Office Action 2: Final Rejection (2025-01-22)
Rejection types: 112 - Written Description/Enablement

CLAIMS:
Reply to Office Action dated August 20, 2024 AMENDMENTS TO THE CLAIMS:

1\. (Currently Amended) A D Domain target binding domain polypeptide that specifically binds CD123 and comprises an amino acid sequence that has at least \[\[94%\]\] 96% sequence identity to 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 Fe 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\. (Previously Presented) The CAR of claim 5, further 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\. (Previously Presented) The CAR of claim 5 comprising the amino acid sequence of SEQ ID NO: 67.

9\. (Previously Presented) 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\. (Previously Presented) 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\. (Previously Presented) The adapter of claim 9, wherein the adapter comprises a single D domain that specifically binds CD123 or two D domains that specifically bind CD123.

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\. (Previously Presented) 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 D domain that binds to CD 123 of claim 1, (ii) a transmembrane domain, and (iii) an intracellular signaling 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 signaling 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 signalingdomain; 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 signalingdomain; and (b) the adapter comprises (i) the D domain that binds to CD 123 of claim 1 and (ii) an AFP p26 AD.

24\. (Previously Presented) 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;

Reply to Office Action dated August 20, 2024 (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;
(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;
(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;
(j) the contacting occurs in a human subject;
(k) the target cell is a cancer cell; and/or (1) the target cell is an acute myeloid leukemia (AML) cell or a high-risk myelodysplastic syndrome cell.

25\. (Previously Presented) 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 D domain that binds to CD 123 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 signaling 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 signaling 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 signaling domain.

27\. (Previously Presented) 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;
(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;
(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;
(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;
(j) the cell expressing the CAR is an autologous immune cell;
(k) the cancer is a hematological cancer; and/or (1) the cancer is acute myeloid leukemia (AML) or high-risk myelodysplastic syndrome.

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

29\. (New) The D Domain target binding domain polypeptide of claim 1, wherein the D Domain target binding domain polypeptide comprises substitutions relative to SEQ ID NO:14, wherein the substitutions are selected from a group consisting of substitutions in positions corresponding to 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.

30\. (New) The D Domain target binding domain polypeptide of claim 1, wherein the D Domain target binding domain polypeptide comprises a serine in position 50.

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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218
733
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SEQ ID NO: 14 aligned with SEQ ID NO: 12
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214
734
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SEQ ID NO: 14 aligned with SEQ ID NO: 13
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215
727
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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
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183
624
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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.

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 .
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 after final submitted on 03/14/2025 is acknowledged and the amendment is entered. Claims 1, 3, and 23 are amended and claims 28-30 are cancelled. Claims 1-27 are pending and found to be allowable for the reasons discussed below.
Withdrawn Objections/Rejections
In the office action of 01/22/2025, claims 1-27 and 29-30 were rejected under 35 USC 112(a) written description. Applicant’s amendment to the independent claim to recite that the amino acid sequence is SEQ ID NO: 14 has overcome the rejection and the rejection is withdrawn.
Reasons for Allowance
Claims 1-27 are allowed.
The following is an examiner’s statement of reasons for allowance: The instant claims are drawn to a D Domain target binding domain polypeptide that binds CD123 comprising the amino acid sequence of 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 novel and 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_image1.png
183
624
media_image1.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 sequence was found to be free of, and non-obvious in view of, the prior art.
Conclusions
Any comments considered necessary by applicant must be submitted no later than the payment of the issue fee and, to avoid processing delays, should preferably accompany the issue fee.  Such submissions should be clearly labeled “Comments on Statement of Reasons for Allowance.”

CITED REFERENCE SUMMARIES: Ref WO2016164308A1: Claims:
A method for purifying a target of interest comprising,
contacting a sample comprising a target of interest with a composition comprising: a polypeptide agent attached to a solid support, wherein the polypeptide agent has an amino acid sequence comprising:
MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALGGSEAELAAFEKEIAAFESEL
QAYKGKG PEVEX 55 LRX 58 X 59 AAX 62 IRX 65 X 66 LQAYr<HN (SEQ ID NO:4), wherein the polypeptide has an amino acid sequence that differs from SEQ ID
wherein the polypeptide specifically binds the target of interest,
wherein the polypeptide's specific binding to the target of interest is greater than binding of a polypeptide according to SEQ ID NO: 1 to the target of interest; the contacting performed under conditions that permit binding of the composition to the target of interest; and
removing a portion of the sample that is not bound to 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 solid support comprises a bead, a glass slide, a chip, a gelatin, or an agarose.
The method of Claim 1, wherein the polypeptide agent is coupled to the solid support through non-covalent association.
The method of Claim 1, wherein the polypeptide agent is coupled to the solid support through covalent bonding.
The method of Claim 1, wherein the polypeptide agent of the composition further comprises a peptide tag, wherein the peptide tag comprises a hexahistidine moiety or a FLAG tag.
The method of Claim I, wherein the polypeptide agent of the composition further comprises a streptavidin moiety.
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.
A method according to of any one of Claims 1 to 8, wherein the target of interest can be eluted from the composition.
The method of Claim 1, wherein a nucleic acid molecule encoding the polypeptide is packaged in an expression vector that is used to transduce a cell line to cause the cell line to express the polypeptide.
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, and SEQ ID NO:6,
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, and SEQ ID NO:6, wherein the polypeptide has an amino acid sequence that differs from SEQ ID
wherein the polypeptide's specific binding to the target of interest is greater than binding of a polypeptide according to SEQ ID NO: 1 to the target of interest; and the contacting performed under conditions that permit binding of the composition to the target of interest; and
The method of Claim 11, wherein the solid support comprises a bead, a glass slide, a chip, a gelatin, or an agarose.
The method of Claim 11, wherein the polypeptide of the composition further comprises a peptide tag, wherein the peptide tag comprises a hexahistidine moiety or a FLAG tag.
The method of Claim 11, wherein the portion of the sample that is not bound to the composition is discarded.
The method of Claim 11, 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.
The method of Claim 15, further comprising contacting the portion of the sample that is not bound to the composition with an antibody directed against the polypeptide of the composition, the antibody being generated from membrane bound virus-like particles (VLP) expressing the polypeptide released from a mammalian cell is engineered to express a fusion protein comprising the polypeptide fused to a chimeric antigen receptor (CAR), the fusion protein being expressed on the generated VLPs,
wherein the antibodies are suitable for use in an assay to detect residual polypeptides detached from the solid support.
A method for removing one or more contaminants from a sample comprising a target of interest comprising,
NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID N0 5, and SEQ ID NO:6, 

 wherein the polypeptide has an amino acid sequence that differs from SEQ ID
wherein the polypeptide specifically binds one or more contaminants to be removed from a sample comprising the target of interest,
wherein the polypeptide's specific binding to one or more contaminants is greater than binding of a polypeptide according to SEQ ID NO: l to the one or more contaminants; and
the contacting performed under conditions that permit binding of the composition to the one or more contaminants; and
collecting a portion of the sample that is not bound to the composition.
The method of Claim 17, 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 17, wherein the solid support comprises a bead, a glass slide, a chip, a gelatin, or an agarose and the virus-like particles is coupled to the solid support through non- covalent association.
The method of Claim 17, wherein the portion of the sample that collected is contacted with the composition a second time to remove additional contaminants from the sample.
An affinity resin comprising a polypeptide agent having an amino acid sequence comprising a sequence selected from the group consisting of:
MGSWX5X6FKX9X10LAX13IKX16X17LEALGGSEAELAX30
FEX33X34IAX37FEX40X41LQX44YKGKGNPEVEALRKEAAAIRDELQAYRHN (SEQ ID NO:2);
MGSWAEFKQRLAAIKTRLEALGGSEAELAAFX 32 X 33 EIX 36 AFX 39 X 40 ELX 43 AY KGKGNPEVEALXsyXssEAXgiAEX^XesELXggAYRHN (SEQ ID NO:3);
MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALGGSEAELAAFEKEIAAFESELQAYK GKGNPEVEX55LRX58X59AAX62IRX65X66LQAYRHN (SEQ ID NO:4); 

 MGSWX 5 X 6 FKX 9 XioLA i 3 lKXi 6 X 17 LEALGGSEAELAAFX 32 X 33 EIX 36 AFX 39 X 4 oE LX 43 AYKGKGNPEVEX 55 LRX 58 X 59 AA X 62 IRX 65 X 66 LQAYRHN (SEQ ID NO: 5);
MGSWX5EFX 8 X9RLXi 2 AIXi5Xi6RLXi9ALGGSEAELAX3oFEX33X34lAX 37 FEX4oX 4iLQX 44 YKGKGNPEVEALX 57 X 58 EAX 6 iAIX 64 X 65 ELX 68 AYRHN (SEQ ID NO:6);
MGSWX5X6FKX9XioLAXi3lKXi 6 Xi 7 LEALZiEAELAX28FEX3iX32lAX35FEX 3 8 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 N PEVEALX 52 X 53 EAX 5 cAIX 59 X 6 oELX 63 AYRHN (SEQ ID NO:8);
MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALZ 1 EAELAAF
EKEIAAFESELQAYZ2NPEVEX50LRX53X54AAX57IRX60X61LQAYRHN (SEQ ID NO: 9);
MGSWX 5 X 6 FKX 9 XioLAXi 3 lKX 16 X 17 LEALZiEAELAAFX 3 oX 3 iEIX 34 AFX 37 X 38 EL X41AYZ2 PEVEX50LRX53X54AAX57IRX60X61 LQAYRHN (SEQ ID NO: 10); and
X 9 RLXi 2 AIXi 5 Xi 6 RLXi 9 ALZiEAELAX 28 FEX 3 iX 32 lAX 35 FEX 38 X 39 LQX 42 YZ 2 PEVEAL X52X53EAX56AIX59X60ELX63AY HN (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; and/or
wherein Zi and/or Z 2 is 2 to 30 natural or non-natural amino acids;
and wherein the amino acid sequence is not SEQ ID NO: 1.
The affinity resin of claim 21, wherein the polypeptide agent has an amino acid sequence that differs from SEQ ID NO: 1 by an amino acid substitution at one or more residues.
The affinity resin of claim 22, wherein the amino acid substitution at one or more residues comprises a conservative substitution.
The affinity resin of claim 22, wherein the amino acid substitution at one or more residues comprises a non-conservative substitution.
An affinity resin according to any one of claims 22-24, wherein the amino acid substitution at one or more residues comprises a substitution at a solvent accessible residue
An affinity resin according to any one of claims 22-24, wherein the amino acid substitution at one or more residues comprises a substitution at a solvent inaccessible residue.
The affinity resin of claim 21, wherein the polypeptide agent has an amino acid sequence that differs from SEQ ID NO: 1 by an amino acid deletion at one or more residues.
A method of making an affinity resin comprising a step of:
attaching to a solid support a polypeptide agent having an amino acid sequence comprising a sequence selected from the group consisting of:
MGS WX5X6FKX9X1 oL AX, 3IKX, 6 X, 7LEALGGSEAEL AX 30
FEX 33 X 34 IAX 37 FEX 40 X 41 LQX 44 YKGKGNPEVEALRKEAAAIRDELQAYRHN (SEQ ID NO:2);
MGSWAEFKQ LAAlKTRLEALGGSEAELAAFX 32 X 33 ETX 36 AFX 39 X 4 oELX 43 AY KGKGNPEVEALX 57 X 58 EAX 6 iAIX 64 X 65 ELX 68 AYRHN (SEQ ID NO:3);
MGSWX 5 EFX 8 X 9 RLX 12 AIX 15 X 16 RLX 19 ALGGSEAELAAFEI EIAAFESELQAYK GKGNPE EX 55 LRX 58 X 59 AAX 62 IRX 65 X 66 LQ AYRUN (SEQ ID NO:4);
MGSWX 5 X 6 FKX 9 XioLAXi 3 lKXi 6 Xi 7 LEALGGSEAELAAFX 32 X 33 EIX 36 AFX 39 X 4 oE LX 43 AYKGKGNPEVEX 55 LRX 58 X 59 AA X 62 IRX 65 X 66 LQAYRHN (SEQ ID NO: 5);
MGSWX5EFX 8 X9RLXi 2 AIXi5Xi6RLXi9ALGGSEAELAX3oFEX33X34lAX37FEX4oX 4iLQX 44 YKGKGNPEVEALX 57 X 58 EAX 6 iAIX 64 X 65 ELX 68 AYRHN (SEQ ID NO:6);
Î08\Î½Î§5Î§6Î¡ÎÎ§9Î§Î¹Î¿ÎÎÎ§Î3ÎÎÎ§ 16 Î§ 17 ÎÎÎÎÎÎ¹ÎÎÎÎÎÎ§2 8 Î¡ÎÎ§3ÎÎ§32ÎÎÎ§35Î¡ÎÎ§38 X 39 LQX 42 YZ 2 NPEVEALRKEAAAIRDELQAYRHN (SEQ ID NO:7);
MGSWAEFKQRLAAIKTRLEALZ1EAELAAFX30X31EIX34AFX37X38ELX41AYZ2N PEVEALX 52 X 53 EAX 56 AIX 59 X 6 oELX 63 AYRHN (SEQ ID NO:8);
MGSWX 5 EFX 8 X 9 RLXi 2 AIXi 5 Xi 6 RLXi 9 ALZiEAELAAF
EKEIAAFESELQAYZ 2 NPEVEX 5 oLRX 53 X 54 AAX 57 lRX 6 oX 6 iLQAYRHN (SEQ ID NO: );
MGSWX 5 X 6 FKX 9 XioLAXi 3 lKXi 6 Xi 7 LEALZiEAELAAFX 3 oX 3 iEIX 34 AFX 37 X 38 EL X41AYZ2NPEVEX50LRX53X54AAX57IRX60X61 LQAYRHN (SEQ ID NO: 10); and
X 9 RLXi 2 AIXi 5 Xi 6 RLXi 9 ALZiEAELAX 28 FEX 3 iX 32 lAX 35 FEX 38 X 39 LQX 42 YZ 2 EVEAL X 52 X 53 EAX 56 AIX 59 X 6 oELX 63 A RHN (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; and/or
The method of claim 28, wherein the polypeptide agent is attached to the solid support by covalent bonding.
The method of claim 28, wherein the polypeptide agent is attached to the solid support by non-covalent association.
A method according to any one of claims 28-30, wherein the solid support comprises a bead, glass slide, chip, gelatin, or agarose.
A composition comprising a solid support coupled to a polypeptide agent having an amino acid sequence comprising a sequence selected from the group consisting of:
FEX 33 X 3 4lAX 37 FEX4oX4iLQX44YKGKGNPEVEALRKEAAAIRDELQAYRHN (SEQ ID NO:2);
MGSWAEFKQRLAAIKTRLEALGGSEAELAAFX 32 X 33 EIX 36 AFX 39 X 4 oELX 43 AY KGKGNPEVEALX 57 58 EAX 6 iAIX 64 X 65 ELX 68 AYRHN (SEQ ID NO:3);
MGSWXsEFXiiXyRLXnAIXisXieRLXiyALGGSEAELAAFEKEIAAFESELQAYK GKGNPE VEX 55 LRX 5 8X59 AAÂ¾ 2 IRX 65 X 66 LQ AYRFIN (SEQ ID NO:4);
MGSWX 5 X 6 FKX 9 XioLAXi 3 lKX 16 X 17 LEALGGSEAELAAFX 32 X 33 EIX 36 AFX 39 X 4 oE LX 43 AYKGKGNPEVEX 55 LRX 58 X 59 AA X 62 IRX 65 X 66 LQAYRHN (SEQ ID NO: 5);
MGSWX5EFX 8 X 9 RLXi2AIXi5Xi6RLXi9ALGGSEAELAX 3 oFEX3 3 X 3 4lAX 37 FEX 4 oX 4iLQX 44 YKGKGNPEVEALX 57 X 58 EAX 6 iAIX 64 X 65 ELX 68 AYRHN (SEQ ID NO:6);
MGSWX5X6FKX9XioLAXi3lKXi 6 Xi 7 LEALZiEAELAX 28 FEX3iX3 2 IAX35FEX 3 8 X 39 LQX 42 YZ 2 NPEVEALRKEAAAIRDELQAYRHN (SEQ ID NO:7);
MGSWAEFKQRLAAIKTRLEALZiEAELAAFX 3 oX 3 iEIX 34 AFX 37 X 38 ELX 4 iAYZ 2 N PEVEALX52 X53EAX56AIX59X6oELX 63 AYRHN (SEQ ID NO:8); 

 MGSWXsEFXsXyRLXnAIXisXieRLXiyALZiEAELAAF
EKEIAAFESELQAYZ 2 NPEVEX 5 oLRX 53 X 54 AAX 57 lRX 6 oX 6 iLQAYRHN (SEQ ID NO: 9);
MGSWX 5 X 6 FKX 9 XioLAXi 3 lKX 16 X 17 LEALZiEAELAAFX 3 oX 3 iEIX 34 AFX 37 X 38 EL X41AYZ2NPEVEX50LRX53X54AAX57IRX60X61 LQAYRHN (SEQ ID NO: 10); and
X 9 RLXi 2 AIXi 5 Xi 6 RLXi 9 ALZ 1 EAELAX 28 FEX 3 iX 32 lAX 35 FEX 38 X 39 LQX 42 YZ 2 NPEVEAL X 52 X 53 EAX 56 AIX 59 X 60 ELX 63 AYRHN (SEQ ID NO: 11); and combinations thereof;
and wherein the amino acid sequence is not SEQ ID NO: 1
The composition of claim 32, wherein the polypeptide agent has an amino acid sequence that differs from SEQ ID NO: l by an amino acid substitution at one or more residues.
The composition of claim 33, wherein the amino acid substitution at one or more residues comprises a conservative substitution.
The composition of claim 33, wherein the amino acid substitution at one or more residues comprises a non-conservative substitution.
A composition according to any one of claims 33-35, wherein the amino acid substitution at one or more residues comprises a substitution at a solvent accessible residue.
The composition of any of claims 33-35, wherein the amino acid substitution at one or more residues comprises a substitution at a solvent inaccessible residue.
The composition of claim 33, wherein the polypeptide agent has an amino acid sequence that differs from SEQ ID NO: l by an amino acid deletion at one or more residues.
A composition according to any one of claims 32 to 38 wherein the solid support comprises a bead, glass slide, chip, gelatin, or agarose.
A composition comprising a polypeptide agent conjugated to a detectable agent and/or wherein the polypeptide agent has an amino acid sequence comprising a sequence selected from the group consisting of:
MGSWXsXeFKXgXioLAXoIKXigXnLEALGGSEAELAXso
MGSWAEFKQRLAAIKTRLEALGGSEAELAAFX 32 X 33 EIX 36 AFX 39 X 40 ELX 43 AY KGKGNPEVEALX 57 X 58 EAÂ¾ X 64 X 65 ELX 68 AYRHN (SEQ ID NO:3);
MGSWX5EFX8X9RLX12AIX15X16RLX19ALGGSEAELAAFEKEIAAFESELQAYK GKGNPE VEX 55 LRX 58 X 59 AAX 62 IRX 65 X 66 LQ AYRUN (SEQ ID NO:4);
MGSWX 5 X 6 FKX 9 XioLAXi 3 lKXi 6 Xi 7 LEALGGSEAELAAFX 32 X 33 EIX 36 AFX 39 X 4 oE LX 43 AYKGKGNPEVEX 55 LRX 58 X 59 AA X 62 lRX 65 X 66 LQAYRHN (SEQ ID NO: 5);
MGSWX5EFX 8 X9RLXi 2 AIXi5Xi6RLXi9ALGGSEAELAX3oFEX33X34lAX37FEX4oX 4iLQX 44 YKGKG PEVEALX57X58EAX6iAlX64X65ELX68AY H (SEQ ID NO:6);
MGSWX5X6FKX9XioLAXi3lKX 16 X 1 7LEALZiEAELAX28FEX3iX32lAX35FEX 3 8 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 N PEVEALX 52 X 53 EAX 56 AIX 59 X 6 oELX 63 AYRHN (SEQ ID NO:8);
EKEIAAFESELQAYZ 2 NPEVEX 50 LRX 53 X 54 AAX 57 IRX 60 X 61 LQAYRHN (SEQ ID NO: 9);
MGSWX 5 X 6 FKX 9 XioLAXi 3 lKXi 6 Xi 7 LEALZiEAELAAFX 3 oX 3 iEIX 34 AFX 37 X 38 EL X4iAYZ 2 NPEVEX5oLRX53X54AAX57lPX 6 oX6i LQAYRHN (SEQ ID NO: 10); and
X 9 RLX, 2 AIX, 5X1 6 RLX, 9ALZ1 EAELAX 28 FEX31 X32IAX35FEX38X39LQX42YZ2NPEVEAL X 52 X 53 EAX 56 AIX 59 X 6 oELX 63 AYRHN (SEQ ID NO: 11); and combinations thereof;
wherein Z \ and/or Z 2 is 2 to 30 natural or non-natural amino acids;
The composition of claim 40, wherein the detectable agent comprises a chromogen.
The composition of claim 40, wherein the detectable agent comprises a fluorescent dye.
The composition of claim 40, wherein the detectable agent comprises a radionuclide.
A composition according to any one of claims 40-43, wherein the detectable agent is quantifiable.
A composition according to any one of claims 40-44, wherein the polypeptide agent is conjugated to a chromatography bead, resin, glass slide, chip, gelatin, or agarose.
The composition of claim 40, wherein the tag comprises polyhistidyl tag, a myc tag, or a FLAG tag.
The composition of claim 40, wherein the polypeptide agent is conjugated to a detectable agent or tag by covalent binding.
A composition according to any one of claims 40-47, wherein the polypeptide agent is a fusion protein.
A composition according to any one of claims 40-48, wherein the polypeptide agent is multimeric.
Ref WO2019099433A2: Claims:
1. A protein comprising a D Domain (DD) target binding domain wherein the DD is a member selected from the group consisting of:
(a) a DD that specifically binds BCMA and comprises the amino acid sequence of SEQ ID NO: 11-305, or 306;
(b) a DD that specifically binds CD123 and comprises the amino acid sequence of SEQ ID NO: 307-739, or 740,
(c) a DD that specifically binds AFP and comprises the amino acid sequence of SEQ ID NO: 741-874, or 886-895,
(d) a DD that specifically binds AFP p26 and comprises the amino acid sequence of SEQ ID NO: 741-874, or 886-895;
(e) a DD that specifically binds CS1 and comprises the amino acid
sequence of SEQ ID NO: 896-909, or 910; and
(f) a DD that specifically binds HER2 and comprises the amino acid sequence of SEQ ID NO: 911-949, or 950.
2. The protein of claim 1 wherein the DD is fused to a heterologous polypeptide.
3. The protein of claim 2, wherein the heterologous polypeptide comprises a full-length antibody or an antibody fragment.
4. The protein of claim 2, wherein the heterologous polypeptide comprises a member selected from the group consisting of.
(a) a transmembrane domain;
(b) a membrane associating domain;
(c) human serum albumin or a fragment thereof;
(d) AFP or a fragment thereof;
(e) AFP p26 or a fragment thereof; and
(f) the extracellular domain of a receptor or a fragment thereof.
5. The protein of claim 3, wherein the DD is fused to: the amino terminus of a full-length antibody heavy chain; the amino terminus of a full-length antibody light chain; the carboxyl terminus of 

 a full-length antibody heavy chain; or the carboxyl terminus of a full-length antibody light chain.
6. The protein of claim 3, wherein the heterologous polypeptide is an Fc.
7. The protein of claim 2, wherein the heterologous polypeptide comprises the extracellular domain, or a fragment of an extracellular domain, of a receptor selected from the group consisting of: BCMA, CD123, CS1, and CD19.
8. The protein according to any one of claims 1-7, which is labeled.
9. The protein according to claim 9, wherein the label is selected from the group consisting of an enzymatic label, a fluorescent label, a luminescent label, a bioluminescent label and a biotin moiety.
10. A protein according to any one of claims 1-10, which conjugated to a therapeutic or cytotoxic agent.
11. A chimeric antigen receptor (CAE.) which comprises a target binding domain comprising the protein according to any one of claims 1-5.
12. 'The CAR of claim 11, which comprises, a target binding domain, a transmembrane domain, and an intracellular signaling domain.
13. The CAR of claim 1 1 or 12, wdierein transmembrane domain comprises a 41BB or CD28 transrn embrane domain .
14. The CAR according to any one of claims 11-13, wherein 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 41 BB domain; a human CD28 domain; and any combination thereof
15. A CAR according to any one of claims 11-14, wherein the intracellular signaling domain comprises the intracellular domain of a eostimulatory molecule selected from the group consisting of CD27, CD28, 41BB, 0X40, CD30, CD4Q, PD1, lymphocyte function- associated antigen- 1 (I..FA-1), CD2, CD7, LIGHT, NKG2C, NKG2D, B7-H3, a ligand that specifically binds with CD83, and any combination thereof.
16. A protein according to any on of claims 1-15, which further comprises a second target binding domain having the same or a different target than the DD target binding domain.
17. An isolated nucleic acid encoding the protein according to any one of claims 1-16.
18. A vector comprising the nucleic acid of claim 17.
19. The vector of claim 18, wherein the nucleic acid is operabiy linked with a nucleotide sequence which regulates the expression of the protein encoded by the nucleic acid.
20. The vector of claim 19 which is a lenti viral vector.
21. A host cell comprising the nucleic acid acording to claim 17 or the vector according to any one of claims 18-21.
22. A cell engineered to express the protein according to any one of claims 1-16.
23. A cell according to claim 21 or 22, wherein the cell is a T cell or a natural killer (NK) ceil.
24. A pharmaceutical composition comprising the protein according to any one of claims 1-16, the nucleic acid of claim 17, the vector of claim 18. 19 o
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