Office Action 1: Non-Final Rejection (2024-08-20)
Rejection types: 102 - Lack of Novelty, 103 - Obviousness, 112 - Written Description/Enablement, Double Patenting

CLAIMS:
AMENDMENTS TO THE CLAIMS

This listing of claims replaces all prior versions and listing of claims in the above-referenced patent application. The following amendments do not constitute an admission regarding the patentability of the amended subject matter and should not be so construed. Amendments to the claims do not add new matter.

What is claimed is:

1\. (Currently Amended) A D Domain target binding domain polypeptide that specifically binds CD 123 and comprises an amino acid sequence that has at least 94% sequence identity to an amino acid sequence of SEQ ID NO: 14.

2\. (Original) A polypeptide comprising the D domain of claim 1 fused to a heterologous polypeptide.

3\. (Original) The polypeptide of claim 2, wherein the heterologous polypeptide comprises.(a) a full-length antibody or an antibody fragment;
(b) an Fc domain;
(c) a transmembrane domain;
(d) a membrane associating domain;
(e) human serum albumin or a fragment thereof;
(f) AFP or a fragment thereof;
(g) AFP p26 or a fragment thereof; or (h) the extracellular domain of a receptor or a fragment thereof.
4\. (Original) The polypeptide of claim 2, which is labeled or conjugated to a therapeutic or cytotoxic agent.

5\. (Original) A chimeric antigen receptor (CAR) which comprises a target binding domain comprising the D domain that specifically binds CD 123 of claim 1.

6\. (Currently Amended) The CAR of claim 52further comprising a transmembrane domain and an intracellular signaling domain.

7\. (Original) The CAR of claim 6, wherein

(a) the transmembrane domain comprises a CD8a, 41BB, or CD28 transmembrane domain;
(b) the intracellular signaling domain is selected from the group consisting of a domain of a human T cell receptor alpha, beta, or zeta chain; a human 41BB domain; a human CD28 domain; and any combination thereof; and/or (c) the intracellular signaling domain comprises the intracellular domain of a costimulatory molecule selected from the group consisting of CD27, CD28, 41BB,OX40, CD30, CD40, PD1, lymphocyte function-associated antigen- 1 (LFA-1),
CD2, CD7, LIGHT, NKG2C, NKG2D, B7-H3, a ligand that specifically binds with CD83, and any combination thereof.

8\. (Currently Amended) The CAR of claim 5 comprising the amino acid sequence of SEQ ID NO: 67.

9\. (Currently Amended) An adapter comprising (a) the D domain target binding domain that specifically binds CD123 of claim 1, and (b) an antigenic determinant (AD).

10\. (Currently Amended) The adapter of claim 9, wherein the AD comprises an AFP p26 polypeptide,

11\. (Currently Amended) The adapter of claim 10, wherein the AFP p26 polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 37- 43 and 44.

12\. (Currently Amended) The adapter of claim 9, wherein the adapter comprises a single D domain that specifically binds CD 123 or two D domains that specifically bind CD 123.

13\. (Original) An isolated polynucleotide encoding the polypeptide of claim 2.

14\. (Original) A method of producing the polypeptide of claim 2, comprising culturing a host cell comprising a polynucleotide encoding the polypeptide under suitable conditions to produce the polypeptide.

15\. (Original) An isolated polynucleotide encoding the CAR of claim 5.

16\. (Original) A lentiviral vector comprising the polynucleotide of claim 15.

17\. (Original) A host cell comprising the polynucleotide of claim 15.

18\. (Original) A cell engineered to express the CAR of claim 5.

19\. (Original) The cell of claim 18, which is a T cell or a natural killer (NK) cell.

20\. (Currently Amended) A pharmaceutical composition comprising the polypeptide of claim 2 and a pharmaceutically acceptable excipient.

21\. (Original) A pharmaceutical composition comprising a cell expressing the CAR of claim 5 and a pharmaceutically acceptable excipient.

22\. (Original) The pharmaceutical composition of claim 21, wherein the cell is a T cell or a natural killer (NK) cell.

23\. (Currently Amended) A method of delivering an immune response to a target cell or killing a target cell comprising (a) contacting a composition comprising the target cell with a cell expressing a chimeric antigen receptor (CAR) comprising (i) the\[\[a\]\] D domain that binds to CD 123 of claim 1, (ii) a transmembrane domain, and (iii) an intracellular domain;(b) contacting a composition comprising the target cell with an adapter,wherein (a) the composition comprising the target cell further comprises a cell expressing a CAR, wherein the CAR comprises (i) an antigenic determinant binding domain (ADBD) that binds to an AFP p26 antigenic determinant (AD), (ii) a transmembrane domain, and (iii) an intracellular domain; and (b) the adapter comprises (i) the D domain that binds to CD 123 of claim 1 and (ii) AFP p26 AD;
(c) contacting a composition comprising the target cell with a cell expressing a CAR,wherein (a) the CAR comprises (i) an antigenic determinant binding domain (ADBD) that binds to an AFP p26 antigenic determinant (AD), (ii) a transmembrane domain, and (iii) an intracellular domain; and (b) the composition comprising the target cell further comprises an adapter comprising (i) the D domain that binds to CD 123 of claim 1 and (ii) an AFP p26 AD; or (d) contacting a composition comprising the target cell with a cell expressing a CAR and an adapter, wherein (a) the CAR comprises (i) an antigenic determinant binding domain (ADBD) that binds to an AFP p26 antigenic determinant (AD), (ii) a transmembrane domain, and (iii) an intracellular domain;

and (b) the adapter comprises (i) the D domain that binds to CD 123 of

claim 1 and (ii) an AFP p26 AD.
24\. (Currently Amended) The method of claim 23, wherein
 (a the transmembrane domain comprises a CD8a, 41BB or CD28 transmembrane domain;
 (b} the intracellular signaling domain is selected from the group consisting of a domain of a human T cell receptor alpha, beta, or zeta chain; a human 41BB domain; a human CD28 domain; and any combination thereof;
 (c} the intracellular signaling domain comprises the intracellular domain of a costimulatory molecule selected from the group consisting of CD27, CD28, 41BB,OX40, CD30, CD40, PD1, lymphocyte function-associated antigen- 1 (LFA-1),
CD2, CD7, LIGHT, NKG2C, NKG2D, B7-H3, a ligand that specifically binds with CD83, and any combination thereof;
((d} the AFP p26 AD comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 37-43 and 44;
 (e} the ADBD that binds to AFP p26 AD comprises a D domain that binds to AFP p26 AD;
 (f the ADBD that binds to AFP p26 AD comprises a D domain comprising the amino acid sequence of SEQ ID NO: 73, 70-72 or 92-94;
(4)(g} the CAR comprising a D domain that binds to AFP p26 AD comprises the amino acid sequence of SEQ ID NO: 68 or 69;
(j)h) the cell expressing the CAR is an immune cell,
 (i} the cell expressing the CAR is a T cell or a natural killer (NK) cell;
(1){j) the contacting occurs in a human subject;
 k)the target cell is a cancer cell; and/or

{ll the target cell is an acute myeloid leukemia (AML) cell or a high-risk myelodysplastic syndrome cell.

25\. (Currently Amended) A method of delivering an immune response to a target cell, killing a target cell or treating cancer in a patient comprising:(a) administering to the patient a cell expressing the chimeric antigen receptor (CAR) comprising (i) the\[\[a\]\] D domain that binds to CD123 of claim 1, (ii) a transmembrane domain, and (iii) an intracellular domain; or (b) administering to the patient an adapter comprising (i) the D domain that binds to CD 123 of claim 1 and (ii) an AFP p26 AD.

26\. (Currently Amended) The method of claim 25, wherein (a) the patient receiving the adapter has been administered a cell expressing a CAR, wherein the CAR comprises (i) an antigenic determinant binding domain (ADBD) that binds to an AFP p26 antigenic determinant (AD), (ii) a transmembrane domain, and (iii) an intracellular domain;(b) the patient receiving the adapter comprises a cell expressing a CAR,wherein the CAR comprises (i) an antigenic determinant binding domain (ADBD) that binds to an AFP p26 antigenic determinant (AD), (ii) a transmembrane domain,
and (iii) an intracellular domain; or (c) the method of (b) further comprises administering a cell expressing a CAR, wherein the CAR comprises (i) an antigenic determinant binding domain (ADBD) that binds to an AFP p26 antigenic determinant (AD), (ii) a transmembrane domain, and (iii) an intracellular domain.

27\. (Currently Amended) The method of claim 26, wherein
 (a the transmembrane domain comprises a CD8a, 41BB or CD28 transmembrane domain;

 (b} the intracellular signaling domain is selected from the group consisting of a domain of a human T cell receptor alpha, beta, or zeta chain; a human 41BB domain; a human CD28 domain; and any combination thereof;
 (c} the intracellular signaling domain comprises the intracellular domain of a costimulatory molecule selected from the group consisting of CD27, CD28, 41BB,OX40, CD30, CD40, PD1, lymphocyte function-associated antigen- 1 (LFA-1),
CD2, CD7, LIGHT, NKG2C, NKG2D, B7-H3, a ligand that specifically binds with CD83, and any combination thereof;
((d} the AFP p26 AD comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 37-43 and 44;
 (el the ADBD that binds to AFP p26 AD comprises a D domain that binds to AFP p26 AD;
 (f the ADBD that binds to AFP p26 AD comprises a D domain comprising the amino acid sequence of SEQ ID NO: 73, 70-72 or 92-94;
(4)(g the CAR comprising a D domain that binds to AFP p26 AD comprises the amino acid sequence of SEQ ID NO: 68 or 69;
j-()h the cell expressing the CAR is an immune cell,
 (i} the cell expressing the CAR is a T cell or a natural killer (NK) cell;
(1){j) the cell expressing the CAR is an autologous immune cell;
 k} the cancer is a hematological cancer; and/or ( the cancer is acute myeloid leukemia (AML) or high-risk myelodysplastic syndrome.

28\. (New) A polypeptide comprising the D domain of claim 1, wherein the D domain comprises the amino acid sequence of SEQ ID NO: 14.

OFFICE ACTION:
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 .
In the event the determination of the status of the application as subject to AIA  35 U.S.C. 102 and 103 (or as subject to pre-AIA  35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Priority
The instant application, filed 10/13/2023, is a continuation of application 18/055,096, filed 11/14/2022, and claims domestic benefit to US provisional application 63/279,489, filed 11/15/2021.
Status of Claims/Application
Applicant’s preliminary amendment of 01/03/2024 is acknowledged. Claims 1, 6, 8-12, 20, and 23-27 are amended and claim 28 is new. Claims 1-28 are currently pending and are examined on the merits herein.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 01/03/2024 are in compliance with the provisions of 37 CFR 1.97.  Accordingly, the information disclosure statements have been considered by the examiner.
Claim Objections
Claim 10 objected to because of the following informalities: the claim is terminated with a comma, correction to terminate the claim with a period is required.
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 1-27 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.
The instant claims are drawn to D domain polypeptides that specifically bind CD123 and comprise an amino acid sequence that has at least 94% sequence identity to an amino acid sequence of SEQ ID NO: 14 and the use of the domain in heterologous polypeptides, CARs, and adapters. The claims allow for up to 6% modification in the recited amino acid sequence (at least 94% identity). Additionally, the claims recite “an” amino acid sequence of SEQ ID NO: 14 suggesting that the claim encompasses fragments of SEQ ID NO: 14 and does not require the full length sequence. Based on the recitation of “at least 94% identity” and “an amino acid sequence”, the claims are drawn to a genus of antibodies all of which are claimed as having the function of specifically binding to CD123. The claims further recite methods in which the D Domain polypeptides are used in methods of delivering an immune response, killing a target cell, or treating cancer.
The disclosure, however, does not provide a representative number of species of the claimed genus nor does the disclosure identify a structure-function relationship which would allow an ordinarily skilled artisan to identify which amino acids in SEQ ID NO: 14 could be modified such that the polypeptide would maintain binding to CD123 and function in methods of delivering immune response, killing target cells, or treating cancer. This is particularly the case as, in the broadest reasonable interpretation of the claim, the 6% variance could be located anywhere in the amino acid sequence including areas that contribute to CD123 binding. Additionally, the disclosure does not provide a representative number of species of fragments of SEQ ID NO: 14 which are shown to perform the claimed functions.
The instant specification discloses 35 D domain sequences that target CD123 in Table 1 (pages 52-54), including SEQ ID NO: 14. These sequences, however, are not representative of the entire claimed genus as the domains disclosed do not comprise modifications that span the entirety of the claimed genus in which up to 6% modification can be made anywhere, and in anyway, in the amino acid sequence of SEQ ID NO: 14 while maintaining binding to CD123 maintaining the function of delivering an immune response, killing target cells, or treating cancer.
Additionally, the disclosure does not describe a structure-function relationship which would allow an ordinarily skilled artisan to predictably identify which amino acid sequences with 94% sequence identity to SEQ ID NO: 14, or fragments of SEQ ID NO: 14, would maintain binding to CD123. Rather, the disclosure demonstrates that modifications in the D domains are not predictable and must be tested in order to establish binding.
The examples of the disclosure describe the isolation of the variant D domains with increased affinity to CD123 (page 214, Example 1). In the example methods of improving affinity of D domains for target antigens, for example CD123, is described as including mutagenesis of existing amino acid sequences. These mutations can be directed towards specific amino acids or randomly distributed through the sequence. Mutated D domains are subsequently assayed for changes in binding characteristics, protein expression, or other biological activity associated with a particular application or function. The example goes on to describe the production and testing of CD123 binding domains.
The instant specification further discloses that the term D domain refers to a target binding polypeptide sharing certain sequences and certain structural features of the reference scaffold sequence of SEQ ID NO: 2. The reference scaffold is a variant of a non-naturally occurring and targetless antiparallel three helical bundle reference polypeptide that has no known target binding activity. It has been discovered that polypeptides containing modifications of the reference scaffold of SEQ ID NO: 1 are able to specifically bind to targets of interest. Therefore, a D domain, or molecule comprising a D domain, can specifically bind to a target molecule. The specification further discloses that it is believed that in designing the D domain the structural constraints of surface-exposed residues, that can be modified, confer the ability of the surface exposed residues to specifically bind a target of interest (page 28, [0040]).
Through these teachings, the instant disclosure demonstrates an unpredictability in modifying D domains while maintaining binding specificity. As discussed in the disclosure, modifications in the surface exposed residues of the antiparallel three helical bundle can change the specific binding of the domain. The disclosure, however, does not identify which of the amino acids in SEQ ID NO: 14 are the surface-exposed residues that are responsible for binding such that the specific binding could be predictably maintained while making modifications. Additionally, as discussed above, in the broadest reasonable interpretation of the claims, the 6% modification could occur anywhere in SEQ ID NO: 14, including areas that could be responsible for binding.
The prior art also does not provide a representative number of species of the claimed genus or a structure-function relationship which would allow for the modification of the D domain with predictable results.
WO 2016/164308 A1 (D.W. Lafleur and D.M. Hilbert) 13 October 2016 teaches de novo binding domain containing polypeptides (DBDpp) that specifically bind a target of interest as well as libraries of DBDpp, methods of producing and screening such libraries, and DBDpp identified from such processes (abstract). WO’308 teaches a reference scaffold which is a variant of a non-naturally occurring and targetless antiparallel three helical bundle peptide of SEQ ID NO: 1. Like the instant disclosure, WO’308 teaches that modification to the structural constraints of surface exposed residues that can be modified confer the ability of the residues to specifically bind a target of interest (page 52, [0151]).
WO’308 further teaches that for known binding proteins, the specific residues that constitute the binding region of the molecule either have been, or theoretically can be, experimentally determined. Natural binding proteins, such as antibodies or protein A, have identifiable residues that promote the binding to their known targets. However, unlike natural ligands and binding proteins, the disclosed reference scaffold is not known to bind to another protein. Therefore endogenous binding residues cannot be utilized as a guide to engineer novel binding specificity. In the construction of DBDpp that bind to targets, residues were considered for mutation if they were surface exposed – exhibiting significant solvent accessibility (pages 54-55, [0156]). WO’308 further teaches that protein secondary structure, such as the alpha helices, can change depending on environmental variables such as temperature, matrix or buffer composition and concentration. WO’308 provides predicted helix residues for the reference polypeptide as well as solvent accessible and low solvent accessible residues (page 55, [0157]).
WO’308 teaches DBDpp sequences obtained from the scaffold sequence that bind to CD137, CD47, CTLA4, DR5, KIR, PD-L1, TIM3, PD1, CD123, CD19, and CD22 (pages 144-151, Table 1), demonstrating that modifications to the DBDpp domain results in binding to different targets. These teachings suggest that modification to SEQ ID NO: 14, particularly in regions that contribute to binding, would likely result in a polypeptide that does not function in specifically binding to CD123.
WO 2019/099433 A2 (D.M. Hilbert and J.S. Swers) 23 May 2019 discloses a sequence which is at least 94% identical to instant SEQ ID NO: 14, but does not bind to CD123, demonstrating that random modifications to SEQ ID NO: 14 could result in a binding peptide that binds to a completely different target and that such a result would be unpredictable.
WO’433 teaches D domain polypeptides as alternative binding domains based on a non-antibody structural scaffold (page 1, [0004]) WO’433 teaches D domain containing polypeptides that specifically bind targets of interest including BCMA, CD123, CS1, HER2, AFP, and AFP p26 (abstract) and teaches a targetless alpha helical protein scaffold of SEQ ID NO: 1 (page 189, [0428]).
WO’433 teaches a D domain binding peptide of SEQ ID NO: 916 which is disclosed as binding to HER2 (page 199, claim 1 (f)) and has at least 94% identity to instant SEQ ID NO: 14 as shown in the ABSS alignment below:
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The teachings of WO’308 and WO’433 demonstrate a lack of predictability in the art concerning modifications to D Domain binding polypeptides and target specificity.
Neither the instant disclosure nor the prior art provide a representative number of species of the claimed genus which allows for up to 6% modification anywhere in SEQ ID NO: 14, or fragments of SEQ ID NO: 14, while maintaining specific binding to CD123. Additionally, there is no disclosed, or art recognized, structure-function relationship which would allow for the modification of instant SEQ ID NO: 14 while predictably maintaining specificity for CD123 and performing the recited functions. Rather, the disclosure and prior art suggest that the structure-function relationship is not predictable. For these reasons, the instantly claimed invention was found to not meet the written description requirements of 35 USC 112(a).
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim 1 is rejected under 35 U.S.C. 102 (a)(1) and (a)(2) as being anticipated by WO 2016/164308 A1 (D.W. Lafleur and D.M. Hilbert) 13 October 2016.
WO’308 teaches de novo binding domain containing polypeptides (DBDpp) that specifically bind a target of interest as well as nucleic acids encoding the polypeptides, vectors, and host cells. WO’308 teaches libraries of DBDpp, methods of producing and screening the libraries, as well as methods of using the DBDpp (abstract).
WO’308 teaches a CD123 specific binding domain of SEQ ID NO: 135 (page 149; page 200, [0525]), which has 94.7% sequence identity to instant SEQ ID NO: 14, as shown in the ABSS alignment below, meeting the instant claim limitation of the sequence having at least 94% identity to instant SEQ ID NO: 14:
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Thus, WO’308 anticipates instant claim 1.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary.  Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 2-7 and 13-27 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2016/164308 A1 (D.W. Lafleur and D.M. Hilbert) 13 October 2016 as applied to claim 1 above.
WO’308 teaches the polypeptide of claim 1 as discussed above.
WO’308 further teaches that the DBDpp is fused to heterologous polypeptide sequences described in the disclosure or otherwise known in the art to facilitate purification (page 118, [0301]). WO’308 also teaches that multimeric DBDpp fusion proteins, containing at least two DBDpp, are fused with other heterologous proteins, or their subdomains, and that by doing so impart the multivalent and multi-specific properties to the fusion partners (page 86, [0218]). WO’308 teaches that examples of fusion partners of a DBDpp include antibodies or antibody subdomains, e.g., scFv or Fc domains, serum albumin, serum albumin subdomains, cell surface receptors and cell surface receptor subdomains, and the alpha or beta chain of a T cell receptor (page 86, [0218]).
WO’308 further teaches that polypeptide is labeled (page 5, [0014]) and/or conjugated to a therapeutic or cytotoxic agent (page 6, [0015]).
WO’308 further teaches a chimeric antigen receptor (CAR) where the CAR includes a targeting domain, a transmembrane domain, and an intracellular signaling domain and that the targeting domain is made up of, at least in part, a target-binding polypeptide disclosed.
WO’308 further teaches that the CAR comprises:
the transmembrane domain of 41BB or CD28 (page 9, [0027]);
the intracellular signaling domain of an alpha, beta, or zeta chain of the T cell receptor (page 9, [0027]). WO’308 further teaches that the intracellular signaling domain is selected from the group consisting of a human CD3 zeta domain, 41BB domain, a CD28 domain, and any combination thereof (page 7, [0021]); and
the intracellular signaling domain comprises the intracellular domain of a costimulatory molecule selected from CD27, CD28, 41BB, OX40, CD30, CD40, PD-1, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, and a ligand that specifically binds with CD83 (page 7, [0021]).
WO’308 further teaches an isolated nucleic acid molecule encoding the polypeptide (page 6, [0017]). WO’308 teaches that the terms “polynucleotide” and “nucleic acid” are used interchangeably and refer to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides (page 46, [0127]).
WO’308 teaches that any type of cells or cultured cell line can be used to express a DBDpp disclosed. WO’308 teaches that the background cell line used to generate an engineered host cell is a phage, a bacterial cell, a yeast cell, a mammalian cell and that a variety of host-expression vector systems may be used to express the coding sequence of a DBDpp fusion protein. WO’308 teaches that mammalian cells can be used as host cell systems transfected with recombinant plasmid DNA or cosmid DNA expression vectors containing the coding sequence of the target of interest and the coding sequence of the fusion polypeptide (page 112, [0285]). An ordinarily skilled artisan would reasonably conclude that WO’308’s teaching of cultured cell lines being used to express the DBDpp indicates that the cells are cultured under suitable conditions to produce the polypeptide.
WO’308 further teaches isolated nucleic acid sequences encoding the CAR that include the target-binding polypeptides as the targeting region (page 7, [0021]).
WO’308 further teaches a lentiviral vector encoding the CAR (page 168, [0427]). WO’308 teaches that the term “vector” refers to a vehicle by which the nucleic acid sequence can be introduced into a host cell, so as to transform the host and promote expression of the introduced sequence (page 46, [0129]).
WO’308 further teaches a host cell comprising the polynucleotide (page 46, [0129]; page 47, [0130]; page 171, [0436]).
WO’308 teaches cells genetically engineered to express the CAR (page 168, [0428]) and further teaches that the cell is a T cell or a natural killer cell (page 9, [0026]).
WO’308 further teaches a pharmaceutical composition comprising the polypeptide and a pharmaceutically acceptable excipient (page 160, [0395]) and that the CAR-modified T cells can be administered alone or as a pharmaceutical composition in combination with diluents and/or with other components (page 171, [0438]).
WO’308 further teaches that the immune cell comprising the CAR can be used in methods of treatment and/or diagnosis of a disease, such as cancer, e.g. a solid or hematological malignancy. WO’308 teaches that upon administration to a subject having cancer, the target binding domain specifically binds to a target of interest expressed by a cancer cell, and the binding of the target of interest induces the immune cell to generate cytotoxic signals that result in cytotoxic effects on the cancer cell, thereby treating the cancer (page 8, [0025]). WO’308 further teaches that cell exhibits an anti-tumor immunity when the polypeptide binds to its corresponding tumor antigen (pages 7-8, [0022]) and that, when T cells are used, the binding of the target of interest stimulates the T cell to initiate intracellular signaling, produces cytokines, and degranulate, leading to the cytotoxic effects on the cancer cell. WO’308 also teaches that the T cell proliferates in response to binding the target of interest (page 9, [0027]). Based on these teachings, one of ordinary skill in the art would reasonably conclude that WO’308 is teaching a method of delivering an immune response to a target cell comprising contacting a composition comprising the target cell with the CAR. An ordinarily skilled artisan would draw this conclusion as WO’308 is teaching that the CAR expressing cell is binding to the target of interest, initiating intracellular signaling, producing cytokines and degranulates leading to a cytotoxic effect and that the cell also proliferates.
WO’308 further teaches that the target cell is a cancer cell and that the cancer is an acute leukemia such as acute myelocytic leukemia and acute myelogenous leukemia (page 165, [0418]). WO’308 further teaches that the contacting occurs in a human subject (page 10, [0033]; page 48, [0137]).
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to have arrived at the instantly claimed invention based on the teachings of WO’308. As discussed above, WO’308 teaches a DBDpp of SEQ ID NO: 135, which specifically binds to CD123. WO’308 also teaches that the DBDpps disclosed may be used in heterologous polypeptides, CARs, adapters, and methods of delivering an immune response. Therefore, it would have been obvious to use the DBDpp of SEQ ID NO: 135 in heterologous polypeptides, CARs, adapters, and in methods of delivering an immune response with a reasonable expectation of success.
In regards to claims 26 and 27, there is no limitation in claims 25, 26, or 27 that require that the patient be administered an adapter. WO’308 anticipates claim 25 part (a). While claim 26 further limits part (b) of claim 25, claim 26 does not limit claim 25 to requiring part (b). Claim 27 is dependent from claim 26. Since claim 25 is met by part (a), the limitations of claims 26 and 27 are also met.
Claims 9-12 and 25-27 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2016/164308 A1 (D.W. Lafleur and D.M. Hilbert) 13 October 2016 in view of WO 2019/099440 A1 (Hilbert, D.M and D.W. Lafleur) 23 MAY 2019.
It is noted that claims 25-27 were rejected above under 35 USC 103 over WO’308. The claims are further rejected here to demonstrate that the alternative limitations were known in the prior art.
The teachings of WO’308 are as discussed above.
WO’308, however, does not disclose that the D domain is comprised in an adapter with an antigenic determinant (AD).
WO’440 teaches multi-functional chimeric antigen receptor (CAR)-based compositions and their use in directing immune responses to target cells for the treatment of hyperproliferative disorders, such as cancer. WO’440 discloses methods including the use of CAR cells in combination with an adapter, where the adapter confers the ability to modulate, alter, and/or redirect CAR cell-mediated immune response in vitro and in vivo (abstract).
WO’440 teaches that adapters are multi-domain soluble proteins that comprise an antigenic determinant (AD) and an antigenic determinant binding domain (ADBD), where the ADBD binds to a second AD. WO’440 further discloses that an adapter can comprise additional AD, additional ADBD, and/or other additional domains (page 61, [0113]). WO’440 teaches that the ADBD(s) are an alternative scaffold binding domain (ASBD) (page 82, [0212]) including a D domain (de novo binding domain) (page 82, [0216]). WO’440 teaches an adapter that comprises an ABDB that binds to CD123 (page 21, [64.]).
WO’440 further teaches that the AD comprises an AFP p26 polypeptide (page 91, [0262]-[0263]).
WO’440 further teaches that the adapter comprises a p26 protein having the sequence of SEQ ID NO: 16, 1117, 1118, 1119, 1120, 1121, 1122, or 1123 (page 91, [0262]-[0263]). The sequences disclosed for p26 in WO’440 match those of instant SEQ ID NO:s 37-43 and 44, as shown in the ABSS alignments below:
WO’440, SEQ ID NO: 16 aligned with instant application SEQ ID NO: 37:
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WO’440, SEQ ID NO: 1117 aligned with instant application SEQ ID NO: 38:
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WO’440, SEQ ID NO: 1118 aligned with instant application SEQ ID NO: 39:
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370
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WO’440, SEQ ID NO: 1119 aligned with instant application SEQ ID NO: 40:
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373
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WO’440, SEQ ID NO: 1120 aligned with instant application SEQ ID NO: 41:
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365
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WO’440, SEQ ID NO: 1121 aligned with instant application SEQ ID NO: 42:
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371
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WO’440, SEQ ID NO: 1122 aligned with instant application SEQ ID NO: 43:
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WO’440, SEQ ID NO: 1123 aligned with instant application SEQ ID NO: 44:
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WO’440 teaches an adapter that comprises an ABDB that binds to CD123 (page 21, [64.]). WO’440 further teaches that the adapter comprises at least one ADBD (page 92, [0268]). WO’440 also teaches a homo-multimeric adapter that contains more than one, including two or more, of the same ADBD (page 92, [0269]).
WO’440 teaches methods of delivering an immune response to a target cell in a patient and/or killing a target cell in a patient comprising administering the adapter. WO’440 further teaches a method of treating cancer comprising administering the adapter (page 142, [0506]).
WO’440 teaches compositions that can be used to treat cancer and teaches that the methods generally include the use of a CAR cell in combination with an adapter where the adapter confers the ability to modulate, alter, and/or redirect CAR cell-mediated immune response in vitro and in vivo (abstract).
WO’440 further teaches a method of delivering an immune response to a patient comprising administering an adapter to a patient with cancer. WO’440 further teaches that the patient has been treated with a cell expressing a chimeric antigen receptor (CAR) comprising an antigenic determinant binding domain that is an ASBD that binds to a first antigenic determinant AD (e.g., AFP p26 or a variant thereof), a transmembrane domain, and an intracellular domain (pages 153-154, [0538]). Additionally, WO’440 teaches an example in which a CD123-p26 adapter (cg06-p26) was studied in combination with a p26-binding CAR to assess cell lysis (page 268, Example 4, [0701]).
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to have modified the teachings of WO’308 and include the CD123 D domain target binding domain in an adapter comprising the D domain target binding domain and an antigenic determinant (AD) as taught by WO’440 and to have applied the adapter in the methods disclosed by WO’440. An ordinarily skilled artisan would have been motivated to make this combination in order to treat hyperproliferative disorders using an adapter that has been known to have the ability to modulate, alter, and/or redirect CAR cell-mediated immune response in vitro and in vivo, as taught by WO’440 (abstract). An ordinarily skilled artisan would have had a reasonable expectation of success as both WO’308 and WO’440 are both teaching D Domain binding polypeptides that bind to CD123 and WO’440 teaches the use of such polypeptides in adapters.
Non-statutory 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.
U.S. Patent No. 11,827,716
Claims 1-28 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-27 of U.S. Patent No. 11,827,716. Although the claims at issue are not identical, they are not patentably distinct from each other.
Claim 1 of US’716 claims a D domain target binding polypeptide that specifically binds CD123 and comprises the amino acid sequence of SEQ ID NOs: 8, 13, or 14. US’716, SEQ ID NO: 14 is identical to instant SEQ ID NO: 14 as shown in the ABSS alignment below:
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Claim 11 of US’716 claims a CAR comprising the amino acid sequence of SEQ ID NO: 67, which is identical to instant SEQ ID NO: 67 as shown in the alignment below:
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Instant claims 2-7 and 9-27 recite the same limitations as the claims of US’716 as follows: Instant claims 2-4 and US’716 claims 2-4, respectively; instant claims 5-7 and US’716 claims 8-10, respectively; instant claims 9-12 and US’716 claims 19-22, respectively; instant claims 13-15 and US’716 claims 5-6, respectively; instant claims 15-19 and US’716 claims 12-16, respectively; instant claim 20 and US’716 claim 7; instant claims 21-22 and US’716 claims 17-18, respectively; instant claims 23-27 and US’716 claims 23-27, respectively
As US’716 claims a D Domain polypeptide matching SEQ ID NO: 14, which is a species of the instantly claimed genus, US’716 anticipates instant claims 1-28.
U.S. Patent No. 11,464,803
Claims 1-3, 13, and 20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-8 of U.S. Patent No. 11,464,803. Although the claims at issue are not identical, they are not patentably distinct from each other.
US’803 claims proteins comprising a D Domain target binding domain fused to an AFP p26 polypeptide, wherein the D Domain specifically binds CD123 and wherein the AFP p26 polypeptide consists of the recited amino acid sequences. US’803 further claims a pharmaceutical composition comprising the protein as well as nucleic acids encoding the proteins. US’803 claims that the DD comprises an amino acid including that of SEQ ID NO: 344, which has 94.7% identity to instant SEQ ID NO: 14 as shown in the ABSS alignment below:
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The claims of US’803 are species of instant claims 1-3, 13, and 20 and, therefore, anticipate the instant claims. See MPEP 2131.02.
Claims 4-12, 14-19, and 21-27 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-8 of U.S. Patent No. 11,464,803 in view of WO 2016/164308 A1 (D.W. Lafleur and D.M. Hilbert) 13 October 2016 and WO 2019/099440 A1 (Hilbert, D.M and D.W. Lafleur) 23 MAY 2019 .
The claims of US’803 are as discussed above.
The claims of US’803 differ from the instantly claimed invention in that US’803 does not claim the use of the CD123 binding D Domain in a CAR, in an adapter, or in methods of delivering an immune response to a target cell, killing a target cell, or treating cancer.
The teachings of WO’308 and WO’440 are as discussed above.
It would have been prima facie obvious to one of ordinary skill in the art to modify the claims of US’803 with the teachings of WO’308 concerning D Domains and CAR expressing cells and the teachings of WO’440 concerning adapters to arrive at the instantly claimed invention. It would have been obvious to one or ordinary skill in the art to modify US’803 with the teachings of WO’308 and WO’440 as all three of US’803, WO’308, and WO’440 are teachings D Domains that bind to CD123 and their use in recombinant proteins and methods of therapy. Thus an ordinarily skilled artisan would have had a reasonable expectation of success.
Conclusion
No claims are allowed.

APPLICANT REBUTTAL: REMARKS
Claims 1-28 were pending prior to entry of the abovementioned amendments. Claims 1, 10, 23 and 26 are herein amended. New claims 29 and 30 herein added. The claim amendments and new claims are fully supported by the application as originally filed, for example, at paragraphs [0441], [0453], [0993] and Table 1. No new matter is added by any of these amendments. Accordingly, upon entry, claims 1-30 will be pending.
Reconsideration and allowance of this application is respectfully requested in light of the abovementioned amendments and the following remarks.
Claim Ob
j
ection
Claim 10 stands objected to for ending in a comma instead of a period. Applicant has amended claim 10 to end in a period. Accordingly, Applicant respectfully requests that the objection to claim 10 be withdrawn.
35 U.S.C.
Claims 1-27 stand rejected under 35 U.S.C. 112(a) as allegedly failing to comply with the written description requirement. Specifically, the Office alleges that "[t]he disclosure . .. does not provide a representative number of species of the claimed genus nor does the disclosure identify a structure-function relationship which would allow an ordinarily skilled artisan to identify which amino acids in SEQ ID NO: 14 could be modified such that the polypeptide would maintain binding to CD123." Office Action, p. 4. Further, the Office alleges that "the claims recite 'an' amino acid sequence of SEQ ID NO: 14 suggesting that the claim encompasses fragments of SEQ ID NO: 14 and does not require the full length sequence." Id. at p. 3.
Without conceding to the basis of the rejection and solely to expedite prosecution of this application, Applicant has amended claim 1 to recite "A D Domain target binding domain polypeptide that specifically binds CD 123 and comprises an amino acid sequence that has at least 96% sequence identity to SEQ ID NO: 14." Applicant submits that amended claim 1 complies with the written description requirement at least for the following reasons.
As a preliminary matter, Applicant submits that amended claim 1 does not encompass mere fragments of SEQ ID NO: 14, and instead encompasses D domain target binding domain polypeptides that each "comprise[] an amino acid sequence that has at least 96% identity to SEQ ID NO: 14."
Additionally, Applicant submits that the disclosure provides a representative number of species of the claimed genus, which is sufficient for one of ordinary skill in the art to understand the inventors had possession of the claimed subject matter. For example, Table 1 of the Application provides 35 exemplary D domains that bind to CD123. The 35 exemplary CD123- binding D domains demonstrate amino acid substitutions relative to SEQ ID NO: 14 in numerous amino acid positions. While the 35 exemplary CD 123-binding D domains do not encompass every possible species, "[d]escription of a representative number of species does not require the description to be of such specificity that it would provide individual support for each species that the genus embraces." MPEP 2163 II.A.3.a.ii. Further, Applicant notes that claim 1 has been amended to encompass only D domains that specifically bind CD 123 and comprise an amino acid sequence that has at least 96% sequence identity to SEQ ID NO: 14 (effectively allowing for only two substitutions relative to SEQ ID NO: 14 and greatly narrowing the number of species within the claimed genus). As the disclosure of the Application (e.g., the 35 exemplary CD123-binding D domains) would allow a person of ordinary skill in the art to reasonably predict the species encompassed by claim 1, the disclosure of the Application provides a representative number of species. Thus, a person of ordinary skill in the art would understand the inventors to be in possession of the claimed subject matter.
Accordingly, Applicant respectfully requests that the written description rejection under § 112(a) of claim 1 be withdrawn. Further, each of claims 2-27 depends, directly or indirectly, from claim 1 and thus include all elements of claim 1. Therefore, for at least the reasons discussed above with respect to independent claim 1, Applicant submits that claims 2-27 comply with the written description requirement. Accordingly, Applicant respectfully requests that the written description rejection under § 112(a) of claims 2-27 be withdrawn.
35 U.S.C.
&
Claim 1 stands rejected under 35 U.S.C. 102(a)(1) and (a)(2) over W02016/164308 ("LaFleur").
Without conceding to the basis of the rejection and solely to expedite prosecution of this application, Applicant has amended claim 1 to recite "A D Domain target binding domain polypeptide that specifically binds CD 123 and comprises an amino acid sequence that has at least 96% sequence identity to SEQ ID NO: 14." Applicant submits that amended claim 1 is novel over LaFleur at least because LaFleur does not disclose all elements of amended claim 1.
Accordingly, Applicant respectfully requests that the § 102(a)(1) and § 102(a)(2) rejections of claim 1 be withdrawn.
35 U.S.C.
&
Claims 2-7 and 13-27 stand rejected under 35 U.S.C. 103 over LaFleur as applied to claim
1 above. Claims 9-12 and 25-27 stand rejected under 35 U.S.C. 103 over LaFleur in view of W02019/099440 ("Hilbert").
Without conceding to the basis of the rejection and solely to expedite prosecution of this application, Applicant has amended claim 1 to recite "A D Domain target binding domain polypeptide that specifically binds CD 123 and comprises an amino acid sequence that has at least 96% sequence identity to SEQ ID NO: 14." Applicant submits that amended claim 1 is non- obvious over the cited references at least because LaFleur and Hilbert, considered alone or in combination, fail to disclose all elements of the amended claims.
Further, each of claims 2-7 and 9-27 depends, directly or indirectly, from claim 1 and thus includes all elements of claim 1. Therefore, for at least the reasons discussed above with respect to independent claim 1, Applicant submits that claims 2-7 and 9-27 are non-obvious over the cited references. Accordingly, Applicant respectfully requests that the § 103 rejections of claims 2-7 and 9-27 be withdrawn.
DOUBLE PATENTING
U.S. Patent No. 11,827,716
The Examiner has rejected claims 1-28 under the judicially created doctrine of obviousness-type double patenting over claims 1-27 of U.S. Patent No. 11,827,716.
A terminal disclaimer with respect to U.S. Pat. No. 11,827,716 is filed concurrent with this response. "The filing of a terminal disclaimer to obviate a rejection based on nonstatutory double patenting is not an admission of the propriety of the rejection. MPEP 804.02(II) (citing Quad Environmental Technologies Corp. v. Union Sanitary District, 946 F.2d 870 (Fed. Cir. 1991). Rather, the "filing of a terminal disclaimer simply serves the statutory function of removing the rejection of double patenting, and raises neither a presumption nor estoppel on the merits of the rejection." Id. Accordingly, in view of submission of the terminal disclaimer, Applicant respectfully requests that the rejection of claims 1-28 over claims 1-27 of U.S. Pat. No. 11,827,716 be withdrawn.
U.S. Patent No. 11,464,803
The Examiner has rejected claims 1-3, 13, and 20 under the judicially created doctrine of obviousness-type double patenting over claims 1-8 of U.S. Patent No. 11,464,803. The Examiner has rejected claims 4-12, 14-19 and 21-27 under the judicially created doctrine of obviousness- type double patenting over claims 1-8 of U.S. Patent No. 11,464,803 in view of LaFleur and Hilbert.
Applicant respectfully traverses these rejections. As amended herein, claim 1 recites a "D Domain target binding domain polypeptide that specifically binds CD 123 and comprises an amino acid sequence that has at least 96% sequence identity to SEQ ID NO: 14." At least because the Office has failed to establish that claims of the cited references disclose a "D Domain target binding domain polypeptide that specifically binds CD 123 and comprises an amino acid sequence that has at least 96% sequence identity to SEQ ID NO: 14" as recited in claim 1 (or nucleic acids that encode the same), Applicant submits that the Office has failed to demonstrate that the pending claims are patentably indistinct from the claims of the cited references.
Accordingly, Applicant respectfully requests that the obviousness-type double patenting rejections be withdrawn.
***
It shall be understood herein that any instance in which Applicant has addressed certain comments set forth by the Office shall not be construed as a concession to other comments or arguments advanced by the Office. Any circumstance in which Applicant has amended or canceled a claim also does not mean that Applicant concedes to the arguments or positions advanced by the Office with respect to that claim or other claims pending herein.
CONCLUSION

NEXT OFFICE ACTION: 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 .
In the event the determination of the status of the application as subject to AIA  35 U.S.C. 102 and 103 (or as subject to pre-AIA  35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Priority
The instant application, filed 10/13/2023, is a continuation of application 18/055,096, filed 11/14/2022, and claims domestic benefit to US provisional application 63/279,489, filed 11/15/2021.
Status of Application, Amendments, and/or Claims
Applicant’s amendment of 11/14/2024 is acknowledged. Claims 1, 10, 23, and 26 are amended and claims 29-30 are new. Claims 1-30 are currently pending and are examined on the merits herein.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 11/14/2024 is in compliance with the provisions of 37 CFR 1.97.  Accordingly, the information disclosure statement has been considered by the examiner.
Withdrawn Objections and Rejections
In the office action of 08/20/2024:
Claim 10 was objected to for being terminated with a comma. Applicant’s amendment to change the comma to a period has overcome the objection and the objection is withdrawn.
Claim 1 was rejected under 35 USC 102(a)(1) and (a)(2) as being anticipated by WO’308. Applicant’s amendment to the claim to further limit the sequence identity to 96% has overcome the rejection and the rejection is withdrawn.
Claims 2-7 and 13-27 were rejected under 35 USC 103 over WO’308 and claims 9-12 and 25-27 were rejected under 35 USC 103 over WO’308 in view of WO’440. Applicant’s amendment to the independent claim to further limit the sequence identity to 96% has overcome the rejection and the rejection is withdrawn.
Claims 1-28 were rejected on the grounds of nonstatutory double patenting over US 11,827,716. Applicant’s filing and the approval of a terminal disclaimer has overcome the rejections and the rejections are withdrawn.
The following grounds of rejection are modified as necessitated by applicant’s amendment to the claims.
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 1-27 and 29-30 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.
The instant claims are drawn to D domain polypeptides that specifically bind CD123 and comprise an amino acid sequence that has at least 96% sequence identity to an amino acid sequence of SEQ ID NO: 14 and the use of the domain in heterologous polypeptides, CARs, and adapters. The claims allow for up to 4% modification in the recited amino acid sequence (at least 96% identity). Based on the recitation of “at least 96% identity”, the claims are drawn to a genus of D domain polypeptides all of which are claimed as having the function of specifically binding to CD123. The claims further recite methods in which the D Domain polypeptides are used in methods of delivering an immune response, killing a target cell, or treating cancer, all of which are functions of the claimed D Domains.
Newly added claim 29 limits the substitutions in SEQ ID NO: 14 to being in amino acid residues 5, 8, 9, 12, 15-17, 19, 21, 24, 30, 33, 34, 37, 40, 41, 44, 48, 50, 55, 57-59, 61, 62, 64-66, and 68. While the limitation narrows the locations of the modifications in SEQ ID NO: 14, the claim remains drawn to a genus of D domain polypeptides in which substitutions can be made in any of the recited locations with any amino acid, as long as the resulting sequence is 96% identical to SEQ ID NO: 14, and are claimed as having the function of specifically binding to CD123.
Newly added claim 30 limits the D domain binding polypeptide to comprising a serine in position 50. The claim, however, remains drawn to a genus in which any amino acids in SEQ ID NO: 14 can be modified, as long as the resulting sequence is 96% identical to SEQ ID NO: 14 and has a serine in position 50. The claim also limits the binding domains as having the function of specifically binding to CD123.
The disclosure, however, does not provide a representative number of species of the claimed genus nor does the disclosure identify a structure-function relationship which would allow an ordinarily skilled artisan to identify which amino acids in SEQ ID NO: 14 could be modified such that the polypeptide would maintain binding to CD123 and function in methods of delivering immune response, killing target cells, or treating cancer. This is particularly the case as, in the broadest reasonable interpretation of the independent claim, the 4% variance could be located anywhere in the amino acid sequence including areas that contribute to CD123 binding.
With regards to claim 29, while the claim acts to further limit the locations of the substitutions, the claim still allows for a large number of possible modifications where amino acids in the recited positions are substituted with any other amino acid, as long as the resulting sequence is 96% identical to SEQ ID NO: 14 and still claimed to have the required function of binding to CD123. The instant disclosure does not provide a representative number of species of the claimed genus performing this function or a structure-function relationship that would allow for the predictable identification of which substitutions in which positions in combination would maintain the claimed function.
With regards to claim 30, while the claim requires that the serine in position 50 be unchanged, the disclosure does not provide a representative number of species of the claimed genus in which any other amino acid could be modified and still result in the claimed function. The instant disclosure also does not suggest that the serine in position 50 is the amino acid that is responsible for the binding function of the polypeptide, such that maintaining this amino acid would maintain binding specificity.
The instant specification discloses 35 D domain sequences that target CD123 in Table 1 (pages 52-54), including SEQ ID NO: 14. Of these, only SEQ ID NOs: 11-14 are species of the instantly claimed genus in which the sequences have at least 96% identity to SEQ ID NO: 14 and bind to CD123. The ABSS alignment of these sequences are shown below.
SEQ ID NO: 14 aligned with SEQ ID NO: 11
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SEQ ID NO: 14 aligned with SEQ ID NO: 12
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SEQ ID NO: 14 aligned with SEQ ID NO: 13
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As shown above:
SEQ ID NO: 11 is 96.5% identical to SEQ ID NO: 14, with 3 substitutions of G8, L21, and I59;
SEQ ID NO: 12 is 97.1% identical to SEQ ID NO: 14, with 3 substitutions of G8, K48, and N50
SEQ ID NO: 13 is 98.1% identical to SEQ ID NO: 14, with 1 substitution of L21
These sequences represent the species of the claimed genus that applicant was in possession of at the time of the effective filing date of the claimed invention.
These sequences, however, are not representative of the entire claimed genus as the sequences disclosed do not comprise modifications that span the entirety of the claimed genus in which up to 4% modification can be made anywhere, and in anyway, in the amino acid sequence of SEQ ID NO: 14 while maintaining binding to CD123 and maintaining the functions of delivering an immune response, killing target cells, or treating cancer. Additionally, the substitutions in these sequences compared to SEQ ID NO: 14 do not encompass all of those recited in claim 29, nor do they all have a serine in position 50 as recited in claim 30, for instance SEQ ID NOs: 12, has an asparagine (N) in position 50.
Furthermore, the disclosure does not describe a structure-function relationship which would allow an ordinarily skilled artisan to predictably identify which amino acid sequences with 96% sequence identity to SEQ ID NO: 14, would maintain binding to CD123. Rather, the disclosure suggests that modifications in the D domains are not predictable.
The examples of the disclosure describe the isolation of the variant D domains with increased affinity to CD123 (page 214, Example 1). The examples disclose that methods of improving affinity of D domains for target antigens, for example CD123, can include mutagenesis of existing amino acid sequences. These mutations can be directed towards specific amino acids or randomly distributed through the sequence. Mutated D domains are subsequently assayed for changes in binding characteristics, protein expression, or other biological activity associated with a particular application or function. The example goes on to describe the production and testing of CD123 binding domains (page 214, [0662]). As the mutations made to the D domain to confer binding properties are disclosed as including both specific targeted mutations as well as randomly distributed mutations and that the mutated D domains then require assay for changes in binding characteristics, it is further suggested that the structure-function of the D domains is not predictable.
The instant specification further discloses that the term D domain refers to a target binding polypeptide sharing certain sequences and certain structural features of the reference scaffold sequence of SEQ ID NO: 2. The reference scaffold is a variant of a non-naturally occurring and targetless antiparallel three helical bundle reference polypeptide that has no known target binding activity. It has been discovered that polypeptides containing modifications of the reference scaffold are able to specifically bind to targets of interest. Therefore, a D domain, or molecule comprising a D domain, can specifically bind to a target molecule. The specification further discloses that it is believed that in designing the D domain the structural constraints of surface-exposed residues, that can be modified, confer the ability of the surface exposed residues to specifically bind a target of interest (page 28, [0040]). However, it is not apparent from the instant disclosure which amino acids are considered to be surface-exposed.
Through these teachings, the instant disclosure demonstrates an unpredictability in modifying D domains while maintaining binding specificity. As discussed in the disclosure, modifications in the surface exposed residues of the antiparallel three helical bundle can change the specific binding of the domain. The disclosure, however, does not identify which of the amino acids in SEQ ID NO: 14 are the surface-exposed residues that are responsible for binding such that the specific binding could be predictably maintained while making modifications. Additionally, as discussed above, in the broadest reasonable interpretation of the claims, the 4% modification could occur anywhere in SEQ ID NO: 14, including areas that could be responsible for binding.
The prior art also does not provide a representative number of species of the claimed genus or a structure-function relationship which would allow for the modification of the D domain with predictable results.
WO 2016/164308 A1 (D.W. Lafleur and D.M. Hilbert) 13 October 2016 teaches de novo binding domain containing polypeptides (DBDpp) that specifically bind a target of interest as well as libraries of DBDpp, methods of producing and screening such libraries, and DBDpp identified from such processes (abstract). WO’308 teaches a reference scaffold which is a variant of a non-naturally occurring and targetless antiparallel three helical bundle peptide of SEQ ID NO: 1. Like the instant disclosure, WO’308 teaches that modification to the structural constraints of surface exposed residues that can be modified confer the ability of the residues to specifically bind a target of interest (page 52, [0151]).
WO’308 further teaches that for known binding proteins, the specific residues that constitute the binding region of the molecule either have been, or theoretically can be, experimentally determined. Natural binding proteins, such as antibodies or protein A, have identifiable residues that promote the binding to their known targets. However, unlike natural ligands and binding proteins, the disclosed reference scaffold is not known to bind to another protein (pages 54-55, [0156]). WO’308 goes on to state that therefore endogenous binding residues cannot be utilized as a guide to engineer novel binding specificity (page 55, lines 3-4). WO’308 teaches that in the construction of DBDpp that bind to targets, residues were considered for mutation if they were surface exposed – exhibiting significant solvent accessibility (pages 54-55, [0156]). WO’308 does study the reference scaffold disclosed, which differs from the reference scaffold of the claimed invention in a single conservative substitution, and identifies potential solvent accessible, alpha helical residues including 2-6, 8-10, 12-13, 15-17, 19-20, 29-30, 32-34, 36-37, 39-40, 41, 43-44, 52, 54-55, 57-59, 61-62, 64-66, and 68-70 (page 55, [0157]). If these residues were used for comparison to the scaffold of the instant disclosure, it would indicate that 26 out of the 29 positions recited in instant claim 29 are in solvent accessible positions that could potentially change binding specificity. In any case, WO’308 goes on to teach that protein secondary structure, such as the alpha helices, can change depending on environmental variables such as temperature, matrix or buffer composition and concentration (page 55, [0157]). This teaching suggests that the identified solvent accessible residues could change further establishing that structure-function of the DBDpps is not predictable.
WO’308 teaches DBDpp sequences obtained from the scaffold sequence that bind to CD137, CD47, CTLA4, DR5, KIR, PD-L1, TIM3, PD1, CD123, CD19, and CD22 (pages 144-151, Table 1), demonstrating that modifications to the DBDpp domain results in binding to different targets. These teachings suggest that modification to SEQ ID NO: 14, particularly in regions that contribute to binding, would likely result in a polypeptide that does not function in specifically binding to CD123.
WO 2019/099433 A2 (D.M. Hilbert and J.S. Swers) 23 May 2019  teaches D domain polypeptides as alternative binding domains based on a non-antibody structural scaffold (page 1, [0004]) WO’433 teaches D domain containing polypeptides that specifically bind targets of interest including BCMA, CD123, CS1, HER2, AFP, and AFP p26 (abstract) and teaches a targetless alpha helical protein scaffold of SEQ ID NO: 1 (page 189, [0428]).
The teachings of WO’308 and WO’433 demonstrate a lack of predictability in the art concerning modifications to D Domain binding polypeptides and target specificity.
Neither the instant disclosure nor the prior art provide a representative number of species of the claimed genus which allows for up to 4% modification in SEQ ID NO: 14, while maintaining specific binding to CD123. Additionally, there is no disclosed, or art recognized, structure-function relationship which would allow for the modification of instant SEQ ID NO: 14 while predictably maintaining specificity for CD123 and performing the recited functions. Rather, the disclosure and prior art suggest that the structure-function relationship is not predictable. For these reasons, the instantly claimed invention was found to not meet the written description requirements of 35 USC 112(a).
Response to Arguments
Applicant’s arguments in the response of 11/14/2024 regarding the rejections under 35 USC 112(a) have been fully considered in so far as they apply to the rejections of the instant office action, but were not found to be persuasive.
In the response, applicant argues that the disclosure provides a representative number of species of the claimed genus sufficient for one of ordinary skill in the art to recognize that the inventor was in possession of the claimed subject matter at the time of filing. Applicant references table 1 as disclosing 35 exemplary D domains that bind to CD123, demonstrating substitutions relative to SEQ ID NO: 14 in numerous amino acid positions. Applicant references MPEP 2163 II.A.3.a.ii as stating that a representative number of species does not require individual support for each species within a claimed genus.
While table 1 does show 35 exemplary D domains that bind to CD123, not all 35 D domains disclosed are encompassed by the instantly claimed invention which require that the D domains have at least 96% identity to SEQ ID NO: 14. As discussed in detail in the rejection above, of the 35 sequences disclosed in table 1, only SEQ ID NOs: 11-14 are species of the instantly claimed invention.
Furthermore, while MPEP 2163 II.A.3.a.ii does state that individual support for each species within the genus is not required, the section of the MPEP states that “A ‘representative number of species’ means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus.”
In this case, the species disclosed do not fully support the entire variation that is within the claimed genus and; therefore, are not a representative number of species. This is particularly the case as the specificity of binding polypeptides depends heavily on the amino acid structure and; therefore, can change drastically based on limited modifications to the amino acid structure. For instance, the applied references WO’308 and WO’433 demonstrate that amino acid modifications to the same scaffold polypeptide results in polypeptides that bind to drastically different antigens.
Applicant argues that the claim is now limited to at least 96% sequence identity, effectively allowing for only two substitutions relative to SEQ ID NO: 14 and greatly narrowing the number of species in the claimed genus.
While the claims have been amended to further limit the sequence identity and narrow the number of species, the claims still encompass a wide genus of species in which any 2-3 amino acids can be changed anywhere in SEQ ID NO: 14. As discussed in detail in the rejection above, neither the disclosure nor the art provide a representative number of species of the claimed genus. Nor does the disclosure or art provide a structure-function correlation that would allow an ordinarily skilled artisan to identify which amino acids in which positions could be substituted such that the binding polypeptide would retain its function of specifically binding CD123. This is particularly the case as neither the disclosure nor the art clearly define which amino acids/positions in SEQ ID NO: 14 are responsible for the claimed function such that the modification could be limited to non-binding regions.
Allowable Subject Matter
Claim 28 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form.
The following is a statement of reasons for the indication of allowable subject matter:  instant claim 28 is drawn to the polypeptide comprising the D domain of claim 1 and further limits the D domain to having 100% identity to instant SEQ ID NO: 14.
In searches of the prior art, no D Domain binding polypeptides that specifically bind CD123 were identified with an amino acid structure identical to instant SEQ ID NO: 14. Additionally, no suggestion was identified in the art that would have encouraged an ordinarily skilled artisan to alter known D domains to arrive at instant SEQ ID NO: 14 with a reasonable expectation that the resulting D domain would be specific for CD123. As such, the claimed sequence was also found to be non-obvious. The following is considered to be the closest prior art:
WO 2016/164308 A1 (Lafleur, D.W. and D.M. Hilbert) 13 OCT 2016
WO’308 is drawn to de novo binding domain containing polypeptides (DBDpp) that specifically bind a target of interest. WO’308 teaches nucleic acids encoding the polypeptides as well as vectors, and host cells containing the nucleic acids. WO’308 also teaches libraries of DBDpp as well as methods of producing and screening the libraries and methods of using the DBDpp (abstract).
WO’308 discloses SEQ ID NO: 1 which is a non-naturally occurring and targetless antiparallel three-helical bundle that can be used as a reference scaffold platform for producing de novo binding domain (DBD) containing polypeptides (DBDpp) that bind to a target of interest.  WO’308 further discloses that the scaffold can be used to create libraries which can be screened for DBDpp that have desired functional and/or biological activity (page 52, [0151]).
WO’308 discloses the generation and selection of CD123 targeting DBDpp based off of the reference sequence of SEQ ID NO: 1 which was modified in a plurality of positions resulting in a library of DBDpp corresponding to the genus SEQ ID NOs: 2, 4, and 6. These sequences represent numerous DBDpp exhibiting specificity for CD123 (page 199, [0520]-[0522]). WO’308 further de-immunized a species of SEQ ID NO: 4 to generate SEQ ID NO: 135, a DBDpp with specificity for CD123 (page 200, [0525]; page 149, SEQ ID NO: 135). WO’308, SEQ ID NO: 135 is identical to the parent D domain of the instant application (instant SEQ ID NO: 5) but differs from instantly claimed SEQ ID NO: 14 by 5 substitutions, as shown in the ABSS alignment below:
Instant SEQ ID NO: 14 aligned with WO’308, SEQ ID NO: 135
PNG
media_image4.png
183
624
media_image4.png
Greyscale
As shown in the alignments above, the claimed sequence differs from WO’308, SEQ ID NO: 135 with the following substitutions: G8S, L21Q, K48E, N50S, and I59L.
WO’308, SEQ ID NOs: 2, 4, and 6 suggest that the amino acids in positions 8 and 59 could be substituted in SEQ ID NO: 135 and result in a DBDpp that maintains specificity for CD123 (pages 207-208, claim 21). WO’308, however, does not provide a reasonable expectation that the substitution of the amino acids in positions 21, 48, or 50 would still result in a binding polypeptide specific for CD123. WO’308 identifies these positions as positions that could be modified in SEQ ID NO: 1, however, SEQ ID NO: 1 is considered by the reference to be targetless and, therefore, there is no suggestion that modifying these amino acids as claimed would maintain specificity for CD123. Additionally, WO’308 does not disclose CD123 binding polypeptides that comprise substitutions in positions 21, 48, or 50.
Based on the nature of binding polypeptide functionality and the sensitivity of the binding polypeptides to variation in the amino acid sequences, it would not have been obvious or predictable to one of ordinary skill in the art prior to the effective filing date of the claimed invention to have modified the teachings of WO’308 to arrive at the exact binding polypeptide structure of the instantly claimed invention without undergoing a significant amount of trial and error experimentation to ensure specificity for CD123. Therefore, the instantly claimed sequences were found to be free of, and non-obvious in view of, the prior art.
Conclusion
THIS ACTION IS MADE FINAL.  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 extension fee 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.

CITED REFERENCE SUMMARIES: Ref US10647775: Claims:
A method for purifying a target of interest comprising: (a) contacting a sample comprising a target of interest with a composition comprising: a polypeptide attached to a solid support, wherein the polypeptide comprises an amino acid sequence selected from the group consisting of:
(a) contacting a sample comprising a target of interest with a composition comprising: a polypeptide attached to a solid support, wherein the polypeptide comprises an amino acid sequence selected from the group consisting of:
a polypeptide attached to a solid support, wherein the polypeptide comprises an amino acid sequence selected from the group consisting of:
(SEQ ID NO: 2) MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALGGSEAELAX 30 FEX 33 X 34 IAX 37 FEX 40 X 41 LQ X 44 YKGKGNPEVEALRKEAAAIRDELQAY RHN, (SEQ ID NO: 3) MGSWAEFKQRLAAIKTRLEALGGSEAELAAFX 32 X 33 EIX 36 AFX 39 X 40 ELX 43 AYKGKGNPEVEALX 57 X 58 EAX 61 AIX 64 X 65 ELX 68 AYRHN, (SEQ ID NO: 4) MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALGGSEAELAAFEKEIAAFE SELQAYKGKGNPEVEX 55 LRX 58 X 59 AAX 62 IRX 65 X 66 LQAYRHN, (SEQ ID NO: 5) MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALGGSEAELAAFX 32 X 33 EI X 36 AFX 39 X 40 ELX 43 AYKGKGNPEVEX 55 LRX 58 X 59 AAX 62 IRX 65 X 66 LQAYRHN, (SEQ ID NO: 6) MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALGGSEAELAX 30 FEX 33 X 34 IAX 37 FEX 40 X 41 LQX 44 YKGKGNPEVEALX 57 X 58 EAX 61 AIX 64 X 65 ELX 68 AYRHN, (SEQ ID NO: 7) MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALZ 1 EAELAX 28 FEX 31 X 32 IAX 35 FEX 38 X 39 LQX 42 YZ 2 NPEVEALRKEAAAIRDELQAYRHN, (SEQ ID NO: 8) MGSWAEFKQRLAAIKTRLEALZ 1 EAELAAFX 30 X 31 EIX 34 AFX 37 X 38 E LX 41 AYZ 2 NPEVEALX 52 X 53 EAX 56 AIX 59 X 60 ELX 63 AYRHN, (SEQ ID NO: 9) MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALZ 1 EAELAAFEKEIAAFES ELQAYZ 2 NPEVEX 50 LRX 53 X 54 AAX 57 IRX 60 X 61 LQAYRHN, (SEQ ID NO: 10) MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALZ 1 EAELAAFX 30 X 31 EI X 34 AFX 37 X 38 ELX 41 AYZ 2 NPEVEX 50 LRX 53 X 54 AAX 57 IRX 60 X 61 LQ AYRHN, and (SEQ ID NO: 11) MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALZ 1 EAELAX 28 FEX 31 X 32 IAX 35 FEX 38 X 39 LQX 42 YZ 2 NPEVEALX 52 X 53 EAX 56 AIX 59 X 60 EL X 63 AYRHN, and combinations thereof; wherein X n is a natural or non-natural amino acid, wherein each X n is the same or different natural or non-natural amino acid, wherein Z 1 and Z 2 comprise between about 2 to about 30 natural or non-natural amino acids, wherein the amino acid sequence differs from SEQ ID NO: 1 and does not comprise SEQ ID NO: 50, wherein the polypeptide specifically binds the target of interest, wherein the contacting is performed under conditions that permit binding of the composition to the target of interest; and (b) removing a portion of the sample that is not bound to the composition.
and combinations thereof; wherein X n is a natural or non-natural amino acid, wherein each X n is the same or different natural or non-natural amino acid, wherein Z 1 and Z 2 comprise between about 2 to about 30 natural or non-natural amino acids, wherein the amino acid sequence differs from SEQ ID NO: 1 and does not comprise SEQ ID NO: 50, wherein the polypeptide specifically binds the target of interest, wherein the contacting is performed under conditions that permit binding of the composition to the target of interest; and
wherein X n is a natural or non-natural amino acid, wherein each X n is the same or different natural or non-natural amino acid,
wherein Z 1 and Z 2 comprise between about 2 to about 30 natural or non-natural amino acids,
wherein the amino acid sequence differs from SEQ ID NO: 1 and does not comprise SEQ ID NO: 50,
wherein the polypeptide specifically binds the target of interest,
wherein the contacting is performed under conditions that permit binding of the composition to the target of interest; and
(b) removing a portion of the sample that is not bound to the composition.
The method of claim 1 , wherein the solid support comprises a bead, and the composition is suitable for use in affinity chromatography to purify the target of interest.
The method of claim 1 , wherein the target of interest can be eluted from the composition.
The method of claim 1 , further comprising dissociating the composition from the target of interest and recovering the target of interest.
The method of claim 1 , wherein the polypeptide is coupled to the solid support through non-covalent association or a covalent bond and the solid support comprises a bead, a glass slide, a chip, a gelatin, or an agarose.
A method for purifying a target of interest comprising, (a) contacting a sample comprising a target of interest with a composition comprising: a virus-like particle coupled to a solid support, wherein the virus-like particle expresses a polypeptide as a membrane protein, the polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, and SEQ ID NO: 11, wherein no cysteine or proline residues are substituted into any of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, and SEQ ID NO: 11, wherein the amino acid sequence differs from SEQ ID NO:1 and does not comprise SEQ ID NO: 50, wherein the polypeptide specifically binds the target of interest, wherein the contacting is performed under conditions that permit binding of the composition to the target of interest; and (b) removing a portion of the sample that is not bound to the composition.
(a) contacting a sample comprising a target of interest with a composition comprising:
a virus-like particle coupled to a solid support, wherein the virus-like particle expresses a polypeptide as a membrane protein, the polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, and SEQ ID NO: 11,
wherein no cysteine or proline residues are substituted into any of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, and SEQ ID NO: 11,
wherein the amino acid sequence differs from SEQ ID NO:1 and does not comprise SEQ ID NO: 50,
The method of claim 6 , wherein the polypeptide of the composition further comprises a peptide tag, wherein the peptide tag comprises a hexahistindine moiety or a FLAG tag.
The method of claim 6 , wherein the portion of the sample that is not bound to the composition is contacted with the composition a second time to capture additional target of interest or is discarded.
A method for removing one or more contaminants from a sample comprising a target of interest comprising, (a) contacting a sample comprising a target of interest with a composition comprising: a virus-like particle coupled to a solid support, wherein the virus-like particle expresses a polypeptide as a membrane protein, the polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, and SEQ ID NO: 11, wherein no cysteine or proline residues are substituted into any of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, and SEQ ID NO: 11, wherein the amino acid sequence differs from SEQ ID NO:1 and does not comprise SEQ ID NO: 50, wherein the polypeptide specifically binds one or more contaminants to be removed from a sample comprising the target of interest, wherein the contacting is performed under conditions that permit binding of the composition to the one or more contaminants; and (b) collecting a portion of the sample that is not bound to the composition.
wherein the polypeptide specifically binds one or more contaminants to be removed from a sample comprising the target of interest,
wherein the contacting is performed under conditions that permit binding of the composition to the one or more contaminants; and
(b) collecting a portion of the sample that is not bound to the composition.
The method of claim 9 , wherein the polypeptide of the composition further comprises a streptavidin moiety or a peptide tag, wherein the peptide tag comprises a hexahistindine moiety or a FLAG tag.
The method of claim 9 , further comprising contacting the portion of the sample that is collected with the composition a second time to remove additional contaminants from the sample.
An affinity resin comprising a polypeptide comprising an amino acid sequence selected from the group consisting of:
(SEQ ID NO: 2) MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALGGSEAELAX 30 FEX 33 X 34 IAX 37 FEX 40 X 41 LQX 44 YKGKGNPEVEALRKEAAAIRDELQAYR HN; (SEQ ID NO: 3) MGSWAEFKQRLAAIKTRLEALGGSEAELAAFX 32 X 33 EIX 36 AFX 39 X 40 ELX 43 AYKGKGNPEVEALX 57 X 58 EAX 61 AIX 64 X 65 ELX 68 AYRHN; (SEQ ID NO: 4) MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALGGSEAELAAFEKEIAAFE SELQAYKGKGNPEVEX 55 LRX 58 X 59 AAX 62 IRX 65 X 66 LQAYRHN; (SEQ ID NO: 5) MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALGGSEAELAAFX 32 X 33 EI X 36 AFX 39 X 40 ELX 43 AYKGKGNPEVEX 55 LRX 58 X 59 AAX 62 IRX 65 X 66 LQAYRHN; (SEQ ID NO: 9) MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALZ 1 EAELAAFEKEIAAFES ELQAYZ 2 NPEVEX 50 LRX 53 X 54 AAX 57 IRX 60 X 61 LQAYRHN; (SEQ ID NO: 10) MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALZ 1 EAELAAFX 30 X 31 EI X 34 AFX 37 X 38 ELX 41 AYZ 2 NPEVEX 50 LRX 53 X 54 AAX 57 IRX 60 X 61 LQ AYRHN; and (SEQ ID NO: 11) MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALZ 1 EAELAX 28 FEX 31 X 32 IAX 35 FEX 38 X 39 LQX 42 YZ 2 NPEVEALX 52 X 53 EAX 56 AIX 59 X 60 EL X 63 AYRHN;
and combinations thereof; wherein X n is a natural or non-natural amino acid; wherein each X n is the same or different natural or non-natural amino acid; and/or wherein Z 1 and/or Z 2 is 2 to 30 natural or non-natural amino acids; and wherein the amino acid sequence differs from SEQ ID NO: 1 and does not comprise SEQ ID NO: 50.
wherein X n is a natural or non-natural amino acid; wherein each X n is the same or different natural or non-natural amino acid; and/or
wherein Z 1 and/or Z 2 is 2 to 30 natural or non-natural amino acids;
and wherein the amino acid sequence differs from SEQ ID NO: 1 and does not comprise SEQ ID NO: 50.
The affinity resin of claim 12 , wherein the amino acid sequence differs from SEQ ID NO: 1 by an amino acid substitution at one or more residues; wherein the amino acid substitution at one or more residues comprises a conservative substitution; or wherein the amino acid substitution at one or more residues comprises a non-conservative substitution.
wherein the amino acid sequence differs from SEQ ID NO: 1 by an amino acid substitution at one or more residues;
wherein the amino acid substitution at one or more residues comprises a conservative substitution; or
wherein the amino acid substitution at one or more residues comprises a non-conservative substitution.
A method of making an affinity resin comprising a step of: attaching to a solid support a polypeptide comprising an amino acid sequence selected from the group consisting of:
attaching to a solid support a polypeptide comprising an amino acid sequence selected from the group consisting of:
(SEQ ID NO: 2) MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALGGSEAELAX 30 FEX 33 X 34 IAX 37 FEX 40 X 41 LQX 44 YKGKGNPEVEALRKEAAAIRDELQAY RHN; (SEQ ID NO: 3) MGSWAEFKQRLAAIKTRLEALGGSEAELAAFX 32 X 33 EIX 36 AFX 39 X 40 ELX 43 AYKGKGNPEVEALX 57 X 58 EAX 61 AIX 64 X 65 ELX 68 AYRHN; (SEQ ID NO: 4) MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALGGSEAELAAFEKEIAAFE SELQAYKGKGNPEVEX 55 LRX 58 X 59 AAX 62 IRX 65 X 66 LQAYRHN; (SEQ ID NO: 5) MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALGGSEAELAAFX 32 X 33 EI X 36 AFX 39 X 40 ELX 43 AYKGKGNPEVEX 55 LRX 58 X 59 AAX 62 IRX 65 X 66 LQAYRHN; (SEQ ID NO: 6) MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALGGSEAELAX 30 FEX 33 X 34 IAX 37 FEX 40 X 41 LQX 44 YKGKGNPEVEALX 57 X 58 EAX 61 AIX 64 X 65 ELX 68 AYRHN; (SEQ ID NO: 7) MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALZ 1 EAELAX 28 FEX 31 X 32 IAX 35 FEX 38 X 39 LQX 42 YZ 2 NPEVEALRKEAAAIRDELQAYRHN; (SEQ ID NO: 8) MGSWAEFKQRLAAIKTRLEALZ 1 EAELAAFX 30 X 31 EIX 34 AFX 37 X 38 E LX 41 AYZ 2 NPEVEALX 52 X 53 EAX 56 AIX 59 X 60 ELX 63 AYRHN; (SEQ ID NO: 9) MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALZ 1 EAELAAFEKEIAAFES ELQAYZ 2 NPEVEX 50 LRX 53 X 54 AAX 57 IRX 60 X 61 LQAYRHN; (SEQ ID NO: 10) MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALZ 1 EAELAAFX 30 X 31 EI X 34 AFX 37 X 38 ELX 41 AYZ 2 NPEVEX 50 LRX 53 X 54 AAX 57 IRX 60 X 61 LQ AYRHN; and (SEQ ID NO: 11) MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALZ 1 EAELAX 28 FEX 31 X 32 IAX 35 FEX 38 X 39 LQX 42 YZ 2 NPEVEALX 52 X 53 EAX 56 AIX 59 X 60 EL X 63 AYRHN; and combinations thereof; wherein X n is a natural or non-natural amino acid; wherein each X n is the same or different natural or non-natural amino acid; and/or wherein Z 1 and/or Z 2 is 2 to 30 natural or non-natural amino acids; and wherein the amino acid sequence differs from SEQ ID NO: 1 and does not comprise SEQ ID NO: 50.
and combinations thereof;
wherein X n is a natural or non-natural amino acid;
wherein each X n is the same or different natural or non-natural amino acid; and/or
The method of claim 14 , wherein the polypeptide agent is attached to the solid support by covalent bonding or non-covalent association and wherein the solid support comprises a bead, glass slide, chip, gelatin, or agarose.
A composition comprising a solid support coupled to a polypeptide comprising an amino acid sequence selected from the group consisting of:
(SEQ ID NO: 2) MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALGGSEAELAX 30 FEX 33 X 34 IAX 37 FEX 40 X 41 LQX 44 YKGKGNPEVEALRKEAAAIRDELQAY RHN; (SEQ ID NO: 3) MGSWAEFKQRLAAIKTRLEALGGSEAELAAFX 32 X 33 EIX 36 AFX 39 X 40 ELX 43 AYKGKGNPEVEALX 57 X 58 EAX 61 AIX 64 X 65 ELX 68 AYRHN; (SEQ ID NO: 4) MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALGGSEAELAAFEKEIAAFE SELQAYKGKGNPEVEX 55 LRX 58 X 59 AAX 62 IRX 65 X 66 LQAYRHN; (SEQ ID NO: 5) MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALGGSEAELAAFX 32 X 33 EI X 36 AFX 39 X 40 ELX 43 AYKGKGNPEVEX 55 LRX 58 X 59 AAX 62 IRX 65 X 66 LQAYRHN; (SEQ ID NO: 6) MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALGGSEAELAX 30 FEX 33 X 34 IAX 37 FEX 40 X 41 LQX 44 YKGKGNPEVEALX 57 X 58 EAX 61 AIX 64 X 65 ELX 68 AYRHN; (SEQ ID NO: 7) MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALZ 1 EAELAX 28 FEX 31 X 32 IAX 35 FEX 38 X 39 LQX 42 YZ 2 NPEVEALRKEAAAIRDELQAYRHN; (SEQ ID NO: 8) MGSWAEFKQRLAAIKTRLEALZ 1 EAELAAFX 30 X 31 EIX 34 AFX 37 X 38 E LX 41 AYZ 2 NPEVEALX 52 X 53 EAX 56 AIX 59 X 60 ELX 63 AYRHN; (SEQ ID NO: 9) MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALZ 1 EAELAAFEKEIAAFES ELQAYZ 2 NPEVEX 50 LRX 53 X 54 AAX 57 IRX 60 X 61 LQAYRHN; (SEQ ID NO: 10) MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALZ 1 EAELAAFX 30 X 31 EI X 34 AFX 37 X 38 ELX 41 AYZ 2 NPEVEX 50 LRX 53 X 54 AAX 57 IRX 60 X 61 LQ AYRHN; and (SEQ ID NO: 11) MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALZ 1 EAELAX 28 FEX 31 X 32 IAX 35 FEX 38 X 39 LQX 42 YZ 2 NPEVEALX 52 X 53 EAX 56 AIX 59 X 60 EL X 63 AYRHN;
combinations thereof;
wherein Z 1 and/or Z 2 is 2 to 30 natural or non-natural amino acids; and
wherein the amino acid sequence differs from SEQ ID NO: 1 and does not comprise SEQ ID NO: 50.
The composition of claim 16 , wherein the amino acid sequence differs from SEQ ID NO: 1 by an amino acid substitution at one or more residues; wherein the amino acid substitution at one or more residues comprises a conservative substitution; or wherein the amino acid substitution at one or more residues comprises a non-conservative substitution.
The composition of claim 16 , wherein the solid support comprises a bead, glass slide, chip, gelatin, or agarose.
A composition comprising a polypeptide conjugated to a detectable agent and/or tag, wherein the polypeptide comprises an amino acid sequence selected from the group consisting of:
wherein the polypeptide comprises an amino acid sequence selected from the group consisting of:
The composition of claim 19 , wherein the detectable agent and/or tag comprises a chromogen, a fluorescent dye, or radionuclide or wherein the tag comprises a polyhistidyl tag, a myc tag, or a FLAG tag.
The composition of claim 19 , wherein the polypeptide is conjugated to a chromatography bead, resin, glass slide, chip, gelatin, or agarose.
The composition of claim 19 , wherein the polypeptide is conjugated to a detectable agent or tag by covalent binding.
The composition of claim 19 , wherein the polypeptide is a fusion protein or is multimeric.
The composition of claim 19 , wherein the detectable agent is quantifiable.
Ref US10662248: Claims:
A polypeptide for binding a target of interest, the polypeptide comprising an amino acid sequence selected from the group consisting of: MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALGGSEAELAX 30 FEX 33 X 34 IAX 37 FEX 40 X 41 LQX 44 YKGKGNPEVEALRKEAAAIRDELQAYRHN (SEQ ID NO:2), MGSWAEFKQRLAAIKTRLEALGGSEAELAAFX 32 X 33 EIX 36 AFX 39 X 40 ELX 43 AYKGKGNPEVEALX 57 X 58 EAX 61 AIX 64 X 65 ELX 68 AYRHN (SEQ ID NO:3), MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALGGSEAELAAFEKEIAAFESELQAYKGKGNPEVEX 55 LRX 58 X 59 AAX 62 IRX 65 X 66 LQAYRHN (SEQ ID NO:4), MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALGGSEAELAAFX 32 X 33 EIX 36 AFX 39 X 40 ELX 43 AYKGKGNPEVEX 55 LRX 58 X 59 AAX 62 IRX 65 X 66 LQAYRHN (SEQ ID NO:5), MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALGGSEAELAX 30 FEX 33 X 34 IAX 37 FEX 40 X 41 LQX 44 YKGKGNPEVEALX 57 X 58 EAX 61 AIX 64 X 65 ELX 68 AYRHN (SEQ ID NO:6), MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALZ 1 EAELAX 28 FEX 31 X 32 IAX 35 FEX 38 X 39 LQX 42 YZ 2 NPEVEALRKEAAAIRDELQAYRHN (SEQ ID NO:7), MGSWAEFKQRLAAIKTRLEALZ 1 EAELAAFX 30 X 31 EIX 34 AFX 37 X 38 ELX 41 AYZ 2 NPEVEALX 52 X 53 EAX 56 AIX 59 X 60 ELX 63 AYRHN (SEQ ID NO:8), MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALZ 1 EAELAAFEKEIAAFESELQAYZ 2 NPEVEX 50 LRX 53 X 54 AAX 57 IRX 60 X 61 LQAYRHN (SEQ ID NO:9), MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALZ 1 EAELAAFX 30 X 31 EIX 34 AFX 37 X 38 ELX 41 AYZ 2 NPEVEX 50 LRX 53 X 54 AAX 57 IRX 60 X 61 LQAYRHN (SEQ ID NO:10), MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALZ 1 EAELAX 28 FEX 31 X 32 IAX 35 FEX 38 X 39 LQX 42 YZ 2 NPEVEALX 52 X 53 EAX 56 AIX 59 X 60 ELX 63 AYRHN (SEQ ID NO: 11), and combinations thereof; wherein X n is a natural or non-natural amino acid, wherein each X n is the same or different natural or non-natural amino acid, wherein Z 1 and Z 2 comprise between about 2 to about 30 natural or non-natural amino acids, wherein the amino acid sequence differs from SEQ ID NO: 1 and does not comprise SEQ ID NO: 50, and wherein the polypeptide specifically binds a target of interest.
MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALGGSEAELAX 30 FEX 33 X 34 IAX 37 FEX 40 X 41 LQX 44 YKGKGNPEVEALRKEAAAIRDELQAYRHN (SEQ ID NO:2),
MGSWAEFKQRLAAIKTRLEALGGSEAELAAFX 32 X 33 EIX 36 AFX 39 X 40 ELX 43 AYKGKGNPEVEALX 57 X 58 EAX 61 AIX 64 X 65 ELX 68 AYRHN (SEQ ID NO:3),
MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALGGSEAELAAFEKEIAAFESELQAYKGKGNPEVEX 55 LRX 58 X 59 AAX 62 IRX 65 X 66 LQAYRHN (SEQ ID NO:4),
MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALGGSEAELAAFX 32 X 33 EIX 36 AFX 39 X 40 ELX 43 AYKGKGNPEVEX 55 LRX 58 X 59 AAX 62 IRX 65 X 66 LQAYRHN (SEQ ID NO:5),
MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALGGSEAELAX 30 FEX 33 X 34 IAX 37 FEX 40 X 41 LQX 44 YKGKGNPEVEALX 57 X 58 EAX 61 AIX 64 X 65 ELX 68 AYRHN (SEQ ID NO:6),
MGSWX 5 X 6 FKX 9 X 10 LAX 13 IKX 16 X 17 LEALZ 1 EAELAX 28 FEX 31 X 32 IAX 35 FEX 38 X 39 LQX 42 YZ 2 NPEVEALRKEAAAIRDELQAYRHN (SEQ ID NO:7),
MGSWAEFKQRLAAIKTRLEALZ 1 EAELAAFX 30 X 31 EIX 34 AFX 37 X 38 ELX 41 AYZ 2 NPEVEALX 52 X 53 EAX 56 AIX 59 X 60 ELX 63 AYRHN (SEQ ID NO:8),
MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALZ 
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