DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Priority- Foreign
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(a)-(d) and (f) or under 35 U.S.C. 120, 121, 365(a) or (b), or 386(a) is acknowledged. The present application is drawn from PCT/EP2021/087618, filed 12/23/2021; and claims benefit under 35 U.S.C. (119(a)-(d) to foreign applications EP20216957.9, filed 12/23/2020, EP21154786.4, filed 2/2/2021, and PCT/EP2021/064427, filed 5/28/2021.
Acknowledgment is made of applicant's claim for foreign priority based on an application filed in Europe on 2/2/2021. It is noted, however, that applicant has not filed a certified copy of the EP21154786.4 application as required by 37 CFR 1.55.
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55 for PCT/EP2021/087618, EP20216957.9 and PCT/EP2021/064427, which were filed on 6/22/2023.
Election/Restrictions
Applicant’s election without traverse of Group I, encompassing claims 1-11 and 16, in the reply filed on 5/26/2026 is acknowledged. Claims 12-15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected Group II, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 5/26/2026. Applicants did not indicate a traversal in the response; therefore it is assumed that election was made without traverse.
Applicant’s election of species of the HFRs 1-4 and LFRs 1-4, the CDR sequences of the antibody species, and the tri-specific antibody embodiment, in the response of 5/26/2026, are acknowledged.
Status of Claims
Claims 1-16 are pending; claims 12-15 are withdrawn; claims 1-11 and 16 are being examined on the merits.
Claim Objections
Claim 4 is objected to for reciting “Tables 1, 2 and 4” in the claim. MPEP 2173.05(s) states:
“Where possible, claims are to be complete in themselves. Incorporation by reference to a specific figure or table ‘is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience.’ Ex parte Fressola, 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993) (citations omitted).”
In the instant case the corresponding FR regions, which are identical across many of the recited sequences, could easily be incorporated into the claims to define the invention. For example, claim 4 could be amended to recite that the antibody comprises the FRs 1-4 of SEQ ID NO: 3 resides 1-25, 37-50, 69-99 and 112-122, respectively. Alternatively, applicants could put the individual FR sequences, comprising the substituted residues, in the sequence listing and recite the appropriate SEQ ID NOs accordingly in the claim. Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
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.
Claims 1-3, 5-9 and 16 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 the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 recites wherein the HFW1-4 are selected from a “VH framework subtype” wherein the regions have one of the following substitutions (AHo numbering), an arginine (R) at amino acid position 12. It is unclear what constitutes “a VH framework subtype” beyond that of SEQ ID NOs: 114-115 and 120-122, as described in the specifications (pg. 25, para. 0054). That is, as numerous VH framework subtypes are presented in the art, it is unclear what the metes and bounds of the claim limitations are. Are any VH framework subtypes not encompassed, do they need to be human VH framework subtypes? Further, AHo numbering is listed in paratheses, whereby it is presumed that the sequences are meant to be defined by that numbering scheme. However, the examples of Tables 1-2 and 4 clearly specify the residue being substituted in the VH is the 11th residue. This contradicts the claim, which specifies the 12th residue. Thus, the combination of uncertainty regarding which VH framework subtypes are encompassed and which residue of those selected subtypes is to be substituted with an arginine creates uncertainty as to the metes and bounds of the claim limitations; thus claim 1 is rendered indefinite. The skilled artisan should not have to take sequences that are provided and translate them into an alternative numbering scheme in order to understand which residues the claim limitations are drawn to. This does not meet the definition of “particularly pointing out and distinctly claiming the subject matter.” When appropriate, the applicant should define the sequences for use in the invention in the sequence listing, recite the appropriate sequences in the claims, and specify the specific residue, of the recited sequences, that are subject to manipulation. Any “translation” of a particular reside number across various alternative numbering schemes should be done by the applicant, such that the appropriate residue is clearly identified in the sequences of the claim(s). Claim 1 is rejected for indefiniteness; claims 2-3, 5-9 and 16 depend from claim 1, but fail to rectify the issue of indefiniteness, thus they are also rejected.
Regarding claims 2-3, 5 and 8-9, the phrase "particular", “particularly” or “more particularly” renders the claims indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Regarding claim 4, the phrase "i.e." renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d). As described above the claims should not recite references to Tables or Figures in the specifications. It is unclear if the claims require the non-italicized residues or the framework regions, by definition in the art, of the recited SEQ ID NOs.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
Claims 1-9 and 16 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 1 recites an antibody variable domain, which specifically binds to a target antigen, comprising the heavy chain framework regions 1-4 (HFR1-4), which are selected from “a VH framework subtype”, wherein, following AHo numbering, there is a substitution of an arginine (R) at position 12 and/or a glutamine (Q) at position 144, with or without a threonine (T) substitution at position 103. Thus claim 1 encompasses a genus of variant antibody heavy chain FRs 1-4, whereby any combination of FRs 1-4 derived from any VH framework subtype may be used, and wherein the frameworks comprise a 12R substitution. MPEP Section 2163 states that the written description for a claimed genus may be satisfied through either a) a representative number of species, or b) disclosed correlation between function and structure.
Applicants describe the VHs, comprising the substitutions, of various antibody species in Tables 1, 2 and 4, as well as some alternate antibody species of Tables 6-8. However, the listed embodiments of Tables 1, 2 and 4 primarily utilizes FRs derived from the VH framework subtype VH3; specifically, every embodiment uses the HFR1 of VH framework subtype VH3. Knappik et al., (WO 97/08320; published 3/6/1997) describes 7 VH subtype consensus sequences, including VH1a, VH1b, VH2, VH3, VH4, VH5 and VH6; whereby each subtype is distinguished based on alternative amino acid sequences of their respective FRs 1-4 (see Fig. 2C, pg. 231). Thus, claim 1 encompasses mixing and matching FRs 1-4 selected from any of the 7 VH subtypes, such that ~2400 different combinations of FRs 1-4 are encompassed. Further, claim 1 encompasses, for example, a 12R substitution in any of the combinations, such that a 12R substitution is universally accepted across any conceived embodiment.
Regarding the state of the art; it is known in the art that the antigen binding domain of an antibody requires the 6 complementarity determining regions (CDR) of the heavy and light chains, whereby the 3 CDRs of the heavy chain and the 3 CDRs of the light chain are structurally inter-dependent in forming the unique binding pocket of the antibody paratope region; and thus the CDRs constitute critical aspects of the antibody paratope and ultimately impart the paratope-epitope binding functionality with regard to specificity and affinity (for review see MacCallum et al., 1996). However, the structure-to-function correlation continues to be highly unpredictable. For example, Chen et al., (1992) teaches that a single amino acid substitution in the VH CDR2 of PC-specific T15 antibody could increase, decrease or ablate binding the target antigen (abstract, Fig. 3), and this occurred in an unpredictable manner based on which residue was mutated. Similarly, a single point mutation in the heavy chain CDR3 region of the high affinity anti-VEGF antibody G6.31, could in some cases enhance, or otherwise completely ablate binding to the target antigen, and this also occurred in an unpredictable manner (Koenig et al., PNAS, 2017). That is, only screening each mutation individually provided insight as to the resulting changes in functionality. In some cases this extends even beyond the CDRs. Within the framework regions, Koenig et al. (PNAS, 2017) teaches that various amino acid point mutations can increase or decrease binding or neutralization capacity. Some amino acid residues are more tolerant to substitution, while other “conserved” residues are less tolerant, such that a single amino acid substitution may defunctionalize the antibody (pg. E487, Fig. 1). Thus, while antibodies share certain characteristics such as Fc regions or hinge regions, these regions are not correlated with the binding function of the antibody. Conversely, the hyper-variable regions, comprising the complementary set of 6 CDRs, are well established in the art as the portion of the binding regions which impart the specificity of the antibody; and yet, there is no way to look at an amino acid sequence and envision, a priori, whether the combination of six CDRs will bind a particular epitope, even when the CDRs are highly related, without teachings of the basic shared amino acid residues that are sufficient to impart functional binding across all variants. Further, even when provided with several related antibodies that bind the desired target, this does not represent the astronomical and potentially unknowable breadth of all possible amino acid sequences which will result in the desired binding properties. This is exemplified by the Court decision in Abbvie (Abbvie v Janssen 759 F.3d 1285 (Fed. Cir. 2014)), where Abbvie developed over 200 antibodies that shared 99.5% identity in the variable regions (pg. 7) and which bound the target, but in no way allowed one to envisage the unique structure of Centocor’s antibodies which bound the same target but shared only 50% sequence similarity (see table on pg. 11). Thus, when claiming a genus of antibodies based on their binding to a common target, the representative examples must cover the full scope of structural variabilities which encompass all species variants that would bind the target.
Regarding MPEP 2163, applicants claiming a genus of species must disclose either a) a representative number of species, or b) disclosed correlation between function and structure. In the instant examples, applicants disclose a 12R substitution in the HFR1 of the VH subtype VH3, whereby most, if not all, of the embodiments also use the FRs 2-4 of the VH subtype VH3. Thus, applicants do not disclose a representative number of species to accommodate the mixing and matching of any of FRs 1-4 of any of the 7 different VH subtypes, nor is it disclosed that a 12R substitution is tolerated across the ~2400 different combinations of FRs 1-4 as claimed. Thus, applicants have not satisfied the disclosure of a representative number of species, as the instant application doesn’t describe a 12R substitution in any other HFR1 beyond that of the VH3 subtype.
Regarding the structure-to-function relationship, the 7 different consensus VH framework subtypes described by Knappik et al., while having some shared residues, are structurally distinct, thus owing to their classifications across 7 distinct subtypes. Further, Knappik teaches an analysis of each subgroup sequences to determine which residues are conserved, and thus more likely to be resistant to mutation, versus the residues that are variant, and thus more likely to tolerate mutation. Knappik teaches the factor “rel. oomcaa” which shows the “relative occurrence of the most common amino acid”, whereby if the rel. oomcaa is higher it is a conserved residue of the consensus sequence, and if the rel. oomcaa is lower it is a residue that is variant across sequences, and would be more likely to tolerate mutation. As described above, the examples of the specifications predominantly utilize the subtype VH3 for HFRs 1-4. Knappik teaches that the “12” residue (residue 11 when not re-numbered by AHo), is an L, and has a rel. oomcaa of 68% (Fig. 6D, pg. 165). Thus, the L12R mutation that is described across the embodiments of instant Tables 1, 2 and 4, has a higher likelihood of tolerating mutation. However, the corresponding residue in the VH4 subtype, which is also an L, has a rel. oomcaa of 100% (Fig. 6E, pg. 174); which suggests that the VH4 subtype is less likely to tolerate a mutation at the L12 residue. Subtype VH5 has a V at the corresponding position, and has a rel. oomcaa of 96%; thus it has a different base reside being substituted and is less likely to tolerate mutation. Similarly, each of subtypes VH1a and VH1b have a V at the corresponding residue, with a 95% and 100% rel. oomcaa, respectively (pgs. 144, 151). Knappik discloses that the FRs 1-4 of the 7 VH framework subtypes have distinct amino acid sequences in Fig. 2C (pg. 231). The different VH framework subtypes have distinct sequence structure, several HFR1s do not even have a L at the corresponding position, and the applicants only show embodiments comprising an L12R substitution of HFR1 of the VH3 subtype. Similarly, regarding the 103T substitution, which is a V103T substitution of the HFR3 of the VH3 subtype, not all subtypes have even a V at the corresponding position (residue position 89 of Knappik Fig. 2C); subtype VH5 has an M at the corresponding position. Further, subtype VH6 has a V, but a rel. oomcaa of 95%, suggesting it is less likely to tolerate mutation. Taken together, the different VH framework subtypes have distinct structures, whereby the proposed residue for substitution is highly conserved in some VH framework subtypes and therefore less likely to tolerate mutation, and the specifications do not teach embodiments of alternative VH framework subtypes (beyond VH3) that tolerate the specified substitutions. Therefore, there is not a sufficient structure-to-function correlation disclosed across the genus of VH framework subtypes of claim 1. Instead, it may be that a 12R substitution in an alternate VH framework subtype FR1 domain will lead to aggregation of the antibody, enhanced immunogenicity, or interfere with the requirement that the antibody variant “specifically binds to a target antigen.”
In view of this uncertainty and the lack of a representative number of examples of the claimed genus, claim 1 is rejected for lack of adequate written description support. Claims 2-3 and 5-9 depend from claim 1 but fail to rectify the lack of descriptive support, thus claims 2-3, 5-9 and 16 are also rejected. Claims 4 and 10-11 limit the substitutions to the specified HFRs 1-4, in the specified combinations, of the representative examples.
Claim 4 recites utilizing the FRs 1-4 of any of the listed SEQ ID NOs, whereby the FRs may have 1, 2 or 3 mutations within the FR at positions different from 12, 103 and 144. Thus the claim encompasses millions of variant FRs whereby any one of 20 amino acids may be substituted across any three residues of the FRs, and whereby any combination of 3 residues may be selected from, for example the VH of SEQ ID NO: 3, which has 81 residues across FRs 1-4. No guidance is provided, beyond the embodiments of sequences of claim 4, as to where the substitutions may occur or with which amino acid. As described above, Koenig et al. (2017) teaches that framework residues also contribute to the proper function of the antibody, whereby mutating a critical residue of a FR domain can defunctionalize the antibody, such that it no longer binds its target antigen. As claim 4 encompasses a vast number of variants comprising up to 3 unidentified mutations, and the specifications provide no more than a few specific examples of substitutions in FR subtypes, beyond the 12, 103 and 144 residues, there is a lack of both a representative number of examples and a structure-to-function relationship. Thus, claim 4 is also rejected for lack of adequate descriptive support.
Claim Rejections - 35 USC § 112
Claim 11 is rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of antibody variable domains is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons:
The antibody variable domains of claim 11 are alternative chemical compounds as a whole. It is known in the art that the amino acid residues that define the structure of the complementarity determining regions (CDR) of an antibody, or antibody variable domain, are critical to the functional specificity and affinity of the antibody for the target antigen, such that the 3 CDRs of the heavy chain and the 3 CDRs of the light chain form the antigen-binding domain of the antibody paratope, where critical contacts with the antigen epitope occur during binding (for review see MacCallum et al., 1996). The CDRs of the VH and VL sequences that define an antibody that binds to CD137 are structurally distinct from the CDRs of the VH and VL that define an antibody that binds to PDL1, or alternatively HSA. Regarding the “single structural similarity” of a proper Markush grouping, the alternatives must share a substantial structural feature from which the common use flows. Here the common use of an anti-CD137 antibody is distinct from the common use of a PDL1 antibody or an HSA antibody, whereby the common use it their specificity to the target antigen. Thus, the single structural similarity must be the CDRs; and the CDRs of the antibody variable domains of anti-CD137 antibodies are distinctly different than those of anti-PDL1 antibodies and anti-HSA antibodies. As the FRs, of claim 1, do not define the specificity of the antibody variable domains, the FRs do not provide a substantial structural feature from which the common use flows. Therefore the alternative antibody variable domains, which distinctly function to bind either CD137, PDL1 or HSA are not functional equivalents, and do not comprise a proper Markush Grouping.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-3, 5-7 and 16 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 5-6, 8-10, 13 and 19 of copending Application No. 18/863208 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the scope of the claims of application ‘208 anticipates that of the instant claims. Specifically, app ‘208 claims mutated heavy chain framework regions which comprise a R substitution at residue 12.
Application ‘208 claims a method for generating modified antibody variable domains which exhibit decreased binding to anti-drug antibodies wherein the heavy chain framework regions comprise a substitution at positions 101, 146 and 148 (claims 1 and 6) or the antibody itself (claims 8-10), wherein the light chain framework regions LFR 1-3 are selected from a human kappa FR and wherein LFR4 is selected from a lambda FR and wherein the LFR4 may be SEQ ID NO: 188 (claim 2), and wherein the antibody additionally comprises an arginine (R) substitution at position 12 (claim 5). whereby the antibody comprises one or more variable domains and wherein the variable domains comprise scFvs (claim 13); as well as nucleic acids, vectors, host cells, methods of making the antibody and pharmaceutical compositions (claims 15-19).
The light chain LFR4 of app ‘208 SEQ ID NO: 188 is 100% identical to that of instant SEQ ID NO: 123, of instant claim 5. Therefore, the embodiments of app ‘208, comprising an HFR1 R12 substitution (e.g. SEQ ID NO: 34, of the specs) and the VL FRs 1-4 (e.g. SEQ ID NO: 184), of the methods of claims 1-2 and 5-6, or the antibody itself of claims 8-11, anticipate that of instant claims 1-3 and 5. The antibody comprising more than one variable domain of app. ‘208 claim 13 anticipates that of instant claims 6-7. The pharmaceutical composition of app. ‘208 claim 19 anticipates that of instant claim 16.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Allowable Subject Matter
Claim 10 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims. Specifically, the VH of SEQ ID NOs: 3-4, 8-9, 13-14, 19-20, 25-26 and 31-32 have been searched and are free of the art when used in a trispecific antibody format. Thus wherein claim 10 requires that at least one VH is selected from c) or d), the trispecific antibody would comprise a novel VH binding domain.
Conclusion
No claims are allowed. Claims 1-9, 11 and 16 are rejected, claim 10 is objected to.
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/JAMES RYLAND MELCHIOR/Examiner, Art Unit 1644
/NELSON B MOSELEY II/Primary Examiner, Art Unit 1642
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