DETAILED ACTION
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 12/8/2025 has been entered.
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 .
Status of Claims
Applicant’s amendments and remarks, filed on December 8, 2025, are acknowledged.
Claims 1-2, 6 and 8 are currently amended.
Claims 10-19 are canceled.
Claims 1-9 and 20-25 are pending and under consideration.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 12/12/25 is acknowledged. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Specification
The disclosure is objected to because there are reference at the end of the specification. Reference should be placed on an Information Disclosure Statement form to be considered by the Examiner.
The use of the terms OPDIVO®, KEYTRUDA®, TGX™, and InstantBlue™, which are trade names or marks used in commerce, have been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Appropriate correction is required.
Claim Objections
Claim 3 is objected to because of the following informalities: full names of amino acids, such as glycine and serine, should not be capitalized unless they begin a sentence. Appropriate correction is required.
Withdrawn Rejections
The rejection of claim 6 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, as set forth at pg.3 of the previous Office action (mailed on September 5, 2025), is withdrawn in view of the amended claims (received on December 8, 2025).
The rejection of claims 1, 3-9, and 20-25 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, as set forth at pg.5-6 of the previous Office action (mailed on September 5, 2025), is withdrawn in view of the amended claim (received on December 8, 2025). The Examiner acknowledges Claim 1 has been amended to limit the scope of the Fc domain to “IgG Fc domain”.
The rejection of claims 1, 2, 6, 7, 9, 21, and 23-25 under 35 U.S.C. 103 as being unpatentable over Carreno et al. (US 7,029,674 B2; issued 18 April 2006) in view of Novarra et al. (2016, MABS 8(6):1118-1125), is withdrawn in view of the amended claims and applicant’s argument (received on December 8, 2025).
The rejection of claims 3 and 22 under 35 U.S.C. 103 as being unpatentable over Carreno et al in view of Novarra et al and Seehra et al. (U.S. Publication No. 2019/0345225), is withdrawn in view of the amended claims and applicant’s argument (received on December 8, 2025).
The rejection of claims 1, 4 and 5 under 35 U.S.C. 103 as being unpatentable over Carreno et al, in view of Novarra et al and Ma et al (U.S. Publication No. 2018/0162939) is withdrawn in view of the amended claims and applicant’s argument (received on December 8, 2025).
The rejection of claim 20 under 35 U.S.C. 103 as being unpatentable over Carreno et al is withdrawn in view of Novarra et al and Mason et al (2001, Protein Expression and Purification 23:142-150), as set force at pg. 6-12 of the previous Office action (mailed December 9, 2025).
New Rejections Necessitated by Applicant’s Amendments
Claim Rejections - 35 USC § 112
Written Description
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.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
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 1-9 and 20-25 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.
The MPEP states that the purpose of the written description requirement is to ensure that the inventor had possession, as of the filing date of the application, of the specific subject matter later claimed. The MPEP lists factors that can be used to determine if sufficient evidence of possession has been furnished in the disclosure of the application. These include “level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention.”
The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, disclosure of drawings, or by disclosure of relevant identifying characteristics, for example, structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the Applicant was in possession of the claimed genus.
In making a determination of whether the application complies with the written description requirement of 35 U.S.C. 112(a), it is necessary to understand what Applicant are claiming and what Applicant have possession of.
The claims are drawn to a fusion protein comprising: an extracellular domain of a mammalian Programmed Cell Death-1 (PD-1) protein, wherein the extracellular domain binds a mammalian PD-L1 protein; and a Fc domain, wherein the Fc domain does not comprise a hinge region, wherein the Fc domain comprises complete CH2 and CH3 domains, wherein the Fc domain is an IgG Fc domain.
Regarding the extracellular domain (ECD) of a mammalian PD-1 protein wherein the ECD binds a mammalian PD-L1 protein, although the claims are inclusive of a few variations of an ECD of a human PD-1 protein as set forth in Claims 6, 8 and 24 (residues 21-170, 21-145, 22-170, 33-145, 35-170 and 35-145 of SEQ ID NO 1, SEQ ID NO 12, and SEQ ID NOs 14&15 whose ECD of PD-1 is 100% identical to SEQ ID 12), the claims also broadly encompass the ECD of other mammalian PD-1 proteins, and any amino acid sequence that shares at least 90% identity with the amino acid sequences examples set forth in the claims. This would represent a large pool of variant polypeptides that must have similar function activity. First, the exact structures/sequences of the ECD of mammalian PD-1 are variable. PD-1 has relatively low conservation across vertebrates (Masubuchi et al, Sci Immunol. 2025 Jan 3;10(103):eads6295). For instance, the human PD-1 and mouse PD-1 share only 64% amino acid sequence identity in the ECD (Zak et al., 2015, Structure 23, 2341–2348. pg. 2342 right col. 2nd para, Fig. S1 legend). Even for human PD-1, the exact structures and sequences of ECD are different based on different literature. For instance, UniProt defines residues 25-170 of human PD-1 (Q15116) as extracellular domain, while Zak et al uses residues 20-155 (Fig. S1 and legend). Second, the sequence variance adds on significantly to the pool of polypeptides. A variance of 10%, for example, in the polypeptide set forth in residues 21-170 of SEQ ID NO:1, which is about 150 amino acids in length, translate into 15 residues that may be added, deleted, substituted, or otherwise mutated along the entire length of the 150 amino acid sequence, as long as the polypeptide can still bind with a mammalian PD-L1 protein. There is no limit in the claims, as written, that the variance be contiguous. Moreover, the specification provides limited guidance regarding which amino acids can be modified in the genus of the ECD of PD-1 protein, while maintaining the claimed function. Therefore, these structures (i.e., sequence variants) are claimed only be their functional characteristics and the specification fails to provide sufficient correlation between the claimed functional characteristics and the necessary structural components (i.e., critical domains or residues within the sequences).
Regarding the Fc domain of the fusion protein, wherein the Fc domain does not comprise a hinge region, wherein the Fc domain comprises complete CH2 and CH3 domains, wherein the Fc domain is an IgG Fc domain, although the claims are inclusive of two sequences as set forth in Claims 7 and 8 (SEQ ID NOs 6 & 28, and SEQ ID NOs 14&15 whose Fc domain sequences are identical to SEQ ID NO 6), the claims also broadly encompass unlimited variations of the structures of the IgG Fc domain. The specification states the term lgG "hinge" region refers to a polypeptide comprising an amino acid sequence that shares sequence identity, or similarity, with a portion of a naturally- occurring lg hinge region sequence, which includes the cysteine residues at which the disulfide bonds link the two heavy chains of the immunoglobulin (inst. specs para. 141). Based on the definition, there could be many variations of the naturally-occurring Ig hinge, as long as it has the cysteine residues to form the disulfide bonds that link the two heavy chains of the immunoglobin together. The length of the naturally-occurring hinge region could be as short as a few residues (such as the core hinge region), to as long as any regions of the Fc domain that is defined as hinge, which could be more than 60 residues in a IgG3 Fc domain. Because the “hinge” region in the claims are any polypeptide that shares sequence identify or similarity with the naturally-occurring hinge region, there could be unlimited structure variations, such as residues added, removed, mutated or substituted to the naturally-occurring hinge region.
The specification fails to define what comprises a complete CH2 and CH3 region. In the state of the art, the exact first residue of CH2 domains is unclear (e.g. in IgG1, whether residues 231-239 are part of the hinge or part of the CH2 domain are unclear). For instance, Rayner et al (JBC, 2015, vol. 290 NO. 13 pp 8420-8438) teaches the hinge is best considered as a three-part structure: upper, middle and lower hinge, and the human IgGH1 hinge is composed of 23 residues (EPKSCDKTHTCPPCPAPELLGGP) between Val215 and Ser239 (pg.8420 right col. 2nd para, also see Fig. 1 legend). Hui et al (J Biol Chem. 2019 May 14;294(28):10789–10806.) teaches the hinge region of human IgG2 is composed of 19 residues (ERKCCVECPPCPAPPVAGP) between Val219-Ser239 (Fig.1 legend). Van der Horst (Immunological Reviews. 2024;328:456–465) teaches that the lower hinge region includes leu234-Ser239 (section 3.1). Morgan et al (Immunology. 1995 86 319-324) teaches residues 231-238 are N-terminal region of the human IgG1 CH2 domain. In the human IgG1 (IGHG1) sequence records on NCBI and UniProt (P01857.2), the CH2 domain starts at residue P115, corresponding to the P232 position in the literatures cited above. Therefore, there could be many variations of the structures/sequences that comprises complete CH2 and CH3 domains. In addition, as stated above, sequence variance adds on significantly to the large pool of polypeptides. A variance of 10%, for example, in the polypeptide set forth in SEQ ID NO:6, which is 214 amino acids in length, translate into about 21 residues that may be added, deleted, substituted, or otherwise mutated along the entire length of the amino acid sequence. Moreover, the specification provides limited guidance regarding which amino acids can be modified.
The specification does not provide adequate written description to identify the broad and variable genus of the fusion protein because, inter alia, the specification does not disclose a correlation between the necessary structure of the protein and the function(s) recited in the claims. A definition by function does not suffice to define the genus because it is only an indication of what the protein does, rather than what it is; therefore, it is only a definition of a useful result rather than a definition of what achieves that result. In addition, because the genus of fusion proteins is highly variable, the generic description of the fusion protein is insufficient to describe the genus. Further, given the highly diverse nature of proteins, even one of skill in the art cannot envision the structure of the fusion protein by knowing a partial structure and its functional characteristics. Thus, the specification does not provide substantive evidence for possession of this large and variable genus, encompassing a potentially massive number of the fusion proteins claimed only by a functional characteristic and/or partial structure.
Furthermore, Applicant has not shown procession of a representative number of species that have the claimed function(s). The specification has written description for the examples: regarding ECD of PD-1 protein, residues 21-170, 21-145, 33-170, 33-145, 35-170 and 35-145 of SEQ ID NO 1, SEQ ID NO 12, and SEQ ID NOs 14 and 15 (both 14 and 15 have the extracellular domain sequence 100% identical to SEQ ID NO 12); regarding IgG Fc domain, seq ID NOs: 6 and 28, and SEQ ID NOs: 14 and 15 (both 14 and 15 have the Fc domain sequence 100% identical to SEQ ID NO 6).
However, as noted above, the claims are not limited to these exemplary fusion protein components, and encompass any extracellular domain that any ECD of a mammalian PD-1 domain that binds a mammalian PD-L1 and any Fc domain of an IgG that does not have the core hinge region but have a complete CH2 and CH3 domain. Thus the genus has substantial variation because of the numerous alternatives and combinations permitted. There is no description of the structure common to the members of the genus such that one of skill in the art can visualize or recognize the members of the genus. Therefore, only a few species have been described and this is not considered to be representative of the breadth of the genus. Given the lack of structure function correlation and the lack of a representative number of species, the specification provides insufficient written description to support the genus encompassed by the claim.
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.)
The skilled artisan cannot envision the detailed chemical structure of the encompassed molecules in the fusion protein as claimed. 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. The nucleic acid and/or protein itself is required. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (CAFC 1993) and Amgen Inc. V. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016. In Fiddes v. Baird, 30 USPQ2d 1481, 1483, 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.
University of California v. Eli Lilly and Co., 43 USPQ2d 1398, 1404. 1405 held that:
...To fulfill the written description requirement, a patent specification must describe an invention and does so in sufficient detail that one skilled in the art can clearly conclude that "the inventor invented the claimed invention." Lockwood v. American Airlines Inc. , 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (1997); In re Gosteli , 872 F.2d 1008, 1012, 10 USPQ2d 1614, 1618 (Fed. Cir. 1989) (" [T]he description must clearly allow persons of ordinary skill in the art to recognize that [the inventor] invented what is claimed."). Thus, an applicant complies with the written description requirement "by describing the invention, with all its claimed limitations, not that which makes it obvious," and by using "such descriptive means as words, structures, figures, diagrams, formulas, etc., that set forth the claimed invention." Lockwood, 107 F.3d at 1572, 41 USPQ2datl966.
Protein chemistry is probably one of the most unpredictable areas of biotechnology. Consequently, the effects of sequence dissimilarities upon protein structure and function cannot be predicted. Punta et al (PLoS Comput Biol 4(10): e1000160, 2008) teaches that homology (both orthology and paralogy) does not guarantee conservation of function. Relatively small difference in sequence can sometimes cause quite radical changes in functional properties, such as a change of enzymatic action, or even loss or acquisition of enzymatic activity itself (pg. 2). It is also apparent that there is no sequence similarity threshold that guarantees that two proteins share the same function (pg. 2). Punta et al. also teaches that homology between two proteins does not guarantee that they have the same function, not even when sequence similarity is very high (including 100% sequence identity) (pg. 2, tab. 2). Proteins live and function in 3D, and therefore structural information is very helpful for predicating function (pg. 4). However, as with sequence, two proteins having the same overall architecture, and even conserved functional residues, can have unrelated functions (pg. 4). Punta et al teaches that still structural knowledge is an extremely powerful tool for computational function prediction (pg. 5).
Similarly, Whisstock et al (Quarterly Reviews in Biophysics. 36(3):307-340, August 2003) teaches that the prediction of protein function from sequence and structure is a difficult problem (abs.). Although many families of proteins contain homologues with the same function, homologous proteins often have different functions as the sequences progressively diverge (pg. 309). Moreover, even closely related proteins can change function, either through divergence to a related function or by recruitment for a very different function (pg. 309). Further, even sequences that are the same can have different functions. For example, eye lens proteins in the duck are identical in sequence to active lactate dehydrogenase and enolase in other tissues, although they do not encounter the substrates in the eye (pg. 310). Whisstock et al. teaches that assigning a function to an amino acid sequence based upon similarity becomes significantly more complex as the similarity between the sequence and a putative homologue fall (pg. 321). Whisstock et al. further teaches that while it is hopeful that similar proteins will share similar functions, substitution of a single, critically placed amino acid in an active-site may be sufficient to alter a protein’s role fundamentally (pg. 321-323).
The sensitivity of proteins to alterations of even a single amino acid in a sequence are exemplified by Burgess et al (J. Cell Biol. 111:2129-2138, 1990) who teaches that replacement of a single lysine reside at position 118 of acidic fibroblast growth factor by glutamic acid led to the substantial loss of heparin binding, receptor binding and biological activity of the protein and by Song et al (Molecular Biology of the Cell, 15:1287–1296, March 2004) who teach that substitution of alanine for aspartate in survivin results in the conversion of survivins’ apoptotic function from anti-apoptotic to proapoptotic and changes in its subcellular localization (pg. 1287-1289). Moreover, Defeo-Jones et al (Molecular and Cellular Biology, Sept. 1989, pg. 4083-4086) teaches that the conservative substitution of lysine for arginine at position 42 completely eliminated biological activity (abs., pg. 4084-4085). These references demonstrate that even a single amino acid substitution will often dramatically affect the biological activity and characteristics of a protein.
Additionally, Bork (Genome Research, 2000; 10:398-400) clearly teaches the pitfalls associated with comparative sequence analysis for predicting protein function because of the known error margins for high-throughput computational methods. Bork specifically teaches that computational sequence analysis is far from perfect, despite the fact that sequencing itself is highly automated and accurate (pg. 398 col. 1). One of the reasons for the inaccuracy is that the quality of data in public sequence databases is still insufficient. This is particularly true for data on protein function. Protein function is context dependent, and both molecular and cellular aspects have to be considered (pg. 398 col. 2). Conclusions from the comparison analysis are often stretched with regard to protein products (pg. 398 col. 3). Further, although gene annotation via sequence database searches is already a routine job, even here the error rate is considerable (pg. 399 col. 2). Most features predicted with an accuracy of greater than 70% are of structural nature and, at best, only indirectly imply a certain functionality (pg. 399 tab.1 legend). As more sequences are added and as errors accumulate and propagate it becomes more difficult to infer correct function from the many possibilities revealed by database search (pg. 399, col. 2 & 3). The reference finally cautions that although the current methods seem to capture important features and explain general trends, 30% of those features are missing or predicted wrongly. This has to be kept in mind when processing the results further (pg. 400, section Taking the 70% Hurdle).
Given not only the teachings of Punta et al, Whisstock et al, Song et al, Burgess et al, and Defeo-Jones et al, but also the limitations and pitfalls of using computational sequence analysis and the unknown effects of alternative splicing, post translational modification and cellular context on protein function as taught by Bork, the claimed proteins having the required function(s) could not be predicted based on sequence identity. Clearly, it could not be predicted that polypeptide or a variant that shares only partial homology with a disclosed protein or that is a fragment of a given SEQ ID NO. will function in a given manner. Therefore, the state of the art supports that even the skilled artisan requires guidance on the critical structures of the fusion protein per se and thereby does not provide adequate written description support for which structural features of any given polypeptide would predictably retain their functional activities.
Applicant is reminded that generally, in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus (Enzo Biochem, Inc. v. Gen- Probe Inc., 323 F.3d 956 (Fed. Cir. 2002); Noelle v. Lederman, 355 F.3d 1343 (Fed. Cir. 2004); Regents of the University of California v. Eli Lilly Co., 119 F.3d 1559 (Fed. Cir. 1997)). A patentee must disclose “a representative number of species within the scope of the genus of structural features common to the members of the genus so that one of skill in the art can visualize or recognize the member of the genus” (see Amgen Inc. v. Sanofi, 124 USPQ2d 1354 (Fed. Cir. 2017) at page 1358). 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).
MPEP § 2163.02 states, “[a]n objective standard for determining compliance with the written description requirement is, ‘does the description clearly allow person of ordinary skill in the art to recognize that he or she invented what is claimed’”. The courts have decided: the purpose of the “written description" requirement is broader than to merely explain how to "make and use"; the 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 Vas-Cath, Inc v. Mahurkar, 935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Federal Circuit, 1991).
Furthermore, the written description provision of 35 USC §112 is severable from its enablement provision; and 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. Fiers v. Revel, 25 USPQ2d 1601, 1606 (CAFC 1993). And Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016. Moreover, an adequate written description of the claimed invention must include sufficient description of at least a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics sufficient to show that Applicant was in possession of the claimed genus. However, factual evidence of an actual reduction to practice has not been disclosed by Applicant in the specification; nor has Applicant shown the invention was “ready for patenting” by disclosure of drawings or structural chemical formulas that show that the invention was complete; nor has the Applicant described distinguishing identifying characteristics sufficient to show that Applicant were in possession of the claimed invention at the time the application was filed.
Therefore, for all these reasons the specification lacks adequate written description, and one of skill in the art cannot reasonably conclude that Applicant had possession of the claimed invention at the time the instant application was filed.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary.
Claims 1, 2, 6, 7, 9, 21, 23 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Carreno et al (US 7,029,674 B2; issued 18 April 2006, referred to as Carreno thereafter) in view of Shiga et al (Mol. Pharmaceutics. 2017 Aug 1, 14: 3025-3035, referred to as Shiga thereafter).
Claim 1 is drawn to a fusion protein comprising: an extracellular domain of a mammalian Programmed Cell Death-1 (PD-1) protein, wherein the extracellular domain binds a mammalian PD-L1 protein; and a Fc domain, wherein the Fc domain does not comprise a hinge region, wherein the Fe domain comprises complete CH2 and CH3 domains, wherein the Fe domain is an IgG Fc domain.
Claim 2 is drawn to the fusion protein according to claim 1, wherein the IgG Fc domain is an IgG1 Fc domain or an IgG2A Fc domain.
Claim 6 is drawn to the fusion protein according to claim 1, wherein the amino acid sequence of the extracellular domain of PD-1 is selected from the group consisting of: (i) the amino acid sequence that shares at least 90% identity with the amino acid sequence consisting of residues 21 to 170 of SEQ ID NO:1; (ii) the amino acid sequence that shares at least 90% identity with the amino acid sequence consisting of residues 21 to 145 of SEQ ID NO:1; (iii) the amino acid sequence that shares at least 90% identity with the amino acid sequence consisting of residues 33 to 170 of SEQ ID NO:1; (iv) the amino acid sequence that shares at least 90% identity with the amino acid sequence consisting of residues 33 to 145 of SEQ ID NO:1; (v) the amino acid sequence that shares at least 90% identity with the amino acid sequence consisting of residues 35 to 170 of SEQ ID NO:1; and (vi) the amino acid sequence that shares at least 90% identity with the amino acid sequence consisting of residues 35 to 145 of SEQ ID NO:1. SEQ ID NO: 1 is the amino acid sequence of PD-1 (UniProt: Q15116) (inst. specs. para [0059]).
Claim 7 is drawn to the fusion protein according to claim 1, wherein the amino acid sequence of the Fc domain is selected from the group consisting of: (i) the amino acid sequence that shares at least 90% identity with the amino acid sequence set forth in SEQ ID NO: 6; and (ii) the amino acid sequence that shares at least 90% identity with the amino acid sequence set forth in SEQ ID NO: 28. SEQ ID NO: 6 is the amino acid sequence of Murine lgG1 containing CH2 and CH3 domains only, and SEQ ID NO: 28 is the amino acid sequence of Murine lgG2A containing CH2 and CH3 domains only (inst. specs. para [0064] & [86]).
Claim 9 is drawn to the fusion protein according to claim 1, wherein the PD-1 is recombinant PD-1.
Claims 21 is drawn to the fusion protein according to claim 1, wherein the Fc domain is from human or mouse immunoglobulin.
Claim 23 is drawn to the fusion protein according claim 1, wherein the fusion protein comprises from the N-terminal to the C-terminal peptide, an extracellular domain of the PD-1 protein, and a Fc domain.
Claim 25 is drawn to the fusion protein according to claim 9, wherein PD-1 is recombinant human PD-1.
Carreno teach a fusion protein comprising, from N-terminal to C-terminal, an extracellular domain of recombinant human PD-1 fused to a human IgG1 or murine IgG2A Fc domain (col. 78 ln. 8-12). This is relevant to claims 1, 2, 9, 21, 23, and 25. Carreno teaches the human PD-1 extracellular domain is about 147 amino acids (col. 27 ln. 19-30), which comprised amino acid sequence that shares at least 90% identity with the amino acid sequence consisting of residues 21-170 of SEQ ID NO:1 as cited in claim 6. The murine IgG2A Fc domains comprised amino acid sequence that are at least 90% identical to instant SEQ ID NOs: 28 in claim 7.
Carreno fails to teach the limitation that the IgG Fc domain lacks a hinge region but comprises complete CH2 and CH3 domains.
However, Shiga teaches that fusion proteins comprising Fc domains can potentially induce antibody-dependent and complement-dependent cytotoxicity and serious side effects, and the Fc hinge region is essential for engaging Fc receptors on immune cells and inducing complement-mediated cel lysis (abs.). Shiga engineered a fusion protein with the human IgG1 Fc domain without the hinge region (hLF-CH2-CH3) (pg. 3028 section Molecular Design and Production of the Hinge-Deficient hLF-Fc Protein, also see abs.). In Fig. 1, Shiga teaches the sequence of the fusion site: a linkage (DP) connects the therapeutic protein (hLF) to CH2-CH3 domain, which starts with residues APELL. The A residue is A114 of human IgG1 (UniProt P01857.2), which corresponds to the first residue of mouse IgG1 CH2 domain in SEQ ID Nos: 6, 14 and 15. Shiga further teaches the fusion protein without the Fc hinge region has superior properties than the recombination therapeutic protein, and does not elicit Fc-mediated effector response potentially damaging for the target cells (abs.). Finally, Shiga concludes conjugation of hinge-deficient Fc to therapeutic proteins is a promising strategy for improving their pharmacokinetic properties without enhancing effector functions (abs.).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the PD-1-Fc constructs of Carreno with the teaching of Shiga, to use a hingeless IgG Fc domain in the fusion protein because removing the hinge region of the Fc domain will improve the pharmacokinetic properties of the therapeutic protein without enhancing effector functions. One of ordinary skill in the art is motivated to do so because the hingeless Fc domains have desirable properties in the context of a fusion protein. One would have a reasonable expectation of success in making the combination because a therapeutic protein fused to a hingeless IgG Fc domain is well established practices in the art for improving the properties of the fusion protein.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that if a technique has been used to improve one method, and a person of ordinary skill would recognize that it would be used in similar methods in the same way, using the technique is obvious unless its application is beyond that person’s skill. It would be obvious to apply a known technique to a known product to be used in a known method that is ready for improvement to yield predictable results. Thus, the combination of prior art references as combined provided a prima facie case of obviousness, absent convincing evidence to the contrary.
Claims 3 and 22 are rejected under 35 U.S.C. 103 as being unpatentable over Carreno in view of Shiga as applied to claims 1, 2, 6, 7, 9, 21, 23 and 25 above, and further in view of Toporik et al (US 2014/0044641 A1, published Feb 13 2014).
Claim 3 is drawn to the fusion protein according to claim 1, wherein the extracellular domain of the PD-1 protein is fused to the Fc domain via one or more flex linkers comprising amino acids Glycine and Serine or via one or more flex pro linkers comprising amino acids Glycine, Proline, and Serine.
Claim 22 is drawn to the fusion protein according to claim 3, wherein the extracellular domain of the PD-1 protein is fused to the Fc domain via one or more peptide linkers comprising the amino acid sequence set forth in SEQ ID NO: 4 or SEQ ID NO: 5. SEQ ID NO:4 is the amino acid sequence of flexible Gly-Ser linker and SEQ ID NO: 5 is the amino acid sequence of flexible Gly-Pro-Ser linker (Flex Pro Linker) (inst. specs. para. [0062]&[0063]).
The teaching of Carreno and Shiga have been discussed previously.
Carreno and Shiga fail to teach the extracellular domain of PD-1 protein is fused to the Fc domain via one or more flex linkers or flex pro linkers (such as SEQ ID NOs:4&5) as cited in claims 3 and 22.
However, the use of flexible linkers to join extracellular domains of membrane –bound proteins to Fc domains was commonly known in the prior art. For example, Toporik teaches a fusion protein therapeutic protein extracellular domain and the IgG Fc domain (where the hinge region might or might not be present), are linked with flexible linker, such as GGGS (identical to instant SEQ ID NO:4) (para. 469-470, 495, 497). Use of a flexible linker provides increased rotational freedom for polypeptides linked compared with linked polypeptides without a flexible linker (para. 497). Such rotational freedom allows the polypeptides to access their binding sites more efficiently (para. 497).
It would have been prima facie obvious before the effective filing date of the claimed invention to modify the hingeless PD-1-Fc constructs taught by the combined teachings of Carreno and Shiga, and inserting a GGGS linker between the PD-1 and Fc domains as taught by Toporik et al because use of such linkers allows for flexibility of the fusion protein. The motivation to do so could have been found in the teachings of Toporik et al, who explains the use of such linkers allows for flexibility of the fusion protein and allow the polypeptides to access their binding sites more efficiently (para. 497). One would have a reasonable expectation of success in making the combination because using a flexible linker is well established practices in the art for improving the properties of the fusion protein.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that if a technique has been used to improve one method, and a person of ordinary skill would recognize that it would be used in similar methods in the same way, using the technique is obvious unless its application is beyond that person’s skill. It would be obvious to apply a known technique to a known product to be used in a known method that is ready for improvement to yield predictable results. Thus, the combination of prior art references as combined provided a prima facie case of obviousness, absent convincing evidence to the contrary.
Claims 4-5 are rejected under 35 U.S.C. 103 as being unpatentable over Carreno in view of Shiga as applied to claims 1, 2, 6, 7, 9, 21, 23 and 25 above, and further in view of Ma et al (US 2018/0162939 A1; effectively filed 29 July 2016).
Claim 4 is drawn to the fusion protein according to claim 1, further comprising a signal sequence, wherein the signal sequence is fused at the N-terminus of the extracellular domain of PD-1 protein.
Claim 5 is drawn to the fusion protein according to claim 4, wherein the signal sequence comprises the amino acid sequence set forth in SEQ ID NO: 3. SEQ ID NO: 3 is the amino acid sequence of Human IL2 signal peptide (inst. specs. para [0061]).
The teaching of Carreno and Shiga have been discussed previously.
Carreno and Shiga fail to teach a signal sequence (such as the one set forth in SEQ ID NO:3) fused at the N-terminus of the extracellular domain of PD-1 protein.
However, the inclusion of a signal sequence is known in the prior art. The codon-optimized human IL-2 signal sequence (identical to instant SEQ ID NO: 3) was particularly preferred. For instance, Ma et al discloses this signal peptide fused to heterologous sequences for highly efficient recombinant protein production (para. 0228 & 0360).
Therefore, It would have been prima facie obvious before the effective filing date of the claimed invention to modify the hingeless PD-1-Fc constructs taught by the combined teaching of Carreno and Shiga to include a signal sequence such as SEQ ID NO: 3 in view of Ma et al because IL-2 signal peptide is a strong signal peptide and doing so would provide a high efficiency of the protein secretion (para. 0368). The motivation to do so would have been known to the ordinary skilled artisan in this field regarding the ability of codon-optimized IL-2 signal sequence to improve yield of recombinantly made proteins, as acknowledged by Ma et al (para. 0360 & 0368). One would have a reasonable expectation of success in making the combination because using signal peptide is well established practices in the art for improving the properties of the fusion protein.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that if a technique has been used to improve one method, and a person of ordinary skill would recognize that it would be used in similar methods in the same way, using the technique is obvious unless its application is beyond that person’s skill. It would be obvious to apply a known technique to a known product to be used in a known method that is ready for improvement to yield predictable results. Thus, the combination of prior art references as combined provided a prima facie case of obviousness, absent convincing evidence to the contrary.
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Carreno in view of Shiga and as applied to claims 1, 2, 6, 7, 9, 21, 23 and 25 above, and further in view of Mason et al (Protein Expression and Purification 23:142-150. 2001).
Claim 20 is drawn to the fusion protein according to claim 1, further comprising a polyhistidine affinity tag.
The teaching of Carreno and Shiga have been discussed previously.
Carreno and Shiga fail to teach the fusion protein further comprising a polyhistidine affinity tag.
However, Mason et al. teaches that the polyhistidine affinity tag has long been used to greatly simplify the purification of a recombinantly made protein from the complex mix of proteins in the media or cell extract in which it is made (abs).
Therefore, It would have been prima facie obvious before the effective filing date of the claimed invention to modify the hingeless PD-1-Fc constructs taught by the combined teaching of Carreno and Shiga, to further including a polyhistidine affinity tag in view of Mason et al because doing so would greatly simplify the purification of a recombinantly made protein from the complex mix of proteins in the media or cell extract in which it is made (abs). The motivation to do so could have been found in the teachings of Mason et al., who explain that the use of such tags allows for easier and higher quality purification. One would have a reasonable expectation of success in making the combination because using a polyhistidine tag is well established practices in the art to help with purification of the fusion protein.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that if a technique has been used to improve one method, and a person of ordinary skill would recognize that it would be used in similar methods in the same way, using the technique is obvious unless its application is beyond that person’s skill. It would be obvious to apply a known technique to a known product to be used in a known method that is ready for improvement to yield predictable results. Thus, the combination of prior art references as combined provided a prima facie case of obviousness, absent convincing evidence to the contrary.
Claims 8 and 24 are rejected under 35 U.S.C. 103 as being unpatentable over Carreno in view of Shiga and Ma et al as applied to claims 1, 2, 4-6, 7, 9, 21, 23 and 25 above, and further in view of Lin et al (PNAS 2008 Feb 26;105(8):3011-6) and Toporik et al (US 2014/0044641 A1, published Feb 13 2014).
Claim 8 is drawn to the fusion protein according to claim 1, wherein the amino acid sequence of the fusion protein is selected from the group consisting of: (i) the amino acid sequence that shares at least 90% identity with the amino acid sequence set forth in SEQ ID NO: 14; and (ii) the amino acid sequence that shares at least 90% identity with the amino acid sequence set forth in SEQ ID NO: 15. SEQ ID NO: 14 is the amino acid sequence of a PD-1 fusion protein (Hull2SS- PD-1(GGGGS)2-Murine lgG1 (CH2, CH3 ONLY) 362 AA Flex Linker), and SEQ ID NO: 15 is the amino acid sequence of a PD-1 fusion protein (Hull2SS- PD-1(GGGPS)2- Murine lgG1 (CH2, CH3 ONLY) 362 AA Flex Pro Linker) (inst. specs. para [0072] & [0073]. The PD-1 sequence defined in SEQ ID NOs: 14 & 15 are identical to residues 33-150 of human PD-1 protein (UniProt Q15116).
Claim 24 is drawn to the fusion protein according claim 6, wherein the amino acid sequence of the extracellular domain of PD-1 comprises a sequence with at least 90% identity with the amino acid sequence set forth in SEQ ID NO: 12. SEQ ID NO: 12 is identical to residues 33-150 of human PD-1 protein (UniProt Q15116).
The teaching of Carreno, Shiga and Ma et al have been discussed previously.
Carreno, Shiga and Ma et al fail to teach that the extracellular domain of the PD-1 that binds with a mammalian PD-L1 protein comprises a sequence with at least 90% identity with the amino acid sequence set forth in SEQ ID NOs: 12, 14 or 15.
However, Lin et al teaches PD-1 and PD-L1 interact through the conserved Ig variable (IgV) domains (see abstract), which includes residues 34-145 of human PD-1 protein (UniProt 15116.3) and shares at least 90% identity with the extracellular domain of PD-1 in the fusion protein as claimed in SEQ ID NOs: 12, 14 and 15.
Therefore, It would have been prima facie obvious before the effective filing date of the claimed invention to modify the hingeless PD-1-Fc constructs that includes a human IL2 signal peptide at the N-terminus, taught by the combined teaching of Carreno, Shiga, and Ma et al, to include the IgV region of the PD-1 extracellular domain in view of Lin et al because this IgV domain is essential for the binding of PD-1 with PD-L1. The rational to do so is IgV domain is part of the extracellular domain of PD-1 protein and it is essential for the claimed function of binding to PD-L1 protein. One would have a reasonable expectation of success in making the modification because the IgV domain retains the binding properties required for the fusion protein.
Carreno, Shiga, Ma et al and Lin et al fail to teach the fusion protein further comprises linkers as set forth in SEQ ID NOs: 14 and 15.
However, the use of flexible linkers to join extracellular domains of membrane –bound proteins to Fc domains was commonly known in the prior art. For example, Toporik teaches a fusion protein therapeutic protein extracellular domain and the IgG Fc domain (where the hinge region might or might not be present), are linked with flexible linker, such as (GGGGS)2 (linker used in SEQ ID NO: 14) (para. 469-470, 495, 497, also see SEQ ID NO: 164). Use of a flexible linker provides increased rotational freedom for polypeptides linked compared with linked polypeptides without a flexible linker (para. 497). Such rotational freedom allows the polypeptides to access their binding sites more efficiently (para. 497).
It would have been prima facie obvious before the effective filing date of the claimed invention to modify the hingeless PD-1-Fc constructs that has a human IL2 signal peptide fused at the N-terminus, taught by the combined teachings of Carreno, Shiga, Ma et al and Lin et al, and inserting a (GGGGS)2 linker between the PD-1 and Fc domains as taught by Toporik et al because the use of such linkers allows for flexibility of the fusion protein. The motivation to do so could have been found in the teachings of Toporik et al, who explains the use of such linkers allows for flexibility of the fusion protein and allow the polypeptides to access their binding sites more efficiently (para. 497). One would have a reasonable expectation of success in making the combination because using a flexible linker is well established practices in the art for improving the properties of the fusion protein.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that if a technique has been used to improve one method, and a person of ordinary skill would recognize that it would be used in similar methods in the same way, using the technique is obvious unless its application is beyond that person’s skill. It would be obvious to apply a known technique to a known product to be used in a known method that is ready for improvement to yield predictable results. Thus, the combination of prior art references as combined provided a prima facie case of obviousness, absent convincing evidence to the contrary.
Conclusion
Claims 1-9 and 20-25 are rejected.
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/TIAN YANG/Examiner, Art Unit 1674
/VANESSA L. FORD/Supervisory Patent Examiner, Art Unit 1674