmodulin and calmodulin binding peptide to enable one of skilled in the art envision the claimed adapter.
Even assuming the first or second binding pair member is SpyCatcher, the specification discloses:
[0125] The first generation SpyCatcher amino acid sequence is: ATHIKFSKRDEDGKELAGATMELRDSSGKTISTWISDGQVKDFYLYPGKYTFVETAA PDGYEVATAITFTVNEQGQVTVN (SEQ ID NO: 17). The SpyCatcher amino acid sequence may also include homologous, variant, and fragment sequences having SpyCatcher function. In some embodiments, the SpyCatcher amino acid sequence includes an amino acid sequence which is 60, 65, 70, 75, 80, 85, 90, 95, or 99% identity to the sequence set forth in SEQ ID NO: 17.
However, the specification does not describe where and what amino acid within the full-length sequence of SEQ ID NO: 17 to be substituted, deleted, added or a combination thereof such that the modified SpyCatcher having 60%, 65, 70, 75, 80, 85, 90, 95% sequence identity still maintains structure and function.
Regarding SpyTag, the specification discloses:
[0126] The first generation SpyTag amino acid sequence is: AHIVMVDAYKPTK (SEQ ID NO: 18). The SpyTag amino acid sequence may also include homologous, variant, and fragment sequences having SpyTag function. In some embodiments, the SpyTag amino acid sequence includes an amino acid sequence which is 60, 65, 70, 75, 80, 85, 90, 95, or 99% identity to the sequence set forth in SEQ ID NO: 18 at the time of filing.
However, the specification does not describe where and what amino acid within the full-length sequence of SEQ ID NO: 18 to be substituted, deleted, added or a combination thereof such that the modified SpyTag having 60%, 65, 70, 75, 80, 85, 90, 95% sequence identity still maintains structure and function, e.g., heterodimerization.
Thus, the specification does not disclose a representative number of species of binding pair of photoreactive antibody binding domains (pAbBDs) and heterodimer comprising any “two protein or peptide moieties” connected via linkers and the two moieties can under click reaction at the time of filing to show Applicants were in possession of the genus at the time of filing.
Thus, a skilled artisan would reasonably conclude that Applicant was not in possession of the genus of all the said adapter at the time the instant application was filed, and hence not in possession of the claimed method of making and using said adapter at the time the instant application was filed.
Vas-Cath Inc. v. Mahurkar, 19 USPQ2d 1111, makes clear that “applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the written description inquiry, whatever is now claimed.” (See page 1117.) The specification does not “clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed.” (See Vas-Cath at page 1116.).
Adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method for isolating it. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (CAFC 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016.
One cannot describe what one has not conceived. See Fiddles v. Baird, 30 USPQ2d 1481, 1483. In Fiddles v. Baird, claims directed to mammalian FGF’s were found unpatentable due to lack of written description for the broad class. The specification provided only the bovine sequence. Thus, the specification fails to describe these DNA sequences.
For genus claims, an adequate written description of a claimed genus requires more than a generic statement of an invention's boundaries. A patent must set forth either a representative number of species falling within the scope of the genus or structural features common to the members of the genus. Kubin, Exparte, 83 USPQ2d 1410 (Bd. Pat. App. & Int. 2007); Ariad Pharms., Inc. v. Eli Lilly& Co., 598 F.3d 1336, 1350 (Fed. Cir. 2010).
Therefore, only (1) an adapter fusion protein comprising a pair of photoreactive IgG-binding domain (pAbBD) from the bacterial protein G or protein Z fused to a member of a binding pair via linkers wherein the binding pair is selected from the group consisting of SpyCatcher (SC) and SpyTag (ST), two complementary halves of a split intein; c-Jun and c-Fos; leucine zippers; split adhesin domains; S-protein and S-Tag; Streptavidin/Streptactin; calmodulin and calmodulin binding peptide, a pair of complementary oligonucleotides, wherein the pAbBD comprising the amino acid sequence set forth in SEQ ID NO: 2 having a photo-reactive amino acid benzoylphenylalanine (BPA) at A24, K28 or both or SEQ ID NO: 1 having a photo-reactive amino acid benzoylphenylalanine (BPA) at Q32BPA, K35BPA, N28BPA, N23BPA, and L17BPA, wherein the interaction between the binding pairs form a heterodimer, (2) the adaptor fusion protein wherein the first and second linkers are flexible Glycine-serine (GS) rich linker and have from 1 to 8 GGS repeats of SEQ ID NO: 44, (3) the adaptor fusion protein is pAbBD-SC-pAbBD or pAbBD-ST-pAbBD, (4) the adaptor fusion protein wherein one of the binding pair comprises an azide and the other binding pair member comprises ADIBO or DBCO, but not the full breadth of the claims meets the written description provision of 35 U.S.C. § 112, first paragraph. Applicant is reminded that Vas-Cath makes clear that the written description provision of 35 U.S.C. § 112 is severable from its enablement provision (see page 1115).
Applicant's arguments filed November 14, 2025 have been fully considered but they are not persuasive.
The present claims recite an adapter comprising a first binding pair member and a pair of photoreactive antibody binding domains (pAbBDs) that site-specifically bind and photo- crosslink to an immunoglobulin, wherein said first binding pair member and a second binding pair member comprise two moieties that form a heterodimer
The application as filed, inter ala, discloses and exemplifies:
an antibody binding domain that crosslinks to the immunoglobulin Fc or Fab region (paragraph [0079]);
AbBDs include Protein A, Protein G, Protein L, CD4 and their subdomains, e.g., B1 domain of Protein G, or engineered subdomains, e.g., Protein Z, HTB1 (paragraph [0120]);
Detailed description of Protein Z (paragraph [0080]), and Protein G (paragraph [0081]), and their properties;
IgG Fc region photocrosslinked with a Protein G-based adapter protein (Fig. 5);
A large number of binding pairs wherein the members of each binding pair contain two moieties that form a heterodimer (paragraphs [0124]-[0135]).
Thus, contrary to the Examiner's contention, based on the disclosure and examples in this application, such as those above, together with a skilled artisan's own knowledge, a skilled artisan would reasonably conclude the inventors had possession of the necessary common attributes or features possessed by the members of the genus, specifically peptides that contain two domains connected via a linker (numerous suitable linkers are described, e.g., in paragraphs [0059] and [0123]), wherein the first domain specifically binds a constant region (Fab or Fc) of an antibody (as exemplified by Protein G in e.g., Figure 5), and the second domain represents a member of a binding pair, which contains a moiety that can form a heterodimer with its counterpart moiety of the second member of the minding pair (wherein the binding pair is selected from a list disclosed in paragraphs [0124]-[0135]).
In addition, the Examiner's apparent to requirement that structure-identifying information, e.g., amino acid sequence be provided for the claimed adapter (Office Action, pg. 7) is inappropriate and unwarranted. While structural formulas may be a convenient way of demonstrating possession of specific molecules, in the case of biological molecules possession can also be demonstrated through disclosure of other identifying characteristics. "There is no per se rule that an adequate written description of an invention that involves a biological macromolecule must contain a recitation of known structure." Falkner v. Inglis, 448 F.3d 1357, 1366, (Fed. Cir. 2006). Furthermore, where the claims are directed to species that bind to various selected targets, it is not fatal that all species are not disclosed as long as the patent provides other means of identifying which species would possess the claimed common structural characteristics or shared traits. Juno Therapeutics, Inc. v. Kite Pharma, Inc., 10 F.4th 1330, 1337, 2021 USPQ2d 893 (Fed. Cir. 2021).
In that regard, Applicant respectfully points out that sequences and even structures of the pAbBDs and peptide binding pair members are known in the art (see, e.g., for Streptavidin (en.wikipedia.org/wiki/Streptavidin), for Streptactin (Mikula et al. (2012) J Bacteriol. 194(4):827-38), and for B1 protein (Zhu et al. (2016) Scientific reports 6(1):1-12)). Thus, these and other sequences that are known in the art do not need to be described in detail.
Furthermore, Applicant notes that amino acid exchanges in proteins and peptides, which do not generally alter the activity of the proteins, or peptides are also known in the art (H. Neurath, R. L. Hill, The Proteins, Academic Press, New York, 1979; Argos EMBO J, 8, 779-785 (1989)). The most commonly occurring exchanges are Ala/Ser, Val/Ile, Asp/Glu, Thr/Ser, Ala/Gly, Ala/Thr, Ser/Asn, Ala/Val, Ser/Gly, Thy/Phe, Ala/Pro, Lys/Arg, Asp/Asn, Leu/Ile, Leu/Val, Ala/Glu and Asp/Gly, in both directions. Furthermore, a skilled artisan can determine whether a particular substitution or a set of substitutions would reasonably be expected to alter functionality of the pAbBDs (i.e., binding to an Fe antibody domain) or of binding pair members (i.e., ability to form heterodimers) using, for example, the criteria defined for an "accepted point mutation" in Dayhoff et al., 5: Atlas of Protein Sequence and Structure, 5: Suppl. 3, chapter 22: 354-352, 5 Nat. Biomed. Res. Foundation, Washington, D.C. (1978) or guidance provided in Bowie et al., Science 247:1306-1310, (1990). Accordingly, contrary to the Examiner's contention, a skilled artisan would recognize that certain amino acids in the pAbBDs and binding pair members listed in the present Specification can be substituted without affecting their functionality, and further will be able to identify such substitutions using well known methods.
Thus, this description is sufficient to allow a skilled artisan to recognize a member of the claimed genus because the Specification discloses a sufficient combination of the number of species (paragraphs [00120] and [0124]-[0135]) and of the functional characteristics common to the genus members (paragraph [0079] and [0124]-[0135]).
In view of the foregoing, the specification includes enough to convince a person of ordinary skill in the art that the inventors possessed the invention, thereby satisfying the written description requirement. Thus, the full scope of the claims has been fully described pursuant to 35 U.S.C. §112.
In response, amended claim 1 encompasses any adapter comprising any first binding pair member and a pair of photoreactive antibody binding domains (pAbBDs) that site-specifically bind and photo-crosslink to any immunoglobulin, wherein said first binding pair member and a second binding pair member comprise two moieties that form a heterodimer, wherein the pair of pAbBDs and the first binding pair member are connected via linkers and wherein the two moieties that form a heterodimer are any two protein or peptide moieties that form a heterodimer, two moieties that can undergo a click reaction, or a pair of complementary oligonucleotides.
Regarding a pair of photoreactive antibody binding domains (pAbBDs) that site-specifically bind and photo-crosslink to any immunoglobulin, the specification discloses recombinantly produce an antibody-binding domain derived from protein Z or protein G with two key features: (1) a photo-crosslinker (benzoylphenylalanine, BPA) within the antibody binding domain and (2) an azide or constrained alkyne moiety (e.g., azadibenzocyclooctyne, ADIBO) at the c-terminus (FIG. 1A). The photocrosslinker allows for covalent linkage to the Fc domain of IgG (FIG. 1B). Protein G variants, each having an Fc-facing amino acid substituted by BPA: V21, A24, K28, I29, K31, Q32, D40, E42, W42 (FIG. 12). Only two variants, A24BPA and K28BPA, that allowed 100% of all human IgG subclasses to be labeled with at least one adapter protein (FIG. 6). The structural stability of the Protein G HTB1 domain gives LASIC adapters a long shelf life even at room temperature, with no detectable loss of activity even after weeks of storage (FIG. 15).
Hui (of record, Bioconjugate Chemistry 25: 1709-1719, 2014; PTO 892) teaches that amino acid substitution in domain Z of protein A at position Q32 for benzoylphenylalanine (BPA) has maximum cross-linking of mIgG1 with 50% of heavy chains. However, mouse IgG2a, mIgG2b, mIgG3 isotypes were not appreciably cross-linked by Q32BPA, see p. 1712, left col. Hui further teaches while the utility of photoreactive Protein Z has been previously demonstrated, it is very challenging to produce such as a recombinant protein with multiple modifications, see p. 1715, Discussion, in particular. Thus, the prior art teaches binding specificity and crosslinking ability of bacterial protein Z and protein G to a target, i.e., immunoglobulin is necessarily determined empirically.
Regarding two peptide moieties that form a heterodimer, the specification does not describe the structure of peptide moieties that form a heterodimer.
Regarding two protein moieties that form a heterodimer, the specification discloses SpyCatcher and SpyTag; two complementary halves of a split intein; c-Jun and c-Fos; leucine zippers; split adhesin domains; SnoopCatcher and SnoopTag; S-protein and S-Tag; Streptavidin/Streptactin, Strep-tag or Strep-tag II; calmodulin and calmodulin binding peptide, see para. [0057].
However, the specification does not describe the structure of protein binding pair members other than SpyCatcher and SpyTag; two complementary halves of a split intein; c-Jun and c-Fos; leucine zippers; split adhesin domains; SnoopCatcher and SnoopTag; S-protein and S-Tag; Streptavidin/Streptactin, Strep-tag or Strep-tag II; calmodulin and calmodulin binding peptide to enable one of skilled in the art envision the claimed adapter.
Even assuming the first or second binding pair member is SpyCatcher, the specification discloses:
[0125] The first generation SpyCatcher amino acid sequence is: ATHIKFSKRDEDGKELAGATMELRDSSGKTISTWISDGQVKDFYLYPGKYTFVETAA PDGYEVATAITFTVNEQGQVTVN (SEQ ID NO: 17). The SpyCatcher amino acid sequence may also include homologous, variant, and fragment sequences having SpyCatcher function. In some embodiments, the SpyCatcher amino acid sequence includes an amino acid sequence which is 60, 65, 70, 75, 80, 85, 90, 95, or 99% identity to the sequence set forth in SEQ ID NO: 17.
However, the specification does not describe where and what amino acid within the full-length sequence of SEQ ID NO: 17 to be substituted, deleted, added or a combination thereof such that the modified SpyCatcher having 60%, 65, 70, 75, 80, 85, 90, 95% sequence identity still maintains structure and function.
Regarding SpyTag, the specification discloses:
[0126] The first generation SpyTag amino acid sequence is: AHIVMVDAYKPTK (SEQ ID NO: 18). The SpyTag amino acid sequence may also include homologous, variant, and fragment sequences having SpyTag function. In some embodiments, the SpyTag amino acid sequence includes an amino acid sequence which is 60, 65, 70, 75, 80, 85, 90, 95, or 99% identity to the sequence set forth in SEQ ID NO: 18 at the time of filing.
However, the specification does not describe where and what amino acid within the full-length sequence of SEQ ID NO: 18 to be substituted, deleted, added or a combination thereof such that the modified SpyTag having 60%, 65, 70, 75, 80, 85, 90, 95% sequence identity still maintains structure and function, e.g., heterodimerization.
For example, Byeon (newly cited, J. Mol Biol 333 141-152, 2003; PTO 892) teaches that single-point mutation A34F in the immunoglobulin-binding domain B1 of streptococcal protein G (GB1), a small (56 residues) can switch the classical monomer GB1 fold into a domain-swapped dimer, and this dimeric structure can be switched further into a tetramer by another single amino acid change of A34F, see entire document, Fig. 1,, p. 147, 149.
The specification exemplifies fusion proteins e.g., pAbBD-SpyCatcher/SpyTag and pAbBD-SpyCatcher/SpyTag-pAbBD, each comprising photoreactive antibody binding domain (pAbBD) comprising SEQ ID NO: 2 having A34 and K28 substitution for benzoylalanine (BPA) is fused to a SpyCatcher comprising the amino acid sequence of SEQ ID NO: 17 and the SpyTag comprising the amino acid sequence of SEQ ID NO: 18 wherein a (GGS).sub.7 (SEQ ID NO: 24) linker is used to connect the pAbBD with SpyCatcher (SC) or SpyTag (ST), see para. [0191].
The pAbBD fusion proteins were added to IgGs and the mixture was exposed to 365 nm UV light to crosslink pAbBD fusion proteins to IgGs at the CH2-CH3 junction, see para. [0195]. IgG crosslinked to pAbBD-SpyCatcher/SpyTag was allowed to bind recombinant protein G resin for purification.
To produce bispecific antibody, crosslinking of two different IgGs, e.g., Trastuzumab (anti-Her2/neu), Cetuximab (anti-EGFR) to either pAbBD-SpyCatcher or pAbBD-SpyTag, respectively, and then using the interaction between SpyCatcher and SpyTag to form a bridge between these two IgG antibodies (FIG. 31A, Scheme 1) or pAbBD-SC-pAbBD or pAbBD-ST-pAbBD in Scheme 2.
A description of a genus may be achieved by means of a recitation of a representative number of species falling within the scope of the genus or of a recitation of structural features common to the members of the genus, which features constitute a substantial portion of the genus. Regents of the University of California v. Eli Lilly & Co., 119 F3d 1559, 1569, 43 USPQ2d 1398, 1406 (Fed. Cir. 1997). In Regents of the University of California v. Eli Lilly (43 USPQ2d 1398-1412), the court held that a generic statement which defines a genus of nucleic acids by only their functional activity does not provide an adequate written description of the genus. The court indicated that, while applicants are not required to disclose every species encompassed by a genus, the description of the genus is achieved by the recitation of a representative number of species falling within the scope of the claimed genus. At section B(1), the court states, “An adequate written description of a DNA ... requires a precise definition, such as by structure, formula, chemical name, or physical properties, not a mere wish or plan for obtaining the claimed chemical invention.”
The disclosure of two pAbBD-SC-pAbBD and pAbBD-ST-pAbBD fusion proteins may provide an adequate written description of a genus when the species disclosed is representative of the genus. However, the present claim encompasses numerous species that are not further described. Applicant is reminded that while “examples explicitly covering the full scope of the claim language” typically will not be required, a sufficient number of representative species must be included to “demonstrate that the patentee possessed the full scope of the [claimed] invention.” Lizardtech v. Earth Resource Mapping, Inc., 424 F.3d 1336, 1345, 76 USPQ2d 1724, 1732 (Fed. Cir. 2005).
“A sufficient description of a genus . . . requires the disclosure of either a representative number of species falling within the scope of the genus or structural features common to the members of the genus so that one of skill in the art can "visualize or recognize" the members of the genus.” See AbbVie, 759 F.3d at 1297, reiterating Eli Lilly, 119 F.3d at 1568-69.
In the absence of sufficient recitation of distinguishing characteristics of the pair of photoreactive antibody binding domain (pAbBDs), binding pair members that are any two protein or peptide moieties that form a heterodimer, and two moieties that can undergo a click reaction, one of skill in the art would not recognize from the disclosure that the applicant was in possession of the full scope of the claimed generic adapters.
Other than (1) an adapter fusion protein comprising a pair of photoreactive IgG-binding domain (pAbBD) from the bacterial protein G or protein Z fused to a member of a binding pair via a first and second linkers wherein the binding pair is selected from the group consisting of SpyCatcher (SC) and SpyTag (ST), two complementary halves of a split intein; c-Jun and c-Fos; leucine zippers; split adhesin domains; S-protein and S-Tag; Streptavidin and Streptactin; calmodulin and calmodulin binding peptide, a pair of complementary oligonucleotides, wherein the pAbBD comprising the amino acid sequence set forth in SEQ ID NO: 2 having a photo-reactive amino acid benzoylphenylalanine (BPA) at A24, K28 or both or SEQ ID NO: 1 having a photo-reactive amino acid benzoylphenylalanine (BPA) at Q32BPA, K35BPA, N28BPA, N23BPA, and L17BPA, wherein the interaction between the binding pairs form a heterodimer, (2) the adaptor fusion protein wherein the first and second linkers are flexible Glycine-serine (GS) rich linker and have from 1 to 8 GGS repeats of SEQ ID NO: 44, (3) the adaptor fusion protein is pAbBD-SC-pAbBD or pAbBD-ST-pAbBD, (4) the adaptor fusion protein wherein one of the binding pair comprises an azide and the other binding pair member comprises ADIBO or DBCO, there is insufficient written description for genus of adapter set forth in claims 1, 3-12 and 16 at the time the invention was made and as disclosed in the specification as filed under the written description provision of 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph.
In response to the argument that amino acid exchanges in proteins and peptides such as Ala/Ser, Val/Ile, Asp/Glu, Thr/Ser, Ala/Gly, Ala/Thr, Ser/Asn, Ala/Val, Ser/Gly, Thy/Phe, Ala/Pro, Lys/Arg, Asp/Asn, Leu/Ile, Leu/Val, Ala/Glu and Asp/Gly which do not generally alter the activity of the proteins, or peptides are also known in the art (H. Neurath, R. L. Hill, The Proteins, Academic Press, New York, 1979; Argos EMBO J, 8, 779-785 (1989)), it is noted that the mutations are not limited to these conservative substitutions. The specification does not teach where and what amino acid within the full-length sequence of pAbBDs, binding pairs such as SpyCatch, SpyTag to be substituted, deleted, added or a combination thereof such that the modified variant of SpyCatch or SpyTag having 60, 65, 70, 75, 80, 85, 90 % identity to the sequence of pAbBDs, SpyCatch, or SpyTag still maintains structure and functions. The specification does not provide a representative number of species of adaptor comprising pAbBD variants, binding pairs SpyCatch, SpyTag variants to describe the claimed genus or structure common to members of the genus.
In response to the argument that a skilled artisan can determine whether a particular substitution or a set of substitutions would reasonably be expected to alter functionality of the pAbBDs pair members listed in the present Specification can be substituted without affecting their functionality, and further will be able to identify such substitutions using well known methods, possession may not be shown by merely described how to obtain possession of members of the claimed genus or how to identify their common structural features. The Court has held that the disclosure of screening assays and general classes of compounds was not adequate to describe compounds having the desired activity: without disclosure of which peptides, polynucleotides, or small organic molecules have the desired characteristic, the claims failed to meet the description requirement of § 112. See University of Rochester v. G.D. Searle & Co., Inc., 69 USPQ2d 1886,1895 (Fed. Cir. 2004).
For these reasons, the rejection is maintained.
Claims 1, 3-12 and 16 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for only (1) an adapter fusion protein comprising a pair of photoreactive IgG-binding domain (pAbBD) from the bacterial protein G or protein Z fused to a member of a binding pair via a first and second linkers wherein the binding pair is selected from the group consisting of SpyCatcher (SC) and SpyTag (ST), two complementary halves of a split intein; c-Jun and c-Fos; leucine zippers; split adhesin domains; S-protein and S-Tag; Streptavidin/Streptactin; calmodulin and calmodulin binding peptide, a pair of complementary oligonucleotides, wherein the pAbBD comprising the amino acid sequence set forth in SEQ ID NO: 2 having a photo-reactive amino acid benzoylphenylalanine (BPA) at A24, K28 or both or SEQ ID NO: 1 having a photo-reactive amino acid benzoylphenylalanine (BPA) at Q32BPA, K35BPA, N28BPA, N23BPA, and L17BPA, wherein the interaction between the binding pairs form a heterodimer, (2) the adaptor fusion protein wherein the first and second linkers are flexible Glycine-serine (GS) rich linker and have from 1 to 8 GGS repeats of SEQ ID NO: 44, (3) the adaptor fusion protein is pAbBD-SC-pAbBD or pAbBD-ST-pAbBD, (4) the adaptor fusion protein wherein one of the binding pair comprises an azide and the other binding pair member comprises ADIBO or DBCO, does not reasonably provide enablement for any adapter as set forth in claims 1-12 and 16. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
Enablement is considered in view of the Wands factors (MPEP 2164.01(a)). These factors include, but are not limited to: (A) The breadth of the claims; (B) The nature of the invention; (C) The state of the prior art; (D) The level of one of ordinary skill; (E) The level of predictability in the art; (F) The amount of direction provided by the inventor; (G) The existence of working examples; and (H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. . In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988).
Claim 1 encompasses any adapter comprising a first binding pair member and a pair of photoreactive antibody binding domains (pAbBDs) that site-specifically bind and photo-crosslink to an immunoglobulin, wherein said first binding pair member and a second binding pair member comprise two moieties that form a heterodimer, wherein the pair of pAbBDs and the first binding pair member are connected via linkers and wherein the two moieties that form a heterodimer are two protein or peptide moieties that form a heterodimer, two moieties that can undergo a click reaction, or a pair of complementary oligonucleotides.
Claim 3 encompasses the adapter of claim 1, wherein the two moieties form a covalently-linked heterodimer.
Claim 4 encompasses the adapter of claim 1, wherein each of said pair of pAbBDs in the adapter site-specifically bind and photo-crosslink to the two heavy chains of a single immunoglobulin.
Claim 5 encompasses the adapter of claim 1, wherein the two protein or peptide moieties that form a heterodimer are selected from the group consisting of SpyCatcher and SpyTag; two complementary halves of a split intein; c-Jun and c-Fos; leucine zippers; split adhesin domains; SnoopCatcher and SnoopTag; S-protein and S-Tag; Streptavidin/Streptactin or variants thereof and Strep-tag or Strep-tag II; calmodulin and calmodulin binding peptide; a leader peptide and a B1 protein pair from a lasso peptide biosynthesis system and a binding pair of a dock-and-lock system.
Claim 6 encompasses the adapter of claim 5, wherein the binding pair members are SpyTag and SpyCatcher.
Claim 7 encompasses the adapter of claim 1, wherein the immunoglobulin is an IgG molecule.
Claim 8 encompasses the adapter of claim 1, wherein the adapter is a fusion protein comprising in series a first pAbBD connected via a first linker to the first binding pair member connected via a second linker to a second pAbBD.
Claim 9 encompasses the adapter of claim 1, wherein the adapter is a fusion protein comprising in series a first pAbBD connected via a first linker to the second pAbBD, and the first binding pair member is connected via a second linker to either the first or the second pAbBD.
Claim 10 encompasses the adapter of claim 8, wherein the first pAbBD and the second pAbBD site-specifically bind and photo-crosslink to the two heavy chains of a single immunoglobulin.
Claim 11 encompasses the adapter of claim 8, wherein the first and the second linkers are flexible GS-rich linkers and wherein the flexible GS-rich linkers have from 1 to 8 GGS repeats (SEQ ID NO: 44).
Claim 12 encompasses the adapter of claim 9, wherein the first linker is between 35 and 100 amino acids in length.
Claim 16 encompasses a composition comprising: (a) a first adapter comprising a first binding pair member and a first pair of any photoreactive antibody binding domains (pAbBDs) that site-specifically bind and photo-crosslink to any first antibody, and wherein the first pair of pAbBDs and the first binding pair member are connected via linkers; and (b) a second adapter comprising any second binding pair member and any second pair of photoreactive antibody binding domains (pAbBDs) that site-specifically bind and photo-crosslink to a second antibody, wherein the second pair of pAbBDs and the second binding pair member are connected via linkers; wherein the first and second binding pair members comprise two moieties that form a heterodimer.
Regarding adapter, the specification discloses:
[0187] Bispecific antibodies (BsAb) refer to a class of biomacromolecules that are capable of binding two antigens or epitopes simultaneously. This can elicit unique biological effects that cannot be achieved with either individual antibody or with two unlinked antibodies. Bispecific antibodies have been used for targeting effector cells to tumor cells, preferential targeting of cells expressing two target biomarkers over cells expressing either target biomarker individually, or to couple two molecular targets on the same cell surface to trigger unique intracellular signaling pathways. In this Example, two related methods are presented that allow direct, rapid assembly of bispecific antibodies from any two “off-the-shelf” Immunoglobulin G (IgG) antibodies, in as little as one day. Both workflows can be summarized into two steps: 1) attach a small photoreactive antibody binding domain (pAbBD) fused to SpyCatcher or SpyTag (peptide-protein partners derived from the S. pyrogenes fibronectin-binding protein FbaB) to each component IgG, respectively; 2) assemble the BsAb through the spontaneous isopeptide bond formation that occurs between SpyTag and SpyCatcher. These approaches allow production of BsAbs from any two IgG molecules without the need to elucidate their amino acid sequences or genetically alter their structure. Binding assays and T cell-mediated cytolysis assays were performed to validate the binding and functional properties of Trastuzumab×Cetuximab BsAb and Cetuximab×OKT3 BsAb, respectively. This approach allows rapid, low-cost production of highly homogenous tetravalent BsAbs in a modular fashion, presenting an opportunity to quickly evaluate antibody pairs in a BsAb format for unique or synergistic functionalities.
[0190] In this Example, two methods are presented for rapid, in vitro assembly of tetravalent, bispecific antibodies from two full-length IgGs. Both methods use small photoreactive antibody binding domains (pAbBDs) fused to SpyCatcher (SC) or SpyTag (ST) to steer full-length IgG molecules into forming heterodimers (FIG. 31). pAbBDs are composed of IgG-binding domains derived from the bacterial protein G or protein Z and allow highly-efficient photocrosslinking to the heavy chains of nearly any IgG, from a diverse range of hosts and subclasses. pAbBDs can be expressed as a fusion protein in series with other proteins of interest to label IgGs covalently and in a site-specific manner. Here, pAbBDs are used to label IgGs with either SpyCatcher or SpyTag. This protein-peptide binding pair was originally developed from the S. pyrogenes fibronectin binding protein FbaB domain and can spontaneously form a covalent isopeptide bond. Therefore, once SpyCatcher and SpyTag are covalently attached to two different antibodies via the pAbBDs, they can drive the formation of a stable BsAb. This eliminates the need for genetic engineering of the component antibodies and allows the use of an off-the shelf IgG to create BsAbs in a modular fashion. Thus, this represents a powerful new approach to test any combination of antibodies in a BsAb format for unique or synergistic functionalities.
However, the specification does not teach the structure-identifying information, e.g., amino acid sequence about the claimed adapter that correlated with site-specifically bind and photo-crosslink to any immunoglobulin and any first member of any binding pair to enable one of skill in the art can make and use adapter themselves without undue experimentation.
Regarding photoreactive antibody binding domains (pAbBDs), the specification discloses:
[0080] “Protein Z” refers to a Z domain based on the B domain of Staphylococcal aureus Protein A. The wild-type Protein Z amino acid sequence is: VDNKFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAP KMRM (SEQ ID NO: 1). Photoreactive Protein Z includes those where an amino acid in protein Z has been replaced with benzoylphenylalanine (BPA), such as F13BPA and F5BPA (underlined amino acids in bold in SEQ ID NO: 1). Examples of other BPA-containing Protein Z mutants include, but are not limited to, Q32BPA, K35BPA, N28BPA, N23BPA, and L17BPA. Examples of Protein Z variants or mutants include, F5I, such as F5I K35BPA. The Protein Z amino acid sequence may also include homologous, variant, and fragment sequences having Z domain function. In some embodiments, the Protein Z amino acid sequence includes an amino acid sequence which is 60, 65, 70, 75, 80, 85, 90, 95, or 99% identity to the sequence set forth in SEQ ID NO: 1.
[0081] “Protein G” refers to a B1 domain based on Streptococcal Protein G. Preferably, the Protein G is a hyperthermophilic variant of a B1 domain based on Streptococcal Protein G. The Protein G amino acid sequence preferably is: MTFKLIINGKTLKGEITIEAVDAAEAEKIFKQYANDYGIDGEWTYDDATKTFTVTE (SEQ ID NO: 2). Nine Protein G variants were successfully designed and expressed, each with an Fc-facing amino acid substituted by BPA: V21, A24, K28, I29, K31, Q32, D40, E42, W42 (underlined and bold in SEQ ID NO: 23). Two variants, A24BPA and K28BPA, allowed ˜100% of all human IgG subtypes to be labeled. The Protein G amino acid sequence may also include homologous, variant, and fragment sequences having B1 domain function. In some embodiments, the Protein G amino acid sequence includes an amino acid sequence which is 60, 65, 70, 75, 80, 85, 90, 95, or 99% identity to the sequence set forth in SEQ ID NO: 2.
Even assuming the pAbBDs is Protein Z, the specification does not teach which amino acid within the full-length sequence of SEQ ID NO: 1 to be substituted, deleted, added or a combination thereof such that the variant maintains binding to all immunoglobulin.
Even assuming the pAbBDs is B1 domain of Protein G, the specification does not teach which amino acid within the full-length sequence of SEQ ID NO: 2 to be substituted, deleted, added or a combination thereof such that the variant maintains binding to all immunoglobulin.
Hui (Bioconjugate Chemistry 25: 1709-1719, 2014; PTO 892) teaches that amino acid substitution in domain Z from protein A at Q32 for benzoylphenylalanine (BPA) has maximum cross-linking of mIgG1 with 50% of heavy chains. However, mouse IgG2a, mIgG2b, mIgG3 isotypes were not appreciably cross-linked by Q32BPA, see p. 1712, left col. Hui further teaches while the utility of photoreactive Protein Z has been previously demonstrated, it is very challenging to produce such as a recombinant protein with multiple modifications, see p. 1715, Discussion, in particular. Thus, the prior art teaches binding specificity and crosslinking ability of bacterial protein Z and protein G to a target, i.e., immunoglobulin is necessarily determined empirically.
Regarding members of the binding pair that form heterodimer such as SpyCatcher and SpyTag (claim 5, elected species), the specification discloses:
[0125] The first generation SpyCatcher amino acid sequence is: ATHIKFSKRDEDGKELAGATMELRDSSGKTISTWISDGQVKDFYLYPGKYTFVETAA PDGYEVATAITFTVNEQGQVTVN (SEQ ID NO: 17). The SpyCatcher amino acid sequence may also include homologous, variant, and fragment sequences having SpyCatcher function. In some embodiments, the SpyCatcher amino acid sequence includes an amino acid sequence which is 60, 65, 70, 75, 80, 85, 90, 95, or 99% identity to the sequence set forth in SEQ ID NO: 17.
Regarding SpyTag, the specification discloses:
[0126] The first generation SpyTag amino acid sequence is: AHIVMVDAYKPTK (SEQ ID NO: 18). The SpyTag amino acid sequence may also include homologous, variant, and fragment sequences having SpyTag function. In some embodiments, the SpyTag amino acid sequence includes an amino acid sequence which is 60, 65, 70, 75, 80, 85, 90, 95, or 99% identity to the sequence set forth in SEQ ID NO: 18.
However, the specification does not teach where and what amino acids within the full-length sequence of SEQ ID NO: 17 or SEQ ID NO: 18 to be substituted, deleted, added or a combination thereof such the SpyCatch and SpyTag variants maintain heterodimerization.
Regarding any variant of Streptavidin/Streptactin and any leader peptide and B1 protein pair from any lasso peptide biosynthesis system and binding pair of any dock-and-lock system, the specification does not teach the structure, e.g., amino acid sequence of such variants and leader peptide and B1 protein pair from which lasso peptide biosynthesis system to enable one of skilled in the art to make and use of such without undue experimentation.
There are insufficient working examples. It is unpredictable which combination of binding pair member and pair of photoreactive antibody binding domain encompassed by the claimed adapter able to photo-crosslink any and all immunoglobulin for making and using bispecific antibody. As such, it would require undue experimentation of one skilled in the art to practice the scope of the claimed invention with a reasonable expectation of success. See page 1338, footnote 7 of Ex parte Aggarwal, 23 USPQ2d 1334 (PTO Bd. Pat App. & Inter. 1992).
The scope of the claims must bear a reasonable correlation with the scope of enablement. See In re Fisher, 166 USPQ 19 24 (CCPA 1970).
Applicant's arguments filed November 14, 2025 have been fully considered but they are not persuasive.
Applicant’s position is that as discussed in the section above, numerous suitable AbBDs and binding pairs are disclosed in the Specification, together with their relevant functional characteristics, and further examples are provided of making and testing adapters comprising AbBD domains and a binding pair member connected by linkers (Examples 3-5). Using this guidance a skilled artisan can easily test functionality of multiple combinations of pAbBDs and binding pair members using routine and conventional methods. Furthermore, both conservative substitutions in amino acid sequences that do not alter polypeptide functionality and methods of identifying such substitutions are well known in the art. Thus, a skilled artisan can easily determine which sequence variants of the disclosed pAbBDs and binding pair members will retain functionality through the use of well known, routine, and conventional methods, and without engaging in undue experimentation. Applicant reminds the Examiner that "a considerable amount of experimentation is permissible, if it is merely routine" In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988) (citing In re Angstadt, 537 F.2d 489, 502- 04, 190 USPQ 214, 217-19 (CCPA 1976)). Time and expense are merely factors in this consideration and are not the controlling factors. United States v. Telectronics Inc., 857 F.2d 778, 785, 8 USPQ2d 1217, 1223 (Fed. Cir. 1988), cert. denied, 490 U.S. 1046 (1989). Thus, as amply stated above, routine experimentation, although time consuming, is permissible.
Furthermore, even assuming, which Applicant does not, that inoperative embodiments are within the scope of the claims, "[t]he presence of inoperative embodiments within the scope of a claim does not necessarily render a claim nonenabled." MPEP § 2164.08(b) Rather, "[t]he standard is whether a skilled person could determine which embodiments that were conceived, but not yet made, would be inoperative or operative with expenditure of no more than is normally required in the art." Atlas Powder Co. v. E.I. du Pont de Nemours & Co., 750 F.2d 1569, 1577, 224 USPQ 409, 414 (Fed. Cir. 1984).
Finally, Applicant needs not disclose all possible variants. As explained above, legal standard for enablement does not require that Applicant demonstrates enablement for all possible claimed iterations. Enablement must bear only a reasonable relationship to the scope of the claims. See MPEP 2164.01(b) (citing In re Fisher, 427 F.2d 833, 839, 166 U.S.P.Q. 18, 24 (CCPA 1970)). For example, a patent applicant is not required to "predict every possible variation, improvement or commercial embodiment of his invention." United States Steel Corp. v. Phillips Petroleum Co., 673 F. Supp. 1278, 1292 (D. Del. 1987), aff'd, 865 F.2d 1247, 1250 (Fed. Cir. 1989) (specifically quoting this statement).
For at least the reasons stated above, Applicant respectfully asserts that the instant application has met the requirements for enablement of the currently pending claims under 35 U.S.C. § 112. Accordingly, Applicant respectfully requests the withdrawal of this rejection.
In response, enablement is not commensurate in scope with how to make and use the claimed adaptor without undue experimentation for the following reasons.
Amended claim 1 encompasses any adapter comprising any first binding pair member and a pair of photoreactive antibody binding domains (pAbBDs) that site-specifically bind and photo-crosslink to any immunoglobulin, wherein said first binding pair member and a second binding pair member comprise two moieties that form a heterodimer, wherein the pair of pAbBDs and the first binding pair member are connected via linkers and wherein the two moieties that form a heterodimer are any two protein or peptide moieties that form a heterodimer, two moieties that can undergo a click reaction, or a pair of complementary oligonucleotides.
Regarding a pair of photoreactive antibody binding domains (pAbBDs) that site-specifically bind and photo-crosslink to any immunoglobulin, the specification discloses recombinantly produce an antibody-binding domain derived from protein Z or protein G with two key features: (1) a photo-crosslinker (benzoylphenylalanine, BPA) within the antibody binding domain and (2) an azide or constrained alkyne moiety (e.g., azadibenzocyclooctyne, ADIBO) at the c-terminus (FIG. 1A). The photocrosslinker allows for covalent linkage to the Fc domain of IgG (FIG. 1B). Protein G variants, each having an Fc-facing amino acid substituted by BPA: V21, A24, K28, I29, K31, Q32, D40, E42, W42 (FIG. 12). Only two variants, A24BPA and K28BPA, that allowed 100% of all human IgG subclasses to be labeled with at least one adapter protein (FIG. 6).
However, the specification does not teach random substitution of any antibody binding domains, much less photoreactive.
Hui (of record, Bioconjugate Chemistry 25: 1709-1719, 2014; PTO 892) teaches that amino acid substitution in domain Z of protein A at position Q32 for benzoylphenylalanine (BPA) has maximum cross-linking of mIgG1 with 50% of heavy chains. However, mouse IgG2a, mIgG2b, mIgG3 isotypes were not appreciably cross-linked by Q32BPA, see p. 1712, left col. Hui further teaches while the utility of photoreactive Protein Z has been previously demonstrated, it is very challenging to produce such as a recombinant protein with multiple modifications, see p. 1715, Discussion, in particular. Thus, the prior art teaches binding specificity and crosslinking ability of bacterial protein Z and protein G to a target, i.e., immunoglobulin is necessarily determined empirically.
Regarding two peptide moieties that form a heterodimer, the specification does not teach the structure of “peptide moieties” that form a heterodimer.
Regarding two “protein moieties” that form a heterodimer, the specification discloses SpyCatcher and SpyTag; two complementary halves of a split intein; c-Jun and c-Fos; leucine zippers; split adhesin domains; SnoopCatcher and SnoopTag; S-protein and S-Tag; Streptavidin/Streptactin, Strep-tag or Strep-tag II; calmodulin and calmodulin binding peptide, see para. [0057].
However, the specification does not teach the structure of protein binding pair members other than SpyCatcher and SpyTag; two complementary halves of a split intein; c-Jun and c-Fos; leucine zippers; split adhesin domains; SnoopCatcher and SnoopTag; S-protein and S-Tag; Streptavidin/Streptactin, Strep-tag or Strep-tag II; calmodulin and calmodulin binding peptide to enable one of skilled in the art envision the claimed adapter.
Even assuming the first or second binding pair member is SpyCatcher, the specification discloses:
[0125] The first generation SpyCatcher amino acid sequence is: ATHIKFSKRDEDGKELAGATMELRDSSGKTISTWISDGQVKDFYLYPGKYTFVETAA PDGYEVATAITFTVNEQGQVTVN (SEQ ID NO: 17). The SpyCatcher amino acid sequence may also include homologous, variant, and fragment sequences having SpyCatcher function. In some embodiments, the SpyCatcher amino acid sequence includes an amino acid sequence which is 60, 65, 70, 75, 80, 85, 90, 95, or 99% identity to the sequence set forth in SEQ ID NO: 17.
However, the specification does not teach where and what amino acid within the full-length sequence of SEQ ID NO: 17 to be substituted, deleted, added or a combination thereof such that the modified SpyCatcher having 60%, 65, 70, 75, 80, 85, 90, 95% sequence identity still maintains structure and function.
Regarding SpyTag, the specification discloses:
[0126] The first generation SpyTag amino acid sequence is: AHIVMVDAYKPTK (SEQ ID NO: 18). The SpyTag amino acid sequence may also include homologous, variant, and fragment sequences having SpyTag function. In some embodiments, the SpyTag amino acid sequence includes an amino acid sequence which is 60, 65, 70, 75, 80, 85, 90, 95, or 99% identity to the sequence set forth in SEQ ID NO: 18 at the time of filing.
However, the specification does not teach where and what amino acid within the full-length sequence of SEQ ID NO: 18 to be substituted, deleted, added or a combination thereof such that the modified SpyTag having 60%, 65, 70, 75, 80, 85, 90 sequence identity still maintains structure and function, e.g., heterodimerization.
For example, Byeon (newly cited, J. Mol Biol 333 141-152, 2003; PTO 892) teaches that single-point mutation A34F in the immunoglobulin-binding domain B1 of streptococcal protein G (GB1), a small (56 residues) can switch the classical monomer GB1 fold into a domain-swapped dimer, and this dimeric structure can be switched further into a tetramer by another single amino acid change of A34F, see entire document, Fig. 1,, p. 147, 149.
The specification exemplifies fusion proteins e.g., pAbBD-SpyCatcher/SpyTag and pAbBD-SpyCatcher/SpyTag-pAbBD, each comprising photoreactive antibody binding domain (pAbBD) comprising SEQ ID NO: 2 having A34 and K28 substitution for benzoylalanine (BPA) is fused to a SpyCatcher comprising the amino acid sequence of SEQ ID NO: 17 and the SpyTag comprising the amino acid sequence of SEQ ID NO: 18 wherein a (GGS).sub.7 (SEQ ID NO: 24) linker is used to connect the pAbBD with SpyCatcher (SC) or SpyTag (ST), see para. [0191].
The pAbBD fusion proteins were added to IgGs and the mixture was exposed to 365 nm UV light to crosslink pAbBD fusion proteins to IgGs at the CH2-CH3 junction, see para. [0195]. IgG crosslinked to pAbBD-SpyCatcher/SpyTag was allowed to bind recombinant protein G resin for purification.
To produce bispecific antibody, crosslinking of two different IgGs, e.g., Trastuzumab (anti-Her2/neu), Cetuximab (anti-EGFR) to either pAbBD-SpyCatcher or pAbBD-SpyTag, respectively, and then using the interaction between SpyCatcher and SpyTag to form a bridge between these two IgG antibodies (FIG. 31A, Scheme 1) or pAbBD-SC-pAbBD or pAbBD-ST-pAbBD in Scheme 2.
There are insufficient working examples. It is unpredictable which combination of binding pair member and pair of photoreactive antibody binding domain encompassed by the claimed adapter able to photo-crosslink any and all immunoglobulin for making and using bispecific antibody. As such, it would require undue experimentation of one skilled in the art to practice the scope of the claimed invention with a reasonable expectation of success.
For these reasons, the rejection is maintained.
Conclusion
No claim is allowed.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PHUONG HUYNH whose telephone number is (571)272-0846. The examiner can normally be reached on 9:00 a.m. to 6:30 p.m. The examiner can also be reached on alternate alternative Friday from 9:00 a.m. to 5:30 p.m.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Misook Yu, can be reached at 571-272-0839. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://portal.uspto.gov/external/portal. Should you have questions about access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free).
/PHUONG HUYNH/ Primary Examiner, Art Unit 1641