DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 82-101 are pending and under examination.
Priority
Claims 82-93 have been assigned the priority date of August 21, 2023, the filing date of the present application.
Applicant argues that support for this claim language, the '974 application teaches that limited substitutions within individual CDRs, and combinations thereof across multiple CDRs, are contemplated, and expressly discloses embodiments in which no more than two amino acid changes are introduced within the CDRs:
In some embodiments, one or more amino acid modifications are made in one or more of the CDRs of the TIGIT antibodies of the invention. In general, only l.. or 2 or 3-amino acids are substituted in any single CDR, and generally no more than from 1, 2 3. 4, 5, 6, 7, 8, 9 or 10 changes are made within a set of CDRs. However, it should be appreciated that any combination of no substitutions, 1, 2 or 3 substitutions in any CDR can be independently and optionally combined with any other substitution. (See, the '974 application at paragraph [00137],
Applicant argues that the '974 application recognizes that while minor sequence variations may be introduced into vh and vl CDRs 1-2 while generally preserving TIGIT binding, CDR3-particularly vhCDR3-is the principal determinant of antibody identity and specificity. the '974 application notes:
Clones were deemed sequence-unique if there were more than one non-conservative differences in heavy chain CDR3. (The '974 application at paragraph [00209]).
Applicant argues that this statement is critical because it articulates the inventor's recognition that vhCDR3 is the defining feature of antibody identity and binding specificity, and that limited sequence variation outside vhCDR3 does not give rise to a distinct antibody species. Applicant argues that by treating antibodies as sequence-unique only when vhCDR3 differs by more than one non-conservative substitution,
the '974 application confirms that variants sharing the same vhCDR3-despite minor
substitutions in vh/vl CDRs 1-2-were understood and possessed by the inventors as functional variants of the same antibody. Applicant argues that this disclosure directly supports the claim element fixing CDR3 while allowing limited substitutions in CDRs 1-2.
Applicant further argues that the prior-filed '974 application discloses anti-TIGIT antibodies with minor CDR sequence variation such as single CDR substitution in up to 2 of vh/vlCDRs 1-2. Applicant argues that it expressly teaches that such limited amino acid substitutions may be introduced without compromising TIGIT binding, while identifying vhCDR3 as determinative of antibody identity and binding specificity. Applicant argues that consistent with this teaching, the '974 application treats antibodies as sequence-unique when vhCDR3 differs by more than one non-conservative substitution. Applicant argues that the presently claimed scope aligned with this disclosed structural framework by fixing vh/vlCDR3 sequences while permitting only tightly constrained substitutions in vh/vlCDRs 1-2.
Applicant’s arguments have been considered but are not persuasive. As Applicant acknowledges, the limitation “wherein the CDRs comprise from 0 to 2 substitutions and wherein no individual CDR comprises more than 1 substitution, and wherein the vhCDR3 and vlCDR3 comprise no substitutions” is not recited in the priority documents or the specification as filed. MPEP 2163.07 recites by which an amendments to the Application are supported in the original description. These include rephrasing or obvious errors. It appears as if Applicant is arguing that the limitation “wherein the CDRs comprise from 0 to 2 substitutions and wherein no individual CDR comprises more than 1 substitution, and wherein the vhCDR3 and vlCDR3 comprise no substitutions” is merely a rephrasing of several paragraphs that are recited in the Application. However, none of the paragraphs are disclosing making substitutions to only the vhCDR1 and/or vhCDR2 without any substitutions within the vhCDR3. In fact one of the phrases “In general, only 1.. or 2 or 3-amino acids are substituted in any single CDR, and generally no more than from 1, 2 3. 4, 5, 6, 7, 8, 9 or 10 changes are made within a set of CDRs” would appear to support making substitutions within the vhCDR3 as well as vhCDR1 and vhCDR2.
Furthermore, the term “anti-TIGIT antigen-binding domains comprising a variable heavy domain comprising vhCDR1, vhCDR2, and vhCDR3 from SEQ ID NO:160; and a variable light domain comprising vlCDR1, vlCDR2, and vlCDR3 from SEQ ID NO:165, wherein the CDRs comprise from 0 to 2 substitutions and wherein no individual CDR comprises more than 1 substitution” is not a rephrasing of the phrase “Clones were deemed sequence-unique if there were more than one non-conservative differences in heavy chain CDR3”.
Objections to claims withdrawn
The objections to the claims are withdrawn in view of Applicant’s amendments to claims 94-97.
Objections to drawings maintained
The drawings are objected to for having SEQ ID NOs: for amino acid sequences less than 4 amino acids. The sequences of SEQ ID Nos: 157 and 167 on pages 69 and 70 are three amino acids.
Objections to Specification maintained
The objections to the specification are maintained. The priority date for the present claims remains August 21, 2023, the filing date of the present application
35 USC § 112(a) rejections
The rejection of claims 82-101 for failing to comply with the written description requirement are maintained.
Applicant argues that the claimed antibodies are structurally bounded to a
defined antibody lineage sharing an identical vh/vlCDR3 sequence, with only narrowly defined substitutions permitted in vh/vl CDRs 1-2-that is, no more than two single CDR substitutions in total for claims 82-93, and only a single substitution across all four vh/vl CDRs1-2 per claims 94-101. Applicant argues that the specification expressly recognizes vhCDR3 as determinative of antibody identity and demonstrates that limited variation within vh/vl CDRs 1-2 can be accommodated while preserving TIGIT binding. Applicant argues that the claimed subject matter is not a broad functional genus untethered to structure, but rather a structurally defined set of variants within a disclosed antibody lineage. Applicant argues that these conserved structural features provide identifying characteristics common to the claimed genus which are sufficient to demonstrate possession under MPEP § 2163.
Applicant further argues that regarding CDR3 that remains unchanged in the claimed TIGIT antibodies, the specification expressly recognizes the determinative role of heavy chain CDR3 in defining antibody identity. As stated in paragraph [00569], antibody clones were deemed sequence-unique and primarily defined by their heavy chain CDR3. Applicant argues that this disclosure reflects the inventors' recognition that CDR3-particularly vhCDR3- serves as a defining structural feature central to antibody species. Applicant argues that by fixing vh/vl CDR3 in the claims, the recited antibodies retain the core structural feature that the specification identifies as determinative of identity and functionality of the antibody clone. Applicant argues that the combination of the largely conserved vh/vl CDRl-2 sequences with unchanged CDR3 sequences constitutes sufficient structural identifying characteristics to demonstrate possession of the claimed genus.
In addition, Applicant argues that with respect to vh/vl CDRs 1-2, which are defined in the claims to at most a single substitution per CDR, the application discloses numerous representative CDR variants exhibiting varying degrees of substitution relative to the parent CDRs of CP A.9.086, whose sequences are recited in the claims. The sequences and alignments of these representative variants are provided
in Exhibits A-D submitted herewith. As shown in the Exhibits, substitutions (highlighted therein) may be introduced across the majority of residues within vh/vl CDRs 1-2 without abolishing TIGIT binding of the corresponding antibody. Indeed, with very limited exceptions, residues across vh/vl CDRs 1-2 are shown to tolerate substitution either individually or in combination with other substitutions. These sequences and alignments thereof demonstrate that the recited single-substitution framework represents a subset of structurally disclosed and functionally validated variants. Applicant argues that a substantial number of the disclosed variants in the Exhibits contain multiple substitutions within CDRs 1-2 and nonetheless retain TIGIT binding, thereby exhibiting greater sequence divergence from the parent CDRs of CPA.9.086 than is permitted under the present claims. Applicant argues that even these more divergent variants retain binding and as such, there is no reasonable basis to surmise that the recited antibody variants cannot tolerate no more than one substitution
in any of vh/vl CDRs 1-2. Applicant argues that the presently claimed antibodies-allowing no more than one substitution per CDR and no more than two substitutions in total-are consistent with retained TIGIT binding.
Applicant’s arguments have been considered but are not persuasive. As an initial note it appears as if several of the clones listed in Exhibits A-D were not present in the priority documents and thus would not be available to demonstrate possession for the present claims. Possession must be demonstrated at the time of the effective filing date of the application. Thus, Exhibits A-D could not be used to demonstrate adequate written description for the genus of anti-TIGIT antibodies that is required to practice the claimed invention.
As previously discussed, Paul states that the amino acid sequences and conformations of each of the heavy and light chain CDRs are critical in maintaining the antigen binding specificity and affinity, which is characteristic of the immunoglobulin. It is expected that all of the heavy and light chain CDRs in their proper order and in the context of framework sequences which maintain their required conformation, are required in order to produce a protein having antigen-binding function and that proper association of heavy and light chain variable regions is required in order to form functional antigen binding sites. The exhibits submitted by Applicant demonstrate that particular substitutions may be made but doesn’t demonstrate that any amino acid may be substituted within any vh/vl CDRs 1-2 with any of the 19 other amino acids. It appears that the amino acid substitutions shown in Exhibits A-D are limited with only 1 or 2 amino acids substituted for a particular position. Furthermore, it appears as if in many cases there is not just one amino acid change when comparing the various CDRs, suggesting that the different amino acid changes may be coordinated. Exhibit D shows that three amino acids were specifically substituted but does not indicate whether one or two amino acids may be substitutes with any of the other 19 amino acids. As Paul states a functional binding site requires the correct conformation of the different CDRs.
The claims are drawn to anti-TIGIT antibodies wherein the CDRs comprise from 0 to 2 substitutions and wherein no individual CDR comprises more than 1 substitution, and wherein the vhCDR3 and vlCDR3 comprise no substitutions. The claims encompass a huge number of possible vh/vl CDRs 1-2 sequences. Given that the vh/vl CDRs 1-2 comprise approximately 22 amino acids and that each position may be substituted by one of 19 amino acids the number of potential species within the genus would be an incredibly large number of sequences. Applicant has only demonstrated a small fraction of the genus of anti-TIGIT antibodies encompassed by the claims are capable of binding TIGIT. Based on the information in the specification one of ordinary skill in the art would not be able to discern which of the very large number of potential species within the genus would be capable of binding TIGIT. The specification does not give one the ability to know which of the amino acids within HCDR1, HCDR2, LCDR1 or LCDR2 may be substituted with any of the 19 other amino acids and be capable of binding TIGIT. The specification and exhibits only disclose a small number of antibodies that fall within the genus of claimed antibodies in which the CDRs comprise from 0 to 2 substitutions and no individual CDR comprises more than 1 substitution and wherein the vhCDR3 and vlCDR3 comprise no substitutions. There are only a couple of examples in the specification and exhibits in which only one amino acid substitution in one or two of HCDR1, HCDR2, LCDR1 or LCDR2 resulted in binding to TIGIT. From the Exhibits it appears that in many cases there are at least two amino acid substitutions in HCDR1, HCDR2, LCDR1 or LCDR2 for the different anti-TIGIT antibody clones. Thus, from the Exhibits it’s not clear the effect of making just one or two amino acid substitutions to HCDR1, HCDR2, LCDR1 or LCDR2 retain binding to TIGIT. The specification does not disclose sufficient information to be able to determine which amino acids in a particular CDR may be substituted by which of one of the other 19 amino acids and retain the capability of binding TIGIT. Thus, the specification does not provide an adequate written description of the genus of anti-TIGIT antibodies that is required to practice the claimed invention.
Applicant also argues that independent studies corroborate that limited substitutions within vh/vl CDRl-2 are generally tolerated without loss of antigen-binding specificity. For example, in Koenig et al. an amino acid substitution was introduced to each amino acid residue in the variable domains for various proteins. See, Koenig at Page E487. Koenig shows that across almost all the amino acid residues in the Fab region, mutations in vh/vlCDRs 1-2 consistently retain binding ability comparable to their non-mutated counterparts. See, Koenig, Figure 1 for binding data on anti-gD and anti-VEGF antibodies, and Figures S 1 and S2 on anti-gD antibody, protein A, and protein L, as well as the section entitled "High Tolerance to Single Mutations in vl and vh for Stable Fab Assembly" describing the results and which is located on page E488 of Koenig.
In addition, Applicant has submitted two more references - Xu et al.
and Gorski et al. that further show the significant role of CDR3 relative to the other CD Rs in mediating antigen-antibody interactions. Xu examines the function of CDRs in a number of haptens and protein antigens and suggests vhCDR3 to be the dominant determinant of binding specificity, whereas all the other CDRs appear to have little impact on antigen recognition and binding affinity. See, Xu, Summary section.
Consistently, Gorski confirms that CDR3 is the sole determinant for fine specificity of
TCR binding to its ligand, stating "[t]he CDR3 is the sole fine specificity-determining ion of normal TCR, as any TCR composed of the same V and J gene is identical elsewhere." Applicant argues that one of skill in the art viewing the references above would recognize that the tolerability of substitutions in vh/vl CD Rs 1-2 is not unique to any particular antibody, but is a phenomenon observed across a broad range of antibodies.
Applicant argues that the teachings of Koenig, Xu, and Gorski support the conclusion that limited substitutions within vh/vl CDRs 1-2 are structurally and functionally tolerable. Applicant argues that this general principle of tolerability is consistent with the alignments of the disclosed CDR variants in Exhibits A-D, which demonstrate that substitutions across the majority of residues within vh/vl CDRs 1-2 can be introduced without abolishing TIGIT binding. Applicant argues that the experimentally validated anti-TIGIT variants disclosed in the instant application therefore corroborate the literature-based structure-function relationship and establish the requisite correlation between structure and function. Together with the structurally conserved vh/vl CDR3 sequences and the largely intact vh/vl CDR1-2 sequences permitting no more than two substitutions (claims 82-93) or a single substation ( claims 94-101 ), the specification provides sufficient structural identifying characteristics common to the claimed genus to demonstrate possession under MPEP § 2163.
Applicant argues that written description does not require that every conceivable variant retain identical functional properties. Rather, it requires disclosure of sufficient identifying characteristics demonstrating possession of the claimed subject matter. Applicant argues that as discussed above, the specification provides adequate identifying features of the relevant CDR sequences together with experimentally validated variants and a demonstrated correlation between structure and retained
TIGIT binding.
Applicant’s arguments have been considered but are not persuasive. ... As an initial note, Koenig was published after the claimed filing date of the present invention. The specification and art that supports the written description requirement for the examined claims must be prior to the effective filing date of the application.
In addition, while it is generally believed that VH/VL CDRs 1-2 play a less decisive role in antibody-antigen binding, and consequently exhibit higher tolerance of single amino acid substitutions than VH CDR3, amino acid substitutions to CDRs 1-2 have been shown to affect binding as pointed out in Cassette and Holm. Koenig involves the determination of variable domain mutations in one anti-VEGF antibody (G6.31) which result in either enhanced or reduced binding. ... Koenig discloses that an amino acid at position 83, a framework residue affected binding more than any other position (page e487, 2nd column). Koenig does disclose that that a few CDR positions (e.g., R94, P100, D101 in the CDRH3) exhibited low tolerance to mutation, suggesting their role in overall stability. ... In response to Applicant’s argument that the vast majority of positions appear to be tolerant to either the full range of mutations or a set of conserved mutations, because mutations at these sites do not exhibit overt depletion, Koenig was discussing mutations within the heavy and light variable domains, not just the CDRs. ... Again, as previously discussed, Koenig was analyzing the mutational characteristics of one specific antibody.
In addition it is not clear the relevance of Gorski, that concerns the importance of the CDR3 of T cell receptors. The art recognizes that, in general, alpha and beta chains comprising six distinct CDR sequences are required to create the TCR peptide-MHC binding site (Janeway et al., Immunobiology, 5th Ed., Garland Science, pages 106-108, 117-118 and 260-263, (2001)). In particular, the art teaches there is a bias where the TCR CDR3s are predominately involved in peptide binding, and the TCR CDR1 and CDR2 regions are predominately involved in MHC binding, although it should be noted that this bias is not absolute (Janeway et al., pages 118 and 263; Manning et al., Immunity, 1998, 8:413-425, specifically page 423, see conclusions). Thus, it is not clear the relevance of Gorski to Applicant’s argument that the vh/vl CDR1-2 sequences of an antibody are of little relevance in the binding of an antibody to its epitope.
It is also not clear the relevance of Xu to Applicant’s argument that the vh/vl CDR1-2 sequences of an antibody are of little relevance in the binding of an antibody to its epitope. Xu disclose that to characterize the antibody responses of an organism with a very limited V region repertoire but full CDR3 diversity, we utilize a previously described trans- gene, HC1, which contains one functional human VH gene segment (VH5–51). Xu found that CDR3 of the VH domain, is sufficient to permit otherwise identical IgM molecules to distinguish between a variety of hapten and protein antigens. Thus, Xu was examining a limited antibody repertoire.
However, even with these caveats for Koenig, Gorski and Xu, as previously discussed, it is generally understood that HCDR3 is more critical for antibody binding than HCDR1 or HCDR2. However, the art does not disclose that HCDR1 or HCDR2 are irrelevant for antibody binding to its epitope. Based on Exhibits A-D it was difficult to determine which amino acids of HCDR1 or HCDR2 could be substituted by one of the other 19 amino acids and retain the binding to TIGIT. From the Exhibits it appears that in many cases there are at least two amino acid substitutions in HCDR1, HCDR2, LCDR1 or LCDR2 for the different anti-TIGIT antibody clones. Thus, from the Exhibits it’s not clear the effect of making just one or two amino acid substitutions to HCDR1, HCDR2, LCDR1 or LCDR2 retain binding to TIGIT. Are two amino acid substitutions in one of HCDR1, HCDR2, LCDR1 or LCDR2 required to retain binding to TIGIT.
In response to Applicant’s argument the specification provides sufficient structural identifying characteristics common to the claimed genus to demonstrate possession under MPEP § 2163, it is not clear that the specification of Exhibits provide sufficient structural identifying characteristics common to the claimed genus to demonstrate possession. There are only a couple of examples in which only one amino acid substitution in one or two of HCDR1, HCDR2, LCDR1 or LCDR2 resulted in binding to TIGIT. The claimed antibodies are defined by function the ability to bind TIGIT. It is not clear what structural identifying characteristics common to the claimed genus to demonstrate possession. One of ordinary skill in the art would not have any way to know which of the numerous species within the claimed genus of anti-TIGIT antibodies would be still capable of binding TIGIT. It is not clear what characteristics could be used to be able to identify those species in the genus which are capable of binding TIGIT.
Applicant further argues that Paul does not address the tolerability of
limited substitutions within vh/vl CDRs 1-2, nor does it evaluate antibodies retaining identical CDR3 sequences with narrowly defined substitutions in CDRs 1-2. Applciant argues that Rudikoff concerns a naturally occurring phosphocholine-binding myeloma protein, rather than engineered antibodies, and reports the functional consequences of a somatic mutation in that specific wild-type protein context. Applicant argues that such wild-type antibodies evolved under physiological constraints in complex natural environments, where evolutionary pressures often favor structural stability and may limit mutational flexibility, resulting in trade-offs between affinity enhancement and structural destabilization. Applicant states the Examiner cites Colman for the proposition that even conservative substitutions may abolish binding or have unpredictable effects. Applicant argues that this characterization overlooks Colman's distinction between substitutions in antigens and substitutions in antibodies. Colman explains that amino acid substitutions in antigens may abolish binding, whereas substitutions within antibody variable domains may increase affinity or otherwise be accommodated. Applicant argues that Colman does not establish that limited substitutions within vh/vl CDRs 1-2 of engineered antibodies necessarily disrupt binding. Applicant argues that Colman is consistent with the principle that minor structural variations can be tolerated within an appropriate structural context. Applicant argues that Colman does not undermine the structure-function correlation demonstrated in the present specification. Applicant states that Holm addresses an isolated structural scenario rather than establishing a general rule that limited substitutions within vh/vl CD Rs 1-2 disrupt antigen binding. Applicant argues that Holm is consistent with the broader understanding that minor structural
variations in CDRl-2 may be tolerated within appropriate structural contexts.
As such, the specification and the supporting literature establish a demonstrated
correlation between structure and function for the claimed antibodies. Applicant argues that one of skill in the art viewing these results together with the teachings of the above references would recognize the recited vh/vl CDRs 1-2, within a defined antibody lineage sharing identical vh/vl CDR3, to be tolerant of amino acid substitutions in preserving binding. Applicant argues that these structural features are common
to the claimed genus and correlated with retained function. Applicant argues that these disclosures constitute sufficient identifying characteristics to demonstrate possession under MPEP § 2163.
Applicant’s arguments have been considered but are not persuasive. There is agreement in the broader understanding that minor structural variations in CDR1-2 may be tolerated within appropriate structural contexts. The issue is whether one of skill in the art would agree that the specification discloses sufficient evidence that Applicant was in possession of anti-TIGIT antigen-binding domain comprising a variable heavy domain comprising vhCDR1, vhCDR2, and vhCDR3 from SEQ ID NO:160; and a variable light domain comprising vlCDR1, vlCDR2, and vlCDR3 from SEQ ID NO:165;
wherein the CDRs comprise from 0 to 2 substitutions and wherein no individual CDR comprises more than 1 substitution, and wherein the vhCDR3 and vlCDR3 comprise no substitutions. The specification only discloses a few examples of anti-TIGIT antibodies in which there is only one substitution in HCDR1, HCDR2, LCDR1 or LCDR2. The issue is not whether single amino acid substitutions in HCDR1, HCDR2, LCDR1 and LCDR2 may be made in the anti-TIGIT antibody and maintained binding to TIGIT. The issue is whether Applicant could identify the species or know the characteristics of anti-TIGIT antibodies having one or two substitutions of any one of the other 19 amino acids in HCDR1, HCDR2, LCDR1 or LCDR2 and maintain binding to TIGIT. Based only on the specification one of ordinary skill in the art would not be able to identify which of the many possible species within the claimed genus would still be capable of binding TIGIT.
It is not clear what structural features are common to the claimed genus and correlated with retained function. Unless one knows which amino acids HCDR1, HCDR2, LCDR1 and LCDR2 may be substituted by which amino acids and maintain binding to TIGIT one would not be able to identify the genus of anti-TIGIT antigen-binding domains comprising a variable heavy domain comprising vhCDR1, vhCDR2, and vhCDR3 from SEQ ID NO:160; and a variable light domain comprising vlCDR1, vlCDR2, and vlCDR3 from SEQ ID NO:165, wherein the CDRs comprise from 0 to 2 substitutions and wherein no individual CDR comprises more than 1 substitution.
102(a1) rejections maintained.
The rejections of claims 82-93 under 35 U.S.C. 102(a)(1) as being anticipated by White et al (US 2018/0305456, published October 25, 2018) are maintained.
Claim 88 is drawn to a composition comprising an anti-TIGIT antigen-binding domain, wherein the anti-TIGIT antigen-binding domain binds to human TIGIT (SEQ ID NO:97), wherein the anti-TIGIT antigen-binding domain comprises: a. a variable heavy domain comprising vhCDR1, vhCDR2, and vhCDR3 from SEQ IDNO:150; and
b. a variable light domain comprising vlCDR1, vlCDR2, and vlCDR3 from SEQ ID NO:155; wherein the CDRs comprising from 0 to 4 substitutions.
White discloses anti-TIGIT antibodies comprising a VH comprising SEQ ID NO: 160 and a VL comprising SEQ ID NO: 165 and anti-TIGIT antibodies comprising a VH comprising SEQ ID NO: 150 and a VL comprising SEQ ID NO: 155 (Figure 53), which are identical to the claimed anti-TIGIT antibodies. White further disclose antibodies comprising a heavy chain comprising VH-CH1-hinge-CH2-CH3, wherein said VH comprises SEQ ID NO: 160 and a light chain comprising VL-VC. (paragraph 15). White discloses that the sequence of the CH1-hingeCH2- CH3 is selected from human IgG1, IgG2 and IgG4, and variants thereof (paragraph 16). White discloses that the antibodies of the invention can be modified to alter the amino acid sequences by amino acid substitutions (paragraphs 195, 207-210, 273).
Applicant argues that because the claimed subject matter is entitled to the earlier priority date, White does not qualify as valid art under 35 U.S.C. § 102(a)(l) with respect to claims 82-93.
In response, as discussed previously, the priority date for the present claims remains August 21, 2023, the filing date of the present application.
Double Patenting rejections maintained
The rejections of claims 82-87 and 94-97 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-22 of U.S. Patent No. 10.751,415 are maintained.
The rejections of claim 82-87 and 94-97 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 4-11 and 16, 87 and 91 of copending Application No. 16/428,856 are maintained.
Applicant has requested that the nonstatutory double patenting rejections be held in abeyance until there is an indication of allowable subject matter.
In response, the rejections are maintained.
Summary
Claims 82-101 stand rejected
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