Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 1-12 and 15 are pending.
Claims 1-12 and 15, drawn to a set of heterodimeric precursor polypeptide that read on (A) first heterodimer polypeptide comprising a first heavy chain polypeptide comprising a knob mutation and a second heavy chain polypeptide comprising a hole mutation, (B)a knob mutation in the first heavy chain and hole mutation in the third heavy chain polypeptide and LeY as the target antigen to which first and second antigen moieties bind, a method for generating said heterodimer polypeptide and a method of treating cancer comprising administering to an individual in need thereof a set of said heterodimeric precursor are being acted upon in this Office Action.
Priority
Receipt is acknowledged of papers submitted under 35 U.S.C. 119(a)-(d), which papers have been placed of record in the file.
Objection and Rejection Withdrawn
The objection to claims 1-9, 12, 15 and 16 is withdrawn in view of the claim amendment.
The rejection of claims 1, 4 and 12 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph is withdrawn in light of the claim amendment.
The provisional rejection of claims 1-12, 15 and 16 on the ground of nonstatutory obviousness-type double patenting as being unpatentable over claims 1-9, 11-15, 18, 19-20 of copending Application No. 17/506,993 is withdrawn in view of the terminal disclaimer filed on December 10, 2025.
The provisional rejection of claims 1-8, 12, 15 and 16 on the ground of nonstatutory obviousness-type double patenting as being unpatentable over claims 1-13, 15-17 of copending Application No. 17/507,029 is withdrawn in view of the terminal disclaimer filed on December 10, 2025.
Claim rejections under - 35 U.S.C. 112
The following is a quotation of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), first paragraph:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-12 and 15 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
The Written Description Guidelines for examination of patent applications indicates, “the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical characteristics and/or other chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show applicant was in possession of the claimed genus.” (see MPEP 2163).
An adequate written description must contain enough information about the actual makeup of the claimed products – “a precise definition, such as structure, formula, chemic name, physical properties of other properties, of species falling with the genus sufficient to distinguish the gene from other materials”, which may be present in “functional terminology when the art has established a correlation between structure and function” (Amgen page 1361).
“When a patent claims a genus using functional language to define a desired result, the specification must demonstrate that the applicant has made a generic invention that achieves the claimed result and do so by showing that the applicant has invented species sufficient to support a claim to the functionally-defined genus.” See Capon v. Eshhar, 418 F.3d 1349 (Fed. Cir. 2005).
Further, “A sufficient description of a genus . . . requires the disclosure of either a representative number of species falling within the scope of the genus or structural features common to the members of the genus so that one of skill in the art can "visualize or recognize" the members of the genus.” See AbbVie, 759 F.3d at 1297, reiterating Eli Lilly, 119 F.3d at 1568-69.
In Amgen v. Sanofi, 872 F.3d 1367 (Fed. Cir. 2017), the court explained in Amgen that when an antibody is claimed, 35 U.S.C § 112(a) requires adequate written description of the antibody itself. Citing its decision in Ariad Pharmaceuticals, Inc. v. Eli Lilly & Co., the court also stressed that the "newly characterized" test could not stand because it contradicted the quid pro quo of the patent system whereby one must describe an invention in order to obtain a patent. Amgen, 872 F.3d at 1378-79, quoting Ariad Pharmaceuticals, Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1345 (Fed. Cir. 2010).
Claim 1 encompasses a set of heterodimeric precursor polypeptides comprising:
a) a first heterodimeric precursor polypeptide comprising
a first heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain selected from a VH domain or a VL domain, and a CH3 domain, wherein the first heavy chain polypeptide comprises at least a part of a first antigen binding moiety; and
a second heavy chain polypeptide comprising from N- to C-terminal direction a CH2 domain and a CH3 domain, wherein the first heavy chain polypeptide and the second heavy chain polypeptide are associated with each other via the CH3 domains and form a heterodimer, wherein one of the CH3 domains comprises a knob mutation and the other CH3 domain comprises a hole mutation; and
b) a second heterodimeric precursor polypeptide comprising
a third heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain selected from a VH domain or a VL domain, and a CH3 domain, wherein the antibody variable domain forms an antigen binding site specifically binding to a target antigen with the antibody variable domain comprised in the first heavy chain polypeptide of the first heterodimeric precursor polypeptide, wherein the third heavy chain polypeptide comprises at least a part of a second antigen binding moiety; and
a fourth heavy chain polypeptide comprising from N- to C-terminal direction a CH2 domain and a CH3 domain; wherein the third heavy chain polypeptide and the fourth heavy chain polypeptide are associated with each other via the CH3 domains and form heterodimer, wherein one of the CH3 domains comprises a knob mutation and the other CH3 domain comprises a hole mutation; wherein
A) either
i) the first heavy chain polypeptide comprises the CH3 domain with the knob mutation and the third heavy chain polypeptide comprises CH3 domain with the hole mutation, or
ii) the first heavy chain polypeptide comprises the CH3 domain with the hole mutation and the third heavy chain polypeptide comprises CH3 domain with the knob mutation; and wherein
B) either
the CH3 domain of the first heterodimeric precursor polypeptide comprising the knob mutation and the CH3 domain of the second heterodimeric precursor polypeptide comprising the hole mutation, or
the CH3 domain of the first heterodimeric precursor polypeptide comprising the hole mutation and the CH3 domain of the second heterodimeric precursor polypeptide comprising the knob mutation comprises one or more amino acid substitution destabilizing the CH3/CH3 interface, wherein the amino acid substitutions are arranged such that the substituted amino acids interact in the CH3/CH3 interface within a pair of said CH3 domains.
Claim 2 encompasses the set of heterodimeric polypeptides according to claim 1, wherein the CH3 domain comprising the knob mutation and the CH3 domain comprising the hole mutation indicated in B) comprise one or more of the following amino acid substitutions, wherein the numbering is according to the Kabat numbering system:
the CH3 domain with the hole mutation comprises at least one amino acid substitution selected from the group of:
replacement of S354 with a hydrophobic amino acid;
replacement of D356 with a positively charged amino acid;
replacement of E357 with a positively charged amino acid or with a hydrophobic amino acid;
replacement of D356 with a positively charged amino acid, and replacement of E357 with a positively charged amino acid or with a hydrophobic amino acid;
replacement of $364 with a hydrophobic amino acid;
replacement of A368 with a hydrophobic amino acid;
replacement of K392 with a negatively charged amino acid;
replacement of T394 with a hydrophobic amino acid;
replacement of D399 with a hydrophobic amino acid and replacement of S400 with a positively charged amino acid;
replacement of D399 with a hydrophobic amino acid and replacement of F405 with a positively charged amino acid;
replacement of V 407 with a hydrophobic amino acid; and
replacement of K409 with a negatively charged amino acid; and
replacement of K439 with a negatively charged amino acid;
the CH3 domain with the knob mutation comprises at least one amino acid substitution selected from the group of:
replacement of Q347 with a positively charged amino acid, and replacement of K360 with a negatively charged amino acid;
replacement of Y349 with a negatively charged amino acid;
replacement of L35 | with a hydrophobic amino acid, and replacement of E357 with a hydrophobic amino acid;
replacement of S364 with a hydrophobic amino acid;
replacement of W366 with a hydrophobic amino acid, and replacement of K409 with a negatively charged amino acid;
replacement of L368 with a hydrophobic amino acid;
replacement of K370 with a negatively charged amino acid;
replacement of K370 with a negatively charged amino acid, and replacement of K439 with a negatively charged amino acid;
replacement of K392 with a negatively charged amino acid;
replacement of T394 with a hydrophobic amino acid;
replacement of V397 with a hydrophobic amino acid;
replacement of D399 with a positively charged amino acid, and replacement of K409 with a negatively charged amino acid;
replacement of S400 with a positively charged amino acid;
F405W;
Y407W; and
replacement of K439 with a negatively charged amino acid.
Claim 3 encompasses the set of heterodimeric polypeptides according to according to claim 1 or claim 2, wherein the CH3 domain comprising the knob mutation and the CH3 domain comprising the hole mutation indicated in B) comprise one or more of the following amino acid substitutions, wherein the numbering is according to the Kabat numbering system:
the CH3 domain with the hole mutation comprises at least one amino acid substitution selected from the group of:
replacement of E357 with a positively charged amino acid;
replacement of $364 with a hydrophobic amino acid;
replacement of A368 with a hydrophobic amino acid; and
replacement of V 407 with a hydrophobic amino acid; and
the CH3 domain with the knob mutation comprises at least one amino acid substitution selected from the group of:
replacement of K370 with a negatively charged amino acid;
replacement of K370 with a negatively charged amino acid, and replacement of K439 with a negatively charged amino acid;
replacement of K392 with a negatively charged amino acid; and
replacement of V397 with a hydrophobic amino acid.
Clam 4 encompasses the set of heterodimeric polypeptides according to claim 1 or claim 2, wherein the first antigen binding moiety and/or the second antigen binding moiety is an antibody antigen-binding fragment thereof.
Clam 5 encompasses the set of heterodimeric polypeptides according to claim 1 or claim 2, wherein
a) the first heterodimeric precursor polypeptide further comprises:
within the first heavy chain polypeptide comprising a CH3 domain a further antibody variable domain (first antibody variable domain), and
a further polypeptide chain that is a light chain polypeptide comprising a second antibody variable domain, wherein the first and second antibody variable domain together form a first antigen binding site specifically binding to a target antigen; and wherein
b) the second heterodimeric precursor polypeptide comprises:
within the third heavy chain polypeptide comprising a CH3 domain a further antibody variable domain (third antibody variable domain), and
a further polypeptide chain that is a light chain polypeptide comprising a fourth antibody variable domain, wherein the third and fourth antibody variable domain together form a second antigen binding site specifically binding to a target antigen.
Claim 6 encompasses the set of heterodimeric polypeptides according to claim 1 or claim 2, wherein in the first heterodimeric polypeptide no interchain disulfide bond is formed between the two polypeptide chains comprising the CH3 domains, and wherein in the second heterodimeric polypeptide no interchain disulfide bond is formed between the two polypeptide chains comprising the CH3 domains.
Claim 7 encompasses the set of heterodimeric precursor polypeptides according to claim 1 or claim 2, wherein the antigen binding moiety of the first heterodimeric precursor polypeptide and the antigen binding moiety of the second heterodimeric precursor polypeptide bind to the same antigen.
Claim 8 encompasses the set of heterodimeric precursor polypeptides according to claim 1 or claim 2, wherein the antibody variable domains comprised in the first heavy chain polypeptide and the third heavy chain polypeptide are capable of forming an antigen binding site specifically binding to CD3.
Claim 9 encompasses a method for generating a heterodimeric polypeptide comprising contacting the first heterodimeric precursor polypeptide and the second heterodimeric precursor polypeptide of claim 1 or claim 2 to form a third heterodimeric polypeptide comprising the first heavy chain polypeptide and the third heavy chain polypeptide.
Claim 10 encompasses the method according to claim 9 comprising contacting the first heterodimeric precursor polypeptide and the second heterodimeric precursor polypeptide to form a fourth heterodimeric polypeptide comprising the second heavy chain polypeptide and the fourth heavy chain polypeptide.
Claim 11 encompasses the method according to claim 9, wherein in the first heterodimeric polypeptide no interchain disulfide bond is formed between the two polypeptide chains comprising the CH3 domains, and wherein in the second heterodimeric polypeptide no interchain disulfide bond is formed between the two polypeptide chains comprising the CH3 domains, and wherein the contacting is performed in absence of a reducing agent.
Claim 12 encompasses a first heterodimeric precursor polypeptide comprising:
a first heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain selected from a VH domain and a VL domain, and a CH3 domain, wherein the first heavy chain polypeptide comprises at least a part of a first antigen binding moiety; and
a second heavy chain polypeptide comprising from N- to C- terminal direction a CH2 domain and a CH3 domain, wherein the first heavy chain polypeptide and the second heavy chain polypeptide are associated with each other via the CH3 domains and form a heterodimer, wherein one of the CH3 domains comprises a knob mutation and the other CH3 domain comprises a hole mutation;
wherein either
i) the CH3 domain of the first heterodimeric precursor polypeptide comprising
the knob mutation and the CH3 domain of the second heterodimeric precursor polypeptide comprising the hole mutation, or
ii) the CH3 domain of the first heterodimeric precursor polypeptide comprising the hole mutation and the CH3 domain of the second heterodimeric precursor polypeptide comprising the knob mutation, comprises one or more amino acid substitutions that destabilize a CH3/CH3 interface, wherein the amino acid substitutions are arranged such that the substituted amino acids interact in the CH3/CH3 interface within a pair of said CH3 domains.
Claim 15 encompasses a pharmaceutical composition comprising the set of heterodimeric precursor polypeptides of any claims 1 to 8 and a pharmaceutically acceptable carrier.
The specification exemplifies:
Example 4
Generation of Monospecific Precursor Polypeptides for the Generation of Activatable Binding Sites Upon Polypeptide Chain Exchange
[0477] This example is a proof-of-concept example for identifying destabilizing mutations assessing efficacy polypeptide chain exchange with a subset of destabilizing mutations identified in Examples 1 to 3, and assessing activation of an antigen binding site by polypeptide chain exchange via a cell based T cell activation assay.
[0478] For assessing formation of bispecific anti-LeY/anti-CD3 antibodies from monospecific precursor polypeptides, monospecific precursor polypeptides of a domain arrangement as depicted for the first and second heterodimeric precursor polypeptides indicated in FIG. 2 and FIG. 3 were generated.
Precursor Polypeptides Devoid of CH2 Domain
[0479] In a first set of experiments, heterodimeric precursor polypeptides with a domain arrangement as depicted in FIG. 2 were provided. The precursor polypeptides are devoid of CH2 domains and comprise an antibody variable domain arranged at the N-terminal end of the CH3 domains.
[0480] In a first alternative, the following precursor polypeptides were provided: [0481] A first heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VH)-knob precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VH)-knob precursor comprised a light chain polypeptide of SEQ ID NO:11 (also referred to as “LeY LC”), a first heavy chain polypeptide of SEQ ID NO:12 (also referred to as “LeY-CD3(VH)-knob HC”) comprising a VH domain derived from an antibody specifically binding to CD3 (“CD3(VH)”) and a second heavy chain polypeptide based on SEQ ID NO:13 (which represents the basic amino acid sequence without destabilizing mutation), with the destabilizing mutations as indicated below and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy-VL-hole” polypeptide) comprised von N- to C-terminal direction a hinge region, a VL domain derived from an antibody specifically binding to digoxigenin (“dig”) and a CH3 domain. [0482] A second heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VL)-hole precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VL)-hole precursor comprised the light chain polypeptide of SEQ ID NO:11, i.e. the LeY LC; a first heavy chain polypeptide of SEQ ID NO:14 (also referred to as “LeY-CD3(VL)-hole HC”) comprising a VL domain derived from an antibody specifically binding to CD3 (“CD3(VL)”) and a second heavy chain polypeptide based on SEQ ID NO: 15 (which represents the basic amino acid sequence without destabilizing mutation) with the destabilizing mutations as indicated below and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy-VH-knob” polypeptide) comprised von N- to C-terminal direction a hinge region, a VH domain derived from a non-binding antibody and a CH3 domain.
[0483] In a second alternative, the following precursor polypeptides were provided: [0484] A first heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VL)-knob precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VL)-knob precursor comprised the light chain polypeptide of SEQ ID NO:11, i.e. the LeY LC, a first heavy chain polypeptide of SEQ ID NO:16 (also referred to as “LeY-CD3(VL)-knob HC”) comprising the CD3(VL) domain and a second heavy chain polypeptide based on SEQ ID NO:17 (which represents the basic amino acid sequence without destabilizing mutation), with the destabilizing mutations as indicated below and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy-VH-hole” polypeptide) comprised von N- to C-terminal direction a hinge region, a VH domain derived from a non-binding antibody and a CH3 domain. [0485] A second heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VH)-hole precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VH)-hole precursor comprised the light chain polypeptide of SEQ ID NO:11, i.e. the LeY LC; a first heavy chain polypeptide of SEQ ID NO: 18 (also referred to as “LeY-CD3(VH)-hole HC”) comprising the CD3(VH) domain and a second heavy chain polypeptide based on SEQ ID NO:19 (which represents the basic amino acid sequence without destabilizing mutation) with the destabilizing mutations as indicated below and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy-VL-knob” polypeptide) comprised von N- to C-terminal direction a hinge region, a VL domain derived from an anti-dig antibody and a CH3 domain.
PNG
media_image1.png
655
628
media_image1.png
Greyscale
Precursor Polypeptides with Fc Domain
[0487] In a second set of experiments, heterodimeric precursor polypeptides with a domain arrangement as depicted in FIG. 3 were provided. The precursor polypeptides comprise a full Fc domain and comprise an antibody variable domain arranged at the N-terminal end of the CH2 domains.
[0488] In a first alternative, the following precursor polypeptides were provided: [0489] A first heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VH)-Fc(knob) precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VH)-Fc(knob) precursor comprised the light chain polypeptide of SEQ ID NO:11, i.e. the LeY LC, a first heavy chain polypeptide of SEQ ID NO:20 (also referred to as “LeY-CD3(VH)-Fc(knob) HC”) comprising the CD3(VH) domain and a second heavy chain polypeptide based on SEQ ID NO:21 (which represents the basic amino acid sequence without destabilizing mutation), with the destabilizing mutations as indicated below and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy-VL-Fc(hole)” polypeptide) comprised von N- to C-terminal direction a hinge region, a VL domain derived from an antibody specifically binding to digoxigenin (“dig”), a CH2 domain and a CH3 domain. [0490] A second heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VL)-Fc(hole) precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VL)-Fc(hole) precursor comprised the LeY LC; a first heavy chain polypeptide of SEQ ID NO:22 (also referred to as “LeY-CD3(VL)-Fc(hole) HC”) comprising the CD3(VL) domain and a second heavy chain polypeptide based on SEQ ID NO:23 (which represents the basic amino acid sequence without destabilizing mutation) with the destabilizing mutations as indicated below and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy-VH-Fc(knob)” polypeptide) comprised von N- to C-terminal direction a hinge region, a VH domain derived from an anti-dig antibody, a CH2 domain and a CH3 domain.
[0491] In a second alternative, the following precursor polypeptides were provided: [0492] A first heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VL)-Fc(knob) precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VL)-Fc(knob) precursor comprised the LeY LC, a first heavy chain polypeptide of SEQ ID NO:24 (also referred to as “LeY-CD3(VL)-Fc(knob) HC”) comprising the CD3(VL) domain and a second heavy chain polypeptide based on SEQ ID NO:25 (which represents the basic amino acid sequence without destabilizing mutation), with the destabilizing mutations as indicated below and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy-VH-Fc(hole)” polypeptide) comprised von N- to C-terminal direction a hinge region, a VH domain derived from an anti-dig antibody, a CH2 domain and a CH3 domain. [0493] A second heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VH)-Fc(hole) precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VH)-Fc(hole) precursor comprised the LeY LC; a first heavy chain polypeptide of SEQ ID NO:26 (also referred to as “LeY-CD3(VH)-Fc(hole) HC”) comprising the CD3(VH) domain and a second heavy chain polypeptide based on SEQ ID NO:27 (which represents the basic amino acid sequence without destabilizing mutation) with the destabilizing mutations as indicated below and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy-VL-Fc(knob)” polypeptide) comprised von N- to C-terminal direction a hinge region, a VL domain derived from an anti-dig antibody, a CH2 domain and a CH3 domain.
[0494] The indicated polypeptide chains comprise the following mutations:
PNG
media_image2.png
375
327
media_image2.png
Greyscale
[0495] Heterodimeric precursor polypeptides were generated comprising dummy VL-hole polypeptides of SEQ ID NO:13 and dummy VH-hole polypeptides of SEQ ID NO:17 as indicated above having the amino acid sequence of the respective dummy polypeptide as indicated above, wherein one of the following amino acid substitutions was made: E357K, A368F, D399A F405W, S364L, Y407W, or S354V.
[0496] Heterodimeric precursor polypeptides were generated comprising dummy VH-knob polypeptides of SEQ ID NO:15 and dummy VL-knob polypeptides of SEQ ID NO:19 as indicated above having the amino acid sequence of the respective dummy polypeptide as indicated above, wherein one of the following amino acid substitutions was made: K370E, no destabilizing mutation, W366I K409D, V397Y, or K392D.
[0497] Heterodimeric precursor polypeptides were generated comprising dummy VL-Fc(hole) polypeptides of SEQ ID NO:21 and dummy-VH-Fc(hole) polypeptides of SEQ ID NO:25 as indicated above having the amino acid sequence of the respective dummy polypeptide as indicated above, wherein one of the following amino acid substitutions was made: E357K, A368F, D399A F405W, S364L, D356K, or S354V.
[0498] Heterodimeric precursor polypeptides were generated comprising dummy-VH-Fc(knob) polypeptides of SEQ ID NO:23 and dummy-VL-Fc(knob) polypeptides of SEQ ID NO:27 as indicated above having the amino acid sequence of the respective dummy polypeptide as indicated above, wherein one of the following amino acid substitutions was made: K370E, no destabilizing mutation, W366I K409D, V397Y, K392D, or K370E K439E.
Example 5
Determination of Polypeptide Chain Exchange Via T Cell Activation Assay
[0517] To assess the impact of different destabilizing mutations on the polypeptide chain exchange, exchange reactions were set up using the precursor polypeptides as generated in Example 4 as a proof-of-concept experiment. The structure of the expected product polypeptides is depicted in FIG. 2 for the precursor polypeptides devoid of a CH2 domain and in FIG. 3 for the precursor polypeptides comprising a full Fc domain. Polypeptide chain exchange results in formation of an antigen binding site specifically binding to CD3. Presence of the bispecific anti-LeY/anti-CD3 product polypeptide was assessed by cell-based assay.
[0518] The influence of different CH3 interface mutations on the efficacy of this chain exchange reaction was evaluated in a cell based reporter assay system composed of LeY-expressing MCF7 cells and a Jurkat reporter cell line (Promega J1621) according to the following principle: Binding of the first and second heterodimeric polypeptides to MCF7 cells and polypeptide chain exchange results in formation of an antigen binding site specifically binding to CD3. Jurkat cells expressing CD3 are bound by the antigen binding site specifically binding to CD3, which results in luciferase expression from the Jurkat cells. Luminescence was detected after addition of BioGlo substrate.
Example 6
[0524] Generation of Monospecific Precursor Polypeptides of the Invention that Bind to FcRn for the Generation of Activatable Binding Sites Upon Polypeptide Chain Exchange
[0525] For assessing formation of bispecific anti-LeY/anti-CD3 antibodies from monospecific precursor polypeptides, monospecific precursor polypeptides of a domain arrangement as depicted for the first and second heterodimeric precursor polypeptides indicated in FIG. 1 were generated.
[0526] The following precursor polypeptides were provided: [0527] A first heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VH)-knob precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VH)-knob precursor comprised a light chain polypeptide of SEQ ID NO:11 (also referred to as “LeY LC”), a first heavy chain polypeptide of SEQ ID NO:12 (also referred to as “LeY-CD3(VH)-knob HC”) comprising a VH domain derived from an antibody specifically binding to CD3 (“CD3(VH)”) and a second heavy chain polypeptide based of SEQ ID NO:28 with the destabilizing mutation E357K and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy hole” polypeptide) comprised von N- to C-terminal direction a mutated hinge region that does not comprise cysteine, a CH2 domain and a CH3 domain. [0528] A second heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VL)-hole precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VL)-hole precursor comprised the light chain polypeptide of SEQ ID NO:11, i.e. the LeY LC; a first heavy chain polypeptide of SEQ ID NO:14 (also referred to as “LeY-CD3(VL)-hole HC”) comprising a VL domain derived from an antibody specifically binding to CD3 (“CD3(VL)”) and a second heavy chain polypeptide based on SEQ ID NO:29 with the destabilizing mutation K370E and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy knob” polypeptide) comprised von N- to C-terminal direction a mutated hinge region that does not comprise cysteine, a CH2 domain and a CH3 domain.
[0529] The indicated polypeptide chains comprise the following mutations:
PNG
media_image3.png
335
635
media_image3.png
Greyscale
However, claim 1 does not make complete binding sites for the same antigen and CD3 because the claim does not provide a second variable (V) domain that pairs to bind the same antigen and CD3 as discussed above in 112 (b) section. Therefore, one of ordinary skill in the art would not be able to envision how to use the heterodimeric precursor polypeptides of claim 1 in the absence of the second V domain that pairs to bind the same antigen or CD3 target. The claimed structure is not useful in the absence of the complementing variable domain that create the target-binding sites.
Furthermore, the structure as claimed in instant claim 1 does not seem to correlate with any of the molecules in the drawing because any molecule in the drawing shows the subpart (ii) of the first polypeptide binding to a second target. The structure in claim 1 is missing the light chain polypeptide comprising VL-CL that pairs with the heavy chain polypeptide comprising VH-CH1-VH-CH2-CH3, see Figure 1 below.
PNG
media_image4.png
403
865
media_image4.png
Greyscale
Therefore, the structure claimed in instant claims are not described in the specification in such a way as to enable one skilled in the art to "visualize or recognize" the members of the genus.”
Even assuming the heterodimeric precursor polypeptides bind to the same antigen, or CD3, the specification does not describe the structure, i.e., the amino acid sequences of the heavy and light chain variable domains of the first antigen binding moiety and/or second antigen binding moiety that correlated with binding to which particular antigen (claims 1-7, 9-12, 15), such as any CD3 (claims 9 and 16). Without such as description, one of ordinary skill in the art would be unable to distinguish which anti-CD3 heterodimer would fall within the scope encompassed by the claim and which do not. Further, the specification does not describe a representative number of species falling with the scope of the genus or structural features common to the members of the genus so the one of skill in the art can visualize or recognize the member of the genus of the actual claimed heterodimer themselves to demonstrate possession at the time of filing.
At the time the invention was made, it was known in the art that antibodies have a large repertoire of distinct structures and that a huge variety of antibodies can be made to bind to a single epitope.
For example, Lloyd et al. taught that hundreds of functional antibody fragments can be isolated from an antibody library that bind to the same antigen wherein these antibodies have distinct heavy and light chain sequences (of record, Lloyd et al. Protein Engineering, Design & Selection 22:159-168, 2009; PTO 892; see, e.g., Discussion).
Similarly, Edwards et al., (of record, J Mol Biol. 334(1): 103-118, 2003; PTO 892), found that over 1000 antibodies, all different in amino acid sequence, were generated to a single protein; 568 different amino acid sequences identified for the V(H) CDR3 domains of these antibodies (Abstract).
Poosarla et al (of record, Biotechn. Bioeng., 114(6): 1331-1342, 2017; PTO 892) teach substantial diversity in designed mAbs (sharing less than 75% sequence similarity to all existing natural antibody sequences) that bind to the same 12-mer peptide, binding to different epitopes on the same peptide. Said reference further teaches “most B-cell epitopes... in nature consist of residues from different regions of the sequence and are discontinuous...de novo antibody designs against discontinuous epitopes present additional challenges...". (See entire reference.)
For example, Yu et al (of record, Investigative Ophthalmology & Visual Science 49(2): 522-527, February 2008; PTO 892) teach bevacizumab, which is a humanized anti-human VEGF-A mAb A.4.6.1 binds specifically to human VEGF-A, the same antibody does not bind to mouse VEGF-A (see page 522, right col., page 523, Figure 1, in particular).
Further, even minor changes in the amino acid sequence of a heavy or light variable region, particularly the CDRs, may dramatically affect antigen-binding function and IgG binding to the neonatal Fc receptor (FcRn) and pharmacokinetics.
For example, Piche-Nicholas et al (of record, MABS 10(1): 81-94, 2018; PTO 892) teaches altering complementary-determining region (CDRs) by 1-5 mutations significantly alter binding affinity to FcRn in vitro, see entire document, abstract, p. 95, right col, in particular. Engineering CDRs by modify local charge and thus maintain affinity to FcRn at 400 nM or weaker in vitro while retaining antigen binding may have far-reaching implications in the half-life optimization efforts of IgG therapeutics with respect to in vivo pharmacokinetics, see p. 90, in particular. Given that hundreds of unique antibody structures may bind a single antigen, the structure of an antibody cannot be predicted from the structure of the antigen (as held in Amgen), and a single species, or small group of species, cannot define a structure-function relationship so as to be representative of all the antibodies that bind to that antigen (as held in AbbVie).
In AbbVie Deutschland GMBH v. Janssen Biotech, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014), a claim drawn to a genus of antibodies having a recited binding affinity and binding specificity to a fully characterized antigen was found to be invalid for lack of written description such that it was not infringed by a subsequently disclosed antibody having all of the recited functional characteristics but a completely different structure (amino acid sequence). The Court held:
“It is true that functionally defined claims can meet the written description requirement if a reasonable structure-function correlation is established, whether by the inventor as described in the specification or known in the art at the time of the filing date... The asserted claims attempt to claim every fully human IL-12 antibody that would achieve a desired result, i.e., high binding affinity and neutralizing activity, and cover an antibody as different as Stelara®, whereas the patents do not describe representative examples to support the full scope of the claims. (AbbVie, 759 F.3d at 1298; 111 USPQ2d at 1791) (emphasis added).
Further, the art teaches contrary to any generalized assumption, is that any anti-CD3 domain can be swapped into a bispecific BiTE® format under the conditions of the formulation much less that would result in functional activity.
Shepard et al (of record, PLOS One 18(6): e0273884, June 22, 2023; PTO 892) teach the unpredictability of swapping CD3 binding domains in the context of a BiTE in so far as the binding requirement to CD3 epsilon much less the extracellular epitope:
“We next sought to test our platform for flexibility with respect to screening novel T-cell engaging domains of the bispecific molecule. We developed a number of novel mouse monoclonal antibodies (mAbs) against human CD3 complex using a multi-antigen immunization strategy in mice and traditional hybridoma screening. Through this process, we were able to identify several monoclonal antibodies with reactivity to Jurkat cells (Fig 4A) and human T cells (Fig 4B). To assess whether scFvs derived from novel CD3-targeted mAbs would be functional within as part of a BiTE molecule, we cloned 4 anti-human CD3 single chain variable fragments into CD19 or EGFRvIII specific BiTE plasmids (Fig 4C). We then generated supernatants using transient transfection of HEK293T as described above. BiTE supernatants were screened for activity using Jurkat cells in co-culture with EGFRvIII-expressing U87-VIII targets or CD19-expressing Raji cells. Previously tested constructs using OKT3 CD3-engager arms showed activity with both EGFRvIII and CD19 specific BiTEs, whereas we detected activity for only one of our novel CD3-engager BiTEs and only when combined with an EGFRvIII-specific scFv (Fig 4D). To confirm these results, we repeated BiTE production and Jurkat co-culture screening of CD19 and EGFRvIII targeted BiTE molecules incorporating OKT3 or the novel 1E2 CD3-targeting single chain variable fragment. Whereas EGFRvIII BiTEs incorporating an scFv derived from the 1E2 mAb or OKT3 showed specific reactivity against EGFRvIII expressing U87-vIII cells, only CD19-OKT3 showed reactivity to CD19-expressing Raji cells (Fig 4E). These results indicate that the novel CD3-targeting 1E2-scFv is functional only for an EGFRvIII-targeting BiTE but not a CD19-targeting BiTE, likely due to the specific binding characteristics of the CD19 or EGFRvIII scFv elements.”
“Similarly, we also find that only one of the novel CD3-targeting scFvs tested here showed activity in BiTE format, and even then, activity was restricted to combination with EGFRvIII-targeting scFv and not with a CD19-specific scFv. Again, we have no insight into the failure rate for BiTE molecules in this assay, as the intent of this assay is to provide a rapid means for testing biological activity rather than focusing on various aspects of antibody characterization. We are currently undertaking molecular studies to test whether incorporating different linker domains may be able to improve the activity of BiTEs using the novel CD3-scFv reported to have activity here, something that may provide further insight into the design constraints for these BiTE molecules.”
Since the disclosure fails to describe common attributes or characteristics that identify members of the genus, and because the genus is highly variant, the disclosure is insufficient to describe the genus. Thus, one of skill in the art would reasonably conclude that the disclosure fails to provide a representative number of species to describe the genus as broadly claimed.
Vas-Cath Inc. v. Mahurkar, 19 USPQ2d 1111, makes clear that “applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the ‘written description’ inquiry, whatever is now claimed.” (see page 1117). The specification does not “clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed.” (see Vas-Cath at page 1116).
Adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method for isolating it. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (CAFC 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016.
One cannot describe what one has not conceived. See Fiddles v. Baird, 30 USPQ2d 1481, 1483. In Fiddles v. Baird, claims directed to mammalian FGF’s were found unpatentable due to lack of written description for the broad class. The specification provided only the bovine sequence.
Therefore, only a set of heterodimeric precursor polypeptides as shown in Figure 1 comprising:
a first heterodimeric precursor polypeptide comprising:
a first heavy chain comprising from N- to C-terminal direction a first VH domain, a CH1 domain, a second VH domain, and a first CH3 domain wherein the first CH3 domain comprises a knob or a hole mutation,
a second heavy chain comprising from N- to C-terminal direction a CH2 domain and a CH3 domain
a third polypeptide from N- to C-terminal direction a first VL domain and a CL domain wherein the first VL domain that pairs with the first VH, and
wherein the first heavy chain and the second heavy chain are associated with each other via the CH3 domain, and form a heterodimer, wherein one of the CH3 domain comprises a knob mutation and the other CH3 domain comprises a hole mutation;
a second heterodimeric precursor polypeptide comprising:
a third heterodimeric precursor polypeptide comprising: from N- to C-terminal direction a first VH domain, a CH1 domain, a second VL domain, and a first CH3 domain wherein the first CH3 domain comprises a knob or a hole mutation,
a forth heavy chain comprising from N- to C-terminal direction a CH2 domain and a CH3 domain
a sixth polypeptide from N- to C-terminal direction a first VL domain and a CL domain wherein the first VL domain pairs with the first VH in the third heterodimeric precursor polypeptide, and
wherein the third heavy chain and the forth heavy chain are associated with each other via the CH3 domain, and form a heterodimer, wherein one of the CH3 domain comprises a knob mutation and the other CH3 domain comprises a hole mutation;
and wherein
A) either
i) the first heavy chain polypeptide comprises the CH3 domain with the knob mutation and the third heavy chain polypeptide comprises CH3 domain with the hole mutation, or
ii) the first heavy chain polypeptide comprises the CH3 domain with the hole mutation and the third heavy chain polypeptide comprises CH3 domain with the knob mutation; or wherein
B) either
the CH3 domain of the first heterodimeric precursor polypeptide comprising the knob mutation and the CH3 domain of the second heterodimeric precursor polypeptide comprising the hole mutation, or
the CH3 domain of the first heterodimeric precursor polypeptide comprising the hole mutation and the CH3 domain of the second heterodimeric precursor polypeptide comprising the knob mutation and one or more amino acid substitution destabilizing the CH3/CH3 interface, wherein the amino acid substitutions are arranged such that the substituted amino acids interact in the CH3/CH3 interface within a pair of said CH3 domains, and
wherein the first heavy chain comprises the amino acid sequence of SEQ ID NO: 12 or SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 23, or SEQ ID NO: 27 wherein the first light chain comprising the amino acid sequence of SEQ ID NO: 11, and
a second heterodimeric precursor comprising a second heavy chain polypeptide and a second light chain polypeptide wherein the second heavy chain from N- to C-terminus comprising a LeY binding heavy chain, a CD3 binding VL domain and a CH3 domain comprising a hole mutation, wherein the
second heavy chain comprising the amino acid sequence of SEQ ID NO: 14, SEQ ID NO: 17, SEQ ID NO:18, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:25 or SEQ ID NO:26 and wherein the second light chain polypeptide comprising the amino acid sequence of SEQ ID NO: 11, (2) a method for generating a heterodimeric polypeptide comprising contacting the first heterodimeric precursor polypeptide with the second heterodimeric precursor polypeptide above to form a third heterodimeric antibody comprises two antigen binding sites that bind to LeY and one antigen binding site that binds to CD3, and a CD3 binding heterodimer comprises a VH domain and a CH3 domain comprises a knob or a hole and a VL domain and a CH3 domain comprising a hole or a knob wherein the CH3 domains heterodimerize, but not the full breadth of the claims meets the written description provision of 35 U.S.C. § 112, first paragraph.
Applicant is reminded that Vas-Cath makes clear that the written description provision of 35 U.S.C. § 112 is severable from its enablement provision (see page 1115).
Applicants’ arguments filed December 10, 2025 have been fully considered but are not found persuasive.
Applicants’ position is that Claim 16 is canceled herein without prejudice, mooting the rejection as to this claim. Claim 1 specifies a first heterodimeric precursor polypeptide that comprises a first heavy chain polypeptide comprising either a VH-CH3 or a VL-CH3, and a second heterodimeric precursor polypeptide that comprises a third heavy chain polypeptide comprising either a VL-CH3 or a VH-CH3 (depending upon which is present in the first heavy chain polypeptide). Moreover, claim 1 specifies that the third heavy chain polypeptide antibody variable domain forms an antigen binding site specifically binding to a target antigen [which according to claim 8 could be CD3] with the antibody variable domain comprised in the first heavy chain polypeptide of the first heterodimeric precursor polypeptide. As such, there is no "absence of the second V domain that pairs to bind the same antigen or CD3 target" as alleged by the Office Action, and the claimed structure is useful.
At page 51 of the specification, the antigen binding moiety (first or second) is described as being, inter alia, an Fv, a Fab, a Fab', a Fab'-SH, a F(ab')2, a diabody, a scFv, or an scFab. As such, given the recitation of "antigen binding moiety" and the various forms such an antigen binding moiety might take, as described in the specification, a person of skill in the art would be able to readily visualize the genus of what is recited in claim 1, and the members of that genus.
The Office Action at page 18 further states that the specification "does not describe the structure, i.e., the amino acid sequences of the heavy and light chain variable domains of the first antigen binding moiety and/or second antigen binding moiety that correlated with binding to which particular antigen." This contention misunderstands the nature of the invention.
The invention is not "antibodies that bind to antigen X"; it is the sets of heterodimeric precursor polypeptides that comprise the specific arrangements of the aforementioned structures that allows chain exchange to produce the exchanged polypeptide labeled, e.g., "Multispecific product polypeptide" in Fig. 1. The pair of polypeptides recited in claim 1 is a part of these heterodimeric precursor polypeptides. The overall structure of each of the claimed sets of heterodimeric precursor polypeptides are the important aspects of the inventions; the particular targets are a secondary, non-material, aspect. An adequate description of the novel and nonobvious arrangements of largely-known components into fusion polypeptide chains that form the and nonobvious structures shown in the Figures is not dependent upon what specific targets are chosen. The specification fully describes the structures that define the claimed sets of heterodimeric precursor polypeptides - the arrangements of the heavy and light chain variable regions (VH and VL), heavy and light chain constant regions (CH and CL) and CH3 regions, as depicted in Figure 1. The sequences of CH, CL and CH3 antibody domains are highly conserved and their sequence is well-known, as is the sequence of VH and VL domains aside from the specific CDRs that give them antigen specificity. The identities of the destabilizing mutations (open circles in Fig. 1), and hole and destabilizing knob mutations in the CH3 domains, is explicitly recited in the claims. Thus, while binding to a particular antigen (such as CD3) may be Page 12 of recited functionally, the vast majority of the claimed sets of heterodimeric precursor polypeptides are recited structurally. As such, the great majority of the structures claimed are already well- described.
As such, the specification provides "a precise definition, such as by structure ... of the claimed subject matter sufficient to distinguish it from other materials", Regents of the University of California v. Eli Lilly & Co., 119 F.3d 1559, 1568 (Fed. Cir. 1997) (quoting Fiers v. Revel, 984 F.2d 1164, 1171 (Fed. Cir. 1993), and "structural features common to the members of the genus [encompassed by claim 1] so that one of skill in the art can 'visualize or recognize' the members of the genus" (Ariad Pharmaceuticals v. Eli Lilly & Co., 598 F.3d 1336, 1350 (Fed. Cir. 2010). To focus solely on, for example, CD3 binding (as the Office Action does at page 20) is to essentially ignore the remainder of the claims.
The Office Action at page 19 further states that the specification "does not describe a representative number of species falling with the scope of the genus or structural features common to the members of the genus so the one of skill in the art can visualize or recognize the member of the genus of the actual claimed heterodimer themselves to demonstrate possession at the time of filing. First, the specification describes the structural features common to the members of the claimed genus of heterodimeric precursor polypeptides, as exemplified at least in the Summary of the Invention and in Figures 1-3. A person of skill in the art would have no difficulty in identifying multispecific polypeptides that fall within and without the claimed genus. The references cited by the Office Action at pages 19-22 are not to the contrary. Second, none of the Office Action, the USPTO, the Federal Circuit nor the Supreme Court have ever defined or described what does constitute a "representative number of species" to support a claim to a genus. Lacking that basic guidepost, an assertion that a specification does not describe a representative number of species is at best arbitrary and capricious.
In response, the amendment to claims 1-9, 11, 12, 15 and 16 is acknowledged.
The structure of claim 1 has no resemblance to the picture shown in Fig. 1, which reproduced below for Applicant’s convenience.
There are at least six polypeptides, 3 polypeptides in the first heterodimeric precursor polypeptide and 3 polypeptides in the second heterodimeric precursor polypeptide.
PNG
media_image5.png
322
416
media_image5.png
Greyscale
Further, note that one of the heavy chains in the first and second heterodimeric precursor polypeptides comprises VH-CH1-connector-VH-CH3 and the other heavy chain comprises a VH-CH1-peptide conector-VL-CH3.
Regarding “at least a part” of the first antigen binding moiety (line 6) and the second antigen binding moiety (line 20) in claim 1, the phrase “at least a part” encompasses a single amino acid of an antigen binding moiety, a CDR, or a VL or a VH or a Fv. Claim 1 does not recite VH-CH1 in the first heterodimeric precursor polypeptide and VH-CH1 in the second heterodimeric precursor polypeptide. As such, it is submitted that a skilled artisan cannot, as one can do with a fully described genus, visualize or recognize the identity of the members of the genus of the set of heterodimeric precursor polypeptides.
In response to the argument that at page 51 of the specification, the antigen binding moiety (first or second) is described as being, inter alia, an Fv, a Fab, a Fab', a Fab'-SH, a F(ab')2, a diabody, a scFv, or an scFab, MPEP 2173.05(s) states that where possible, claims are to be complete in themselves.
Further, M.P.E.P. § 2106 (II) states:
USPTO personnel are to give claims their broadest reasonable interpretation in light of the supporting disclosure. In re Morris, 127 F.3d 1048, 1054-55, 44 USPQ2d 1023, 1027-28 (Fed. Cir. 1997). Limitations appearing in the specification but not recited in the claim should not be read into the claim. E-Pass Techs., Inc. v. 3Com Corp., 343 F.3d 1364, 1369, 67 USPQ2d 1947, 1950 (Fed. Cir. 2003) (claims must be interpreted “in view of the specification” without importing limitations from the specification into the claims unnecessarily). In re Prater, 415 F.2d 1393, 1404-05, 162 USPQ 541, 550- 551 (CCPA 1969). See also In re Zletz, 893 F.2d 319, 321-22, 13 USPQ2d 1320, 1322 (Fed. Cir. 1989) (“During patent examination the pending claims must be interpreted as broadly as their terms reasonably allow.... The reason is simply that during patent prosecution when claims can be amended, ambiguities should be recognized, scope and breadth of language explored, and clarification imposed.... An essential purpose of patent examination is to fashion claims that are precise, clear, correct, and unambiguous. Only in this way can uncertainties of claim scope be removed, as much as possible, during the administrative process.”) (Emboldened added for emphasis).
M.P.E.P. § 2106 (II) continues:
While it is appropriate to use the specification to determine what applicant intends a term to mean, a positive limitation from the specification cannot be read into a claim that does not itself impose that limitation. A broad interpretation of a claim by USPTO personnel will reduce the possibility that the claim, when issued, will be interpreted more broadly than is justified or intended. An applicant can always amend a claim during prosecution to better reflect the intended scope of the claim.
Further, Claim 1 does not recite the one or more amino acid substitution that destabilize the CH3/CH3 interface. Claims 2 and 3 do not recite the particular substitutions in CH3 can destabilize the CH3/CH3 interface.
Regarding a first antigen binding site specifically binding to any target antigen and a second antigen binding site specifically binding to a target antigen (claim 5) and antibody variable domain comprised in the first heavy chain polypeptide and the third heavy chain polypeptide are capable of forming an antigen binding site specifically binds to CD3 (claim 8), the specification does not describe the structure, e.g., amino acid sequence of the heavy and light chain variable domains or structure common to members of the genus of first and second antigen binding site that specifically binds to any and all target antigen or CD3 from any species. A person of skill in the art would have difficulty in identifying multispecific polypeptides that fall within the scope of the claimed genus to demonstrate possession at the time of filing.
At the time the invention was made, it was known in the art that antibodies have a large repertoire of distinct structures and that a huge variety of antibodies can be made to bind to a single epitope.
For example, Lloyd et al. taught that hundreds of functional antibody fragments can be isolated from an antibody library that bind to the same antigen wherein these antibodies have distinct heavy and light chain sequences (of record, Lloyd et al. Protein Engineering, Design & Selection 22:159-168, 2009; PTO 892; see, e.g., Discussion).
Similarly, Edwards et al., (of record, J Mol Biol. 334(1): 103-118, 2003; PTO 892), found that over 1000 antibodies, all different in amino acid sequence, were generated to a single protein; 568 different amino acid sequences identified for the V(H) CDR3 domains of these antibodies (Abstract).
Poosarla et al (of record, Biotechn. Bioeng., 114(6): 1331-1342, 2017; PTO 892) teach substantial diversity in designed mAbs (sharing less than 75% sequence similarity to all existing natural antibody sequences) that bind to the same 12-mer peptide, binding to different epitopes on the same peptide. Said reference further teaches “most B-cell epitopes... in nature consist of residues from different regions of the sequence and are discontinuous...de novo antibody designs against discontinuous epitopes present additional challenges...". (See entire reference.)
For example, Yu et al (of record, Investigative Ophthalmology & Visual Science 49(2): 522-527, February 2008; PTO 892) teach bevacizumab, which is a humanized anti-human VEGF-A mAb A.4.6.1 binds specifically to human VEGF-A, the same antibody does not bind to mouse VEGF-A (see page 522, right col., page 523, Figure 1, in particular).
Further, even minor changes in the amino acid sequence of a heavy or light variable region, particularly the CDRs, may dramatically affect antigen-binding function and IgG binding to the neonatal Fc receptor (FcRn) and pharmacokinetics.
For example, Piche-Nicholas et al (of record, MABS 10(1): 81-94, 2018; PTO 892) teaches altering complementary-determining region (CDRs) by 1-5 mutations significantly alter binding affinity to FcRn in vitro, see entire document, abstract, p. 95, right col, in particular. Engineering CDRs by modify local charge and thus maintain affinity to FcRn at 400 nM or weaker in vitro while retaining antigen binding may have far-reaching implications in the half-life optimization efforts of IgG therapeutics with respect to in vivo pharmacokinetics, see p. 90, in particular.
Given that hundreds of unique antibody structures may bind a single antigen, the structure of an antibody cannot be predicted from the structure of the antigen (as held in Amgen), and a single species, or small group of species, cannot define a structure-function relationship so as to be representative of all the antibodies that bind to that antigen (as held in AbbVie).
Given the lack of disclosing the “full scope” of species representative of the diversity in antibody structures that satisfy the functional limits of the claims, e.g., target antigen, or CD3, the specification amounts to no more than a trial and error approach for identifying such species of VH, VL, Fv, domain by screening library. Such a disclosure fails to comport with the purpose of the written description requirement as expressly held by this Court. See Lilly, 119 F.3d at 1568 (stating that “[t]he [written] description requirement of the patent statute requires a description of an invention, not an indication of a result that one might achieve if one made that invention.”); Ariad, 598 F.3d at 1353 (citing Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916 (Fed. Cir. 2004) (quoting Brenner v. Manson, 383 U.S. 519, 536 (1966)) (A "patent is not a hunting license. It is not a reward for the search, but compensation for its successful conclusion.”).
As such, it is submitted that a skilled artisan cannot, as one can do with a fully described genus, visualize or recognize the identity of the members of the genus of the set of heterodimeric precursor polypeptides.
Vas-Cath Inc. v. Mahurkar, 19USPQ2d 1111 (Fed. Cir. 1991), clearly states “applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the ‘written description’ inquiry, whatever is now claimed” (pg. 1117). The specification does not “clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed” (pg. 1116).
Adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method of isolating it. The compound itself is required. See Fiers v. Revel, 25 USPQ2d 1601 at 1606 (CAFC 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016 (Fed. Cir. 1991). One cannot describe what one has not conceived. See Fiddes v. Baird, 30 USPQ2d 1481 at 1483 (BPAI 1993). In Fiddes, claims directed to mammalian FGFs were found to be unpatentable due to lack of written description for that broad class. The specification provided only the bovine sequence.
Further, it is not enough for the specification to show how to make and use the invention, i.e., to enable it (see Amgen at page 1361).
Therefore, there is insufficient written description for genus of heterodimeric precursor polypeptides encompassed the claims at the time the invention was made and as disclosed in the specification as filed under the written description provision of 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph.
For these reasons, the rejection is maintained.
Claims 1-12 and 15 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a set of heterodimeric precursor polypeptides as shown in Figure 1 comprising:
a first heterodimeric precursor polypeptide comprising:
a first heavy chain comprising from N- to C-terminal direction a first VH domain, a CH1 domain, a second VH domain, and a first CH3 domain wherein the first CH3 domain comprises a knob or a hole mutation,
a second heavy chain comprising from N- to C-terminal direction a CH2 domain and a CH3 domain
a third polypeptide from N- to C-terminal direction a first VL domain and a CL domain wherein the first VL domain that pairs with the first VH, and
wherein the first heavy chain and the second heavy chain are associated with each other via the CH3 domain, and form a heterodimer, wherein one of the CH3 domain comprises a knob mutation and the other CH3 domain comprises a hole mutation;
a second heterodimeric precursor polypeptide comprising:
a third heterodimeric precursor polypeptide comprising: from N- to C-terminal direction a first VH domain, a CH1 domain, a second VL domain, and a first CH3 domain wherein the first CH3 domain comprises a knob or a hole mutation,
a forth heavy chain comprising from N- to C-terminal direction a CH2 domain and a CH3 domain
a sixth polypeptide from N- to C-terminal direction a first VL domain and a CL domain wherein the first VL domain pairs with the first VH in the third heterodimeric precursor polypeptide, and
wherein the third heavy chain and the forth heavy chain are associated with each other via the CH3 domain, and form a heterodimer, wherein one of the CH3 domain comprises a knob mutation and the other CH3 domain comprises a hole mutation;
and wherein
A) either
i) the first heavy chain polypeptide comprises the CH3 domain with the knob mutation and the third heavy chain polypeptide comprises CH3 domain with the hole mutation, or
ii) the first heavy chain polypeptide comprises the CH3 domain with the hole mutation and the third heavy chain polypeptide comprises CH3 domain with the knob mutation; or wherein
B) either
the CH3 domain of the first heterodimeric precursor polypeptide comprising the knob mutation and the CH3 domain of the second heterodimeric precursor polypeptide comprising the hole mutation, or
the CH3 domain of the first heterodimeric precursor polypeptide comprising the hole mutation and the CH3 domain of the second heterodimeric precursor polypeptide comprising the knob mutation and one or more amino acid substitution destabilizing the CH3/CH3 interface, wherein the amino acid substitutions are arranged such that the substituted amino acids interact in the CH3/CH3 interface within a pair of said CH3 domains, and
wherein the first heavy chain comprises the amino acid sequence of SEQ ID NO: 12 or SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 23, or SEQ ID NO: 27 wherein the first light chain comprising the amino acid sequence of SEQ ID NO: 11, and
a second heterodimeric precursor comprising a second heavy chain polypeptide and a second light chain polypeptide wherein the second heavy chain from N- to C-terminus comprising a LeY binding heavy chain, a CD3 binding VL domain and a CH3 domain comprising a hole mutation, wherein the
second heavy chain comprising the amino acid sequence of SEQ ID NO: 14, SEQ ID NO: 17, SEQ ID NO:18, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:25 or SEQ ID NO:26 and wherein the second light chain polypeptide comprising the amino acid sequence of SEQ ID NO: 11, (2) a method for generating a heterodimeric polypeptide comprising contacting the first heterodimeric precursor polypeptide with the second heterodimeric precursor polypeptide above to form a third heterodimeric antibody comprises two antigen binding sites that bind to LeY and one antigen binding site that binds to CD3, and a CD3 binding heterodimer comprises a VH domain and a CH3 domain comprises a knob or a hole and a VL domain and a CH3 domain comprising a hole or a knob wherein the CH3 domains heterodimerize, does not enable for making and using a set of any heterodimeric precursor set forth in claims 1-8, 12 as a pharmaceutical composition set forth in claim 15 for treating any cancer as set forth in claim 16 and a method for producing a heterodimeric polypeptide as set forth in claims 9-11. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
Enablement is considered in view of the Wands factors (MPEP 2164.01(a)). These factors include, but are not limited to: (A) The breadth of the claims; (B) The nature of the invention; (C) The state of the prior art; (D) The level of one of ordinary skill; (E) The level of predictability in the art; (F) The amount of direction provided by the inventor; (G) The existence of working examples; and (H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. . In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988).
Claim 1 encompasses a set of heterodimeric precursor polypeptides comprising:
a) a first heterodimeric precursor polypeptide comprising
a first heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain selected from a VH domain or a VL domain, and a CH3 domain, wherein the first heavy chain polypeptide comprises at least a part of a first antigen binding moiety; and
a second heavy chain polypeptide comprising from N- to C-terminal direction a CH2 domain and a CH3 domain, wherein the first heavy chain polypeptide and the second heavy chain polypeptide are associated with each other via the CH3 domains and form a heterodimer, wherein one of the CH3 domains comprises a knob mutation and the other CH3 domain comprises a hole mutation; and
b) a second heterodimeric precursor polypeptide comprising
a third heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain selected from a VH domain or a VL domain, and a CH3 domain, wherein the antibody variable domain forms an antigen binding site specifically binding to a target antigen with the antibody variable domain comprised in the first heavy chain polypeptide of the first heterodimeric precursor polypeptide, wherein the third heavy chain polypeptide comprises at least a part of a second antigen binding moiety; and
a fourth heavy chain polypeptide comprising from N- to C-terminal direction a CH2 domain and a CH3 domain; wherein the third heavy chain polypeptide and the fourth heavy chain polypeptide are associated with each other via the CH3 domains and form heterodimer, wherein one of the CH3 domains comprises a knob mutation and the other CH3 domain comprises a hole mutation; wherein
A) either
i) the first heavy chain polypeptide comprises the CH3 domain with the knob mutation and the third heavy chain polypeptide comprises CH3 domain with the hole mutation, or
ii) the first heavy chain polypeptide comprises the CH3 domain with the hole mutation and the third heavy chain polypeptide comprises CH3 domain with the knob mutation; and wherein
B) either
the CH3 domain of the first heterodimeric precursor polypeptide comprising the knob mutation and the CH3 domain of the second heterodimeric precursor polypeptide comprising the hole mutation, or
the CH3 domain of the first heterodimeric precursor polypeptide comprising the hole mutation and the CH3 domain of the second heterodimeric precursor polypeptide comprising the knob mutation comprises one or more amino acid substitution destabilizing the CH3/CH3 interface, wherein the amino acid substitutions are arranged such that the substituted amino acids interact in the CH3/CH3 interface within a pair of said CH3 domains.
Claim 2 encompasses the set of heterodimeric polypeptides according to claim 1, wherein the CH3 domain comprising the knob mutation and the CH3 domain comprising the hole mutation indicated in B) comprise one or more of the following amino acid substitutions, wherein the numbering is according to the Kabat numbering system:
the CH3 domain with the hole mutation comprises at least one amino acid substitution selected from the group of:
replacement of S354 with a hydrophobic amino acid;
replacement of D356 with a positively charged amino acid;
replacement of E357 with a positively charged amino acid or with a hydrophobic amino acid;
replacement of D356 with a positively charged amino acid, and replacement of E357 with a positively charged amino acid or with a hydrophobic amino acid;
replacement of $364 with a hydrophobic amino acid;
replacement of A368 with a hydrophobic amino acid;
replacement of K392 with a negatively charged amino acid;
replacement of T394 with a hydrophobic amino acid;
replacement of D399 with a hydrophobic amino acid and replacement of S400 with a positively charged amino acid;
replacement of D399 with a hydrophobic amino acid and replacement of F405 with a positively charged amino acid;
replacement of V 407 with a hydrophobic amino acid; and
replacement of K409 with a negatively charged amino acid; and
replacement of K439 with a negatively charged amino acid;
the CH3 domain with the knob mutation comprises at least one amino acid substitution selected from the group of:
replacement of Q347 with a positively charged amino acid, and replacement of K360 with a negatively charged amino acid;
replacement of Y349 with a negatively charged amino acid;
replacement of L35 | with a hydrophobic amino acid, and replacement of E357 with a hydrophobic amino acid;
replacement of S364 with a hydrophobic amino acid;
replacement of W366 with a hydrophobic amino acid, and replacement of K409 with a negatively charged amino acid;
replacement of L368 with a hydrophobic amino acid;
replacement of K370 with a negatively charged amino acid;
replacement of K370 with a negatively charged amino acid, and replacement of K439 with a negatively charged amino acid;
replacement of K392 with a negatively charged amino acid;
replacement of T394 with a hydrophobic amino acid;
replacement of V397 with a hydrophobic amino acid;
replacement of D399 with a positively charged amino acid, and replacement of K409 with a negatively charged amino acid;
replacement of S400 with a positively charged amino acid;
F405W;
Y407W; and
replacement of K439 with a negatively charged amino acid.
Claim 3 encompasses the set of heterodimeric polypeptides according to according to claim 1 or claim 2, wherein the CH3 domain comprising the knob mutation and the CH3 domain comprising the hole mutation indicated in B) comprise one or more of the following amino acid substitutions, wherein the numbering is according to the Kabat numbering system:
the CH3 domain with the hole mutation comprises at least one amino acid substitution selected from the group of:
replacement of E357 with a positively charged amino acid;
replacement of $364 with a hydrophobic amino acid;
replacement of A368 with a hydrophobic amino acid; and
replacement of V 407 with a hydrophobic amino acid; and
the CH3 domain with the knob mutation comprises at least one amino acid substitution selected from the group of:
replacement of K370 with a negatively charged amino acid;
replacement of K370 with a negatively charged amino acid, and replacement of K439 with a negatively charged amino acid;
replacement of K392 with a negatively charged amino acid; and
replacement of V397 with a hydrophobic amino acid.
Clam 4 encompasses the set of heterodimeric polypeptides according to claim 1 or claim 2, wherein the first antigen binding moiety and/or the second antigen binding moiety is an antibody antigen-binding fragment thereof.
Clam 5 encompasses the set of heterodimeric polypeptides according to claim 1 or claim 2, wherein
a) the first heterodimeric precursor polypeptide further comprises:
within the first heavy chain polypeptide comprising a CH3 domain a further antibody variable domain (first antibody variable domain), and
a further polypeptide chain that is a light chain polypeptide comprising a second antibody variable domain, wherein the first and second antibody variable domain together form a first antigen binding site specifically binding to a target antigen; and wherein
b) the second heterodimeric precursor polypeptide comprises:
within the third heavy chain polypeptide comprising a CH3 domain a further antibody variable domain (third antibody variable domain), and
a further polypeptide chain that is a light chain polypeptide comprising a fourth antibody variable domain, wherein the third and fourth antibody variable domain together form a second antigen binding site specifically binding to a target antigen.
Claim 6 encompasses the set of heterodimeric polypeptides according to claim 1 or claim 2, wherein in the first heterodimeric polypeptide no interchain disulfide bond is formed between the two polypeptide chains comprising the CH3 domains, and wherein in the second heterodimeric polypeptide no interchain disulfide bond is formed between the two polypeptide chains comprising the CH3 domains.
Claim 7 encompasses the set of heterodimeric precursor polypeptides according to claim 1 or claim 2, wherein the antigen binding moiety of the first heterodimeric precursor polypeptide and the antigen binding moiety of the second heterodimeric precursor polypeptide bind to the same antigen.
Claim 8 encompasses the set of heterodimeric precursor polypeptides according to claim 1 or claim 2, wherein the antibody variable domains comprised in the first heavy chain polypeptide and the third heavy chain polypeptide are capable of forming an antigen binding site specifically binding to CD3.
Claim 9 encompasses a method for generating a heterodimeric polypeptide comprising contacting the first heterodimeric precursor polypeptide and the second heterodimeric precursor polypeptide of claim 1 or claim 2 to form a third heterodimeric polypeptide comprising the first heavy chain polypeptide and the third heavy chain polypeptide.
Claim 10 encompasses the method according to claim 9 comprising contacting the first heterodimeric precursor polypeptide and the second heterodimeric precursor polypeptide to form a fourth heterodimeric polypeptide comprising the second heavy chain polypeptide and the fourth heavy chain polypeptide.
Claim 11 encompasses the method according to claim 9, wherein in the first heterodimeric polypeptide no interchain disulfide bond is formed between the two polypeptide chains comprising the CH3 domains, and wherein in the second heterodimeric polypeptide no interchain disulfide bond is formed between the two polypeptide chains comprising the CH3 domains, and wherein the contacting is performed in absence of a reducing agent.
Claim 12 encompasses a first heterodimeric precursor polypeptide comprising:
a first heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain selected from a VH domain and a VL domain, and a CH3 domain, wherein the first heavy chain polypeptide comprises at least a part of a first antigen binding moiety; and
a second heavy chain polypeptide comprising from N- to C- terminal direction a CH2 domain and a CH3 domain, wherein the first heavy chain polypeptide and the second heavy chain polypeptide are associated with each other via the CH3 domains and form a heterodimer, wherein one of the CH3 domains comprises a knob mutation and the other CH3 domain comprises a hole mutation;
wherein either
i) the CH3 domain of the first heterodimeric precursor polypeptide comprising
the knob mutation and the CH3 domain of the second heterodimeric precursor polypeptide comprising the hole mutation, or
ii) the CH3 domain of the first heterodimeric precursor polypeptide comprising the hole mutation and the CH3 domain of the second heterodimeric precursor polypeptide comprising the knob mutation, comprises one or more amino acid substitutions that destabilize a CH3/CH3 interface, wherein the amino acid substitutions are arranged such that the substituted amino acids interact in the CH3/CH3 interface within a pair of said CH3 domains.
Claim 15 encompasses a pharmaceutical composition comprising the set of heterodimeric precursor polypeptides of any claims 1 to 8 and a pharmaceutically acceptable carrier.
Enablement is not commensurate with how to make and use any heterodimeric precursor polypeptides for treating cancer without guidance as to the structure of the VH and VL that correlated with binding specificity of said heterodimeric precursor polypeptides.
The specification exemplifies:
Example 4
Generation of Monospecific Precursor Polypeptides for the Generation of Activatable Binding Sites Upon Polypeptide Chain Exchange
[0477] This example is a proof-of-concept example for identifying destabilizing mutations assessing efficacy polypeptide chain exchange with a subset of destabilizing mutations identified in Examples 1 to 3, and assessing activation of an antigen binding site by polypeptide chain exchange via a cell based T cell activation assay.
[0478] For assessing formation of bispecific anti-LeY/anti-CD3 antibodies from monospecific precursor polypeptides, monospecific precursor polypeptides of a domain arrangement as depicted for the first and second heterodimeric precursor polypeptides indicated in FIG. 2 and FIG. 3 were generated.
Precursor Polypeptides Devoid of CH2 Domain
[0479] In a first set of experiments, heterodimeric precursor polypeptides with a domain arrangement as depicted in FIG. 2 were provided. The precursor polypeptides are devoid of CH2 domains and comprise an antibody variable domain arranged at the N-terminal end of the CH3 domains.
[0480] In a first alternative, the following precursor polypeptides were provided: [0481] A first heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VH)-knob precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VH)-knob precursor comprised a light chain polypeptide of SEQ ID NO:11 (also referred to as “LeY LC”), a first heavy chain polypeptide of SEQ ID NO:12 (also referred to as “LeY-CD3(VH)-knob HC”) comprising a VH domain derived from an antibody specifically binding to CD3 (“CD3(VH)”) and a second heavy chain polypeptide based on SEQ ID NO:13 (which represents the basic amino acid sequence without destabilizing mutation), with the destabilizing mutations as indicated below and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy-VL-hole” polypeptide) comprised von N- to C-terminal direction a hinge region, a VL domain derived from an antibody specifically binding to digoxigenin (“dig”) and a CH3 domain. [0482] A second heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VL)-hole precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VL)-hole precursor comprised the light chain polypeptide of SEQ ID NO:11, i.e. the LeY LC; a first heavy chain polypeptide of SEQ ID NO:14 (also referred to as “LeY-CD3(VL)-hole HC”) comprising a VL domain derived from an antibody specifically binding to CD3 (“CD3(VL)”) and a second heavy chain polypeptide based on SEQ ID NO: 15 (which represents the basic amino acid sequence without destabilizing mutation) with the destabilizing mutations as indicated below and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy-VH-knob” polypeptide) comprised von N- to C-terminal direction a hinge region, a VH domain derived from a non-binding antibody and a CH3 domain.
[0483] In a second alternative, the following precursor polypeptides were provided: [0484] A first heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VL)-knob precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VL)-knob precursor comprised the light chain polypeptide of SEQ ID NO:11, i.e. the LeY LC, a first heavy chain polypeptide of SEQ ID NO:16 (also referred to as “LeY-CD3(VL)-knob HC”) comprising the CD3(VL) domain and a second heavy chain polypeptide based on SEQ ID NO:17 (which represents the basic amino acid sequence without destabilizing mutation), with the destabilizing mutations as indicated below and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy-VH-hole” polypeptide) comprised von N- to C-terminal direction a hinge region, a VH domain derived from a non-binding antibody and a CH3 domain. [0485] A second heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VH)-hole precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VH)-hole precursor comprised the light chain polypeptide of SEQ ID NO:11, i.e. the LeY LC; a first heavy chain polypeptide of SEQ ID NO: 18 (also referred to as “LeY-CD3(VH)-hole HC”) comprising the CD3(VH) domain and a second heavy chain polypeptide based on SEQ ID NO:19 (which represents the basic amino acid sequence without destabilizing mutation) with the destabilizing mutations as indicated below and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy-VL-knob” polypeptide) comprised von N- to C-terminal direction a hinge region, a VL domain derived from an anti-dig antibody and a CH3 domain.
PNG
media_image1.png
655
628
media_image1.png
Greyscale
Precursor Polypeptides with Fc Domain
[0487] In a second set of experiments, heterodimeric precursor polypeptides with a domain arrangement as depicted in FIG. 3 were provided. The precursor polypeptides comprise a full Fc domain and comprise an antibody variable domain arranged at the N-terminal end of the CH2 domains.
[0488] In a first alternative, the following precursor polypeptides were provided: [0489] A first heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VH)-Fc(knob) precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VH)-Fc(knob) precursor comprised the light chain polypeptide of SEQ ID NO:11, i.e. the LeY LC, a first heavy chain polypeptide of SEQ ID NO:20 (also referred to as “LeY-CD3(VH)-Fc(knob) HC”) comprising the CD3(VH) domain and a second heavy chain polypeptide based on SEQ ID NO:21 (which represents the basic amino acid sequence without destabilizing mutation), with the destabilizing mutations as indicated below and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy-VL-Fc(hole)” polypeptide) comprised von N- to C-terminal direction a hinge region, a VL domain derived from an antibody specifically binding to digoxigenin (“dig”), a CH2 domain and a CH3 domain. [0490] A second heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VL)-Fc(hole) precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VL)-Fc(hole) precursor comprised the LeY LC; a first heavy chain polypeptide of SEQ ID NO:22 (also referred to as “LeY-CD3(VL)-Fc(hole) HC”) comprising the CD3(VL) domain and a second heavy chain polypeptide based on SEQ ID NO:23 (which represents the basic amino acid sequence without destabilizing mutation) with the destabilizing mutations as indicated below and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy-VH-Fc(knob)” polypeptide) comprised von N- to C-terminal direction a hinge region, a VH domain derived from an anti-dig antibody, a CH2 domain and a CH3 domain.
[0491] In a second alternative, the following precursor polypeptides were provided: [0492] A first heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VL)-Fc(knob) precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VL)-Fc(knob) precursor comprised the LeY LC, a first heavy chain polypeptide of SEQ ID NO:24 (also referred to as “LeY-CD3(VL)-Fc(knob) HC”) comprising the CD3(VL) domain and a second heavy chain polypeptide based on SEQ ID NO:25 (which represents the basic amino acid sequence without destabilizing mutation), with the destabilizing mutations as indicated below and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy-VH-Fc(hole)” polypeptide) comprised von N- to C-terminal direction a hinge region, a VH domain derived from an anti-dig antibody, a CH2 domain and a CH3 domain. [0493] A second heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VH)-Fc(hole) precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VH)-Fc(hole) precursor comprised the LeY LC; a first heavy chain polypeptide of SEQ ID NO:26 (also referred to as “LeY-CD3(VH)-Fc(hole) HC”) comprising the CD3(VH) domain and a second heavy chain polypeptide based on SEQ ID NO:27 (which represents the basic amino acid sequence without destabilizing mutation) with the destabilizing mutations as indicated below and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy-VL-Fc(knob)” polypeptide) comprised von N- to C-terminal direction a hinge region, a VL domain derived from an anti-dig antibody, a CH2 domain and a CH3 domain.
[0494] The indicated polypeptide chains comprise the following mutations:
PNG
media_image6.png
404
352
media_image6.png
Greyscale
[0495] Heterodimeric precursor polypeptides were generated comprising dummy VL-hole polypeptides of SEQ ID NO:13 and dummy VH-hole polypeptides of SEQ ID NO:17 as indicated above having the amino acid sequence of the respective dummy polypeptide as indicated above, wherein one of the following amino acid substitutions was made: E357K, A368F, D399A F405W, S364L, Y407W, or S354V.
[0496] Heterodimeric precursor polypeptides were generated comprising dummy VH-knob polypeptides of SEQ ID NO:15 and dummy VL-knob polypeptides of SEQ ID NO:19 as indicated above having the amino acid sequence of the respective dummy polypeptide as indicated above, wherein one of the following amino acid substitutions was made: K370E, no destabilizing mutation, W366I K409D, V397Y, or K392D.
[0497] Heterodimeric precursor polypeptides were generated comprising dummy VL-Fc(hole) polypeptides of SEQ ID NO:21 and dummy-VH-Fc(hole) polypeptides of SEQ ID NO:25 as indicated above having the amino acid sequence of the respective dummy polypeptide as indicated above, wherein one of the following amino acid substitutions was made: E357K, A368F, D399A F405W, S364L, D356K, or S354V.
[0498] Heterodimeric precursor polypeptides were generated comprising dummy-VH-Fc(knob) polypeptides of SEQ ID NO:23 and dummy-VL-Fc(knob) polypeptides of SEQ ID NO:27 as indicated above having the amino acid sequence of the respective dummy polypeptide as indicated above, wherein one of the following amino acid substitutions was made: K370E, no destabilizing mutation, W366I K409D, V397Y, K392D, or K370E K439E.
Example 5
Determination of Polypeptide Chain Exchange Via T Cell Activation Assay
[0517] To assess the impact of different destabilizing mutations on the polypeptide chain exchange, exchange reactions were set up using the precursor polypeptides as generated in Example 4 as a proof-of-concept experiment. The structure of the expected product polypeptides is depicted in FIG. 2 for the precursor polypeptides devoid of a CH2 domain and in FIG. 3 for the precursor polypeptides comprising a full Fc domain. Polypeptide chain exchange results in formation of an antigen binding site specifically binding to CD3. Presence of the bispecific anti-LeY/anti-CD3 product polypeptide was assessed by cell-based assay.
[0518] The influence of different CH3 interface mutations on the efficacy of this chain exchange reaction was evaluated in a cell based reporter assay system composed of LeY-expressing MCF7 cells and a Jurkat reporter cell line (Promega J1621) according to the following principle: Binding of the first and second heterodimeric polypeptides to MCF7 cells and polypeptide chain exchange results in formation of an antigen binding site specifically binding to CD3. Jurkat cells expressing CD3 are bound by the antigen binding site specifically binding to CD3, which results in luciferase expression from the Jurkat cells. Luminescence was detected after addition of BioGlo substrate.
Example 6
[0524] Generation of Monospecific Precursor Polypeptides of the Invention that Bind to FcRn for the Generation of Activatable Binding Sites Upon Polypeptide Chain Exchange
[0525] For assessing formation of bispecific anti-LeY/anti-CD3 antibodies from monospecific precursor polypeptides, monospecific precursor polypeptides of a domain arrangement as depicted for the first and second heterodimeric precursor polypeptides indicated in FIG. 1 were generated.
[0526] The following precursor polypeptides were provided: [0527] A first heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VH)-knob precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VH)-knob precursor comprised a light chain polypeptide of SEQ ID NO:11 (also referred to as “LeY LC”), a first heavy chain polypeptide of SEQ ID NO:12 (also referred to as “LeY-CD3(VH)-knob HC”) comprising a VH domain derived from an antibody specifically binding to CD3 (“CD3(VH)”) and a second heavy chain polypeptide based of SEQ ID NO:28 with the destabilizing mutation E357K and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy hole” polypeptide) comprised von N- to C-terminal direction a mutated hinge region that does not comprise cysteine, a CH2 domain and a CH3 domain. [0528] A second heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VL)-hole precursor”) comprised a Fab fragment specifically binding to LeY. The anti-LeY-CD3(VL)-hole precursor comprised the light chain polypeptide of SEQ ID NO:11, i.e. the LeY LC; a first heavy chain polypeptide of SEQ ID NO:14 (also referred to as “LeY-CD3(VL)-hole HC”) comprising a VL domain derived from an antibody specifically binding to CD3 (“CD3(VL)”) and a second heavy chain polypeptide based on SEQ ID NO:29 with the destabilizing mutation K370E and a histidine tag. The second heavy chain polypeptide (also referred to as “dummy knob” polypeptide) comprised von N- to C-terminal direction a mutated hinge region that does not comprise cysteine, a CH2 domain and a CH3 domain.
[0529] The indicated polypeptide chains comprise the following mutations:
PNG
media_image3.png
335
635
media_image3.png
Greyscale
However, claim 1 does not make complete binding sites for targeting the same antigen or CD3 because the claim does not provide a second variable (V) domain that pairs to bind the same antigen and CD3 as discussed above in 112 (b) section. Therefore, one of ordinary skill in the art would not be able to envision how to use the heterodimeric precursor polypeptides of claim 1 in the absence of the second V domain that pairs to bind the same antigen or CD3 target.
Furthermore, the structure as claimed in instant claim 1 does not seem to correlate with any of the molecules in the drawing because any molecule in the drawing shows the subpart (ii) of the first polypeptide binding to a second target. The structure in claim 1 is missing the light chain polypeptide comprising VL-CL that pairs with the heavy chain polypeptide comprising VH-CH1-VH-CH2-CH3, see Figure below.
PNG
media_image4.png
403
865
media_image4.png
Greyscale
The claimed structure is not useful in the absence of the complementing variable domain that create the target-binding sites. Therefore, the structure claimed in instant claims are not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Even assuming the same antigen is LeY or CD3, the specification does not teach the structure, e.g., the amino acid sequences of the heavy chain variable domain and the light chain variable domains of the first antigen binding moiety and/or second antigen binding moiety that correlated with binding to which particular same antigen (claim 7), or the first heavy chain polypeptide and the third heavy chain polypeptide that binds to any CD3 (claim 8, 16), any second antigen encompassed by the claimed heterodimeric precursor polypeptides to enable one of skill in the art to make and use without undue experimentation.
At the time the invention was made, it was known in the art that antibodies have a large repertoire of distinct structures and that a huge variety of antibodies can be made to bind to a single epitope.
For example, Lloyd et al. taught that hundreds of functional antibody fragments can be isolated from an antibody library that bind to the same antigen wherein these antibodies have distinct heavy and light chain sequences (of record, Lloyd et al. Protein Engineering, Design & Selection 22:159-168, 2009; PTO 892; see, e.g., Discussion).
Similarly, Edwards et al., (of record, J Mol Biol. 334(1): 103-118, 2003; PTO 892), found that over 1000 antibodies, all different in amino acid sequence, were generated to a single protein; 568 different amino acid sequences identified for the V(H) CDR3 domains of these antibodies (Abstract).
Poosarla et al (of record, Biotechn. Bioeng., 114(6): 1331-1342, 2017; PTO 892) teach substantial diversity in designed mAbs (sharing less than 75% sequence similarity to all existing natural antibody sequences) that bind to the same 12-mer peptide, binding to different epitopes on the same peptide. Said reference further teaches “most B-cell epitopes... in nature consist of residues from different regions of the sequence and are discontinuous...de novo antibody designs against discontinuous epitopes present additional challenges...". (See entire reference.)
For example, Yu et al (Investigative Ophthalmology & Visual Science 49(2): 522-527, February 2008; PTO 892) teach bevacizumab, which is a humanized anti-human VEGF-A mAb A.4.6.1 binds specifically to human VEGF-A, the same antibody does not bind to mouse VEGF-A (see page 522, right col., page 523, Figure 1, in particular).
Further, even minor changes in the amino acid sequence of a heavy or light variable region, particularly the CDRs, may dramatically affect antigen-binding function and IgG binding to the neonatal Fc receptor (FcRn) and pharmacokinetics.
For example, Piche-Nicholas et al (of record, MABS 10(1): 81-94, 2018; PTO 892) teaches altering complementary-determining region (CDRs) by 1-5 mutations significantly alter binding affinity to FcRn in vitro, see entire document, abstract, p. 95, right col, in particular. Engineering CDRs by modify local charge and thus maintain affinity to FcRn at 400 nM or weaker in vitro while retaining antigen binding may have far-reaching implications in the half-life optimization efforts of IgG therapeutics with respect to in vivo pharmacokinetics, see p. 90, in particular. Given that hundreds of unique antibody structures may bind a single antigen, the structure of an antibody cannot be predicted from the structure of the antigen, and a single species, or small group of species, cannot define a structure-function relationship so as to be representative of all the antibodies that bind to that antigen.
Further, the art teaches contrary to any generalized assumption, is that any anti-CD3 domain can be swapped into a bispecific BiTE® format under the conditions of the formulation much less that would result in functional activity.
Shepard et al (of record, PLOSOne 18(6): e0273884, June 22, 2023; PTO 892) teach the unpredictability of swapping CD3 binding domains in the context of a BiTE in so far as the binding requirement to CD3 epsilon much less the extracellular epitope:
“We next sought to test our platform for flexibility with respect to screening novel T-cell engaging domains of the bispecific molecule. We developed a number of novel mouse monoclonal antibodies (mAbs) against human CD3 complex using a multi-antigen immunization strategy in mice and traditional hybridoma screening. Through this process, we were able to identify several monoclonal antibodies with reactivity to Jurkat cells (Fig 4A) and human T cells (Fig 4B). To assess whether scFvs derived from novel CD3-targeted mAbs would be functional within as part of a BiTE molecule, we cloned 4 anti-human CD3 single chain variable fragments into CD19 or EGFRvIII specific BiTE plasmids (Fig 4C). We then generated supernatants using transient transfection of HEK293T as described above. BiTE supernatants were screened for activity using Jurkat cells in co-culture with EGFRvIII-expressing U87-VIII targets or CD19-expressing Raji cells. Previously tested constructs using OKT3 CD3-engager arms showed activity with both EGFRvIII and CD19 specific BiTEs, whereas we detected activity for only one of our novel CD3-engager BiTEs and only when combined with an EGFRvIII-specific scFv (Fig 4D). To confirm these results, we repeated BiTE production and Jurkat co-culture screening of CD19 and EGFRvIII targeted BiTE molecules incorporating OKT3 or the novel 1E2 CD3-targeting single chain variable fragment. Whereas EGFRvIII BiTEs incorporating an scFv derived from the 1E2 mAb or OKT3 showed specific reactivity against EGFRvIII expressing U87-vIII cells, only CD19-OKT3 showed reactivity to CD19-expressing Raji cells (Fig 4E). These results indicate that the novel CD3-targeting 1E2-scFv is functional only for an EGFRvIII-targeting BiTE but not a CD19-targeting BiTE, likely due to the specific binding characteristics of the CD19 or EGFRvIII scFv elements.”
“Similarly, we also find that only one of the novel CD3-targeting scFvs tested here showed activity in BiTE format, and even then, activity was restricted to combination with EGFRvIII-targeting scFv and not with a CD19-specific scFv. Again, we have no insight into the failure rate for BiTE molecules in this assay, as the intent of this assay is to provide a rapid means for testing biological activity rather than focusing on various aspects of antibody characterization. We are currently undertaking molecular studies to test whether incorporating different linker domains may be able to improve the activity of BiTEs using the novel CD3-scFv reported to have activity here, something that may provide further insight into the design constraints for these BiTE molecules.”
In Amgen Inc. et al. v. Sanofi et al., 598 U.S. 594, 2023 USPQ2d 602 (2023), the Supreme Court, held that claims drawn to a genus of monoclonal antibodies, which were functionally claimed by their ability to bind to a specific protein, PCSK9, were invalid due to lack of enablement. The claims at issue were functional, in that they defined the genus by its function (the ability to bind to specific residues of PCSK9) as opposed to reciting a specific structure (the amino acid sequence of the antibodies in the genus). The Supreme Court concluded that the patents at issue failed to adequately enable the full scope of the genus of antibodies that performed the function of binding to specific amino acid residues on PCSK9 and blocking the binding of PCSK9 to a particular cholesterol receptor, LDLR.
The Court clarified that the specification does not always need to "describe with particularity how to make and use every single embodiment within a claimed class." Id. at 610-11. However, "[i]f a patent claims an entire class of processes, machines, manufactures, or compositions of matter, the patent’s specification must enable a person skilled in the art to make and use the entire class….The more one claims, the more one must enable." Id.
There are no in vivo working examples. It is unpredictable which undisclosed heterodimeric precursor polypeptides are effective for treating which cancer. As such, it would require undue experimentation of one skilled in the art to make and use the claimed invention, commensurate in scope with the claims. See page 1338, footnote 7 of Ex parte Aggarwal, 23 USPQ2d 1334 (PTO Bd. Pat App. & Inter. 1992).
The scope of the claims must bear a reasonable correlation with the scope of enablement. See In re Fisher, 166 USPQ 19 24 (CCPA 1970).
Applicants’ arguments filed December 10, 2025 have been fully considered but are not found persuasive.
Applicants’ position is that as explained above, the invention in this application is not "an antibody that binds to antigen X", but sets of heterodimeric precursor polypeptides that initially dissociate under specific conditions, and then reassociate to form active antigen-binding moieties. The structures that enable such dissociation, and subsequent reassociation, are not dependent upon antigen-binding, but are dependent upon well-known and well-understood interactions between VH and VL domains, and between CH3 domains. To focus primarily on the antigen-binding portions of the VH and VL domains, as the Office Action does, or example at page 34, is to misunderstand what has been invented. In any event, the recited VH, VL, and CH3 domains have well-known and highly conserved sequences, and the specific CDR sequences do not determine how VH and VL domains pair, or how CH3 domains pair (with or without knob-and-hole mutations). The destabilizing mutations are well-described in the Examples. As such, the claims readily enable the making and using of the claimed heterodimeric precursor polypeptides where the CDRs are a matter of choice for the person of skill in the art.
The Office Action at age 34 states that "[e]nablement is not commensurate with how to make and use any heterodimeric precursor polypeptides for treating cancer without guidance as to the structure of the VH and VL that correlated with binding specificity of said heterodimeric precursor polypeptides. Applicant respectfully notes that claims 1-12 and 15 are not directed to a method of treating cancer.
At page 38, the Office Action states that "claim 1 does not make complete binding sites for targeting the same antigen or CD3 because the claim does not provide a second variable (V) domain that pairs to bind the same antigen and CD3 as discussed above in 112 (b) section.
Therefore, one of ordinary skill in the art would not be able to envision how to use the heterodimeric precursor polypeptides of claim 1 in the absence of the second V domain that pairs to bind the same antigen or CD3 target." This objection, as noted above, appears to arise from a misreading of claim 1. As explained above, claim 1 specifies a first heterodimeric precursor polypeptide that comprises a first heavy chain polypeptide comprising either a VH-CH3 or a VL- CH3, and a second heterodimeric precursor polypeptide that comprises a third heavy chain polypeptide comprising either a VL-CH3 or a VH-CH3 (depending upon which is present in the first heavy chain polypeptide). After domain exchange, the first and third heavy chain polypeptides associate, as is shown in Figures 1-3, to form in part an active VH-VL pair. As such, claim 1 does, in fact, provide a "second variable (V) domain that pairs to bind the same antigen [or] CD3". (Office Action at page 38.)
The Office Action further states at page 39 that the "structure in claim 1 is missing the light chain polypeptide comprising VL-CL that pairs with the heavy chain polypeptide comprising VH-CH1-VH-CH2-CH3, see Figure below [reproducing Figure 3 of the application as filed]".
Claim 1 specifies that the first heavy chain polypeptide comprises "at least a part of a first antigen binding moiety", and the third heavy chain polypeptide comprises "at least a part of a second antigen binding moiety"; this corresponds to the VH-CH1 in black in the long heavy chain under "First heterodimeric precursor polypeptide" and the VH-CH1 in white in the long heavy chain under "Second heterodimeric precursor polypeptide". The Fab depicted in Figure 3 (in black ovals or white ovals) is only one of several well-known antigen-binding configurations, some of which do not comprise a VL-CL. At page 51 of the specification, the antigen binding moiety (first or second) is described as being, inter alia, an Fv, a Fab, a Fab', a Fab'-SH, a F(ab')2, a diabody, a scFv, or an scFab. As such, given the recitation of "antigen binding moiety" and the various forms such an antigen binding moiety might take, as described in the specification, a person of skill in the art would be enabled to make and use the claimed heterodimeric precursor polypeptide sets.
In this light, the references cited in the Office Action at pages 40-42 are not to the contrary.
Thus, for at least the above reasons, the pending claims are sufficiently enabled in
satisfaction of 35 U.S.C. § 112(a). Applicant requests withdrawal of this rejection of the claims.
In response, claim 1 has no resemblance to the picture shown in Fig. 1 and reproduced below for Applicant’s convenience.
PNG
media_image5.png
322
416
media_image5.png
Greyscale
There are at least six polypeptides, 3 polypeptides in the first heterodimeric precursor polypeptide and 3 polypeptides in the second heterodimeric precursor polypeptide.
Further, note that one of the heavy chains in the first and second heterodimeric precursor polypeptides comprise VH-CH1-connector-VH-CH3 and the other heavy chain comprises a VH-CH1-peptide conector-VL-CH3.
Regarding “at least a part” of the first antigen binding moiety (line 6) and the second antigen binding moiety (line 20) in claim 1, the phrase “at least a part” encompasses a single amino acid of an antigen binding moiety, a CDR, or a VL or a VH or a Fv. Claim 1 does not recite VH-CH1 in the first heterodimeric precursor polypeptide and VH-CH1 in the second heterodimeric precursor polypeptide.
In response to the argument that at page 51 of the specification, the antigen binding moiety (first or second) is described as being, inter alia, an Fv, a Fab, a Fab', a Fab'-SH, a F(ab')2, a diabody, a scFv, or an scFab, MPEP 2173.05(s) states that where possible, claims are to be complete in themselves.
Further, M.P.E.P. § 2106 (II) states:
USPTO personnel are to give claims their broadest reasonable interpretation in light of the supporting disclosure. In re Morris, 127 F.3d 1048, 1054-55, 44 USPQ2d 1023, 1027-28 (Fed. Cir. 1997). Limitations appearing in the specification but not recited in the claim should not be read into the claim. E-Pass Techs., Inc. v. 3Com Corp., 343 F.3d 1364, 1369, 67 USPQ2d 1947, 1950 (Fed. Cir. 2003) (claims must be interpreted “in view of the specification” without importing limitations from the specification into the claims unnecessarily). In re Prater, 415 F.2d 1393, 1404-05, 162 USPQ 541, 550- 551 (CCPA 1969). See also In re Zletz, 893 F.2d 319, 321-22, 13 USPQ2d 1320, 1322 (Fed. Cir. 1989) (“During patent examination the pending claims must be interpreted as broadly as their terms reasonably allow.... The reason is simply that during patent prosecution when claims can be amended, ambiguities should be recognized, scope and breadth of language explored, and clarification imposed.... An essential purpose of patent examination is to fashion claims that are precise, clear, correct, and unambiguous. Only in this way can uncertainties of claim scope be removed, as much as possible, during the administrative process.”) (Emboldened added for emphasis).
M.P.E.P. § 2106 (II) continues:
While it is appropriate to use the specification to determine what applicant intends a term to mean, a positive limitation from the specification cannot be read into a claim that does not itself impose that limitation. A broad interpretation of a claim by USPTO personnel will reduce the possibility that the claim, when issued, will be interpreted more broadly than is justified or intended. An applicant can always amend a claim during prosecution to better reflect the intended scope of the claim.
Further, Claim 1 does not recite the one or more amino acid substitution that destabilize the CH3/CH3 interface. Claims 2 and 3 do not recite the particular substitutions in CH3 can destabilize the CH3/CH3 interface.
Regarding a first antigen binding site specifically binding to any target antigen and a second antigen binding site specifically binding to a target antigen (claim 5) and antibody variable domain comprised in the first heavy chain polypeptide and the third heavy chain polypeptide are capable of forming an antigen binding site specifically binds to CD3 (claim 8), the specification does not teach the structure, e.g., amino acid sequence of the heavy and light chain variable domains or structure common to members of the genus of first and second antigen binding site that specifically binds to any and all target antigen or CD3 from any species.
Enablement is not commensurate in scope with how to make and use the claimed heterodimeric precursor polypeptides, not just how to make the claimed heterodimeric precursor polypeptide as a pharmaceutical composition (claim 15).
Enablement is considered in view of the Wands factors (MPEP 2164.01(a)). These factors include, but are not limited to: (A) The breadth of the claims; (B) The nature of the invention; (C) The state of the prior art; (D) The level of one of ordinary skill; (E) The level of predictability in the art; (F) The amount of direction provided by the inventor; (G) The existence of working examples; and (H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. . In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988).
Considering an antibody will have six CDRs, each CDR comprising approximately ten amino acid residues. With twenty naturally occurring amino acids, the potential size of the CDR variation, of just human antibodies within this indeterminate genus, is 2060. This does not even consider the potential variation with the variable and constant regions of human. Given the genus of antibodies is unknown, both in terms of size and structural diversity, and neither applicant’s specification nor the knowledge in the art, allows the skilled artisan to predict the undisclosed members of the genus.
Even assuming the first or second antigen is CD3 (Claim 9), there is no correlation disclosed in the specification between the function of the antibody to bind to all CD3 from mammalian species. There is no information in the specification how much variation is permissible for it still bind CD3. Without such as description, one of ordinary skill in the art would be unable to distinguish which anti-CD3 heterodimer would fall within the scope encompassed by the claim and which do not. The specification does not teach a representative number of species falling with the scope of the genus or structural features common to the members of the genus so the one of skill in the art can make and use without undue experimentation.
At the time the invention was made, it was known in the art that antibodies have a large repertoire of distinct structures and that a huge variety of antibodies can be made to bind to a single epitope.
For example, Lloyd et al. taught that hundreds of functional antibody fragments can be isolated from an antibody library that bind to the same antigen wherein these antibodies have distinct heavy and light chain sequences (of record, Lloyd et al. Protein Engineering, Design & Selection 22:159-168, 2009; PTO 892; see, e.g., Discussion).
Similarly, Edwards et al., (of record, J Mol Biol. 334(1): 103-118, 2003; PTO 892), found that over 1000 antibodies, all different in amino acid sequence, were generated to a single protein; 568 different amino acid sequences identified for the V(H) CDR3 domains of these antibodies (Abstract).
Poosarla et al (of record, Biotechn. Bioeng., 114(6): 1331-1342, 2017; PTO 892) teach substantial diversity in designed mAbs (sharing less than 75% sequence similarity to all existing natural antibody sequences) that bind to the same 12-mer peptide, binding to different epitopes on the same peptide. Said reference further teaches “most B-cell epitopes... in nature consist of residues from different regions of the sequence and are discontinuous...de novo antibody designs against discontinuous epitopes present additional challenges...". (See entire reference.)
For example, Yu et al (of record, Investigative Ophthalmology & Visual Science 49(2): 522-527, February 2008; PTO 892) teach bevacizumab, which is a humanized anti-human VEGF-A mAb A.4.6.1 binds specifically to human VEGF-A, the same antibody does not bind to mouse VEGF-A (see page 522, right col., page 523, Figure 1, in particular).
Further, even minor changes in the amino acid sequence of a heavy or light variable region, particularly the CDRs, may dramatically affect antigen-binding function and IgG binding to the neonatal Fc receptor (FcRn) and pharmacokinetics.
For example, Piche-Nicholas et al (of record, MABS 10(1): 81-94, 2018; PTO 892) teaches altering complementary-determining region (CDRs) by 1-5 mutations significantly alter binding affinity to FcRn in vitro, see entire document, abstract, p. 95, right col, in particular. Engineering CDRs by modify local charge and thus maintain affinity to FcRn at 400 nM or weaker in vitro while retaining antigen binding may have far-reaching implications in the half-life optimization efforts of IgG therapeutics with respect to in vivo pharmacokinetics, see p. 90, in particular.
Given that hundreds of unique antibody structures may bind a single antigen, the structure of an antibody cannot be predicted from the structure of the antigen, and a single species, or small group of species, cannot define a structure-function relationship so as to be representative of all the antibodies that bind to that antigen. There are insufficient working examples. As such, undue experimentation would be required to produce the invention commensurate with the breadth of the claims based on the disclosure of the instant specification and the knowledge in the art. Reasonable correlation must exist between the scope of the claims and scope of enablement set forth. In view of the quantity of experimentation necessary, the limited working examples, the unpredictability of the art, the lack of sufficient guidance in the specification, and the breadth of the claims, it would take undue trials and errors to practicethe claimed invention.
For these reasons, the rejection is maintained.
New Ground of Objection necessitated by the amendment filed December 10, 2025
Claim objection
Claims 2-6 are objected to because of the following informality: The preamble is inconsistent with the preamble of claim 1. Amending the preamble of claims 2-6 to recite “The set of heterodimeric precursor polypeptides …claim 1…” would obviate this objection.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1 and 12 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claim 1 recites the limitation “at least a part” of the first antigen binding moiety (line 6) and the “at least a part” of second antigen binding moiety (lines 20-21). It is indefinite as to what would be considered a part of an antigen binding moiety because “at least a part” is a relative term which is not defined in the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Does a part include a single amino acid of an antigen binding moiety, a CDR or a VL or a VH or a Fv? An artisan would not be reasonably apprised of the metes and bounds of the claim.
Amending the claim to recite “VH-CH1” for “at least a part of a first antigen binding moiety” and “at least a part of a second antigen binding moiety” for example, would obviate this rejection.
Claim 12 recites “selected from a VH domain and a VL domain, and a CH3 domain” is indefinite because it is not clear the first heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain VH, VL or a CH3 domain, or a VH-CH3, or a VL-CH3. Clarification is required. One skilled in the art could not determine the boundaries of the claimed invention in order to avoid infringing on the claim.
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PHUONG HUYNH whose telephone number is (571)272-0846. The examiner can normally be reached on 9:00 a.m. to 6:30 p.m. The examiner can also be reached on alternate alternative Friday from 9:00 a.m. to 5:30 p.m.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Misook Yu, can be reached at 571-270-3497. The fax phone number for the organization where this application or proceeding is assigned is 571-272-0839.
Information regarding the status of an application may be obtained from Patent Center. Status information for published applications may be obtained from Patent Center. Status information for unpublished applications is available through Patent Center for authorized users only. Should you have questions about access to Patent Center, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free).
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) Form at https://www.uspto.gov/patents/uspto-automated- interview-request-air-form.
/PHUONG HUYNH/ Primary Examiner, Art Unit 1641