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 1-8 and 41-76 are pending.
Applicant’s election without traverse of Group I that read on (A) GGSALQG as the non-naturally occurring sequence, (B) 295 as the species of binding site, 295-296-297 as the heavy chain binding sites, and HC180 as the heavy chain binding site, (C) para-azidomethylphenylalanine as the non-natural amino acid, (D) gamma as the heavy chain, (E) kappa as the light chain, (F) IgG1 as the particular class or subclass, (G) a full-length antibody as the particular form, in the reply filed on August 27, 2025 is acknowledged.
Claims 55-62 and 64-76 are withdrawn from further consideration by the examiner, 37 C.F.R. 1.142(b) as being drawn to non-elected inventions.
Claims 1-8, 41-54 and 63, drawn to an antibody comprising one or more non-natural occurring sequences of amino acids that read on (A) GGSALQG as the non-naturally occurring sequence, (B) 295 as the species of binding site, 295-296-297 as the heavy chain binding sites, and HC180 as the heavy chain binding site, (C) para-azidomethylphenylalanine as the non-natural amino acid, (D) gamma as the heavy chain, (E) kappa as the light chain, (F) IgG1 as the particular class or subclass, (G) a full-length antibody as the particular form, are being acted upon in this Office Action.
Priority
Applicant’ claim priority to provisional application 62/984,698, filed March 3, 2020, is acknowledged.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on September 1, 2022 has been considered by the examiner and an initialed copy of the IDS is included with this Office Action.
Drawings
The drawings filed on September 1, 2022 are acceptable.
Specification
The amendment to the specification filed on September 1, 2022 has been entered.
The specification is objected to because it contains disclosures of amino acid sequences -GGSXLQGPP or GGSLXQGPP that are not accompanied by SEQ ID NOS, at least with respect to the sequences shown in para. [00290]. While it appears those sequences are included in the sequence listing, a sequence identifier must accompany each sequence, each time it appears in the specification. 37 C.F.R. 1.821 (a) and (c); M.P.E.P. 2422.01-03. Amending the specification GGSXLQGPP (SEQ ID NO: 4) and GGSLXQGPP (SEQ ID NO: 7) would obviate this objection.
The lengthy specification has not been checked to the extent necessary to determine the presence of all possible minor errors. Applicant's cooperation is requested in correcting any errors of which applicant may become aware in the specification.
Claim Objection
Claims 5-8, 41-43 are objected to because the claims recite amino acid sequence of at least four amino acid residues and are not accompanied by SEQ ID NO. 37 C.F.R. 1.821 (a) to (d); M.P.E.P. 2422.01, 2422.03.
Claim 49 is objected to because of the following informalities:
duplicate “consisting of” at line 3 should be deleted.
The claim recites non-elected embodiments.
Claim 63 is objected to because of the following informality: the claim recites non-elected “antibody conjugate”.
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 1-8, 41-54 and 63 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 “295, 296, 297, 120, 375 or 400, when the heavy chain is numbered according to Kabat or EU numbering scheme” is indefinite because position 295, 296, 297, 375 or 400 in the Fc should be numbering according to EU numbering scheme, not Kabat. Further, position 120 should be numbering according to Kabat, not EU numbering scheme. One skilled in the art could not determine the boundaries of the claimed invention in order to avoid infringing on the claims.
Claim 3 recites the limitation "294", “298”, “119”, “121”, “374”, “376”, “399” and “401” in claim 1. There is insufficient antecedent basis for this limitation in the claim.
Claim 8 recites the limitation "the amino acid sequence G-G-S-X1-L-Q-G-P-P" in claims 5 and 1. There is insufficient antecedent basis for this limitation in the claim.
Claim 41 recites the limitation "the amino acid sequence G-G-S-L-X2-Q-G-P-P" in claims 5 and 1. There is insufficient antecedent basis for this limitation in the claim.
Claim 42 recites the limitation "the amino acid sequence G-G-S-X1-L-Q-G-P-P" in claims 6 and 1. There is insufficient antecedent basis for this limitation in the claim.
Claim 43 recites the limitation "the amino acid sequence G-G-S-L-X2-Q-G-P-P" in claims 6 and 1. There is insufficient antecedent basis for this limitation in the claim.
Claim 46 recites the limitation “optimally substitutable positions”, which is indefinite and vague because one of skilled in the art could not determine the boundaries of the claimed invention in order to avoid infringing on the claim.
Claim 49 is confusing by mixing heavy chain or light chain residues HC404, HC121, HC180, LC22, LC7, LC42, LC152, HC136, HC25, HC40, HC119, HC190, HC222, HC19, HC52, HC70, HC110, or HC221 according to different EU, Kabat or Chothia numbering scheme. It is noted that the numbering schemes differ between EU, Kabat and Chothia. The amino acid positions will vary between antibodies, and the amino acid at that position will vary between antibodies. One skilled in the art could not determine the boundaries of the claimed invention in order to avoid infringing on the claims.
Claim 53 recites a broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) is considered indefinite, since the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c).
Note the explanation given by the Board of Patent Appeals and Interferences in Ex parte Wu, 10 USPQ2d 2031, 2033 (Bd. Pat. App. & Inter. 1989), as to where broad language is followed by "such as" and then narrow language. The Board stated that this can render a claim indefinite by raising a question or doubt as to whether the feature introduced by such language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims. Note also, for example, the decisions of Ex parte Steigewald, 131 USPQ 74 (Bd. App. 1961); Ex parte Hall, 83 USPQ 38 (Bd. App. 1948); and Ex parte Hasche, 86 USPQ 481 (Bd. App. 1949).
In this case, claim 53 recites the broad limitation of “IgA”, “IgG”, and the claim also recites “IgA2”, “IgG1”, “IgG2” and “IgG3” which is a narrower statement of the range/limitation.
Claim 54 recites the limitation “Fv, Fab, (Fab')2, single chain Fv (scFv)” in claim 1. There is insufficient antecedent basis for this limitation in the claim because positions 295, 296, 297, 375 or 400 are located in the Fc region and antibody Fv, Fab, (Fab')2, single chain Fv (scFv) do not contain Fc.
Claim 63 recites the limitation "antibody conjugate" in claim 1. There is insufficient antecedent basis for this limitation in the claim.
Claims 2, 4-7, 44-48, 50-53 are included in the rejection because they are dependent on rejected claim 1 and do not correct the deficiency of the claim from which they depend. Appropriate correction is required.
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.
Claim 49 is 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. “comprising one or more site-specific non-natural amino acid residues at sequence positions corresponding to residues selected from the group consisting of consisting of heavy chain or light chain residues HC404, HC121, HC180, LC22, LC7, LC42, LC152, HC136, HC25, HC40, HC119, HC190, HC222, HC19, HC52, HC70, HC110, or HC221 according to the EU, Kabat or Chothia numbering scheme, or a post-translationally modified variant thereof” in claim 49 is not further limiting the subject matter of claim 1. Claim 49 fails to limit the parent claim from which claim 49 depends as the parent claim 1 is drawn to antibody comprising one or more non-naturally occurring sequences of amino acids having:
the sequence leucine (L) - glutamine (Q) - arginine (R), wherein the Q residue of one, or up to all, of the non-naturally occurring sequences is at heavy chain site 295, 296, 297, 120, 375, or 400, when the heavy chain is numbered according to the Kabat or EU numbering scheme; or,
alternatively, having:
the sequence X1 - leucine (L) - glutamine (Q) - glycine (G),
wherein X1 is an amino acid selected from the group consisting of glycine (G), alanine (A), isoleucine (I), methionine (M), proline (P), tryptophan (W), tyrosine (Y)), serine (S), threonine (T), asparagine (N), glutamine (Q), histidine (H), lysine (K), arginine (R), aspartate (D), and glutamate (E), or
leucine (L) - X2- glutamine (Q) - glycine (G), wherein X2 is an amino acid selected from the group consisting of isoleucine (I),phenylalanine (F), threonine (T), glutamine (Q), histidine (H), arginine (R), and glutamate (E),
wherein the non-naturally occurring amino acid sequence comprising X1-L-Q-G or L-X2- Q-G is at the C-terminus of an antibody light chain or an antibody heavy chain.
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 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 1-8, 41-54 and 63 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
MPEP § 2163 lists factors that can be used to determine if sufficient evidence of possession has been furnished in the disclosure of the Application. These include: (1) Actual reduction to practice, (2) Disclosure of drawings or structural chemical formulas, (3) Sufficient relevant identifying characteristics (such as: i. Complete structure, ii. Partial structure, iii. Physical and/or chemical properties, iv. Functional characteristics when coupled with a known or disclosed, and correlation between function and structure), (4) Method of making the claimed invention, (5) Level of skill and knowledge in the art, and (6) Predictability in the art. “Disclosure of any combination of such identifying characteristics that distinguish the claimed invention from other materials and would lead one of skill in the art to the conclusion that the applicant was in possession of the claimed species is sufficient.” MPEP § 2163.
The U.S. Court of Appeals for the Federal Circuit recently reaffirmed, in an en banc decision, that the written description requirement for a genus may be satisfied either by (i) the disclosure of a representative number of species falling within the scope of the genus or (ii) 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. Ariad Pharmaceuticals', Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1350, 94 U.S.P.Q.2d 1161, 1171 (en banc) (Fed. Cir. 2010), citing Regents" of the University of California v. Eli Lilly & Co., 119 F.3d 1559, 1568-69, 43 U.S.P.Q.2d 1398, 1406 (Fed. Cir. 1997) and AbbVie v. Janssen Biotech and Centocor Biologics (Fed. Cir. 2014).
Claim 1 encompasses any antibody comprising one or more non-naturally occurring sequences of amino acids having:
the sequence leucine (L) - glutamine (Q) - arginine (R), wherein the Q residue of one, or up to all, of the non-naturally occurring sequences is at heavy chain site 295, 296, 297, 120, 375, or 400, when the heavy chain is numbered according to the Kabat or EU numbering scheme; or,
alternatively, having:
the sequence X1 - leucine (L) - glutamine (Q) - glycine (G),
wherein X1 is an amino acid selected from the group consisting of glycine (G), alanine (A), isoleucine (I), methionine (M), proline (P), tryptophan (W), tyrosine (Y)), serine (S), threonine (T), asparagine (N), glutamine (Q), histidine (H), lysine (K), arginine (R), aspartate (D), and glutamate (E), or
leucine (L) - X2- glutamine (Q) - glycine (G), wherein X2 is an amino acid selected from the group consisting of isoleucine (I),phenylalanine (F), threonine (T), glutamine (Q), histidine (H), arginine (R), and glutamate (E),
wherein the non-naturally occurring amino acid sequence comprising X1-L-Q-G or L-X2- Q-G is at the C-terminus of an antibody light chain or an antibody heavy chain.
Claim 2 encompasses the antibody of claim 1 wherein the Q residue of one, up to all, of the non-naturally occurring sequences is capable of accepting a primary amine in a transglutaminase reaction.
Claim 3 encompasses the antibody of claim 1 comprising the sequence LQR at one or more of the following heavy chain sites, when the heavy chain is numbered according to the EU numbering scheme: a. 294-295-296
b. 295-296-297
c. 296-297-298
d. 119-120-121
e. 374-375-376; and
f. 399-400-401.
Claim 4 encompasses the antibody of claim 1 comprising sequences LQR at two, three, four, five, or six of the heavy chain sites.
Claim 5 encompasses the antibody of claim 1 comprising the amino acid sequence X1-L-Q- G or L-X2-Q-G at the C-terminus of one or both light chains.
Claim 6 encompasses the antibody of claim 1 comprising the amino acid sequence X1-L-Q- G or L-X2-Q-G at the C-terminus of one or both heavy chains.
Claim 7 encompasses the antibody of claim 1 comprising the amino acid sequence Xi-L-Q- G or L-X2-Q-G at the C-terminus of at least one heavy and at least one light chain.
Claim 8 encompasses the antibody of claim 5, comprising the amino acid sequence G-G-S- Xi-L-Q-G-P-P at the C-terminus of one or both light chains.
Claim 41 encompasses the antibody of claim 5, comprising the amino acid sequence G-G-S-L-X2-Q-G-P-P at the C-terminus of one or both light chains.
Claim 42 encompasses the antibody of claim 6, comprising the amino acid sequence G-G-S-X1-L-Q-G-P-P at the C-terminus of one or both heavy chains.
Claim 43 encompasses the antibody of claim 6, comprising the amino acid sequence G-G-S-L-X2-Q-G-P-P at the C-terminus of one or both heavy chains.
Claim 44 encompasses the antibody of claim 5, wherein X1 is an amino acid selected from the group comprising G, A, I, M, P, W, Y, S, T, N, Q, H, K, R, D, and E.
Claim 45 encompasses the antibody of claim 5, wherein X2 is an amino acid selected from the group comprising I, F, T, Q, H, R and E.
Claim 46 encompasses the antibody of claim 1, further comprising a non-natural amino acid residue at a specific site selected from the group consisting of optimally substitutable positions of any polypeptide chain of said antibody.
Claim 47 encompasses the antibody of claim 1, further comprising two or more site-specific non-natural amino acid residues.
Claim 48 encompasses the antibody of claim 1, further comprising two to six non-natural amino acid residues.
Claim 49 encompasses the antibody of claim 1, further comprising one or more site-specific non-natural amino acid residues at sequence positions corresponding to residues selected from the group consisting of consisting of heavy chain or light chain residues HC404, HC121, HC180, LC22, LC7, LC42, LC152, HC136, HC25, HC40, HC119, HC190, HC222, HC19, HC52, HC70, HC110, or HC221 according to the EU, Kabat or Chothia numbering scheme, or a post-translationally modified variant thereof.
Claim 50 encompasses the antibody of claim 49, wherein at least one of said non- natural amino acid residues is a para-azidophenylalanine or para-azidomethylphenylalanine residue.
Claim 51 encompasses the antibody of claim 1 comprising a heavy chain of a type selected from the group consisting of γ, α, δ, ε and μ.
Claim 52 encompasses the antibody of claim 1 comprising a light chain of a type selected from λ and κ.
Claim 53 encompasses the antibody claim 1 that is of a class or subclass selected from the group consisting of IgA, IgA2, IgD, IgE, IgG, IgG1, IgG2, IgG3 and IgM.
Claim 54 encompasses the antibody of claim 1 that is in a form selected from the group consisting of Fv, Fc, Fab, (Fab')2, single chain Fv (scFv) and full-length antibody.
Claim 63 encompasses a composition comprising the antibody or antibody conjugate of claim 1, wherein said antibody or antibody conjugate is at least 95% by mass of the total antibody or antibody conjugate mass of said composition.
The specification discloses:
Example 1: Identifying Modified Antibodies for Optimal Stability and Conjugation
[0309] In this example, several IgG1 HC LQR variants were developed and tested as transglutaminase conjugation substrates with higher conjugation efficiency than parent antibody molecule.
[0310] First, the crystal structure of IgG (PDB 1HZH) was analyzed to select beneficial positions for LQR insertion. The positions were selected in flexible loops with exposed residues in constant regions of the heavy chain and light chain. The loops between constant domains CH.sub.2 and CH.sub.3 were avoided because mutations at these sites might affect antibody properties.
[0311] Second, the IgG HC-Q295 was mutated to A to avoid parent IgG Q conjugation. LQR variants were constructed for Trastuzumab Light Chain and αFolR1_1848-B10_Hc_Q295A heavy chain and subcloned into a pUG expression vector.
[0312] The LQR mutants were synthesized using cell-free technology by co-expressing αFolR1_1848-B10_Hc_Q295A and Trastuzumab LC. The parent and mutant antibody molecules were purified and reacted with TAMRA-cadaverine, which was catalyzed by ZsmTG, a transglutaminase of Streptomyces mobrensis (Zedria GmbH). These IgG variants were also catalyzed by shTG, a transglutaminase of Streptomyces hydroscopicus produced recombinantly in house. The final conjugation efficiency of IgG variants were analyzed by SDS-PAGE and quantified by fluorescence intensity. The normalized fluorescence intensity catalyzed by ZsmTG and shTG at 10 U/ml and 1 U/ml respectively are shown in FIG. 1 (heavy chains) and FIG. 2 (light chains).
[0313] Six HC sites showed appreciable Gln conjugation activity, while all LC sites were inactive. Three LQR variants (HC-E294LQR, A295LQR & Y296LQR) are clustered around the native Q295 conjugation site. The HC-E295LQR sequence has higher fluorescence intensity than the native HC sequence. Three other locations showed activity as TGase substrates include HC-S122LQR, HC-P374LQR, and HC-D399LQR. These mutants are promising candidate molecules for conjugation.
Example 2: Simultaneous Transglutaminase and Click Conjugation
[0314] This example demonstrates transglutaminase conjugation at mutant LQR sequences.
[0315] Dual conjugation of the transglutaminase (TGase) active primary amine-linker-TLR 7/8 agonist drug (Compound 1002) and DBCO-linker-warhead (Compound 101) were performed in a single-step reaction.
[0316] The DBCO-Azide SPAAC reaction was performed using the p-azido-methyl-phenylalanine (pAMF) non-natural amino acid incorporated into the protein at LC position K42 and HC position Y180 (Kabat) to give an overall drug antibody ratio (DAR) of 4 for Compound 101. The transglutaminase reaction was carried out at HC position Y296 by introducing the mutations Q295L/Y296Q/N297R into the protein sequence to give an overall DAR of 2 for Compound 1002.
[0317] The conjugation reaction was performed with 1 mg/mL mAb, 0.1 U/mL TGase (Zedria GmbH, T001), 67 μM SC664, 80 μM SC239, 10 mM EDTA, and 100 mM Tris HCl, pH 8.0. The conjugation reaction was carried out for 16 hours at 37′° C. Unreacted drug and TGase enzyme were removed by preparative size exclusion chromatography (Superdex 200 Increase 10/300 GL, GE Life Sciences, 28990944) and the conjugate was stored in 10 mM Citrate, 9% Sucrose, pH 6.0. DAR analysis was performed by LCMS (Agilent Technologies 6520 Accurate-Mass Q-TOF LC/MS).
Example 3: C-Term Transglutaminase Tag Library Design and Screening
[0318] A library was designed to screen for TGase conjugation to genetically encoded peptide tags appended to the carboxy terminus of trastuzumab LC. This library was based around mutating the leucine residues at the −1 and −2 positions upstream of the acceptor glutamine residue in the TG consensus sequence of LLQG (Ota et al., (1999) Biopolymers, 50:193-200, and Strop et al., (2013) Chem. Biol., 20:161-167) and to identify TGase acceptor sequences with improved performance. A C-term LC library was constructed by appending the sequences -GGSXLQGPP or -GGSLXQGPP to the LC, where X is any of the 19 natural amino acids other than cysteine.
[0319] C-term library variants were synthesized using cell-free technology by co-expressing an anti-folate receptor antibody heavy chain (HC) with a Q295A mutation and trastuzumab LC with a C-terminal transglutaminase tag. The antibody molecules were purified and reacted with TAMRA-cadaverine, which was catalyzed by ZsmTG, a transglutaminase of Streptomyces mobrensis (Zedria GmbH). These IgG variants were also catalyzed by shTG, a transglutaminase of Streptomyces hydroscopicus produced recombinantly.
[0320] The final conjugation efficiency of IgG variants were analyzed by SDS-PAGE and quantified by fluorescence intensity. The normalized fluorescence intensities catalyzed by ZsmTG and shTG at 10 U/ml and 1 U/ml respectively are shown in FIG. 3. FIG. 4 shows the mean fluorescence intensity of the transglutaminase tag library members sorted by residue type and position. The −2 position is more accommodating to sequence variation than the −1 position. Several sequences identified in the −2 sub-library have greater fluorescence intensity than the LLQR consensus sequence. The sequences measured resulted in a fluorescence intensity of between 75-151% in comparison to the reference LLQG consensus sequence. Less sequence variation is tolerated in the −1 position however, with a fluorescence intensity that is 31-121% of that of the reference LLQG consensus sequence. See, FIG. 4. Surprisingly, at the −2 position, the amino acid residues G, A, I, M, P, W, Y, S, T, N, Q, H, K, R, D, and E showed similar or even greater activity compared to the consensus. Also surprisingly, at the −1 position, the amino acid residues I, F, T, Q, H, R and E showed similar or even greater activity compared to the consensus.
However, it does not appear, based upon the disclosure of just two antibodies anti-folate receptor antibody heavy chain (HC) with a Q295A mutation and trastuzumab LC with a C-terminal transglutaminase tag is not representative of the genus of antibodies having diverse structures correlated with binding. The specification does not describe i. Complete structure, e.g., amino acid sequences of heavy and light chains variable domains, ii. Partial structure, e.g., six CDRs of all antibodies having one or more non-naturally occurring LQR sequence at one or more positions such as 295, 296, 297, 120, 375 or 400 numbering according to Kabat or EU numbering.
The specification does not describe a representative number of species falling within the scope of the genus or structural common to the members of the genus so the one of skill in the art can visualize or recognize the member of the genus of the actual claimed multi-specific antibodies or bi-specific antibodies themselves. Thus, one of skill in the art would reasonably conclude that the disclosure fails to provide a representative number of species to describe the genus as broadly claimed at the time of filing.
It is 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 (Lloyd et al. Protein Engineering, Design & Selection 22:159-168, 2009; PTO 892; see, e.g., Discussion).
Similarly, Edwards et al (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 (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.) 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 cannot define a structure-function relationship so as to be representative of all the antibodies that bind to that antigen (as held in Abbvie).
The specification does not describe incorporating different types of non-natural amino acids at multiple sites in the heavy and light chains of all antibodies such as IgG1 isotype.
Gao et al (Frontiers in Pharmacology 10(611): 1-8, 2019; PTO 892) teaches that incorporating different types of unnatural amino acids at multiple sites is still a dauting task, see p. 5, left col.
Tsuchikama (Protein Cell 9(1): 33-46, 2018; PTO 892) teaches non-natural amino acid-based methodology generally requires special techniques, e.g., E coli using amber codon suppression with an engineered orthogonal amino acyl tRNAse/tRNA pair from M. Janaschii and biological agents for the genetic engineering process and the incorporated non-natural amino acid residues could potentially invoke undesired immunological response, see p. 37 to 38. The site-specific conjugation method gives a defined DAR value depending on the number of non-natural residues that are genetically incorporated. Further, the choice of target antigens, payloads (drug) is important, antibody-payload conjugation methods and linker chemistry are also crucial elements for producing successful ADCs. In particular, instability of the linker and heterogeneity of the product (i.e., broad distribution of DARs) often negatively impacts ADC efficacy and therapeutic window, which often leads to difficulty or limitation in the optimization of clinical application and eventual failure in clinical trials, see p. 42-43.
Regarding claim 49, the specification does not teach one or more non-natural amino acid residues at position in the heavy or light chain at positions such as HC404, HC121, HC180, LC22, LC7, LC42, LC152, HC136, HC25, HC40, HC119, HC190, HC222, HC19, HC52, HC70, HC110, or HC221, numbering according to the EU, Kabat or Chothia scheme, or a post-translationally modified variant thereof.
Regarding one or more non-natural amino acid at the specified sites in the heavy or light chain (claim 50), the specification exemplifies just p-azido-L-phenylalanine (pAzF) or para-azido methyl phenylalanine (pAzMeF).
Wang et al (Chemistry & Biology 16: 323-336, March 27, 2009; PTO 892) teach incorporating various unnatural amino acids in E coli are encouraging, it remained a challenge to incorporate various unnatural amino acids in mammalian cells with high efficiency and fidelity, see page 328, left col. Wang et al further teach incorporating unnatural amino acid into protein, i.e., TNF-a leads to a strong immune response directed at the unnatural mutant in mice, even in the absence of adjuvant, see page 333, left col. Thus, the prior art does not support an antibody having multiple non-natural amino acid residues at various sites in the heavy or light chain.
Regarding any non-natural amino acid residue at any optimally substitutable positions of any polypeptide chain of any antibody (claim 46), other than the particular site 295, 296, 297, 120, 375 or 400 from heavy chain of IgG1 antibody, the specification does not describe different non-natural amino acid residue at any location in the heavy and/or light chains of all antibody such as IgA, IgA2, IgD, IgE, IgG, IgG1, IgG2, IgG3 and IgM. Thus, the application at best describes a roadmap for producing various combinations of non-natural amino acid residue at any optimally substitutable positions and then determining which actually function as claimed.
Regarding heavy chain from γ, α, δ, ε and μ (claim 51), the specification discloses the position on the heavy chain is from just IgG1 (aka γ). However, the specification does not disclose the heavy chain site 295, 296, 297, 120, 375 or 400 are from the heavy chain of IgA, IgD, IgE or IgM.
Regarding antibody is of class or subclass from IgA, IgA2, IgD, IgE, IgG, IgG1, IgG2, IgG3 and IgM (claim 53), the specification discloses heavy chain site 295, 296, 297 from Trastuzumab of IgG1 isotype. The specification does not describe the heavy chain site 295, 296, 297, 120, 375 or 400 are from the heavy chain of IgA, IgA2, IgD, IgE, IgM, given these heavy chains are different from IgG1 heavy chain.
Regarding the form of Fv, Fc, Fab, (Fab')2, single chain Fv (scFv) in claim 54, the one or more non-naturally occurring sequences such as LGR are located at heavy chain site 295, 296, 297, 375 and/or 400, which these sites are located in the Fc of IgG1 antibody. Neither the art nor the specification teaches Fv, Fab, (Fab')2, or single chain Fv (scFv) comprises Fc. As such, it is not clear how Fv, Fab, (Fab')2, or single chain Fv (scFv) having one or more non-naturally occurring sequences such as LQG is at heavy chain site 295, 296, 297, 375 and/or 400. Likewise, Fc does not comprise antigen binding region. As such, it is not clear how an Fc can have one or more non-naturally occurring sequences such as LQG at heavy chain site 120, which is located in the antigen binding fragment. Thus, one of skill in the art would conclude that the specification fails to provide adequate written description to demonstrate that Applicant was in possession of the claimed genus. See Eli Lilly, 119 F. 3d 1559, 43, USPQ2d 1398.
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).
For a claim to a genus, a generic statement that defines a genus of substances by only their functional activity does not provide an adequate written description of the genus. Reagents of the University of California v. Eli Lilly, 43 USPQ2d 1398 (CAFC 1997). The recitation of a functional property alone, which must be shared by the members of the genus, is merely descriptive of what the members of the genus must be capable of doing, not of the substance and structure of the members. The Federal Circuit has cautioned that, for claims reciting a genus of antibodies with particular functional properties (e.g., high affinity, neutralization activity, competing with a reference antibody for binding), "[claiming antibodies with specific properties, e.g., an antibody that binds to human TNF-a with A2 specificity, can result in a claim that does not meet written description even if the human TNF-a protein is disclosed because antibodies with those properties have not been adequately described." Centocor Ortho Biotech Inc. v. Abbott Labs., 97 USPQ2d 1870, 1875, 1877-78 (Fed. Cir. 2011).
"[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." Ariad, 598 F.3d at 1350 (quoting Eli Lilly, 119 F.3d at 1568-69). A "representative number of species" means that those species that are adequately described are representative of the entire genus. AbbVie Deutschland GMBH v. Janssen Biotech, 111 USPQ2d 1780,1790 (Fed. Cir. 2014) ("The '128 and '485 patents, however, only describe species of structurally similar antibodies that were derived from Joe-9. Although the number of the described species appears high quantitatively, the described species are all of the similar type and do not qualitatively represent other types of antibodies encompassed by the genus."). Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus to provide a "representative number" of species.
The "structural features common to the members of the genus" needed for one of skill in the art to 'visualize or recognize' the members of the genus takes into account the state of the art at the time of the invention. For antibodies, the Federal Circuit has found that possession of a mouse antibody heavy and light chain variable regions provides a structural "stepping stone" to the corresponding chimeric antibody, but not to human antibodies. Centocor, 97 USPQ2d at 1875 ("[T]he application only provides amino acid sequence information (a molecular description of the antibody) for a single mouse variable region, i.e., the variable region that the mouse A2 antibody and the chimeric antibody have in common. However, the mouse variable region sequence does not serve as a stepping stone to identifying a human variable region within the scope of the claims."). A chimeric antibody shares the full heavy and light chain variable regions with the corresponding mouse antibody; that is, the structure shared between a mouse and chimeric antibody would generally be expected to conserve the antigen binding activity.
Lastly, possession may not be shown by screening assays. Ariad, 94 USPQ2d at 1167; Centocor at 1876 ("The fact that a fully-human antibody could be made does not suffice to show that the inventors of the '775 patent possessed such an antibody.")
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).
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).
Vas-Cath Inc. v. Mahurkar, 19 USPQ2d 1111, makes clear that “applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the ‘written description’ inquiry, whatever is now claimed.” (see page 1117). The specification does not “clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed.” (see Vas-Cath at page 1116).
Adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method for isolating it. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (CAFC 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016.
One cannot describe what one has not conceived. See Fiddles v. Baird, 30 USPQ2d 1481, 1483. In Fiddles v. Baird, claims directed to mammalian FGF’s were found unpatentable due to lack of written description for the broad class. The specification provided only the bovine sequence.
Therefore, only (1) an IgG1 antibody wherein the heavy chain (HC) comprising one or more non-naturally occurring leucine (L) - glutamine (Q) - arginine (R) or LQR sequences positioning the Q of the LQR sequence at one or more positions selected from the group consisting of 295, 296, 297, 122, 374 and 399, wherein the position is numbering according to EU scheme, or a sequence GGSX1LQGPP (SEQ ID NO: 4) or GGSLX2QGPP (SEQ ID NO: 7) appending at the C-terminus of at least one light chain or one heavy chain, wherein X1 is an amino acid selected from the group consisting of G, A, I, M, P, W, Y, S, T, N, Q, H, K, R, D, and E, wherein X2 is an amino acid selected from the group consisting of I, F, T, Q, H, R or E, and wherein the IgG1 antibody is trastuzumab, (2) the IgG1 antibody above wherein at least one of said LQR sequence comprises a para-azidomethylphenylalanine, but not the full breadth of the claims meets the written description provision of 35 U.S.C. § 112, first paragraph.
Applicant is reminded that Vas-Cath makes clear that the written description provision of 35 U.S.C. § 112 is severable from its enablement provision (see page 1115).
Claims 1-8, 41-54 and 63 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 (1) an IgG1 antibody wherein the heavy chain (HC) comprising one or more non-naturally occurring leucine (L) - glutamine (Q) - arginine (R) or LQR sequences positioning the Q of the LQR sequence at one or more positions selected from the group consisting of 295, 296, 297, 122, 374 and 399, wherein the position is numbering according to EU scheme, or a sequence GGSX1LQGPP (SEQ ID NO: 4) or GGSLX2QGPP (SEQ ID NO: 7) appending at the C-terminus of at least one light chain or one heavy chain, wherein X1 is an amino acid selected from the group consisting of G, A, I, M, P, W, Y, S, T, N, Q, H, K, R, D, and E, wherein X2 is an amino acid selected from the group consisting of I, F, T, Q, H, R or E, and wherein the IgG1 antibody is trastuzumab, (2) the IgG1 antibody above wherein at least one of said LQR sequence comprises a para-azidomethylphenylalanine, does not reasonably provide enablement for any antibody as set forth in claims 1-8, 41-54 and 63. 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.
The factors considered when determining if the disclosure satisfies the enablement requirement and whether any necessary experimentation is undue include, but are not limited to: 1) nature of the invention, 2) state of the prior art, 3) relative skill of those in the art, 4) level of predictability in the art, 5) existence of working examples, 6) breadth of claims, 7) amount of direction or guidance by the inventor, and 8) quantity of experimentation needed to make or use the invention. In re wands, 858 F.2d 731, 737.8 USPQ2d 1400, 1404 (Fed. Cir. 1988).
Enablement is not commensurate in scope with claims as how to make and use any antibody above for treating disease.
Claim 1 encompasses any antibody comprising one or more non-naturally occurring sequences of amino acids having:
the sequence leucine (L) - glutamine (Q) - arginine (R), wherein the Q residue of one, or up to all, of the non-naturally occurring sequences is at heavy chain site 295, 296, 297, 120, 375, or 400, when the heavy chain is numbered according to the Kabat or EU numbering scheme; or,
alternatively, having:
the sequence X1 - leucine (L) - glutamine (Q) - glycine (G),
wherein X1 is an amino acid selected from the group consisting of glycine (G), alanine (A), isoleucine (I), methionine (M), proline (P), tryptophan (W), tyrosine (Y)), serine (S), threonine (T), asparagine (N), glutamine (Q), histidine (H), lysine (K), arginine (R), aspartate (D), and glutamate (E), or
leucine (L) - X2- glutamine (Q) - glycine (G), wherein X2 is an amino acid selected from the group consisting of isoleucine (I),phenylalanine (F), threonine (T), glutamine (Q), histidine (H), arginine (R), and glutamate (E),
wherein the non-naturally occurring amino acid sequence comprising X1-L-Q-G or L-X2- Q-G is at the C-terminus of an antibody light chain or an antibody heavy chain.
Claim 2 encompasses the antibody of claim 1 wherein the Q residue of one, up to all, of the non-naturally occurring sequences is capable of accepting a primary amine in a transglutaminase reaction.
Claim 3 encompasses the antibody of claim 1 comprising the sequence LQR at one or more of the following heavy chain sites, when the heavy chain is numbered according to the EU numbering scheme: a. 294-295-296
b. 295-296-297
c. 296-297-298
d. 119-120-121
e. 374-375-376; and
f. 399-400-401.
Claim 4 encompasses the antibody of claim 1 comprising sequences LQR at two, three, four, five, or six of the heavy chain sites.
Claim 5 encompasses the antibody of claim 1 comprising the amino acid sequence X1-L-Q- G or L-X2-Q-G at the C-terminus of one or both light chains.
Claim 6 encompasses the antibody of claim 1 comprising the amino acid sequence X1-L-Q- G or L-X2-Q-G at the C-terminus of one or both heavy chains.
Claim 7 encompasses the antibody of claim 1 comprising the amino acid sequence Xi-L-Q- G or L-X2-Q-G at the C-terminus of at least one heavy and at least one light chain.
Claim 8 encompasses the antibody of claim 5, comprising the amino acid sequence G-G-S- Xi-L-Q-G-P-P at the C-terminus of one or both light chains.
Claim 41 encompasses the antibody of claim 5, comprising the amino acid sequence G-G-S-L-X2-Q-G-P-P at the C-terminus of one or both light chains.
Claim 42 encompasses the antibody of claim 6, comprising the amino acid sequence G-G-S-X1-L-Q-G-P-P at the C-terminus of one or both heavy chains.
Claim 43 encompasses the antibody of claim 6, comprising the amino acid sequence G-G-S-L-X2-Q-G-P-P at the C-terminus of one or both heavy chains.
Claim 44 encompasses the antibody of claim 5, wherein X1 is an amino acid selected from the group comprising G, A, I, M, P, W, Y, S, T, N, Q, H, K, R, D, and E.
Claim 45 encompasses the antibody of claim 5, wherein X2 is an amino acid selected from the group comprising I, F, T, Q, H, R and E.
Claim 46 encompasses the antibody of claim 1, further comprising a non-natural amino acid residue at a specific site selected from the group consisting of optimally substitutable positions of any polypeptide chain of said antibody.
Claim 47 encompasses the antibody of claim 1, further comprising two or more site-specific non-natural amino acid residues.
Claim 48 encompasses the antibody of claim 1, further comprising two to six non-natural amino acid residues.
Claim 49 encompasses the antibody of claim 1, further comprising one or more site-specific non-natural amino acid residues at sequence positions corresponding to residues selected from the group consisting of consisting of heavy chain or light chain residues HC404, HC121, HC180, LC22, LC7, LC42, LC152, HC136, HC25, HC40, HC119, HC190, HC222, HC19, HC52, HC70, HC110, or HC221 according to the EU, Kabat or Chothia numbering scheme, or a post-translationally modified variant thereof.
Claim 50 encompasses the antibody of claim 49, wherein at least one of said non- natural amino acid residues is a para-azidophenylalanine or para-azidomethylphenylalanine residue.
Claim 51 encompasses the antibody of claim 1 comprising a heavy chain of a type selected from the group consisting of γ, α, δ, ε and μ.
Claim 52 encompasses the antibody of claim 1 comprising a light chain of a type selected from λ and κ.
Claim 53 encompasses the antibody claim 1 that is of a class or subclass selected from the group consisting of IgA, IgA2, IgD, IgE, IgG, IgG1,IgG2, IgG3 and IgM.
Claim 54 encompasses the antibody of claim 1 that is in a form selected from the group consisting of Fv, Fc, Fab, (Fab')2, single chain Fv (scFv) and full-length antibody.
Claim 63 encompasses a composition comprising the antibody or antibody conjugate of claim 1, wherein said antibody or antibody conjugate is at least 95% by mass of the total antibody or antibody conjugate mass of said composition.
The specification discloses:
Example 1: Identifying Modified Antibodies for Optimal Stability and Conjugation
[0309] In this example, several IgG1 HC LQR variants were developed and tested as transglutaminase conjugation substrates with higher conjugation efficiency than parent antibody molecule.
[0310] First, the crystal structure of IgG (PDB 1HZH) was analyzed to select beneficial positions for LQR insertion. The positions were selected in flexible loops with exposed residues in constant regions of the heavy chain and light chain. The loops between constant domains CH.sub.2 and CH.sub.3 were avoided because mutations at these sites might affect antibody properties.
[0311] Second, the IgG HC-Q295 was mutated to A to avoid parent IgG Q conjugation. LQR variants were constructed for Trastuzumab Light Chain and αFolR1_1848-B10_Hc_Q295A heavy chain and subcloned into a pUG expression vector.
[0312] The LQR mutants were synthesized using cell-free technology by co-expressing αFolR1_1848-B10_Hc_Q295A and Trastuzumab LC. The parent and mutant antibody molecules were purified and reacted with TAMRA-cadaverine, which was catalyzed by ZsmTG, a transglutaminase of Streptomyces mobrensis (Zedria GmbH). These IgG variants were also catalyzed by shTG, a transglutaminase of Streptomyces hydroscopicus produced recombinantly in house. The final conjugation efficiency of IgG variants were analyzed by SDS-PAGE and quantified by fluorescence intensity. The normalized fluorescence intensity catalyzed by ZsmTG and shTG at 10 U/ml and 1 U/ml respectively are shown in FIG. 1 (heavy chains) and FIG. 2 (light chains).
[0313] Six HC sites showed appreciable Gln conjugation activity, while all LC sites were inactive. Three LQR variants (HC-E294LQR, A295LQR & Y296LQR) are clustered around the native Q295 conjugation site. The HC-E295LQR sequence has higher fluorescence intensity than the native HC sequence. Three other locations showed activity as TGase substrates include HC-S122LQR, HC-P374LQR, and HC-D399LQR. These mutants are promising candidate molecules for conjugation.
Example 2: Simultaneous Transglutaminase and Click Conjugation
[0314] This example demonstrates transglutaminase conjugation at mutant LQR sequences.
[0315] Dual conjugation of the transglutaminase (TGase) active primary amine-linker-TLR 7/8 agonist dru