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 1-13, 15-16 and 18 are pending.
Claims 1-13, 15-16 and 18, drawn to a set of heterodimeric precursor polypeptides that read on (A) E357 and V397Y as the combination of hole and knob mutation in the CH3 domain of the first and second precursor polypeptides, (B) the CH3 domain comprising a knob mutation of the first heterodimeric precursor polypeptide comprises a cysteine mutation and the CH3 domain comprising the hole mutation of the second heterodimeric precursor polypeptide comprising a cysteine mutation in claim 5 subpart (i), 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Objection and Rejection Withdrawn
The objection to claims 1, 7 and 8 is withdrawn in light of the claim amendment.
The objection to claims 4-10, 15 and 16 under 37 CFR 1.75(c) as being in improper form is withdrawn in view of the claim amendment.
The rejection of claims 7-8 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph
The rejection of claims 1-7, 10-13, 15 and 16 under 35 U.S.C. 102 (a)(1) as being anticipated by Brinkmann et al (US20170369595, published December 28, 2017; PTO 892) is withdrawn in view of the argument at p. 19.
Applicant’s arguments, see p. 19, filed November 17, 2025, with respect to the rejection of claims 1-7, 10-13, 15 and 16 under 35 U.S.C. 102 (a)(1) have been fully considered and are persuasive. Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground(s) of rejection is made in view of WO2016087416 publication (published; PTO 892).
The rejection of claims 8 and 9 under 35 U.S.C. 103 as being unpatentable over Brinkmann et al (20170369595, published December 28, 2017; PTO 892) in view of Ng et al (US20180193477, published July 12, 2018; PTO 892) is withdrawn because the addition of Ng does not cure the deficiency of Brinkmann.
The provisional rejection of claims 1-13, 15 and 16 on the ground of nonstatutory obviousness-type double patenting as being unpatentable over claims 1-8, 12-16 of copending Application No. 17/507,511 is withdrawn in view of the terminal disclaimer filed on November 17, 2025.
The provisional rejection of claims 1-13, 15 and 16 on the ground of nonstatutory obviousness-type double patenting as being unpatentable over claims 1-9, 11-12, 19-20 of copending Application No. 17/506,993 is withdrawn in view of the terminal disclaimer filed on November 17, 2025.
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, 2 and 6 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 (lines 7-8) and the second antigen binding moiety (line 16). It is indefinite 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.
Claim 2 is indefinite in the recitation of “the CH3 domain comprising the knob mutation and the CH3 domain comprising the hole mutation” because it is not clear if “the CH3 domain comprising the knob mutation and the CH3 domain comprising the hole mutation” is referring to the first heterodimeric precursor polypeptide or the second heterodimeric precursor polypeptide.
Regarding claim 6, the “antibody fragment” is indefinite and ambiguous because the term “fragment” could be as little as one or two amino acids. Further, it is not clear the “antibody fragment” is referring to the antigen-binding fragment or the Fc fragment. Finally, it is not clear the “antibody fragment” is from the same or different antibody.
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 1-13, 15-16 and 18 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 first heterodimeric precursor polypeptide comprising at least two polypeptide chains comprising a CH3 domain, wherein the two polypeptide chains comprising the CH3 domain are associated with each other via the CH3 domains and form a heterodimer, wherein one of the CH3 domains comprises any knob mutation and the other CH3 domain comprises any hole mutation, wherein the first heterodimeric precursor polypeptide comprises a first antigen binding moiety, wherein at least a part of the first antigen binding moiety is arranged on one of the two polypeptide chains comprising the CH3 domain, and
a second heterodimeric precursor polypeptide comprising at least two polypeptide chains comprising a CH3 domain, wherein the two polypeptide chains comprising the CH3 domain are associated with each other via the CH3 domains and form a heterodimer, wherein one of the CH3 domains comprises any knob mutation and the other CH3 domain comprises any hole mutation, wherein the second heterodimeric precursor polypeptide comprises a second antigen binding moiety, wherein at least a part of the second antigen binding moiety is arranged on one of the two polypeptide chains comprising the CH3 domain;
wherein A) either
within the first heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain comprising the knob mutation comprises at least a part of the first antigen binding moiety and within the second heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain with the hole mutation comprises at least a part of the second antigen binding moiety, or
ii) within the first heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain comprising the hole mutation comprises at least a part of the first antigen binding moiety and within the second heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain with the knob mutation comprises at least a part of the second antigen binding moiety; and wherein
B) either
i) the first heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VL domain and the CH3 domain, and wherein the second heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VH domain and the CH3 domain, wherein said VL domain and said VH domain specifically bind to any antigen when associated to a pair of a VH domain and a VL domain; or
ii) the first heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VH domain and the CH3 domain, and wherein the second heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VL domain and the CH3 domain, wherein said VL domain and said VH domain specifically bind to any antigen when associated to a pair of a VH domain and a VL domain; and
wherein C) 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
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 comprise 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 consisting of:
replacement of E357 with a positively charged amino acid (elected species);
replacement of S364 with a hydrophobic amino acid;
replacement of A368 with a hydrophobic amino acid; and
replacement of V407 with a hydrophobic amino acid; and
the CH3 domain with the knob mutation comprises at least one amino acid substitution selected from the group consisting 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 (elected species).
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 C) comprise one of the amino acid substitutions selected from the group indicated in the following table:
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Claim 3 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 C) comprise one of the amino acid substitutions selected from the group indicated in the following table:
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Claim 4 encompasses the set of heterodimeric polypeptides according to claim 1, wherein in case the CH3 domain with the knob mutation indicated in C) comprises a mutation E357K, the CH3 domain with the hole mutation indicated in C) does not comprise a mutation K370E.
Claim 5 encompasses the set of heterodimeric polypeptides according to claim 1, wherein either i) the CH3 domain comprising the knob mutation of the first heterodimeric precursor polypeptide comprises a cysteine mutation and the CH3 domain comprising the hole mutation of the second heterodimeric precursor polypeptide comprises a cysteine mutation, or ii) the CH3 domain comprising the hole mutation of the first heterodimeric precursor polypeptide comprises a cysteine mutation and the CH3 domain comprising the knob mutation of the second heterodimeric precursor polypeptide comprises a cysteine mutation.
Claim 6 encompasses the set of heterodimeric polypeptides according to claim 1, wherein the first antigen binding moiety and/or the second antigen binding moiety is any antibody fragment.
Claim 7 encompasses the set of heterodimeric polypeptides according to claim 1, wherein
the first heterodimeric precursor polypeptide comprises:
a first heavy chain polypeptide comprising from N- to C-terminal direction a first VH domain, a CH1 domain, a second antibody variable domain selected from a VH domain and a VL domain, and a CH3 domain,
a second heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain capable of associating with the second antibody variable domain of the first heavy chain polypeptide, 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
a light chain polypeptide comprising from N- to C-terminal direction a first VL domain and a CL domain, wherein the first VH domain and the first VL domain are associated with each other and form an antigen binding site specifically binding to a target antigen; and wherein
b) the second heterodimeric precursor polypeptide comprises:
a third heavy chain polypeptide comprising from N- to C-terminal direction a second VH domain, a CH1 domain, a third antibody variable domain selected from a VH domain and a VL domain, and a CH3 domain,
a fourth heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain capable of associating with the third antibody variable domain of the third heavy chain polypeptide, 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 a heterodimer, wherein one of the CH3 domains comprises a knob mutation and the other CH3 domain comprises a hole mutation; and
a light chain polypeptide comprising from N- to C-terminal direction a second VL domain and a CL domain, wherein the second VH domain and the second VL domain are associated with each other and form an antigen binding site specifically binding to a target antigen; and wherein
either i) the first heavy chain polypeptide comprises a CH3 domain comprising a knob mutation and the third heavy chain polypeptide comprises a CH3 domain comprising a hole mutation; or
ii) the first heavy chain polypeptide comprises a CH3 domain comprising a hole mutation and the third heavy chain polypeptide comprises a CH3 domain comprising a knob mutation; and wherein d) the variable domains of the first heavy chain polypeptide and the third heavy chain polypeptide are capable of forming an antigen binding site specifically binding to a target antigen.
Claim 8 encompasses the set of heterodimeric polypeptides according to claim 1, wherein
a) the first heterodimeric precursor polypeptide comprises:
a first heavy chain polypeptide comprising from N- to C-terminal direction a first VH domain, a CH1 domain, a second antibody variable domain selected from a VH domain and a VL domain, a CH2 domain and a CH3 domain,
a second heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain capable of associating with the second antibody variable domain of the first heavy chain polypeptide, 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
a light chain polypeptide comprising from N- to C-terminal direction a first VL domain and a CL domain, wherein the first VH domain and the first VL domain are associated with each other and form an antigen binding site specifically binding to a target antigen; and wherein
the second heterodimeric precursor polypeptide comprises:
a third heavy chain polypeptide comprising from N- to C-terminal direction a second VH domain, a CH1 domain, a third antibody variable domain selected from a VH domain and a VL domain, a CH2 domain and a CH3 domain,
a fourth heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain capable of associating with the third antibody variable domain of the third heavy chain polypeptide, 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 a heterodimer, wherein one of the CH3 domains comprises a knob mutation and the other CH3 domain comprises a hole mutation; and
a light chain polypeptide comprising from N- to C-terminal direction a second VL domain and a CL domain, wherein the second VH domain and the second VL domain are associated with each other and form an antigen binding site specifically binding to a target antigen; and wherein
c) either i) the first heavy chain polypeptide comprises a CH3 domain comprising a knob mutation and the third heavy chain polypeptide comprises a CH3 domain comprising a hole mutation; or ii) the first heavy chain polypeptide comprises a CH3 domain comprising a hole mutation and the third heavy chain polypeptide comprises a CH3 domain comprising a knob mutation; and wherein
d) the variable domains of the first heavy chain polypeptide and the third heavy chain polypeptide are capable of forming an antigen binding site specifically binding to a target antigen.
Claim 9 encompasses the set of heterodimeric precursor polypeptides according to claim 1, wherein the VH domain and the VL domain indicated in B) are capable of forming an antigen binding site specifically binding to any CD3.
Claim 10 encompasses the set of heterodimeric precursor polypeptides according to claim 1, wherein no interchain disulfide bond is formed between the two polypeptide chains comprising the CH3 domains of the first and second heterodimeric polypeptide.
Claim 11 encompasses a heterodimeric polypeptide comprising a first heterodimeric precursor polypeptide and a second heterodimeric precursor polypeptide, as defined in claim 1, wherein said heterodimeric polypeptide is generated by contacting said first heterodimeric precursor polypeptide and said second heterodimeric precursor polypeptide to form a third heterodimeric polypeptide comprising at least one polypeptide chain comprising a CH3 domain from the first heterodimeric precursor polypeptide and at least one polypeptide chain comprising a CH3 domain from the second heterodimeric polypeptide.
Claim 12 encompasses the heterodimeric polypeptide of claim 11, wherein the second heterodimeric precursor polypeptide comprises an antigen binding moiety specifically binding to a second antigen, and wherein the third heterodimeric polypeptide comprises the antigen binding moiety specifically binding to the first antigen and the antigen binding moiety specifically binding to the second antigen, and a third antigen binding moiety is formed by the VL domain and the VH domain indicated in B).
Claim 13 encompasses the heterodimeric polypeptide of claim 11, wherein no interchain disulfide bond is formed between the two polypeptide chains comprising the CH3 domains of the first and second heterodimeric polypeptide, and wherein the contacting is performed in absence of a reducing agent.
Claim 15 encompasses a first heterodimeric precursor polypeptide as defined in claim 1.
Claim 16 encompasses a second heterodimeric precursor polypeptide as defined in claim 1.
Claim 18 encompasses the set of heterodimeric polypeptide of claim 6, wherein said fragment is any variable fragment (Fv), any Fab fragment, any Fab’ fragment, any Fab’-SH fragment, any F(ab’)2 fragment, any diabody, any linear antibody, any single-chain Fv (scFv), or any single chain Fab (scFab).
The specification exemplifies:
Example 1
Generation of Monospecific Precursor Polypeptides Comprising a Full Fc Domain
[0416] In order to assess efficacy of polypeptide chain exchange to result in bispecific anti-biocytinamid/anti-fluorescein antibodies from monospecific precursor polypeptides, the following monospecific precursor polypeptides were generated:
[0417] The first heterodimeric precursor polypeptide (also referred to as “anti-bio precursor”) comprised a Fab fragment specifically binding to biocytinamid (“bio”), a biotin derivative, with a VL domain of SEQ ID NO:01 and a VH domain of SEQ ID NO:02. The first precursor polypeptide comprised a light chain polypeptide of SEQ ID NO:03 (also referred to as “bio LC”), a first heavy chain polypeptide of SEQ ID NO:04 (also referred to as “bio HC”) and a second heavy chain polypeptide based on SEQ ID NO:05 (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 hole” polypeptide) comprised von N- to C-terminal direction a hinge region, a CH2 domain and a CH3 domain.
[0418] The second heterodimeric precursor polypeptide (also referred to as “anti-fluo precursor”) comprised a Fab fragment specifically binding to fluorescein (“fluo”) with a VL domain of SEQ ID NO:06 and a VH domain of SEQ ID NO:07. The second precursor polypeptide comprised a light chain polypeptide of SEQ ID NO:08 (also referred to as “fluo LC”), a first heavy chain polypeptide of SEQ ID NO:09 (also referred to as “fluo HC”) and a second heavy chain polypeptide based on SEQ ID NO:10 (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 knob” polypeptide) comprised von N- to C-terminal direction a hinge region, a CH2 domain and a CH3 domain.
[0419] The CH3 domains of the indicated polypeptide chains comprise the following mutations:
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[0420] Anti-bio precursors were generated comprising dummy hole polypeptides having an amino acid sequence of SEQ ID NO:05, wherein one of the following amino acid substitutions was made: E357K, D356K, A368F, V407Y, D399A F405W, S354V, or S364L.
[0421] Anti-fluo precursors were generated comprising dummy knob polypeptides having an amino acid sequence of SEQ ID NO:10, wherein one of the following amino acid substitutions was made: K370E, W3661 K409E, K370E K439E, or K392D.
Example 3
Generation of Monospecific Precursor Polypeptides for the Generation of Activatable Binding Sites Upon Polypeptide Chain Exchange
[0453] 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 and FIG. 2 were generated.
Precursor polypeptides devoid of CH2 domain
[0454] In a first set of experiments, heterodimeric precursor polypeptides with a domain arrangement as depicted in FIG. 1 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.
[0455] In a first alternative, the following precursor polypeptides were provided:
[0456] 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.
[0457] 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.
[0458] In a second alternative, the following precursor polypeptides were provided:
[0459] 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. [0460] 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 from N- to C-terminal direction a hinge region, a VL domain derived from an anti-dig antibody and a CH3 domain.
[0461] The indicated polypeptide chains comprise the following mutations:
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Precursor Polypeptides with Fc Domain
[0462] In a second set of experiments, heterodimeric precursor polypeptides with a domain arrangement as depicted in FIG. 2 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.
[0463] In a first alternative, the following precursor polypeptides were provided:
[0464] 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. [0465] 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.
[0466] In a second alternative, the following precursor polypeptides were provided:
[0467] 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. [0468] 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.
[0469] The indicated polypeptide chains comprise the following mutations:
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[0470] 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.
[0471] 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, W3661 K409D, V397Y, or K392D.
[0472] 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.
[0473] 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, W3661 K409D, V397Y, K392D, or K370E K439E.
Example 6
Generation of Further Monospecific Precursor Polypeptides Comprising a Full Fc Domain
[0499] For assessing formation of bispecific anti-biocytinamid/anti-fluorescein 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. Note that in this experiments the knobs and holes mutations were arranged on the opposite chains.
[0500] The first heterodimeric precursor polypeptide (also referred to as “anti-fluo precursor”) comprised a Fab fragment specifically binding to fluorescein (“fluo”), a biotin derivative, with a VL domain of SEQ ID NO:06 and a VH domain of SEQ ID NO:07. The first precursor polypeptide comprised a light chain polypeptide of SEQ ID NO:08 (also referred to as “fluo LC”), a first heavy chain polypeptide of SEQ ID NO:29 (also referred to as “fluo HC”) and a second heavy chain polypeptide based on SEQ ID NO:05 (which represents the basic amino acid sequence without destabilizing mutation), with the destabilizing mutations as indicated below and a C-tag. The second heavy chain polypeptide (also referred to as “dummy hole” polypeptide) comprised von N- to C-terminal direction a hinge region, a CH2 domain and a CH3 domain.
[0501] The second heterodimeric precursor polypeptide (also referred to as “anti-bio precursor”) comprised a Fab fragment specifically binding to biocytinamid (“bio”) with a VL domain of SEQ ID NO:01 and a VH domain of SEQ ID NO:02. The second precursor polypeptide comprised a light chain polypeptide of SEQ ID NO:03 (also referred to as “bio LC”), a first heavy chain polypeptide of SEQ ID NO:28 (also referred to as “bio HC”) and a second heavy chain polypeptide based on SEQ ID NO:10 (which represents the basic amino acid sequence without destabilizing mutation) with the destabilizing mutations as indicated below and a C-tag. The second heavy chain polypeptide (also referred to as “dummy knob” polypeptide) comprised von N- to C-terminal direction a hinge region, a CH2 domain and a CH3 domain.
Regarding “at least a part” of the first antigen binding moiety (lines 7-8) and the second antigen binding moiety (line 16) 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. Further, the part is arranged on any one of the two polypeptide chains in the first and second heterodimeric precursor.
Regarding “antibody fragment” in claim 6, the phrase “antibody fragment” encompasses any amino acid, Fc or antigen binding fragment. It is known in the art that Fc fragment or single amino acid does not bind to any antigen.
Regarding “variable domain of the first heavy chain polypeptide and the third heavy chain heavy chain polypeptide form an antigen binding site specifically binding to any target antigen, 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 second antigen binding moiety that correlated with binding to which particular antigen (claims 1-8, 15, 16), such as any CD3 (claim 9), any second antigen (claims 12, 13, 15, 16) encompassed by the claimed heterodimeric precursor polypeptides.
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. One of skill in the art would conclude that the specification fails to disclose a representative number of species to describe the claimed 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 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 that bind to any and all first and second antigens. One of skill in the art would reasonably conclude that the disclosure does not provide a representative number of species of heterodimer polypeptide or heterodimeric precursor polypeptide that specifically bind any and all target antigen, such as “CD3” that would be sufficient to describe the claimed genus of heterodimeric precursor polypeptides.
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.
Applicants’ arguments filed November 17, 2025 have been fully considered but are not found persuasive.
Applicants’ position is that Claim 1 is not directed to, and therefore need not recite, the entire three-chain polypeptide depicted in Fig. 1. Instead, claim 1 is drawn to the boxed portion of Fig. 1, as shown below:
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The first polypeptide comprising VH(black oval)-CH3(gray oval) and VL(gray oval)-CH3(black oval) will undergo chain exchange with the second polypeptide comprising VL(black oval)- CH3(gray oval) and VH(gray oval)-CH3(black oval) to produce a functional exchanged pair of VH(black oval)-CH3(gray oval) and VL(black oval)-CH3(gray oval). The exchanged pair defines a Fab comprising a VH:VL pair that forms a functional antigen-binding site. As such, a person of skill in the art would immediately recognize this structure as being useful. The precursor pairs have utility in their ability to form the exchanged pair. As such, the structures claimed in claim 1 have written description under 35 U.S.C. § 112(a).
Second, the Office Action at page 19 contends 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 second antigen binding moiety that correlated with binding to which particular antigen (claims 1-8, 15, 16), such as any CD3 (claim 9), any second antigen (claim 12, 13, 15, 16) encompassed by the claimed heterodimeric precursor polypeptides." 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 "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 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 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 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 continues in this vein from page 19 to page 23.
Applicant is aware that the current Federal Circuit law regarding the written description of antibodies requires a structural definition of the antibodies and not simply a functional definition. See, e.g., Juno Therapeutics, Inc. v. Kite Pharma, Inc., 10 F.4th 1330, 1342 (Fed. Cir. 2021), cert. denied, No. 21-1566, 2022 WL 16726060 (U.S. Nov. 7, 2022), and cases cited therein. However, this body of caselaw was developed either outside the antibody field, or within the antibody field almost solely with monoclonal antibodies. Generally, because the overall structure of a monoclonal antibody per se is well-known, the inventive aspect is the particular CDRs that bind to a target. Even in the case of Juno v. Kite, the inventive aspect was the use of one particular sequence in the context of a chimeric antigen receptor (CAR), and not the overall structure of the CAR. In the present application, however, Applicant has developed a new set of antibody structures that interact with each other in a specific way to produce a specific result, as shown in Figure 1 or Figure 2. To limit these new sets of structures to ones that bind only to Ley, as the office action proposes on pages 23-25, would be to deny Applicant the full scope of the presently-pending claims, because persons of ordinary skill in the art can ready envision similar sets of antibody structures with the same components but that target different antigens.
Thus, for at least the reasons above, the claims have adequate written description support in the specification as filed. Applicant requests withdrawal of this rejection of the claims.
In response to claim 1 is drawn to the boxed portion of Fig. 1, claim 1 has no resemblance to the picture shown in Fig. 1. In particular, nowhere in claim 1 recites a first polypeptide comprising VH-CH3 and VL-CH3 will undergo chain exchange with the second polypeptide comprising VL-CH3 and VH-CH3 to produce a functional exchanged pair of VH(black oval)-CH3(gray oval) and VL(black oval)-CH3(gray oval) as argued. Further, the term “comprising” or “comprises” is open ended. It expands the heavy chain polypeptides in the first and second heterodimeric precursor polypeptide to include additional domains, e.g., VH-CH1 domains.
Regarding “at least a part” of the first antigen binding moiety (lines 7-8) and the second antigen binding moiety (line 16) 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. Further, the part is arranged on any one of the two polypeptide chains in the first and second heterodimeric precursor.
None of the claims define 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. One of skill in the art cannot envision the arrangement of a single amino acid of an antigen binding moiety, a CDR, or a VL or a VH or a Fv on any one of the two polypeptide chains in the first and second heterodimeric precursor.
Regarding “antibody fragment” in claim 6, the phrase “antibody fragment” encompasses any amino acid, Fc or antigen binding fragment. It is known in the art that Fc fragment or single amino acid does not bind to any antigen.
Regarding “variable domain of the first heavy chain polypeptide and the third heavy chain heavy chain polypeptide form an antigen binding site specifically binding to any target antigen, 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 second antigen binding moiety that correlated with binding to which particular antigen (claims 1-8, 15, 16), such as any CD3 (claim 9), any second antigen (claims 12, 13, 15, 16) encompassed by the claimed heterodimeric precursor polypeptides.
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. One of skill in the art would conclude that the specification fails to disclose a representative number of species to describe the claimed 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 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 that bind to any and all first and second antigens. One of skill in the art would reasonably conclude that the disclosure does not provide a representative number of species of heterodimer polypeptide or heterodimeric precursor polypeptide that specifically bind any and all target antigen, such as “CD3” that would be sufficient to describe the claimed genus of heterodimeric precursor polypeptides.
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 1-13, 15-16 and 18 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 comprising:
a first heterodimeric precursor polypeptide (an anti-LeY-CD3(VH)-Fc(knob) precursor) comprises:
a first light chain polypeptide of SEQ ID NO:11,
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, and
a second heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VL)-Fc(hole) precursor”) comprises:
a first light chain polypeptide comprising SEQ ID NO:11,
a first heavy chain polypeptide comprising 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 comprises the amino acid sequence of SEQ ID NO:23, or
a first heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VH)-knob precursor”) comprises:
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), and
a second heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VL)-hole precursor”) comprises:
a light chain polypeptide of SEQ ID NO:11;
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, also referred to as “dummy-VH-knob” polypeptide, or
a first heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VL)-knob precursor”) comprising:
a light chain polypeptide of SEQ ID NO:11,
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 and
a second heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VH)-hole precursor”) comprises:
a light chain polypeptide of SEQ ID NO:11,
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, or
a first heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VL)-Fc(knob) precursor”) comprising:
a LeY specific light chain polypeptide of SEQ ID NO:11,
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 and
a second heterodimeric precursor polypeptide (also referred to as “anti-LeY-CD3(VH)-Fc(hole) precursor”) comprising:
a LeY specific light chain polypeptide of SEQ ID NO:11,
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, does not reasonably provide enablement for a set of any heterodimeric precursor set forth in claims 1-13, 15 and 16 for treating any cancer. 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 first heterodimeric precursor polypeptide comprising at least two polypeptide chains comprising a CH3 domain, wherein the two polypeptide chains comprising the CH3 domain are associated with each other via the CH3 domains and form a heterodimer, wherein one of the CH3 domains comprises any knob mutation and the other CH3 domain comprises any hole mutation, wherein the first heterodimeric precursor polypeptide comprises a first antigen binding moiety, wherein at least a part of the first antigen binding moiety is arranged on one of the two polypeptide chains comprising the CH3 domain, and
a second heterodimeric precursor polypeptide comprising at least two polypeptide chains comprising a CH3 domain, wherein the two polypeptide chains comprising the CH3 domain are associated with each other via the CH3 domains and form a heterodimer, wherein one of the CH3 domains comprises any knob mutation and the other CH3 domain comprises any hole mutation, wherein the second heterodimeric precursor polypeptide comprises a second antigen binding moiety, wherein at least a part of the second antigen binding moiety is arranged on one of the two polypeptide chains comprising the CH3 domain;
wherein A) either
within the first heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain comprising the knob mutation comprises at least a part of the first antigen binding moiety and within the second heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain with the hole mutation comprises at least a part of the second antigen binding moiety, or
ii) within the first heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain comprising the hole mutation comprises at least a part of the first antigen binding moiety and within the second heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain with the knob mutation comprises at least a part of the second antigen binding moiety; and wherein
B) either
i) the first heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VL domain and the CH3 domain, and wherein the second heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VH domain and the CH3 domain, wherein said VL domain and said VH domain specifically bind to any antigen when associated to a pair of a VH domain and a VL domain; or
ii) the first heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VH domain and the CH3 domain, and wherein the second heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VL domain and the CH3 domain, wherein said VL domain and said VH domain specifically bind to any antigen when associated to a pair of a VH domain and a VL domain; and
wherein C) 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
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 comprise 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 consisting of:
replacement of E357 with a positively charged amino acid (elected species);
replacement of S364 with a hydrophobic amino acid;
replacement of A368 with a hydrophobic amino acid; and
replacement of V407 with a hydrophobic amino acid; and
the CH3 domain with the knob mutation comprises at least one amino acid substitution selected from the group consisting 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 (elected species).
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 C) comprise one of the amino acid substitutions selected from the group indicated in the following table:
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Claim 3 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 C) comprise one of the amino acid substitutions selected from the group indicated in the following table:
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Claim 4 encompasses the set of heterodimeric polypeptides according to claim 1, wherein in case the CH3 domain with the knob mutation indicated in C) comprises a mutation E357K, the CH3 domain with the hole mutation indicated in C) does not comprise a mutation K370E.
Claim 5 encompasses the set of heterodimeric polypeptides according to claim 1, wherein either i) the CH3 domain comprising the knob mutation of the first heterodimeric precursor polypeptide comprises a cysteine mutation and the CH3 domain comprising the hole mutation of the second heterodimeric precursor polypeptide comprises a cysteine mutation, or ii) the CH3 domain comprising the hole mutation of the first heterodimeric precursor polypeptide comprises a cysteine mutation and the CH3 domain comprising the knob mutation of the second heterodimeric precursor polypeptide comprises a cysteine mutation.
Claim 6 encompasses the set of heterodimeric polypeptides according to claim 1, wherein the first antigen binding moiety and/or the second antigen binding moiety is any antibody fragment.
Claim 7 encompasses the set of heterodimeric polypeptides according to claim 1, wherein
the first heterodimeric precursor polypeptide comprises:
a first heavy chain polypeptide comprising from N- to C-terminal direction a first VH domain, a CH1 domain, a second antibody variable domain selected from a VH domain and a VL domain, and a CH3 domain,
a second heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain capable of associating with the second antibody variable domain of the first heavy chain polypeptide, 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
a light chain polypeptide comprising from N- to C-terminal direction a first VL domain and a CL domain, wherein the first VH domain and the first VL domain are associated with each other and form an antigen binding site specifically binding to a target antigen; and wherein
b) the second heterodimeric precursor polypeptide comprises:
a third heavy chain polypeptide comprising from N- to C-terminal direction a second VH domain, a CH1 domain, a third antibody variable domain selected from a VH domain and a VL domain, and a CH3 domain,
a fourth heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain capable of associating with the third antibody variable domain of the third heavy chain polypeptide, 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 a heterodimer, wherein one of the CH3 domains comprises a knob mutation and the other CH3 domain comprises a hole mutation; and
a light chain polypeptide comprising from N- to C-terminal direction a second VL domain and a CL domain, wherein the second VH domain and the second VL domain are associated with each other and form an antigen binding site specifically binding to a target antigen; and wherein
either i) the first heavy chain polypeptide comprises a CH3 domain comprising a knob mutation and the third heavy chain polypeptide comprises a CH3 domain comprising a hole mutation; or
ii) the first heavy chain polypeptide comprises a CH3 domain comprising a hole mutation and the third heavy chain polypeptide comprises a CH3 domain comprising a knob mutation; and wherein d) the variable domains of the first heavy chain polypeptide and the third heavy chain polypeptide are capable of forming an antigen binding site specifically binding to a target antigen.
Claim 8 encompasses the set of heterodimeric polypeptides according to claim 1, wherein
a) the first heterodimeric precursor polypeptide comprises:
a first heavy chain polypeptide comprising from N- to C-terminal direction a first VH domain, a CH1 domain, a second antibody variable domain selected from a VH domain and a VL domain, a CH2 domain and a CH3 domain,
a second heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain capable of associating with the second antibody variable domain of the first heavy chain polypeptide, 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
a light chain polypeptide comprising from N- to C-terminal direction a first VL domain and a CL domain, wherein the first VH domain and the first VL domain are associated with each other and form an antigen binding site specifically binding to a target antigen; and wherein
the second heterodimeric precursor polypeptide comprises:
a third heavy chain polypeptide comprising from N- to C-terminal direction a second VH domain, a CH1 domain, a third antibody variable domain selected from a VH domain and a VL domain, a CH2 domain and a CH3 domain,
a fourth heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain capable of associating with the third antibody variable domain of the third heavy chain polypeptide, 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 a heterodimer, wherein one of the CH3 domains comprises a knob mutation and the other CH3 domain comprises a hole mutation; and
a light chain polypeptide comprising from N- to C-terminal direction a second VL domain and a CL domain, wherein the second VH domain and the second VL domain are associated with each other and form an antigen binding site specifically binding to a target antigen; and wherein
c) either i) the first heavy chain polypeptide comprises a CH3 domain comprising a knob mutation and the third heavy chain polypeptide comprises a CH3 domain comprising a hole mutation; or ii) the first heavy chain polypeptide comprises a CH3 domain comprising a hole mutation and the third heavy chain polypeptide comprises a CH3 domain comprising a knob mutation; and wherein
d) the variable domains of the first heavy chain polypeptide and the third heavy chain polypeptide are capable of forming an antigen binding site specifically binding to a target antigen.
Claim 9 encompasses the set of heterodimeric precursor polypeptides according to claim 1, wherein the VH domain and the VL domain indicated in B) are capable of forming an antigen binding site specifically binding to any CD3.
Claim 10 encompasses the set of heterodimeric precursor polypeptides according to claim 1, wherein no interchain disulfide bond is formed between the two polypeptide chains comprising the CH3 domains of the first and second heterodimeric polypeptide.
Claim 11 encompasses a heterodimeric polypeptide comprising a first heterodimeric precursor polypeptide and a second heterodimeric precursor polypeptide, as defined in claim 1, wherein said heterodimeric polypeptide is generated by contacting said first heterodimeric precursor polypeptide and said second heterodimeric precursor polypeptide to form a third heterodimeric polypeptide comprising at least one polypeptide chain comprising a CH3 domain from the first heterodimeric precursor polypeptide and at least one polypeptide chain comprising a CH3 domain from the second heterodimeric polypeptide.
Claim 12 encompasses the heterodimeric polypeptide of claim 11, wherein the second heterodimeric precursor polypeptide comprises an antigen binding moiety specifically binding to a second antigen, and wherein the third heterodimeric polypeptide comprises the antigen binding moiety specifically binding to the first antigen and the antigen binding moiety specifically binding to the second antigen, and a third antigen binding moiety is formed by the VL domain and the VH domain indicated in B).
Claim 13 encompasses the heterodimeric polypeptide of claim 11, wherein no interchain disulfide bond is formed between the two polypeptide chains comprising the CH3 domains of the first and second heterodimeric polypeptide, and wherein the contacting is performed in absence of a reducing agent.
Claim 15 encompasses a first heterodimeric precursor polypeptide as defined in claim 1.
Claim 16 encompasses a second heterodimeric precursor polypeptide as defined in claim 1.
Claim 18 encompasses the set of heterodimeric polypeptide of claim 6, wherein said fragment is any variable fragment (Fv), any Fab fragment, any Fab’ fragment, any Fab’-SH fragment, any F(ab’)2 fragment, any diabody, any linear antibody, any single-chain Fv (scFv), or any single chain Fab (scFab).
The specification exemplifies:
Example 1
Generation of Monospecific Precursor Polypeptides Comprising a Full Fc Domain
[0416] In order to assess efficacy of polypeptide chain exchange to result in bispecific anti-biocytinamid/anti-fluorescein antibodies from monospecific precursor polypeptides, the following monospecific precursor polypeptides were generated:
[0417] The first heterodimeric precursor polypeptide (also referred to as “anti-bio precursor”) comprised a Fab fragment specifically binding to biocytinamid (“bio”), a biotin derivative, with a VL domain of SEQ ID NO:01 and a VH domain of SEQ ID NO:02. The first precursor polypeptide comprised a light chain polypeptide of SEQ ID NO:03 (also referred to as “bio LC”), a first heavy chain polypeptide of SEQ ID NO:04 (also referred to as “bio HC”) and a second heavy chain polypeptide based on SEQ ID NO:05 (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 hole” polypeptide) comprised von N- to C-terminal direction a hinge region, a CH2 domain and a CH3 domain.
[0418] The second heterodimeric precursor polypeptide (also referred to as “anti-fluo precursor”) comprised a Fab fragment specifically binding to fluorescein (“fluo”) with a VL domain of SEQ ID NO:06 and a VH domain of SEQ ID NO:07. The second precursor polypeptide comprised a light chain polypeptide of SEQ ID NO:08 (also referred to as “fluo LC”), a first heavy chain polypeptide of SEQ ID NO:09 (also referred to as “fluo HC”) and a second heavy chain polypeptide based on SEQ ID NO:10 (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 knob” polypeptide) comprised von N- to C-terminal direction a hinge region, a CH2 domain and a CH3 domain.
[0419] The CH3 domains of the indicated polypeptide chains comprise the following mutations:
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[0420] Anti-bio precursors were generated comprising dummy hole polypeptides having an amino acid sequence of SEQ ID NO:05, wherein one of the following amino acid substitutions was made: E357K, D356K, A368F, V407Y, D399A F405W, S354V, or S364L.
[0421] Anti-fluo precursors were generated comprising dummy knob polypeptides having an amino acid sequence of SEQ ID NO:10, wherein one of the following amino acid substitutions was made: K370E, W3661 K409E, K370E K439E, or K392D.
Example 3
Generation of Monospecific Precursor Polypeptides for the Generation of Activatable Binding Sites Upon Polypeptide Chain Exchange
[0453] 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 and FIG. 2 were generated.
Precursor polypeptides devoid of CH2 domain
[0454] In a first set of experiments, heterodimeric precursor polypeptides with a domain arrangement as depicted in FIG. 1 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.
[0455] In a first alternative, the following precursor polypeptides were provided:
[0456] 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.
[0457] 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.
[0458] In a second alternative, the following precursor polypeptides were provided:
[0459] 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. [0460] 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 from N- to C-terminal direction a hinge region, a VL domain derived from an anti-dig antibody and a CH3 domain.
[0461] The indicated polypeptide chains comprise the following mutations:
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Precursor Polypeptides with Fc Domain
[0462] In a second set of experiments, heterodimeric precursor polypeptides with a domain arrangement as depicted in FIG. 2 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.
[0463] In a first alternative, the following precursor polypeptides were provided:
[0464] 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. [0465] 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.
[0466] In a second alternative, the following precursor polypeptides were provided:
[0467] 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. [0468] 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.
[0469] The indicated polypeptide chains comprise the following mutations:
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[0470] 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.
[0471] 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, W3661 K409D, V397Y, or K392D.
[0472] 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.
[0473] 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, W3661 K409D, V397Y, K392D, or K370E K439E.
Example 6
Generation of Further Monospecific Precursor Polypeptides Comprising a Full Fc Domain
[0499] For assessing formation of bispecific anti-biocytinamid/anti-fluorescein 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. Note that in this experiments the knobs and holes mutations were arranged on the opposite chains.
[0500] The first heterodimeric precursor polypeptide (also referred to as “anti-fluo precursor”) comprised a Fab fragment specifically binding to fluorescein (“fluo”), a biotin derivative, with a VL domain of SEQ ID NO:06 and a VH domain of SEQ ID NO:07. The first precursor polypeptide comprised a light chain polypeptide of SEQ ID NO:08 (also referred to as “fluo LC”), a first heavy chain polypeptide of SEQ ID NO:29 (also referred to as “fluo HC”) and a second heavy chain polypeptide based on SEQ ID NO:05 (which represents the basic amino acid sequence without destabilizing mutation), with the destabilizing mutations as indicated below and a C-tag. The second heavy chain polypeptide (also referred to as “dummy hole” polypeptide) comprised von N- to C-terminal direction a hinge region, a CH2 domain and a CH3 domain.
[0501] The second heterodimeric precursor polypeptide (also referred to as “anti-bio precursor”) comprised a Fab fragment specifically binding to biocytinamid (“bio”) with a VL domain of SEQ ID NO:01 and a VH domain of SEQ ID NO:02. The second precursor polypeptide comprised a light chain polypeptide of SEQ ID NO:03 (also referred to as “bio LC”), a first heavy chain polypeptide of SEQ ID NO:28 (also referred to as “bio HC”) and a second heavy chain polypeptide based on SEQ ID NO:10 (which represents the basic amino acid sequence without destabilizing mutation) with the destabilizing mutations as indicated below and a C-tag. The second heavy chain polypeptide (also referred to as “dummy knob” polypeptide) comprised von N- to C-terminal direction a hinge region, a CH2 domain and a CH3 domain.
Regarding “at least a part” of the first antigen binding moiety (lines 7-8) and the second antigen binding moiety (line 16) 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. Further, the part is arranged on any one of the two polypeptide chains in the first and second heterodimeric precursor.
None of the claims define 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.
Regarding “antibody fragment” in claim 6, the phrase “antibody fragment” encompasses any amino acid, Fc or antigen binding fragment. It is known in the art that Fc fragment or single amino acid does not bind to any antigen.
Regarding “variable domain of the first heavy chain polypeptide and the third heavy chain heavy chain polypeptide form an antigen binding site specifically binding to any target antigen, the specification does not describe the structure, e.g., the amino acid sequences of the heavy and light chain variable domains of the first antigen binding moiety and second antigen binding moiety that correlated with binding to which particular antigen (claims 1-8, 15, 16), such as any CD3 (claim 9), any second antigen (claims 12, 13, 15, 16) encompassed by the claimed heterodimeric precursor polypeptides. Enablement is not commensurate in scope with how to use the claimed heterodimeric precursor polypeptides without guidance as to the binding specificity of such polypeptides.
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.
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.
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. It is unpredictable which undisclosed heterodimeric precursor polypeptides are effective for treating all cancer given the lack of specific guidance as to binding specificity of the heterodimeric precursor polypeptides.
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). 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).
Applicants’ arguments filed November 17, 2025 have been fully considered but are not found persuasive.
Applicants’ position is that Claim 1 is not directed to, and therefore need not recite, the entire three-chain polypeptide depicted in Fig. 1. Instead, claim 1 is drawn to the boxed portion of Fig. 1, as shown below:
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The first polypeptide comprising VH(black oval)-CH3(gray oval) and VL(gray oval)-CH3(black oval) will undergo chain exchange with the second polypeptide comprising VL(black oval)- CH3(gray oval) and VH(gray oval)-CH3(black oval) to produce a functional exchanged pair of VH(black oval)-CH3(gray oval) and VL(black oval)-CH3(gray oval). The exchanged pair defines a Fab comprising a VH:VL pair that forms a functional antigen-binding site. As such, a person of skill in the art would immediately recognize this structure as being useful.
The precursor pairs have utility in their ability to form the exchanged pair, including exchanged pairs that comprise a light chain (as depicted in Fig. 1). The specification, including the working examples and accompanying figures, describe these precursor pairs in sufficient detail so as to enable a person of skill in the art to make and use them. As such, the structures claimed in claim 1 are enabled under35U.S.C..112(a).
The Office Action further contends at pages 4 1-42 that "specification does not teach the structure, e.g., 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 (claims1-8,15,16), such as anyCD3 (claim 9), any second antigen (claims 12, 13, 15, 16) encompassed by the claimed heterodimeric precursor polypeptides to enable one of skill in the art to make and use without undue experimentation." Again, focusing on binding to particular epitopes (as the Office Action does at pages 42-44) misunderstands the nature of the invention. The Office Action at page 44 cites Amgen v. Sanofi, 598 U.S. 594, 2023 USPQ2d 602 (2023) as holding that "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". However, the invention in this application is not "an antibody that binds to antigen X".
The important aspect of the invention is the overall structure of each of the claimed sets of heterodimeric precursor polypeptides, and how the structures facilitate chain exchange to produce a functional bispecific antibody, as depicted in Figure 1; 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 recited functionally, the vast majority of the claimed sets of heterodimeric precursor polypeptides are recited structurally in sufficient detail so as to enable a person of skill in the art to make and use the claimed polypeptide precursor pairs. In fact, the specification "enables a person skilled in the art to make and use the entire class". Amgen at 610-611; Office action at page 44. Amgen's holding does not apply here.
Thus, for at least the above reasons, the pending claims are enabled by the specification. Applicant requests withdrawal of this rejection of the claims.
In response to claim 1 is drawn to the boxed portion of Fig. 1, claim 1 has no resemblance to the picture shown in Fig. 1. In particular, nowhere in claim 1 recites a first polypeptide comprising VH-CH3 and VL-CH3 will undergo chain exchange with the second polypeptide comprising VL-CH3 and VH-CH3 to produce a functional exchanged pair of VH(black oval)-CH3(gray oval) and VL(black oval)-CH3(gray oval) as argued. Further, the term “comprising” or “comprises” is open ended. It expands the heavy chain polypeptides in the first and second heterodimeric precursor polypeptide to include additional domains, e.g., VH-CH1 domains.
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 first heterodimeric precursor polypeptide comprising at least two polypeptide chains comprising a CH3 domain, wherein the two polypeptide chains comprising the CH3 domain are associated with each other via the CH3 domains and form a heterodimer, wherein one of the CH3 domains comprises any knob mutation and the other CH3 domain comprises any hole mutation, wherein the first heterodimeric precursor polypeptide comprises a first antigen binding moiety, wherein at least a part of the first antigen binding moiety is arranged on one of the two polypeptide chains comprising the CH3 domain, and
a second heterodimeric precursor polypeptide comprising at least two polypeptide chains comprising a CH3 domain, wherein the two polypeptide chains comprising the CH3 domain are associated with each other via the CH3 domains and form a heterodimer, wherein one of the CH3 domains comprises any knob mutation and the other CH3 domain comprises any hole mutation, wherein the second heterodimeric precursor polypeptide comprises a second antigen binding moiety, wherein at least a part of the second antigen binding moiety is arranged on one of the two polypeptide chains comprising the CH3 domain;
wherein A) either
within the first heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain comprising the knob mutation comprises at least a part of the first antigen binding moiety and within the second heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain with the hole mutation comprises at least a part of the second antigen binding moiety, or
ii) within the first heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain comprising the hole mutation comprises at least a part of the first antigen binding moiety and within the second heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain with the knob mutation comprises at least a part of the second antigen binding moiety; and wherein
B) either
i) the first heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VL domain and the CH3 domain, and wherein the second heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VH domain and the CH3 domain, wherein said VL domain and said VH domain specifically bind to any antigen when associated to a pair of a VH domain and a VL domain; or
ii) the first heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VH domain and the CH3 domain, and wherein the second heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VL domain and the CH3 domain, wherein said VL domain and said VH domain specifically bind to any antigen when associated to a pair of a VH domain and a VL domain; and
wherein C) 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
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 comprise 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 consisting of:
replacement of E357 with a positively charged amino acid (elected species);
replacement of S364 with a hydrophobic amino acid;
replacement of A368 with a hydrophobic amino acid; and
replacement of V407 with a hydrophobic amino acid; and
the CH3 domain with the knob mutation comprises at least one amino acid substitution selected from the group consisting 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 (elected species).
Regarding “at least a part” of the first antigen binding moiety (lines 7-8) and the second antigen binding moiety (line 16) 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. Further, the part is arranged on any one of the two polypeptide chains in the first and second heterodimeric precursor.
None of the claims define 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.
Regarding “antibody fragment” in claim 6, the phrase “antibody fragment” encompasses any amino acid, Fc or antigen binding fragment. It is known in the art that Fc fragment or single amino acid does not bind to any antigen.
Regarding “variable domain of the first heavy chain polypeptide and the third heavy chain heavy chain polypeptide form an antigen binding site specifically binding to any target antigen, 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 second antigen binding moiety that correlated with binding to which particular antigen (claims 1-8, 15, 16), such as any CD3 (claim 9), any second antigen (claims 12, 13, 15, 16) encompassed by the claimed heterodimeric precursor polypeptides. Enablement is not commensurate in scope with how to use the claimed heterodimeric precursor polypeptides as therapeutic.
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 and Rejection necessitated by the amendment filed November 17, 2024
Claim objection
Claims 2-8 are objected to because of the following informality: The preamble is inconsistent with the preamble of claim 1. Amending the preamble of claims 2-8 to recite “The set of heterodimeric precursor polypeptides …claim 1…” would obviate this objection.
Claim 10 is objected to because of the following informality: “claim 1” should have been “of claim 1”.
Claim 18 is objected to because of the following informality: The preamble is inconsistent with the preamble of claim 6. The set of heterodimeric precursor polypeptides …claim 6…” would obviate this objection.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 7 and 8 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
“the first heterodimeric precursor polypeptide comprises:
a first heavy chain polypeptide comprising from N- to C-terminal direction a first VH domain, a CH1 domain, a second antibody variable domain selected from a VH domain and a VL domain, and a CH3 domain,
a second heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain capable of associating with the second antibody variable domain of the first heavy chain polypeptide, 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
a light chain polypeptide comprising from N- to C-terminal direction a first VL domain and a CL domain, wherein the first VH domain and the first VL domain are associated with each other and form an antigen binding site specifically binding to a target antigen; and wherein
b) the second heterodimeric precursor polypeptide comprises:
a third heavy chain polypeptide comprising from N- to C-terminal direction a second VH domain, a CH1 domain, a third antibody variable domain selected from a VH domain and a VL domain, and a CH3 domain,
a fourth heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain capable of associating with the third antibody variable domain of the third heavy chain polypeptide, 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 a heterodimer, wherein one of the CH3 domains comprises a knob mutation and the other CH3 domain comprises a hole mutation; and
a light chain polypeptide comprising from N- to C-terminal direction a second VL domain and a CL domain, wherein the second VH domain and the second VL domain are associated with each other and form an antigen binding site specifically binding to a target antigen; and wherein
either i) the first heavy chain polypeptide comprises a CH3 domain comprising a knob mutation and the third heavy chain polypeptide comprises a CH3 domain comprising a hole mutation; or
ii) the first heavy chain polypeptide comprises a CH3 domain comprising a hole mutation and the third heavy chain polypeptide comprises a CH3 domain comprising a knob mutation; and wherein d) the variable domains of the first heavy chain polypeptide and the third heavy chain polypeptide are capable of forming an antigen binding site specifically binding to a target antigen” in claim 7 is not further limiting the subject matter of claim 1.
Claim 7 fails to limit the parent claim from which claim 7 depends as the parent claim 1 is drawn to a set of heterodimeric precursor polypeptides comprising:
a first heterodimeric precursor polypeptide comprising at least two polypeptide chains comprising a CH3 domain, wherein the two polypeptide chains comprising the CH3 domain are associated with each other via the CH3 domains and form a heterodimer, wherein one of the CH3 domains comprises any knob mutation and the other CH3 domain comprises any hole mutation, wherein the first heterodimeric precursor polypeptide comprises a first antigen binding moiety, wherein at least a part of the first antigen binding moiety is arranged on one of the two polypeptide chains comprising the CH3 domain, and
a second heterodimeric precursor polypeptide comprising at least two polypeptide chains comprising a CH3 domain, wherein the two polypeptide chains comprising the CH3 domain are associated with each other via the CH3 domains and form a heterodimer, wherein one of the CH3 domains comprises any knob mutation and the other CH3 domain comprises any hole mutation, wherein the second heterodimeric precursor polypeptide comprises a second antigen binding moiety, wherein at least a part of the second antigen binding moiety is arranged on one of the two polypeptide chains comprising the CH3 domain;
wherein A) either
within the first heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain comprising the knob mutation comprises at least a part of the first antigen binding moiety and within the second heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain with the hole mutation comprises at least a part of the second antigen binding moiety, or
ii) within the first heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain comprising the hole mutation comprises at least a part of the first antigen binding moiety and within the second heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain with the knob mutation comprises at least a part of the second antigen binding moiety; and wherein
B) either
i) the first heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VL domain and the CH3 domain, and wherein the second heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VH domain and the CH3 domain, wherein said VL domain and said VH domain specifically bind to any antigen when associated to a pair of a VH domain and a VL domain; or
ii) the first heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VH domain and the CH3 domain, and wherein the second heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VL domain and the CH3 domain, wherein said VL domain and said VH domain specifically bind to any antigen when associated to a pair of a VH domain and a VL domain; and
wherein C) 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
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 comprise 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 consisting of:
replacement of E357 with a positively charged amino acid (elected species);
replacement of S364 with a hydrophobic amino acid;
replacement of A368 with a hydrophobic amino acid; and
replacement of V407 with a hydrophobic amino acid; and
the CH3 domain with the knob mutation comprises at least one amino acid substitution selected from the group consisting 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 (elected species).
Claim 8 fails to limit the parent claim from which claim 8 depends as the parent claim 1 because claim 1 limits to the boxed portion of Fig. 1 indicated above whereas claim 8 comprises the set of heterodimeric precursor polypeptides, wherein
a) the first heterodimeric precursor polypeptide comprises:
a first heavy chain polypeptide comprising from N- to C-terminal direction a first VH domain, a CH1 domain, a second antibody variable domain selected from a VH domain and a VL domain, a CH2 domain and a CH3 domain,
a second heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain capable of associating with the second antibody variable domain of the first heavy chain polypeptide, 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
a light chain polypeptide comprising from N- to C-terminal direction a first VL domain and a CL domain, wherein the first VH domain and the first VL domain are associated with each other and form an antigen binding site specifically binding to a target antigen; and wherein
the second heterodimeric precursor polypeptide comprises:
a third heavy chain polypeptide comprising from N- to C-terminal direction a second VH domain, a CH1 domain, a third antibody variable domain selected from a VH domain and a VL domain, a CH2 domain and a CH3 domain,
a fourth heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain capable of associating with the third antibody variable domain of the third heavy chain polypeptide, 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 a heterodimer, wherein one of the CH3 domains comprises a knob mutation and the other CH3 domain comprises a hole mutation; and
a light chain polypeptide comprising from N- to C-terminal direction a second VL domain and a CL domain, wherein the second VH domain and the second VL domain are associated with each other and form an antigen binding site specifically binding to a target antigen; and wherein
c) either i) the first heavy chain polypeptide comprises a CH3 domain comprising a knob mutation and the third heavy chain polypeptide comprises a CH3 domain comprising a hole mutation; or ii) the first heavy chain polypeptide comprises a CH3 domain comprising a hole mutation and the third heavy chain polypeptide comprises a CH3 domain comprising a knob mutation; and wherein
d) the variable domains of the first heavy chain polypeptide and the third heavy chain polypeptide are capable of forming an antigen binding site specifically binding to a target antigen.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103(a) are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 1-3, 5-7, 10-13, 15-16 and 18 are rejected under 35 U.S.C. 103 as being unpatentable over WO2016087416 publication (published; PTO 892) in view of Brinkmann et al (of record, US20170369595, published December 28, 2017; PTO 892).
Claim 1 recites a set of heterodimeric precursor polypeptide comprising:
a first heterodimeric precursor polypeptide comprising at least two polypeptide chains comprising a CH3 domain, wherein the two polypeptide chains comprising the CH3 domain are associated with each other via the CH3 domains and form a heterodimer, wherein one of the CH3 domains comprises any knob mutation and the other CH3 domain comprises any hole mutation, wherein the first heterodimeric precursor polypeptide comprises a first antigen binding moiety, wherein at least a part of the first antigen binding moiety is arranged on one of the two polypeptide chains comprising the CH3 domain, and
a second heterodimeric precursor polypeptide comprising at least two polypeptide chains comprising a CH3 domain, wherein the two polypeptide chains comprising the CH3 domain are associated with each other via the CH3 domains and form a heterodimer, wherein one of the CH3 domains comprises any knob mutation and the other CH3 domain comprises any hole mutation, wherein the second heterodimeric precursor polypeptide comprises a second antigen binding moiety, wherein at least a part of the second antigen binding moiety is arranged on one of the two polypeptide chains comprising the CH3 domain;
wherein A) either
within the first heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain comprising the knob mutation comprises at least a part of the first antigen binding moiety and within the second heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain with the hole mutation comprises at least a part of the second antigen binding moiety, or
ii) within the first heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain comprising the hole mutation comprises at least a part of the first antigen binding moiety and within the second heterodimeric precursor polypeptide the polypeptide chain comprising the CH3 domain with the knob mutation comprises at least a part of the second antigen binding moiety; and wherein
B) either
i) the first heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VL domain and the CH3 domain, and wherein the second heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VH domain and the CH3 domain, wherein said VL domain and said VH domain specifically bind to any antigen when associated to a pair of a VH domain and a VL domain; or
ii) the first heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VH domain and the CH3 domain, and wherein the second heterodimeric precursor polypeptide comprises one polypeptide chain comprising a VL domain and the CH3 domain, wherein said VL domain and said VH domain specifically bind to any antigen when associated to a pair of a VH domain and a VL domain; and
wherein C) 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
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 comprise 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 consisting of:
replacement of E357 with a positively charged amino acid (elected species);
replacement of S364 with a hydrophobic amino acid;
replacement of A368 with a hydrophobic amino acid; and
replacement of V407 with a hydrophobic amino acid; and
the CH3 domain with the knob mutation comprises at least one amino acid substitution selected from the group consisting 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 (elected species).
As per Applicant’s argument at p. 17 that claim 1 is drawn to the boxed portion of Fig. 1, as shown below:
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The WO2016/087416 publication teaches a first heterodimer precursor comprising at least two heavy chains comprising a VH3 or VL3 fused to a CH3 domain, e.g., VH-CH1-linker-VH3-CH3 and VH-CH1-linker-VL3-CH3 of LeY-Bio(SS)-LeY, respectively, wherein the two heavy chains comprising the CH3 domains are associated with each other via the CH3 domain and form a heterodimer, wherein one of the CH3 domains comprises a hole mutation (left) and the other comprises a knob mutation (right), wherein the first precursor polypeptide comprises a first antigen binding moiety that binds to antigen 1, wherein at least a part of the first antigen binding moiety, e.g., the VH3 (CH2 domains replaced with VL3 and VH3) paired with the VL3 fused to a second CH3 domain to form a third antigen binding site that binds to Biotin (antigen 2), see p. 86, Fig. 1A-C, Fig. 2A and 2B), wherein the VH3 paired with the VL3 forms a third binding site that binds to biotin as per claims 1, and 15, in particular.
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The term “comprising” is open ended. It expands the two heavy chains to include additional domains at the N-terminus to include VH-CH1 domains that paired with the light chain to form a Fab that binds to various antigen, e.g., LeY, and Biotin or (Bio), see Table 5.
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The WO2016/087416 publication teaches a second heterodimer precursor
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comprising at least two heavy chains e.g., VH-CH1-linker-VH3-CH3 and VH-CH1-linker-VL3-CH3 of CD33-Bio(SS)-CD33, respectively), wherein the two polypeptide chains comprising the CH3 domains that are associated with each other via the CH3 domain and form a heterodimer, wherein one of the CH3 domains comprises a hole mutation and the other comprises a knob mutation, wherein the first precursor polypeptide comprises a first antigen binding moiety that binds to antigen 3, e.g., biotin, wherein at least a part of the first antigen binding moiety, e.g., VH3 or VL3 (CH2 domains replaced with VL3 and VH3) is arranged on one of the two polypeptide chains comprising the CH3 domain that binds to Biotin, see Table 5, in particular.
The term “comprising” is open ended. It expands the two heavy chains each to include additional domains at the N-terminus to include VH-CH1 domains that paired with the light chain to form a Fab that binds to various antigen, e.g., CD33 or GPC3, see Tables 5, 7 to form a trivalent, bispecific antibody having the structure shown in Fig. 3D below as per claims 11-12, without interchain disulfide bond (aka no hinge disulfide bonds) as per claims 10 and 13.
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Regarding claim 5, WO2016/087416 publication teaches that the CH3 domains are altered by introduction of at least one cysteine residue in each CH3 domain such that a disulfide bond is formed between the CH3 domains, see Table 5, BsAb LeY-Bio(SS)-LeY, BsAb CD33-Bio(SS)-CD33, BsAb GPC3-Bio(SS)-GPC3, in particular.
Regarding claims 6 and 18, WO2016/087416 publication teaches that the first antigen binding moiety, e.g., VH-CH1 paired with VL-CL or Fab, and the second binding moiety is an antigen binding fragment, e.g., VL2-CL paired with VH2-CH1 (Fab), see Fig. 3B, or single chain antibody, see Fig. 3E.
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Claims 7 and 16 are included because it is within the purview of one of ordinary skill in the art to have produced a second heterodimer precursor having the structure as taught by WO2016087416 publication that binds to different antigens, e.g., BsAb CD33-Bio(SS)-CD33, or BsAb GPC3-Bio(SS)-GPC3 each comprises a third heavy chain polypeptide comprising from N- to C- terminal direction as second VH domain, a CH1 domain, a third antibody variable domain selected from VH or VL domain and a CH3 domain, a fourth heavy chain polypeptide comprising from N- to C-terminal direction an antibody variable domain that associates with the third antibody variable domain of the third heavy chain polypeptide, a CH3 domain, wherein the third heavy chain polypeptide and the fourth heavy chain polypeptide 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, see structure below.
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The WO2016087416 publication does not teach the CH3 domain with a hole mutation comprises E357 replaced with a positively charged amino acid and the CH3 domain with the knob mutation comprises V397 replaced with a hydrophobic amino acid as per claim 1, wherein the hole mutation comprises E357K and the knob mutation comprises V397Y or K370E as per claims 2 and 3.
However, Brinkmann teaches typically, in the heterodimerization approaches known in the art, the CH3 domain of one heavy chain and the CH3 domain of the other heavy chain are both engineered in a complementary manner so that the heavy chain comprising one engineered CH3 domain can no longer homodimerize with another heavy chain of the same structure. Thereby the heavy chain comprising one engineered CH3 domain is forced to heterodimerize with the other heavy chain comprising the CH3 domain, which is engineered in a complementary manner, see para. [0119]. One heterodimerization approach known in the art is the so-called “knobs-into-holes” technology, see para. [0120]. The CH3 domain of one heavy chain (the heavy chain comprising the “knob”) having K370E mutation, and the CH3 domain of the other heavy chain (the heavy chain comprising the “hole”) comprises E357K mutations (numberings according to EU index of Kabat), see para. [0252], [0203], as per claims 2-4.
Regarding claim 5, Brinkmann teaches the CH3 domains are disulfide stabilized by a E356C or a S354C mutation in one of the CH3 domains comprise a Y349C mutation in the other CH3 domain (numberings according to EU index of Kabat), see para. [0252].
In view of the combined teachings of the references, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filling date of the claimed invention to have included Brinkmann’s CH3 domain comprising the hole mutation having a E357K (positively charged amino acid) and the other CH3 domain comprising a knob mutation having K370E substitution (numberings according to EU index of Kabat), in the set of heterodimeric precursor of the WO2016087416 publication to arrive at the claimed invention with a reasonable expectation success, e.g., promoting heterodimerization between the two heavy chains.
One of ordinary skill in the art would have been motivated to do so because Brinkmann teaches that engineered multispecific antibody wherein the CH3 domain of the one heavy chain (the heavy chain comprising the “knob”) comprises K370E mutations, and the CH3 domain of the other heavy chain (the heavy chain comprising the “hole”) comprises E357K mutations (numberings according to EU index of Kabat) for heterodimerization is known in the art, see para. [0203], [0204].
“The combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007).
“The test of obviousness is not express suggestion of the claimed invention in any or all of the references but rather what the references taken collectively would suggest to those of ordinary skill in the art presumed to be familiar with them.” See In re Rosselet 146 USPQ 183, 186 (CCPA 1965).
“There is no requirement (under 35 USC 103(a)) that the prior art contain an express suggestion to combine known elements to achieve the claimed invention. Rather, the suggestion to combine may come from the prior art, as filtered through the knowledge of one skilled in the art.,” Motorola, Inc, v. Interdigital Tech. Corn., 43 USPQ2d 1481, 1489 (Fed. Cir. 1997).
Accordingly, the claimed invention as a whole was prima facie obvious to one of ordinary skill in the art before the effective filling date of the claimed invention especially in the absence of evidence to the contrary.
Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over WO2016087416 publication (published; PTO 892) in view of Brinkmann et al (of record, US20170369595, published December 28, 2017; PTO 892) as applied to claims 1-3, 5-7, 10-13, 15-16 and 18 mentioned above and further in view of Liu (US20140112926, published April 24, 2014; PTO 892).
The teachings of the WO2016087416 publication and Brinkmann have been discussed supra.
The references above do not teach wherein in case the CH3 domain with the knob mutation comprises a mutation E357K, the CH3 domain with the hole mutation does not comprise a mutation K370E as per claim 4.
However, Liu teaches that the general examples of charge pair substitutions include K370D or K370E in one chain plus E357R (aka does not comprises K370E) in the other can enhance heterodimer formation, see para. [0050].
In view of the combined teachings of the references, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filling date of the claimed invention to have included Liu’s CH3 domain comprising the hole mutation having a knob mutation having K370E substitution (numberings according to EU index of Kabat), and E357R in the other CH3 domain having a hole mutation in the set of heterodimeric precursor of the WO2016087416 publication to arrive at the claimed invention with a reasonable expectation success, e.g., promoting heterodimerization between the two heavy chains.
One of ordinary skill in the art would have been motivated to do so because Liu teaches that the pair of substitutions can enhance heterodimer formation, see para. [0050].
“The combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007).
“The test of obviousness is not express suggestion of the claimed invention in any or all of the references but rather what the references taken collectively would suggest to those of ordinary skill in the art presumed to be familiar with them.” See In re Rosselet 146 USPQ 183, 186 (CCPA 1965).
“There is no requirement (under 35 USC 103(a)) that the prior art contain an express suggestion to combine known elements to achieve the claimed invention. Rather, the suggestion to combine may come from the prior art, as filtered through the knowledge of one skilled in the art.,” Motorola, Inc, v. Interdigital Tech. Corn., 43 USPQ2d 1481, 1489 (Fed. Cir. 1997).
Accordingly, the claimed invention as a whole was prima facie obvious to one of ordinary skill in the art before the effective filling date of the claimed invention especially in the absence of evidence to the contrary.
Claims 8-9 are rejected under 35 U.S.C. 103 as being unpatentable over WO2016087416 publication (published; PTO 892) in view of Brinkmann et al (of record, US20170369595, published December 28, 2017; PTO 892) as applied to claims 1-3, 5-7, 10-13, 15-16 and 18 mentioned above and further in view of Ng et al (of record, US20180193477, published July 12, 2018; PTO 892).
The teachings of the WO2016087416 publication and Brinkmann have been discussed supra.
The references above do not teach that the VL3 and VH3 binds to CD3 as per claim 9 and the first and second heavy chain polypeptides in the first heterodimeric and the second heterodimeric precursors each comprises a CH2 domain as per claim 8.
However, Ng teaches bispecific antibody that binds to CD3 and any tumor antigen of interest, e.g., CD19, LeY, see para. [0113]. Ng teaches a humanized variant of OKT3 antibody comprising VH and VL sequences, see entire document, para. [0012], [0015], FIG. 2, in particular. Ng teaches that the bispecific antibodies are capable of targeting T cells to tumor cells, see para. [0004] to [0006]. The bispecific antibody comprises two heavy chains. Each antibody heavy chain typically comprises an Fc that comprises a CH2 domain in addition to CH3 domains, see para. [0138]. The CH2 domain of the Fc binds to Fc receptors and complement and is thus involved in mediating effector cell functions, see para. [0138] to [0142].
In view of the combined teachings of the references, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filling date of the claimed invention to combine the teachings of the WO2016087416 publication, Brinkmann and Ng by including Ng’ CH2 domain in each of the heavy chain of the first and second heterodimer and/or substituting the VH3 and VL3 domain that binds to biotin in B of the WO2016087416 publication for the VH and VL domain that binds to CD3 as taught by Ng to arrive at the claimed invention with a reasonable expectation of success, e.g. targeting CD3 expressing T cells to any cell that expressed tumor antigen.
One of ordinary skill in the art would have been motivated to do so because Ng teaches that the CH2 domain of the bispecific antibody binds to Fc receptors and complement and is thus involved in mediating effector cell functions (see para. [0138] to [0142]) and CD3 binding domain is expected to target T cell expressing CD3 to tumor cell that expressed any tumor antigen of interest.
One of ordinary skill in the art would have been motivated to do so because Brinkmann teaches that when the variable domains VH.sub.3 and VL.sub.3 are directly connected to the respective CH3 domains advantageously prevents mispairing of the cysteine residues, which are located in close proximity, when forming the desired interchain disulfide bonds; the smaller size of the antibody can penetrate tissues and tumors more rapidly, see para. [0011].
One of ordinary skill in the art would have been motivated to include the CH2 domain because Brinkmann teaches that no CH2 domains present in the antibodies, the effector functions of the antibodies is abolished (see para. [0050]) and Ng teaches that CH2 domain of the Fc binds to Fc receptors and complement and is thus involved in mediating effector cell functions, see para. [0138] to [0142].
“The combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007).
“The test of obviousness is not express suggestion of the claimed invention in any or all of the references but rather what the references taken collectively would suggest to those of ordinary skill in the art presumed to be familiar with them.” See In re Rosselet 146 USPQ 183, 186 (CCPA 1965).
“There is no requirement (under 35 USC 103(a)) that the prior art contain an express suggestion to combine known elements to achieve the claimed invention. Rather, the suggestion to combine may come from the prior art, as filtered through the knowledge of one skilled in the art.,” Motorola, Inc, v. Interdigital Tech. Corn., 43 USPQ2d 1481, 1489 (Fed. Cir. 1997).
Accordingly, the claimed invention as a whole was prima facie obvious to one of ordinary skill in the art before the effective filling date of the claimed invention especially in the absence of evidence to the contrary.
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.
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/PHUONG HUYNH/ Primary Examiner, Art Unit 1641